examples/DaskArray.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Install dependencies for this example\n",
    "# Note: This does not include itkwidgets, itself\n",
    "import sys\n",
    "!{sys.executable} -m pip install dask toolz scikit-image matplotlib itk-io"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from urllib.request import urlretrieve\n",
    "import os\n",
    "import zipfile\n",
    "\n",
    "import itk\n",
    "import dask.array.image\n",
    "\n",
    "from itkwidgets import view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Download data\n",
    "file_name = 'emdata_janelia_822252.zip'\n",
    "if not os.path.exists(file_name):\n",
    "    url = 'https://data.kitware.com/api/v1/file/5bf232498d777f2179b18acc/download'\n",
    "    urlretrieve(url, file_name)\n",
    "with zipfile.ZipFile(file_name, 'r') as zip_ref:\n",
    "    zip_ref.extractall()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This example is based on\n",
    "\n",
    "  http://matthewrocklin.com/blog/work/2017/01/17/dask-images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "3c08813adad5424fb491e2141c8d679a",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageUC2; proxy …"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "sample = itk.imread('emdata_janelia_822252/3000_3100_4010.png')\n",
    "view(sample)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
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       "<table>\n",
       "<tr>\n",
       "<td>\n",
       "<table>\n",
       "  <thead>\n",
       "    <tr><td> </td><th> Array </th><th> Chunk </th></tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr><th> Bytes </th><td> 8.00 MB </td> <td> 40.00 kB </td></tr>\n",
       "    <tr><th> Shape </th><td> (200, 200, 200) </td> <td> (1, 200, 200) </td></tr>\n",
       "    <tr><th> Count </th><td> 200 Tasks </td><td> 200 Chunks </td></tr>\n",
       "    <tr><th> Type </th><td> uint8 </td><td> numpy.ndarray </td></tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</td>\n",
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      ],
      "text/plain": [
       "dask.array<imread, shape=(200, 200, 200), dtype=uint8, chunksize=(1, 200, 200), chunktype=numpy.ndarray>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "stack = dask.array.image.imread('emdata_janelia_822252/*')\n",
    "stack"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f10f86ee619a4c5ca3eb60396d81ba64",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Viewer(geometries=[], gradient_opacity=0.4, point_sets=[], rendered_image=<itkImagePython.itkImageUC3; proxy o…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "view(stack, shadow=False, gradient_opacity=0.4, ui_collapsed=True)"
   ]
  }
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