{ "cells": [ { "cell_type": "markdown", "id": "9db0f5d6", "metadata": {}, "source": [ "# Aligning partial coronal brain sections with the Allen Brain Altas" ] }, { "cell_type": "markdown", "id": "2e1c99be", "metadata": {}, "source": [ "In this notebook, we align a STARmap dataset of a the right hemisphere of a mouse brain to the Allen Brain Atlas.\n", "\n" ] }, { "cell_type": "markdown", "id": "4077bfd7", "metadata": {}, "source": [ "We will use STalign to achieve this alignment. We will first load the relevant code libraries." ] }, { "cell_type": "code", "execution_count": 1, "id": "5e1fca44", "metadata": {}, "outputs": [], "source": [ "#Import dependencies\n", "\n", "import numpy as np\n", "%matplotlib notebook\n", "import matplotlib.pyplot as plt\n", "import pandas as pd # for csv.\n", "from matplotlib import cm\n", "from matplotlib.lines import Line2D\n", "import os\n", "from os.path import exists,split,join,splitext\n", "from os import makedirs\n", "import glob\n", "import requests\n", "from collections import defaultdict\n", "import nrrd\n", "import torch\n", "from torch.nn.functional import grid_sample\n", "import tornado\n", "from STalign import STalign\n", "import copy\n", "import pandas as pd" ] }, { "cell_type": "markdown", "id": "1c34f0f3", "metadata": {}, "source": [ "We have already downloaded STARmap datasets and stored them in a folder called starmap_data.\n" ] }, { "cell_type": "markdown", "id": "e79c8329", "metadata": {}, "source": [ "Now, we can read in the cell infomation using pandas as pd.\n", "\n", "We must load all cell x and y positions into the variable x and y respectively. Importantly, the *scale* of the loaded data must approximately match the Allen Brain Atlas, where ~1 pixel unit is ~1 um" ] }, { "cell_type": "code", "execution_count": 2, "id": "bf2bd38d", "metadata": {}, "outputs": [], "source": [ "#Load file\n", "\n", "filename = '__'\n", "df = pd.read_csv(r\"/home/manju/Documents/STalign-master/STalign_build/docs/starmap_data/well11_spatial.csv.gz\")\n", "\n", "#Load x position\n", "x = np.array(df['X'])[1:].astype(float) #change to x positions of cells\n", "\n", "#Load y position\n", "y = np.array(df['Y'])[1:].astype(float) #change to column y positions of cells\n" ] }, { "cell_type": "code", "execution_count": 3, "id": "86b24f39", "metadata": {}, "outputs": [], "source": [ "dx=50\n", "blur = 1" ] }, { "cell_type": "markdown", "id": "28ce7757", "metadata": {}, "source": [ "Now we can load in data from the Allen Brain Altas.\n", "\n", "We need to load in and save files containing the ontology of regions, a 3D cell density atlas, and annotations of brain regions in the aforementioned 3D atlas.\n", "\n", "Depending on which Allen Atlas you would like to use, you can change the url that you download these files from. In this example, we are aligning the adult mouse (P56) Allen Atlas." ] }, { "cell_type": "code", "execution_count": 4, "id": "782404c6", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "url = 'http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Structure,rma::criteria,[ontology_id$eq1],rma::options[order$eq%27structures.graph_order%27][num_rows$eqall]'\n", "\n", "ontology_name,namesdict = STalign.download_aba_ontology(url, 'allen_ontology.csv') #url for adult mouse" ] }, { "cell_type": "code", "execution_count": 5, "id": "33002025", "metadata": {}, "outputs": [], "source": [ "imageurl = 'http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/ara_nissl/ara_nissl_50.nrrd'\n", "labelurl = 'http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_50.nrrd'\n", "imagefile, labelfile = STalign.download_aba_image_labels(imageurl, labelurl, 'aba_nissl.nrrd', 'aba_annotation.nrrd')" ] }, { "cell_type": "markdown", "id": "368f08e6", "metadata": {}, "source": [ "Our first step in this alignment will be to rasterize the single cell centroid positions into an image. This converts our x and y arrays of cells into a pixelated image. For this example, we choose to rasterize at a resolution of 15 (um). \n", "\n" ] }, { "cell_type": "code", "execution_count": 6, "id": "4e0e27c3", "metadata": {}, "outputs": [], "source": [ "#Rasterize Image\n", "X_,Y_,W = STalign.rasterize(x,y,dx=dx, blur = blur,draw=False) " ] }, { "cell_type": "code", "execution_count": 7, "id": "e32e9616", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([-1.42879227e+03, -1.37879227e+03, -1.32879227e+03, -1.27879227e+03,\n", " -1.22879227e+03, -1.17879227e+03, -1.12879227e+03, -1.07879227e+03,\n", " -1.02879227e+03, -9.78792270e+02, -9.28792270e+02, -8.78792270e+02,\n", " -8.28792270e+02, -7.78792270e+02, -7.28792270e+02, -6.78792270e+02,\n", " -6.28792270e+02, -5.78792270e+02, -5.28792270e+02, -4.78792270e+02,\n", " -4.28792270e+02, -3.78792270e+02, -3.28792270e+02, -2.78792270e+02,\n", " -2.28792270e+02, -1.78792270e+02, -1.28792270e+02, -7.87922701e+01,\n", " -2.87922701e+01, 