Boxesplot.ipynb

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   "source": [
    "from skimage.measure import regionprops, label\n",
    "import skimage.io\n",
    "import matplotlib.pyplot as plt\n",
    "from matplotlib.patches import Rectangle as drawrect\n",
    "import numpy as np\n",
    "\n",
    "%matplotlib qt\n",
    "\n",
    "z =5   # int(input(\"how many z slices do you have in your movie?\"))\n",
    "t = 64 #int(input(\"how many time slices do you have in your movie?\"))\n",
    "masks_list = []\n",
    "labels = []\n",
    "Regions = []\n",
    "\n",
    "for j in range(t):\n",
    "    Regions_temp = []\n",
    "    masks_list_temp = []\n",
    "    labels_temp = []\n",
    "    for i in range(1, z+1):\n",
    "        mask = skimage.io.imread(\"C1-movie-%i_cp_masks.tif\" % (int(i)))\n",
    "        masks_list_temp.append(mask[j])\n",
    "        labelled = label(mask[j])\n",
    "        labels_temp.append(labelled)\n",
    "        Regions_temp.append(regionprops(labelled))\n",
    "    Regions.append(Regions_temp)\n",
    "    masks_list.append(masks_list_temp)\n",
    "    labels.append(labels_temp)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "print(len(Regions[0][1]))\n",
    "\n",
    "\n",
    "# Regions = np.reshape(Regions, (64, 5))\n",
    "# masks_list = np.reshape(masks_list, (64, 5))\n",
    "# labels = np.reshape(labels, (64, 5))\n",
    "\n",
    "\n",
    "data = skimage.io.imread(\"movie.tif\")\n",
    "\n",
    "# this just requires you to load the movie\n",
    "\n",
    "data = np.moveaxis(data, 3, 0)\n",
    "data = np.moveaxis(data, 4, 1)\n",
    "\n",
    "cells = data[:,:,:,:,0]\n",
    "\n",
    "Areas = []\n",
    "BBoxes = []\n",
    "Centroids = []\n",
    "\n",
    "for i in range(t):\n",
    "    Areas_temp = []\n",
    "    BBoxes_temp = []\n",
    "    Centroids_temp = []\n",
    "    for j in range(z):\n",
    "        Areas_temp.append([thisRegion.area for thisRegion in Regions[i][j]])\n",
    "        BBoxes_temp.append([thisRegion.bbox for thisRegion in Regions[i][j]])\n",
    "        Centroids_temp.append([thisRegion.centroid for thisRegion in Regions[i][j]])\n",
    "    Areas.append(Areas_temp)\n",
    "    BBoxes.append(BBoxes_temp)\n",
    "    Centroids.append(Centroids_temp)\n",
    "\n",
    "\n",
    "np.random.seed(19680801)\n",
    "\n",
    "class IndexTracker:\n",
    "    def __init__(self, ax, X, areas, bboxes, centroids):\n",
    "        self.ax = ax\n",
    "        ax.set_title(\"use arrow keys. up/down = scroll z-stack, left/right = scroll time series\")\n",
    "\n",
    "        self.X = X\n",
    "        self.areas = areas\n",
    "        self.bboxes = bboxes\n",
    "        self.centroids = centroids\n",
    "        rows, cols, self.tslices, self.zslices = X.shape\n",
    "        self.zind = self.zslices // 2\n",
    "        self.tind = self.tslices // 2\n",
    "\n",
    "        # requires [x, y, t, z] shape\n",
    "        self.im = ax.imshow(self.X[:, :, self.tind, self.zind])\n",
    "        self.update()\n",
    "\n",
    "    def on_key_press(self, event):\n",
    "        print(\"%s\" % (event.key))\n",
    "        if event.key == 'up':\n",
    "            self.zind = (self.zind + 1) % self.zslices\n",
    "        if event.key == 'down':\n",
    "            self.zind = (self.zind - 1) % self.zslices\n",
    "        if event.key == 'left':\n",
    "            self.tind = (self.tind - 1) % self.tslices\n",
    "        if event.key == 'right':\n",
    "            self.tind = (self.tind + 1) % self.tslices\n",
    "        # add try except here to account for not necessarily having all 3 channels\n",
    "        self.ax.clear()\n",
    "        self.update()\n",
    "\n",
    "    def update(self):\n",
    "        ax.set_title(\"use arrow keys. up/down = scroll z-stack, left/right = scroll time series\")\n",
    "        self.im.set_data(self.X[:, :, self.tind, self.zind])\n",
    "        self.im = ax.imshow(self.X[:, :, self.tind, self.zind])\n",
    "        self.ax.set_ylabel('z-slice %s, t-slice %s' % (self.zind, self.tind))\n",
    "        for (bb, area, centroid) in zip(self.bboxes[self.tind][self.zind], self.areas[self.tind][self.zind], self.centroids[self.tind][self.zind]):\n",
    "            r = drawrect((float(bb[1] - 1), float(bb[0] - 1)), bb[3] - bb[1], bb[2] - bb[0], edgecolor='r', facecolor='none')\n",
    "            self.ax.add_patch(r)\n",
    "            plt.scatter(centroid[1] - 1, centroid[0] - 1, c='r', s=2)\n",
    "        self.im.axes.figure.canvas.draw()\n",
    "\n",
    "fig, ax = plt.subplots(1, 1)\n",
    "\n",
    "\n",
    "\n",
    "tracker = IndexTracker(ax, cells, Areas, BBoxes, Centroids)\n",
    "\n",
    "fig.canvas.mpl_connect('key_press_event', tracker.on_key_press)\n",
    "plt.show()\n",
    "\n",
    "\n",
    "# Areas = [thisRegion.area for thisRegion in Regions]\n",
    "# BBs = [thisRegion.bbox for thisRegion in Regions]\n",
    "# Centroids = [thisRegion.centroid for thisRegion in Regions]\n",
    "# fig, ax = plt.subplots()\n",
    "# ax.imshow(cells)\n",
    "# ax.axis('off')\n",
    "# for (bb,area,centroid) in zip(BBs,Areas,Centroids):\n",
    "#     r = drawrect((float(bb[1]-1),float(bb[0]-1)), bb[3]-bb[1],bb[2]-bb[0], edgecolor='r', facecolor='none')\n",
    "#     ax.add_patch(r)\n",
    "#     plt.scatter(centroid[1]-1, centroid[0]-1, c='r', s=2)"
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