TimeLapseData3d-Copy1.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[Errno 2] No such file or directory: u'/Users/markslabodnick/.gputools'\n",
      "<pyopencl.Device 'Intel(R) HD Graphics 530' on 'Apple' at 0x1024500>\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/local/lib/python2.7/site-packages/pyopencl/cffi_cl.py:1476: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.\n",
      "  \"to see more.\", CompilerWarning)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[Errno 2] No such file or directory: '/Users/markslabodnick/.spimagine'\n",
      "<pyopencl.Device 'Intel(R) HD Graphics 530' on 'Apple' at 0x1024500>\n"
     ]
    }
   ],
   "source": [
    "import time\n",
    "import copy\n",
    "import numpy as np\n",
    "from skimage.filters import gaussian_filter\n",
    "\n",
    "from tifffile import imread, imsave\n",
    "import cPickle as pickle\n",
    "\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "from spimagine import volfig, volshow\n",
    "from spimagine import EllipsoidMesh, Mesh\n",
    "\n",
    "%reload_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "from netsurface3d import NetSurf3d\n",
    "from data4d import Data4d\n",
    "\n",
    "%matplotlib qt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load time-lapse data..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "filenames = ['/Users/markslabodnick/Dropbox/ProjectGoldstein/3dseg/Imaging_Strain-01_Embryo2.tif']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dimensions of frame 0 :  (25, 514, 326)\n"
     ]
    }
   ],
   "source": [
    "data = Data4d( filenames, pixelsize=(1.,1.,8.), silent=False )\n",
    "data.set_seg_params(K=120,max_delta_k=6)\n",
    "objects = []\n",
    "ecells = []"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Min radius and max radius at which to look for cells (around center points (seed points))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "max_rs = (data.images[0].shape[2] / 1,\n",
    "          data.images[0].shape[1] / 1,\n",
    "          data.images[0].shape[0] / 1)\n",
    "\n",
    "min_rs = (5,5,1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## adding A cells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "Ea = data.init_object(\"Ea\")\n",
    "objects.append(Ea)\n",
    "ecells.append(Ea)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Added appearance for \"Ea\" in frame 0 with seed coordinates [ 226.   84.   10.]\n",
      "      Optimum energy:  806626.0\n",
      "      Nodes in/out:  13218 48222\n"
     ]
    }
   ],
   "source": [
    "data.add_object_at( Ea, min_rs, max_rs, frame=0, seed=(226,84,10), frame_to=0, seed_to=(448,569,8), segment_it=True )\n",
    "#data.add_object_at( Ea, min_rs, max_rs, frame=0, seed=(429,576,0), segment_it=True )\n",
    "#data.track(Ea, seed_frame=0, target_frames=range(1,len(data.images)), recenter_iterations=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Visualisation stuff "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "w = data.show_frame(0,stackUnits=[1.,1.,8.],raise_window=True)\n",
    "data.show_objects(ecells, show_surfaces=True, show_centers=True, colors=data.colors_gold)\n",
    "try:\n",
    "    data.show_objects(neighbors, show_surfaces=True, show_centers=True, colors=data.colors_green)\n",
    "    data.show_objects(others, show_surfaces=True, show_centers=True, colors=data.colors_blue)\n",
    "except:\n",
    "    None"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Exporting frame  1 of 1\n"
     ]
    },
    {
     "ename": "AttributeError",
     "evalue": "'MainWidget' object has no attribute 'glWidget'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-25-4a277694ce2b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mf\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mimages\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m     \u001b[0;32mprint\u001b[0m \u001b[0;34m'Exporting frame '\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'of'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mimages\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m     \u001b[0mw\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshow_frame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mstackUnits\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1.\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1.\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m5.\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mraise_window\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m     \u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshow_objects\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecells\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mshow_surfaces\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mshow_centers\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcolors\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolors_gold\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/Users/markslabodnick/Dropbox/Bobseg/BobSeg/data4d.pyc\u001b[0m in \u001b[0;36mshow_frame\u001b[0;34m(self, f, show_surfaces, show_centers, stackUnits, raise_window)\u001b[0m\n\u001b[1;32m    306\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspimagine\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvolshow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mimages\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstackUnits\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstackUnits\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mraise_window\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mraise_window\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mautoscale\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    307\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 308\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspimagine\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mglWidget\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrenderer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mimages\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    309\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspimagine\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mglWidget\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrefresh\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    310\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'MainWidget' object has no attribute 'glWidget'"
     ]
    }
   ],
   "source": [
    "for f in range(len(data.images)):\n",
    "    print 'Exporting frame ',f+1,'of',len(data.images)\n",
    "    w = data.show_frame(f,stackUnits=[1.,1.,5.],raise_window=False)\n",
    "    data.show_objects(ecells, show_surfaces=True, show_centers=True, colors=data.colors_gold)\n",
    "    try:\n",
    "        data.show_objects(neighbors, show_surfaces=True, show_centers=True, colors=data.colors_green)\n",
    "        data.show_objects(others, show_surfaces=True, show_centers=True, colors=data.colors_blue)\n",
    "    except:\n",
    "        None\n",
    "    data.save_current_visualization( 'frame'+str(f)+'.jpg' )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}