2.12077299e+01, 7.12077299e+01, 1.21207730e+02,\n", " 1.71207730e+02, 2.21207730e+02, 2.71207730e+02, 3.21207730e+02,\n", " 3.71207730e+02, 4.21207730e+02, 4.71207730e+02, 5.21207730e+02,\n", " 5.71207730e+02, 6.21207730e+02, 6.71207730e+02, 7.21207730e+02,\n", " 7.71207730e+02, 8.21207730e+02, 8.71207730e+02, 9.21207730e+02,\n", " 9.71207730e+02, 1.02120773e+03, 1.07120773e+03, 1.12120773e+03,\n", " 1.17120773e+03, 1.22120773e+03, 1.27120773e+03, 1.32120773e+03,\n", " 1.37120773e+03, 1.42120773e+03, 1.47120773e+03, 1.52120773e+03,\n", " 1.57120773e+03, 1.62120773e+03, 1.67120773e+03, 1.72120773e+03,\n", " 1.77120773e+03, 1.82120773e+03, 1.87120773e+03, 1.92120773e+03,\n", " 1.97120773e+03, 2.02120773e+03, 2.07120773e+03, 2.12120773e+03,\n", " 2.17120773e+03, 2.22120773e+03, 2.27120773e+03, 2.32120773e+03,\n", " 2.37120773e+03, 2.42120773e+03, 2.47120773e+03, 2.52120773e+03,\n", " 2.57120773e+03, 2.62120773e+03, 2.67120773e+03, 2.72120773e+03,\n", " 2.77120773e+03, 2.82120773e+03, 2.87120773e+03, 2.92120773e+03,\n", " 2.97120773e+03, 3.02120773e+03, 3.07120773e+03, 3.12120773e+03,\n", " 3.17120773e+03, 3.22120773e+03, 3.27120773e+03, 3.32120773e+03,\n", " 3.37120773e+03, 3.42120773e+03, 3.47120773e+03, 3.52120773e+03,\n", " 3.57120773e+03, 3.62120773e+03, 3.67120773e+03, 3.72120773e+03,\n", " 3.77120773e+03, 3.82120773e+03, 3.87120773e+03, 3.92120773e+03,\n", " 3.97120773e+03, 4.02120773e+03, 4.07120773e+03, 4.12120773e+03,\n", " 4.17120773e+03, 4.22120773e+03, 4.27120773e+03, 4.32120773e+03,\n", " 4.37120773e+03, 4.42120773e+03, 4.47120773e+03, 4.52120773e+03,\n", " 4.57120773e+03, 4.62120773e+03, 4.67120773e+03, 4.72120773e+03,\n", " 4.77120773e+03, 4.82120773e+03, 4.87120773e+03, 4.92120773e+03,\n", " 4.97120773e+03, 5.02120773e+03, 5.07120773e+03, 5.12120773e+03,\n", " 5.17120773e+03, 5.22120773e+03, 5.27120773e+03, 5.32120773e+03,\n", " 5.37120773e+03, 5.42120773e+03, 5.47120773e+03, 5.52120773e+03,\n", " 5.57120773e+03, 5.62120773e+03, 5.67120773e+03, 5.72120773e+03,\n", " 5.77120773e+03, 5.82120773e+03, 5.87120773e+03, 5.92120773e+03,\n", " 5.97120773e+03, 6.02120773e+03, 6.07120773e+03, 6.12120773e+03,\n", " 6.17120773e+03, 6.22120773e+03, 6.27120773e+03, 6.32120773e+03,\n", " 6.37120773e+03, 6.42120773e+03, 6.47120773e+03, 6.52120773e+03,\n", " 6.57120773e+03, 6.62120773e+03, 6.67120773e+03, 6.72120773e+03,\n", " 6.77120773e+03, 6.82120773e+03, 6.87120773e+03, 6.92120773e+03,\n", " 6.97120773e+03, 7.02120773e+03, 7.07120773e+03, 7.12120773e+03,\n", " 7.17120773e+03, 7.22120773e+03, 7.27120773e+03, 7.32120773e+03,\n", " 7.37120773e+03, 7.42120773e+03, 7.47120773e+03, 7.52120773e+03,\n", " 7.57120773e+03, 7.62120773e+03, 7.67120773e+03, 7.72120773e+03,\n", " 7.77120773e+03, 7.82120773e+03, 7.87120773e+03, 7.92120773e+03,\n", " 7.97120773e+03, 8.02120773e+03, 8.07120773e+03, 8.12120773e+03,\n", " 8.17120773e+03, 8.22120773e+03, 8.27120773e+03, 8.32120773e+03,\n", " 8.37120773e+03, 8.42120773e+03, 8.47120773e+03, 8.52120773e+03,\n", " 8.57120773e+03, 8.62120773e+03, 8.67120773e+03, 8.72120773e+03,\n", " 8.77120773e+03, 8.82120773e+03, 8.87120773e+03, 8.92120773e+03,\n", " 8.97120773e+03, 9.02120773e+03, 9.07120773e+03, 9.12120773e+03,\n", " 9.17120773e+03, 9.22120773e+03, 9.27120773e+03, 9.32120773e+03,\n", " 9.37120773e+03, 9.42120773e+03, 9.47120773e+03, 9.52120773e+03,\n", " 9.57120773e+03, 9.62120773e+03, 9.67120773e+03, 9.72120773e+03,\n", " 9.77120773e+03, 9.82120773e+03, 9.87120773e+03, 9.92120773e+03,\n", " 9.97120773e+03, 1.00212077e+04, 1.00712077e+04, 1.01212077e+04,\n", " 1.01712077e+04, 1.02212077e+04, 1.02712077e+04, 1.03212077e+04,\n", " 1.03712077e+04, 1.04212077e+04, 1.04712077e+04, 1.05212077e+04,\n", " 1.05712077e+04, 1.06212077e+04, 1.06712077e+04, 1.07212077e+04,\n", " 1.07712077e+04, 1.08212077e+04, 1.08712077e+04, 1.09212077e+04,\n", " 1.09712077e+04, 1.10212077e+04, 1.10712077e+04, 1.11212077e+04,\n", " 1.11712077e+04, 1.12212077e+04, 1.12712077e+04, 1.13212077e+04,\n", " 1.13712077e+04, 1.14212077e+04, 1.14712077e+04, 1.15212077e+04,\n", " 1.15712077e+04, 1.16212077e+04, 1.16712077e+04, 1.17212077e+04,\n", " 1.17712077e+04, 1.18212077e+04, 1.18712077e+04, 1.19212077e+04,\n", " 1.19712077e+04, 1.20212077e+04, 1.20712077e+04, 1.21212077e+04,\n", " 1.21712077e+04, 1.22212077e+04, 1.22712077e+04, 1.23212077e+04,\n", " 1.23712077e+04, 1.24212077e+04, 1.24712077e+04, 1.25212077e+04,\n", " 1.25712077e+04, 1.26212077e+04, 1.26712077e+04, 1.27212077e+04,\n", " 1.27712077e+04, 1.28212077e+04, 1.28712077e+04, 1.29212077e+04,\n", " 1.29712077e+04, 1.30212077e+04, 1.30712077e+04, 1.31212077e+04,\n", " 1.31712077e+04, 1.32212077e+04, 1.32712077e+04, 1.33212077e+04,\n", " 1.33712077e+04, 1.34212077e+04, 1.34712077e+04, 1.35212077e+04,\n", " 1.35712077e+04, 1.36212077e+04, 1.36712077e+04, 1.37212077e+04,\n", " 1.37712077e+04, 1.38212077e+04, 1.38712077e+04, 1.39212077e+04,\n", " 1.39712077e+04, 1.40212077e+04, 1.40712077e+04, 1.41212077e+04,\n", " 1.41712077e+04, 1.42212077e+04, 1.42712077e+04, 1.43212077e+04,\n", " 1.43712077e+04, 1.44212077e+04, 1.44712077e+04, 1.45212077e+04,\n", " 1.45712077e+04, 1.46212077e+04, 1.46712077e+04, 1.47212077e+04,\n", " 1.47712077e+04, 1.48212077e+04, 1.48712077e+04, 1.49212077e+04,\n", " 1.49712077e+04, 1.50212077e+04, 1.50712077e+04, 1.51212077e+04,\n", " 1.51712077e+04, 1.52212077e+04, 1.52712077e+04, 1.53212077e+04,\n", " 1.53712077e+04, 1.54212077e+04, 1.54712077e+04, 1.55212077e+04,\n", " 1.55712077e+04, 1.56212077e+04, 1.56712077e+04, 1.57212077e+04,\n", " 1.57712077e+04, 1.58212077e+04, 1.58712077e+04, 1.59212077e+04,\n", " 1.59712077e+04, 1.60212077e+04, 1.60712077e+04, 1.61212077e+04,\n", " 1.61712077e+04, 1.62212077e+04, 1.62712077e+04, 1.63212077e+04,\n", " 1.63712077e+04, 1.64212077e+04, 1.64712077e+04, 1.65212077e+04,\n", " 1.65712077e+04, 1.66212077e+04, 1.66712077e+04, 1.67212077e+04,\n", " 1.67712077e+04, 1.68212077e+04, 1.68712077e+04, 1.69212077e+04,\n", " 1.69712077e+04, 1.70212077e+04, 1.70712077e+04, 1.71212077e+04,\n", " 1.71712077e+04, 1.72212077e+04, 1.72712077e+04, 1.73212077e+04,\n", " 1.73712077e+04, 1.74212077e+04, 1.74712077e+04, 1.75212077e+04,\n", " 1.75712077e+04, 1.76212077e+04, 1.76712077e+04, 1.77212077e+04,\n", " 1.77712077e+04, 1.78212077e+04, 1.78712077e+04, 1.79212077e+04,\n", " 1.79712077e+04, 1.80212077e+04, 1.80712077e+04, 1.81212077e+04,\n", " 1.81712077e+04, 1.82212077e+04, 1.82712077e+04, 1.83212077e+04,\n", " 1.83712077e+04, 1.84212077e+04, 1.84712077e+04, 1.85212077e+04,\n", " 1.85712077e+04, 1.86212077e+04, 1.86712077e+04, 1.87212077e+04,\n", " 1.87712077e+04, 1.88212077e+04, 1.88712077e+04, 1.89212077e+04,\n", " 1.89712077e+04, 1.90212077e+04, 1.90712077e+04, 1.91212077e+04,\n", " 1.91712077e+04, 1.92212077e+04, 1.92712077e+04, 1.93212077e+04,\n", " 1.93712077e+04, 1.94212077e+04, 1.94712077e+04, 1.95212077e+04,\n", " 1.95712077e+04, 1.96212077e+04, 1.96712077e+04, 1.97212077e+04,\n", " 1.97712077e+04, 1.98212077e+04, 1.98712077e+04, 1.99212077e+04,\n", " 1.99712077e+04, 2.00212077e+04, 2.00712077e+04, 2.01212077e+04,\n", " 2.01712077e+04, 2.02212077e+04, 2.02712077e+04, 2.03212077e+04,\n", " 2.03712077e+04, 2.04212077e+04, 2.04712077e+04, 2.05212077e+04,\n", " 2.05712077e+04, 2.06212077e+04, 2.06712077e+04, 2.07212077e+04,\n", " 2.07712077e+04, 2.08212077e+04, 2.08712077e+04, 2.09212077e+04,\n", " 2.09712077e+04, 2.10212077e+04, 2.10712077e+04, 2.11212077e+04,\n", " 2.11712077e+04, 2.12212077e+04, 2.12712077e+04, 2.13212077e+04,\n", " 2.13712077e+04, 2.14212077e+04, 2.14712077e+04, 2.15212077e+04,\n", " 2.15712077e+04, 2.16212077e+04, 2.16712077e+04, 2.17212077e+04,\n", " 2.17712077e+04, 2.18212077e+04, 2.18712077e+04, 2.19212077e+04,\n", " 2.19712077e+04, 2.20212077e+04, 2.20712077e+04, 2.21212077e+04,\n", " 2.21712077e+04, 2.22212077e+04, 2.22712077e+04, 2.23212077e+04,\n", " 2.23712077e+04, 2.24212077e+04, 2.24712077e+04, 2.25212077e+04,\n", " 2.25712077e+04, 2.26212077e+04, 2.26712077e+04, 2.27212077e+04,\n", " 2.27712077e+04, 2.28212077e+04, 2.28712077e+04, 2.29212077e+04,\n", " 2.29712077e+04, 2.30212077e+04, 2.30712077e+04, 2.31212077e+04,\n", " 2.31712077e+04, 2.32212077e+04, 2.32712077e+04, 2.33212077e+04,\n", " 2.33712077e+04, 2.34212077e+04, 2.34712077e+04, 2.35212077e+04,\n", " 2.35712077e+04, 2.36212077e+04, 2.36712077e+04, 2.37212077e+04,\n", " 2.37712077e+04, 2.38212077e+04, 2.38712077e+04, 2.39212077e+04,\n", " 2.39712077e+04, 2.40212077e+04, 2.40712077e+04, 2.41212077e+04,\n", " 2.41712077e+04, 2.42212077e+04, 2.42712077e+04, 2.43212077e+04,\n", " 2.43712077e+04, 2.44212077e+04, 2.44712077e+04, 2.45212077e+04,\n", " 2.45712077e+04, 2.46212077e+04, 2.46712077e+04, 2.47212077e+04,\n", " 2.47712077e+04, 2.48212077e+04, 2.48712077e+04, 2.49212077e+04,\n", " 2.49712077e+04, 2.50212077e+04, 2.50712077e+04, 2.51212077e+04,\n", " 2.51712077e+04, 2.52212077e+04, 2.52712077e+04, 2.53212077e+04,\n", " 2.53712077e+04, 2.54212077e+04, 2.54712077e+04, 2.55212077e+04,\n", " 2.55712077e+04, 2.56212077e+04, 2.56712077e+04, 2.57212077e+04,\n", " 2.57712077e+04, 2.58212077e+04, 2.58712077e+04, 2.59212077e+04,\n", " 2.59712077e+04, 2.60212077e+04, 2.60712077e+04, 2.61212077e+04,\n", " 2.61712077e+04, 2.62212077e+04, 2.62712077e+04, 2.63212077e+04,\n", " 2.63712077e+04, 2.64212077e+04, 2.64712077e+04, 2.65212077e+04,\n", " 2.65712077e+04, 2.66212077e+04, 2.66712077e+04, 2.67212077e+04,\n", " 2.67712077e+04, 2.68212077e+04, 2.68712077e+04, 2.69212077e+04,\n", " 2.69712077e+04, 2.70212077e+04, 2.70712077e+04, 2.71212077e+04,\n", " 2.71712077e+04, 2.72212077e+04, 2.72712077e+04, 2.73212077e+04,\n", " 2.73712077e+04, 2.74212077e+04, 2.74712077e+04, 2.75212077e+04,\n", " 2.75712077e+04, 2.76212077e+04, 2.76712077e+04, 2.77212077e+04,\n", " 2.77712077e+04, 2.78212077e+04, 2.78712077e+04, 2.79212077e+04,\n", " 2.79712077e+04, 2.80212077e+04, 2.80712077e+04, 2.81212077e+04,\n", " 2.81712077e+04, 2.82212077e+04, 2.82712077e+04, 2.83212077e+04,\n", " 2.83712077e+04, 2.84212077e+04, 2.84712077e+04, 2.85212077e+04,\n", " 2.85712077e+04, 2.86212077e+04, 2.86712077e+04, 2.87212077e+04,\n", " 2.87712077e+04, 2.88212077e+04, 2.88712077e+04, 2.89212077e+04,\n", " 2.89712077e+04, 2.90212077e+04, 2.90712077e+04, 2.91212077e+04,\n", " 2.91712077e+04, 2.92212077e+04, 2.92712077e+04, 2.93212077e+04,\n", " 2.93712077e+04, 2.94212077e+04, 2.94712077e+04, 2.95212077e+04,\n", " 2.95712077e+04, 2.96212077e+04, 2.96712077e+04, 2.97212077e+04,\n", " 2.97712077e+04, 2.98212077e+04, 2.98712077e+04, 2.99212077e+04,\n", " 2.99712077e+04, 3.00212077e+04, 3.00712077e+04, 3.01212077e+04,\n", " 3.01712077e+04, 3.02212077e+04, 3.02712077e+04, 3.03212077e+04,\n", " 3.03712077e+04, 3.04212077e+04, 3.04712077e+04, 3.05212077e+04,\n", " 3.05712077e+04, 3.06212077e+04, 3.06712077e+04, 3.07212077e+04,\n", " 3.07712077e+04, 3.08212077e+04, 3.08712077e+04, 3.09212077e+04,\n", " 3.09712077e+04, 3.10212077e+04, 3.10712077e+04, 3.11212077e+04,\n", " 3.11712077e+04, 3.12212077e+04, 3.12712077e+04, 3.13212077e+04,\n", " 3.13712077e+04, 3.14212077e+04, 3.14712077e+04, 3.15212077e+04,\n", " 3.15712077e+04, 3.16212077e+04, 3.16712077e+04, 3.17212077e+04,\n", " 3.17712077e+04, 3.18212077e+04, 3.18712077e+04, 3.19212077e+04,\n", " 3.19712077e+04, 3.20212077e+04, 3.20712077e+04, 3.21212077e+04,\n", " 3.21712077e+04, 3.22212077e+04, 3.22712077e+04, 3.23212077e+04,\n", " 3.23712077e+04, 3.24212077e+04, 3.24712077e+04, 3.25212077e+04,\n", " 3.25712077e+04, 3.26212077e+04, 3.26712077e+04, 3.27212077e+04,\n", " 3.27712077e+04, 3.28212077e+04, 3.28712077e+04, 3.29212077e+04,\n", " 3.29712077e+04, 3.30212077e+04, 3.30712077e+04, 3.31212077e+04,\n", " 3.31712077e+04, 3.32212077e+04, 3.32712077e+04, 3.33212077e+04,\n", " 3.33712077e+04, 3.34212077e+04, 3.34712077e+04, 3.35212077e+04,\n", " 3.35712077e+04, 3.36212077e+04, 3.36712077e+04, 3.37212077e+04,\n", " 3.37712077e+04, 3.38212077e+04, 3.38712077e+04, 3.39212077e+04,\n", " 3.39712077e+04, 3.40212077e+04, 3.40712077e+04, 3.41212077e+04,\n", " 3.41712077e+04, 3.42212077e+04, 3.42712077e+04, 3.43212077e+04,\n", " 3.43712077e+04, 3.44212077e+04, 3.44712077e+04, 3.45212077e+04,\n", " 3.45712077e+04, 3.46212077e+04, 3.46712077e+04, 3.47212077e+04,\n", " 3.47712077e+04, 3.48212077e+04, 3.48712077e+04, 3.49212077e+04,\n", " 3.49712077e+04, 3.50212077e+04, 3.50712077e+04, 3.51212077e+04,\n", " 3.51712077e+04, 3.52212077e+04, 3.52712077e+04, 3.53212077e+04,\n", " 3.53712077e+04, 3.54212077e+04, 3.54712077e+04, 3.55212077e+04,\n", " 3.55712077e+04, 3.56212077e+04, 3.56712077e+04, 3.57212077e+04,\n", " 3.57712077e+04, 3.58212077e+04, 3.58712077e+04, 3.59212077e+04,\n", " 3.59712077e+04, 3.60212077e+04, 3.60712077e+04, 3.61212077e+04,\n", " 3.61712077e+04, 3.62212077e+04, 3.62712077e+04, 3.63212077e+04,\n", " 3.63712077e+04, 3.64212077e+04, 3.64712077e+04, 3.65212077e+04])" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "X_" ] }, { "cell_type": "markdown", "id": "8d869ee1", "metadata": {}, "source": [ "We can visualize the resulting rasterized image." ] }, { "cell_type": "code", "execution_count": 8, "id": "411690d8", "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "Text(0.5, 1.0, 'Rasterized')" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Plot unrasterized/rasterized images\n", "fig,ax = plt.subplots(1,2)\n", "ax[0].scatter(x,y,s=0.5,alpha=0.25)\n", "ax[0].invert_yaxis()\n", "ax[0].set_title('List of cells')\n", "ax[0].set_aspect('equal')\n", "\n", "W = W[0]\n", "extent = (X_[0],X_[-1],Y_[0],Y_[-1]) \n", "ax[1].imshow(W, origin='lower') \n", "ax[1].invert_yaxis() \n", "ax[1].set_title('Rasterized')\n", "\n", "# save figure\n", "#fig.canvas.draw() \n", "#fig.savefig(outname[:-4]+'_image.png')" ] }, { "cell_type": "markdown", "id": "f950a150", "metadata": {}, "source": [ "Now we need to find an approximate slice number in the Allen Atlas to initialize the alignment. Evaluate whether the value of slice is similar to the target image by viewing a side by side comparison of the ABA slice and the target image. If not, change the value of slice. In this example, slice = 0 is anterior and slice = 264 is posterior." ] }, { "cell_type": "code", "execution_count": 9, "id": "998e061f", "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "#find slice\n", "#peruse through images in atlas\n", "# Loading the atlas\n", "slice = 140\n", "\n", "vol,hdr = nrrd.read(imagefile)\n", "A = vol \n", "vol,hdr = nrrd.read(labelfile)\n", "L = vol\n", "\n", "dxA = np.diag(hdr['space directions'])\n", "nxA = A.shape\n", "xA = [np.arange(n)*d - (n-1)*d/2.0 for n,d in zip(nxA,dxA)]\n", "XA = np.meshgrid(*xA,indexing='ij')\n", "\n", "fig,ax = plt.subplots(1,2)\n", "extentA = STalign.extent_from_x(xA[1:])\n", "ax[0].imshow(A[slice],extent=extentA)\n", "ax[0].set_title('Atlas Slice')\n", "\n", "ax[1].imshow(W,extent=extentA)\n", "ax[1].set_title('Target Image')\n", "fig.canvas.draw() \n" ] }, { "cell_type": "code", "execution_count": 10, "id": "0c7e273c", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "228" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "len(xA[2])" ] }, { "cell_type": "markdown", "id": "a6e13a8e", "metadata": {}, "source": [ "Next, we need to find an approximate rotation angle of the Allen Atlas to initialize the alignment. Evaluate whether the rotation of the atlas is similar to the target image by viewing a side by side comparison of the ABA slice and the target image. If not, change the value of theta_deg. Note: the rotation here is defined in degrees." ] }, { "cell_type": "code", "execution_count": 11, "id": "827f4af1", "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from scipy.ndimage import rotate\n", "\n", "theta_deg = 90\n", "\n", "fig,ax = plt.subplots(1,2)\n", "extentA = STalign.extent_from_x(xA[1:])\n", "ax[0].imshow(rotate(A[slice], angle=theta_deg),extent=extentA)\n", "ax[0].set_title('Atlas Slice')\n", "\n", "ax[1].imshow(W,extent=extentA)\n", "ax[1].set_title('Target Image')\n", "fig.canvas.draw() \n" ] }, { "cell_type": "markdown", "id": "b6f65ae8", "metadata": {}, "source": [ "Next, specify if there are any points on the image above that can be approximately matched with eachother and add them in the following format. This helps speed up alignment. (OPTIONAL)\n" ] }, { "cell_type": "code", "execution_count": 12, "id": "ca2a06fb", "metadata": {}, "outputs": [], "source": [ "points_atlas = np.array([[0,0]]) #(-y,-x)\n", "points_target = np.array([[-3700,0]]) # (-y,-x)\n", "Li,Ti = STalign.L_T_from_points(points_atlas,points_target)" ] }, { "cell_type": "markdown", "id": "e634925d", "metadata": {}, "source": [ "We can define atlas and target points, xI and xJ, as well as atlas and target images, I and J. " ] }, { "cell_type": "code", "execution_count": 13, "id": "c760097a", "metadata": {}, "outputs": [], "source": [ "xJ = [Y_,X_]\n", "J = W[None]/np.mean(np.abs(W))\n", "xI = xA\n", "I = A[None] / np.mean(np.abs(A),keepdims=True)\n", "I = np.concatenate((I,(I-np.mean(I))**2))\n", "Inorm = STalign.normalize(I, t_min=0, t_max=1)\n", "Jnorm = STalign.normalize(J, t_min=0, t_max=1)" ] }, { "cell_type": "markdown", "id": "cdc55aca", "metadata": {}, "source": [ "Now that we can chosen the slice number and rotation angle, we are ready to initialize parameters related to our alignment. " ] }, { "cell_type": "code", "execution_count": 14, "id": "3b6b485b", "metadata": {}, "outputs": [], "source": [ "sigmaA = 0.1 #standard deviation of artifact intensities\n", "sigmaB = 0.1 #standard deviation of background intensities\n", "sigmaM = 0.1 #standard deviation of matching tissue intenities\n", "muA = torch.tensor([0.7,0.7,0.7],device='cpu') #average of artifact intensities\n", "muB = torch.tensor([0,0,0],device='cpu') #average of background intensities\n" ] }, { "cell_type": "markdown", "id": "5ed166ed", "metadata": {}, "source": [ "We can change the parameters above by looking at the intensity histogram of our target image (below). We need to consider intensities of artifacts (tissue that is present in the target image and absent in the atlas), which is usually in the upper range of intensity values. We also need to find the intensity of the background values that does not correspond to any tissue, usually around 0, and standard deviations for these values. The matching tissue intensities are regions that should have tissue that can be aligned in both the atlas and the target image." ] }, { "cell_type": "code", "execution_count": 15, "id": "b28c0d31", "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "Text(0.5, 1.0, 'Intensity Histogram of Target Image')" ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fig,ax = plt.subplots()\n", "ax.hist(Jnorm.ravel())\n", "plt.xlabel('Intensity')\n", "plt.ylabel('Number of Pixels')\n", "plt.title('Intensity Histogram of Target Image')" ] }, { "cell_type": "markdown", "id": "0ea40ace", "metadata": {}, "source": [ "The following parameters vary depending on your target image and the duration & accuracy of the alignment. The scale parameters refer to a scaling of the atlas in (x, y, z) to match the size of the target image. The nt parameter ensures smoothness and invertibility of the image transformation. The niter refers to the number of iteration steps in gradient descent to achieve minimum error between the altas and the target image." ] }, { "cell_type": "code", "execution_count": 16, "id": "096f76b0", "metadata": {}, "outputs": [], "source": [ "# initialize variables\n", "scale_x = 4 #default = 0.9\n", "scale_y = 4 #default = 0.9\n", "scale_z = 0.9 #default = 0.9\n", "theta0 = (np.pi/180)*theta_deg\n", "\n", "# get an initial guess\n", "if 'Ti' in locals():\n", " T = np.array([-xI[0][slice],np.mean(xJ[0])-(Ti[0]*scale_y),np.mean(xJ[1])-(Ti[1]*scale_x)])\n", "else:\n", " T = np.array([-xI[0][slice],np.mean(xJ[0]),np.mean(xJ[1])])\n", "#T = np.array([-xI[0][slice],0,0])\n", "\n", "\n", "scale_atlas = np.array([[scale_z,0,0],\n", " [0,scale_x,0],\n", " [0,0,scale_y]])\n", "L = np.array([[1.0,0.0,0.0],\n", " [0.0,np.cos(theta0),-np.sin(theta0)],\n", " [0.0,np.sin(theta0),np.cos(theta0)]])\n", "L = np.matmul(L,scale_atlas)#np.identity(3)" ] }, { "cell_type": "markdown", "id": "70abfa6d", "metadata": {}, "source": [ "Now, we can perform alignment of the atlas to our target slice." ] }, { "cell_type": "code", "execution_count": 24, "id": "dcf9bf8a", "metadata": { "scrolled": false }, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stderr", "output_type": "stream", "text": [ "/home/manju/.local/lib/python3.8/site-packages/STalign/STalign.py:1617: UserWarning: Data has no positive values, and therefore cannot be log-scaled.\n", " axE[2].set_yscale('log')\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 2h 36min 26s, sys: 1h 16min 5s, total: 3h 52min 32s\n", "Wall time: 13min 27s\n" ] } ], "source": [ "%%time\n", "#returns mat = affine transform, v = velocity, xv = pixel locations of velocity points\n", "transform = STalign.LDDMM_3D_to_slice(\n", " xI,Inorm,xJ,Jnorm,\n", " T=T,L=L,\n", " nt=4,niter=800,\n", " a=250,\n", " device='cpu',\n", " sigmaA = sigmaA, #standard deviation of artifact intensities\n", " sigmaB = sigmaB, #standard deviation of background intensities\n", " sigmaM = sigmaM, #standard deviation of matching tissue intenities\n", " muA = muA, #average of artifact intensities\n", " muB = muB #average of background intensities\n", ")\n" ] }, { "cell_type": "code", "execution_count": 25, "id": "9525db36", "metadata": {}, "outputs": [], "source": [ "A = transform['A']\n", "v = transform['v']\n", "xv = transform['xv']\n", "Xs = transform['Xs']" ] }, { "cell_type": "code", "execution_count": 26, "id": "75324682", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "tensor([[ 1.2073e+00, 3.4987e-02, -1.3848e-02, -6.5878e+02],\n", " [-6.2258e-02, 2.3100e-02, -4.8150e+00, 2.6193e+04],\n", " [ 1.2410e-02, 4.6378e+00, -4.3118e-02, 1.8045e+04],\n", " [ 0.0000e+00, 0.0000e+00, 0.0000e+00, 1.0000e+00]],\n", " dtype=torch.float64)\n" ] } ], "source": [ "print(A)" ] }, { "cell_type": "markdown", "id": "ed8f5242", "metadata": {}, "source": [ "Once we have aligned the atlas to our target image, we can project the brain regions defined in the atlas to our target image and export these annotations, along with information about the positions of the atlas that align with the slice." ] }, { "cell_type": "code", "execution_count": 27, "id": "e32e9356", "metadata": { "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/manju/.local/lib/python3.8/site-packages/STalign/STalign.py:1726: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).\n", " A = torch.tensor(A)\n", "/home/manju/.local/lib/python3.8/site-packages/STalign/STalign.py:1727: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).\n", " v = torch.tensor(v)\n", "/home/manju/.local/lib/python3.8/site-packages/STalign/STalign.py:1739: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).\n", " XJ = torch.tensor(XJ)\n" ] } ], "source": [ "df = STalign.analyze3Dalign(labelfile, xv,v,A, xJ, dx, scale_x=scale_x, scale_y=scale_y,x=x,y=y, X_=X_, Y_=Y_, namesdict=namesdict,device='cpu')" ] }, { "cell_type": "code", "execution_count": 28, "id": "d364f7b9", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
coord0coord1coord2xystruct_idacronym
0714.048218-3618.1585165537.46592010834.2727271488.4545450bg
1712.695551-3561.5760815562.22888712139.406780864.7881360bg
2712.907165-3574.6757305547.68541611848.1320751225.679245527AUDd1
3713.804790-3607.2795545543.68864711090.9803921342.5392160bg
4713.301162-3589.9135005543.61323611517.9056601351.7358490bg
........................
43336667.020365-2502.1250954416.02759334741.96363625621.7045450bg
43337668.244750-2520.2969344459.33617234380.79411824686.5735290bg
43338668.459205-2534.3515184446.84132434106.06818225049.7803030bg
43339667.999837-2508.4499474465.79970634648.20000024484.6941180bg
43340667.127079-2502.2885214422.37080234753.99038525492.1346150bg
\n", "

43341 rows × 7 columns

\n", "
" ], "text/plain": [ " coord0 coord1 coord2 x y \n", "0 714.048218 -3618.158516 5537.465920 10834.272727 1488.454545 \\\n", "1 712.695551 -3561.576081 5562.228887 12139.406780 864.788136 \n", "2 712.907165 -3574.675730 5547.685416 11848.132075 1225.679245 \n", "3 713.804790 -3607.279554 5543.688647 11090.980392 1342.539216 \n", "4 713.301162 -3589.913500 5543.613236 11517.905660 1351.735849 \n", "... ... ... ... ... ... \n", "43336 667.020365 -2502.125095 4416.027593 34741.963636 25621.704545 \n", "43337 668.244750 -2520.296934 4459.336172 34380.794118 24686.573529 \n", "43338 668.459205 -2534.351518 4446.841324 34106.068182 25049.780303 \n", "43339 667.999837 -2508.449947 4465.799706 34648.200000 24484.694118 \n", "43340 667.127079 -2502.288521 4422.370802 34753.990385 25492.134615 \n", "\n", " struct_id acronym \n", "0 0 bg \n", "1 0 bg \n", "2 527 AUDd1 \n", "3 0 bg \n", "4 0 bg \n", "... ... ... \n", "43336 0 bg \n", "43337 0 bg \n", "43338 0 bg \n", "43339 0 bg \n", "43340 0 bg \n", "\n", "[43341 rows x 7 columns]" ] }, "execution_count": 28, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df" ] }, { "cell_type": "markdown", "id": "b9e5f4fe", "metadata": {}, "source": [ "Now, we can explore our alignment and brain region annotations! " ] }, { "cell_type": "markdown", "id": "687c263d", "metadata": {}, "source": [ "We can visualize the MERFISH slice overlayed with the matched section in the Allen Brain Atlas." ] }, { "cell_type": "code", "execution_count": 29, "id": "a08d4fb0", "metadata": { "scrolled": false }, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "It = torch.tensor(I,device='cpu',dtype=torch.float64)\n", "AI = STalign.interp3D(xI,It,Xs.permute(3,0,1,2),padding_mode=\"border\")\n", "Ishow_source = ((AI-torch.amin(AI,(1,2,3))[...,None,None])/(torch.amax(AI,(1,2,3))-torch.amin(AI,(1,2,3)))[...,None,None,None]).permute(1,2,3,0).clone().detach().cpu()\n", "Jt = torch.tensor(J,device='cpu',dtype=torch.float64)\n", "Ishow_target = Jt.permute(1,2,0).cpu()/torch.max(Jt).item()\n", "\n", "import matplotlib as mpl\n", "fig,ax = plt.subplots(1,3, figsize=(15,5))\n", "ax0 = ax[0].imshow(Ishow_target, cmap = mpl.cm.Blues,alpha=0.9)\n", "ax[0].set_title('STARmap Slice')\n", "ax1 = ax[1].imshow(Ishow_source[0,:,:,0], cmap = mpl.cm.Reds,alpha=0.2)\n", "ax[1].set_title('z=0 slice of Aligned 3D Allen Brain Atlas')\n", "ax2 = ax[2].imshow(Ishow_target, cmap = mpl.cm.Blues,alpha=0.9)\n", "ax2 = ax[2].imshow(Ishow_source[0,:,:,0], cmap = mpl.cm.Reds,alpha=0.3)\n", "ax[2].set_title('Overlayed')\n", "\n", "plt.show()" ] }, { "cell_type": "code", "execution_count": 30, "id": "0dfa941e", "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "Text(0.5, 0, 'z')" ] }, "execution_count": 30, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from mpl_toolkits import mplot3d\n", "\n", "x=df['coord0']\n", "y=-df['coord1']\n", "z=df['coord2']\n", "\n", "fig = plt.figure()\n", "ax = plt.axes(projection='3d')\n", "\n", "ax.scatter3D(x,y,z,s=0.05)\n", "ax.set_xlabel('x')\n", "ax.set_ylabel('y')\n", "ax.set_zlabel('z')" ] }, { "cell_type": "markdown", "id": "4b6b3506", "metadata": {}, "source": [ "We can also plot all of the brain regions that are captured in the slice, as defined by our alignment." ] }, { "cell_type": "code", "execution_count": 31, "id": "f883aec3", "metadata": { "scrolled": false }, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "STalign.plot_brain_regions(df)" ] }, { "cell_type": "markdown", "id": "ba928a77", "metadata": {}, "source": [ "If we also interested in only a few regions, in this example let's take VISp4 and VISp5, we can plot those regions using the following function." ] }, { "cell_type": "code", "execution_count": 32, "id": "558efc39", "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. ' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.'\n", " );\n", " }\n", "};\n", "\n", "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = this.ws.binaryType !== undefined;\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById('mpl-warnings');\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent =\n", " 'This browser does not support binary websocket messages. ' +\n", " 'Performance may be slow.';\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = document.createElement('div');\n", " this.root.setAttribute('style', 'display: inline-block');\n", " this._root_extra_style(this.root);\n", "\n", " parent_element.appendChild(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message('supports_binary', { value: fig.supports_binary });\n", " fig.send_message('send_image_mode', {});\n", " if (fig.ratio !== 1) {\n", " fig.send_message('set_device_pixel_ratio', {\n", " device_pixel_ratio: fig.ratio,\n", " });\n", " }\n", " fig.send_message('refresh', {});\n", " };\n", "\n", " this.imageObj.onload = function () {\n", " if (fig.image_mode === 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function () {\n", " fig.ws.close();\n", " };\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "};\n", "\n", "mpl.figure.prototype._init_header = function () {\n", " var titlebar = document.createElement('div');\n", " titlebar.classList =\n", " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", " var titletext = document.createElement('div');\n", " titletext.classList = 'ui-dialog-title';\n", " titletext.setAttribute(\n", " 'style',\n", " 'width: 100%; text-align: center; padding: 3px;'\n", " );\n", " titlebar.appendChild(titletext);\n", " this.root.appendChild(titlebar);\n", " this.header = titletext;\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", "\n", "mpl.figure.prototype._init_canvas = function () {\n", " var fig = this;\n", "\n", " var canvas_div = (this.canvas_div = document.createElement('div'));\n", " canvas_div.setAttribute('tabindex', '0');\n", " canvas_div.setAttribute(\n", " 'style',\n", " 'border: 1px solid #ddd;' +\n", " 'box-sizing: content-box;' +\n", " 'clear: both;' +\n", " 'min-height: 1px;' +\n", " 'min-width: 1px;' +\n", " 'outline: 0;' +\n", " 'overflow: hidden;' +\n", " 'position: relative;' +\n", " 'resize: both;' +\n", " 'z-index: 2;'\n", " );\n", "\n", " function on_keyboard_event_closure(name) {\n", " return function (event) {\n", " return fig.key_event(event, name);\n", " };\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'keydown',\n", " on_keyboard_event_closure('key_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'keyup',\n", " on_keyboard_event_closure('key_release')\n", " );\n", "\n", " this._canvas_extra_style(canvas_div);\n", " this.root.appendChild(canvas_div);\n", "\n", " var canvas = (this.canvas = document.createElement('canvas'));\n", " canvas.classList.add('mpl-canvas');\n", " canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'pointer-events: none;' +\n", " 'position: relative;' +\n", " 'z-index: 0;'\n", " );\n", "\n", " this.context = canvas.getContext('2d');\n", "\n", " var backingStore =\n", " this.context.backingStorePixelRatio ||\n", " this.context.webkitBackingStorePixelRatio ||\n", " this.context.mozBackingStorePixelRatio ||\n", " this.context.msBackingStorePixelRatio ||\n", " this.context.oBackingStorePixelRatio ||\n", " this.context.backingStorePixelRatio ||\n", " 1;\n", "\n", " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", " 'canvas'\n", " ));\n", " rubberband_canvas.setAttribute(\n", " 'style',\n", " 'box-sizing: content-box;' +\n", " 'left: 0;' +\n", " 'pointer-events: none;' +\n", " 'position: absolute;' +\n", " 'top: 0;' +\n", " 'z-index: 1;'\n", " );\n", "\n", " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", " if (this.ResizeObserver === undefined) {\n", " if (window.ResizeObserver !== undefined) {\n", " this.ResizeObserver = window.ResizeObserver;\n", " } else {\n", " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", " this.ResizeObserver = obs.ResizeObserver;\n", " }\n", " }\n", "\n", " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", " var nentries = entries.length;\n", " for (var i = 0; i < nentries; i++) {\n", " var entry = entries[i];\n", " var width, height;\n", " if (entry.contentBoxSize) {\n", " if (entry.contentBoxSize instanceof Array) {\n", " // Chrome 84 implements new version of spec.\n", " width = entry.contentBoxSize[0].inlineSize;\n", " height = entry.contentBoxSize[0].blockSize;\n", " } else {\n", " // Firefox implements old version of spec.\n", " width = entry.contentBoxSize.inlineSize;\n", " height = entry.contentBoxSize.blockSize;\n", " }\n", " } else {\n", " // Chrome <84 implements even older version of spec.\n", " width = entry.contentRect.width;\n", " height = entry.contentRect.height;\n", " }\n", "\n", " // Keep the size of the canvas and rubber band canvas in sync with\n", " // the canvas container.\n", " if (entry.devicePixelContentBoxSize) {\n", " // Chrome 84 implements new version of spec.\n", " canvas.setAttribute(\n", " 'width',\n", " entry.devicePixelContentBoxSize[0].inlineSize\n", " );\n", " canvas.setAttribute(\n", " 'height',\n", " entry.devicePixelContentBoxSize[0].blockSize\n", " );\n", " } else {\n", " canvas.setAttribute('width', width * fig.ratio);\n", " canvas.setAttribute('height', height * fig.ratio);\n", " }\n", " /* This rescales the canvas back to display pixels, so that it\n", " * appears correct on HiDPI screens. */\n", " canvas.style.width = width + 'px';\n", " canvas.style.height = height + 'px';\n", "\n", " rubberband_canvas.setAttribute('width', width);\n", " rubberband_canvas.setAttribute('height', height);\n", "\n", " // And update the size in Python. We ignore the initial 0/0 size\n", " // that occurs as the element is placed into the DOM, which should\n", " // otherwise not happen due to the minimum size styling.\n", " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", " fig.request_resize(width, height);\n", " }\n", " }\n", " });\n", " this.resizeObserverInstance.observe(canvas_div);\n", "\n", " function on_mouse_event_closure(name) {\n", " /* User Agent sniffing is bad, but WebKit is busted:\n", " * https://bugs.webkit.org/show_bug.cgi?id=144526\n", " * https://bugs.webkit.org/show_bug.cgi?id=181818\n", " * The worst that happens here is that they get an extra browser\n", " * selection when dragging, if this check fails to catch them.\n", " */\n", " var UA = navigator.userAgent;\n", " var isWebKit = /AppleWebKit/.test(UA) && !/Chrome/.test(UA);\n", " if(isWebKit) {\n", " return function (event) {\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We\n", " * want to control all of the cursor setting manually through\n", " * the 'cursor' event from matplotlib */\n", " event.preventDefault()\n", " return fig.mouse_event(event, name);\n", " };\n", " } else {\n", " return function (event) {\n", " return fig.mouse_event(event, name);\n", " };\n", " }\n", " }\n", "\n", " canvas_div.addEventListener(\n", " 'mousedown',\n", " on_mouse_event_closure('button_press')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseup',\n", " on_mouse_event_closure('button_release')\n", " );\n", " canvas_div.addEventListener(\n", " 'dblclick',\n", " on_mouse_event_closure('dblclick')\n", " );\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " canvas_div.addEventListener(\n", " 'mousemove',\n", " on_mouse_event_closure('motion_notify')\n", " );\n", "\n", " canvas_div.addEventListener(\n", " 'mouseenter',\n", " on_mouse_event_closure('figure_enter')\n", " );\n", " canvas_div.addEventListener(\n", " 'mouseleave',\n", " on_mouse_event_closure('figure_leave')\n", " );\n", "\n", " canvas_div.addEventListener('wheel', function (event) {\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " on_mouse_event_closure('scroll')(event);\n", " });\n", "\n", " canvas_div.appendChild(canvas);\n", " canvas_div.appendChild(rubberband_canvas);\n", "\n", " this.rubberband_context = rubberband_canvas.getContext('2d');\n", " this.rubberband_context.strokeStyle = '#000000';\n", "\n", " this._resize_canvas = function (width, height, forward) {\n", " if (forward) {\n", " canvas_div.style.width = width + 'px';\n", " canvas_div.style.height = height + 'px';\n", " }\n", " };\n", "\n", " // Disable right mouse context menu.\n", " canvas_div.addEventListener('contextmenu', function (_e) {\n", " event.preventDefault();\n", " return false;\n", " });\n", "\n", " function set_focus() {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'mpl-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'mpl-button-group';\n", " continue;\n", " }\n", "\n", " var button = (fig.buttons[name] = document.createElement('button'));\n", " button.classList = 'mpl-widget';\n", " button.setAttribute('role', 'button');\n", " button.setAttribute('aria-disabled', 'false');\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", "\n", " var icon_img = document.createElement('img');\n", " icon_img.src = '_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " fig.canvas_div.style.cursor = msg['cursor'];\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "function getModifiers(event) {\n", " var mods = [];\n", " if (event.ctrlKey) {\n", " mods.push('ctrl');\n", " }\n", " if (event.altKey) {\n", " mods.push('alt');\n", " }\n", " if (event.shiftKey) {\n", " mods.push('shift');\n", " }\n", " if (event.metaKey) {\n", " mods.push('meta');\n", " }\n", " return mods;\n", "}\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * https://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " // from https://stackoverflow.com/q/1114465\n", " var boundingRect = this.canvas.getBoundingClientRect();\n", " var x = (event.clientX - boundingRect.left) * this.ratio;\n", " var y = (event.clientY - boundingRect.top) * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " modifiers: getModifiers(event),\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "brain_regions = ['CA1']\n", "STalign.plot_subset_brain_regions(df, brain_regions)" ] }, { "cell_type": "code", "execution_count": null, "id": "c661a492", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.3" } }, "nbformat": 4, "nbformat_minor": 5 }