notebooks/setup_images_to_stack.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Combine individual z-layers and channels to multichannel z-stacks (Setup)\n",
    "\n",
    "This is a setup notebook for adjusting parameters for [run_images_to_stack.ipynb](run_images_to_stack.ipynb).\n",
    "\n",
    "Run this notebook cell-by-cell and follow the instructions.\n",
    "\n",
    "## Requirements\n",
    "\n",
    "- A folder with images to convert\n",
    "\n",
    "Individual channels and z-layers must be clearly tagged in the filename, and the naming pattern must be consistent across the dataset. The naming pattern should follow the following scheme: \n",
    "\n",
    "`[SAMPLENAME][Z_CODE][Z#][CHANNEL_CODE][CHANNEL#].tif` or `[SAMPLENAME][CHANNEL_CODE][CHANNEL#][Z_CODE][Z#].tif`\n",
    "\n",
    "**Example**: `\"condition1/my_sample_position-3_Z00_C01.tif”`\n",
    "\n",
    "`[SAMPLENAME]` may include subfolders but must be the same for all files that will be combined.\n",
    "\n",
    "<hr style=\"height:2px;\">\n",
    "\n",
    "## Config\n",
    "\n",
    "<hr style=\"height:2px;\">\n",
    "\n",
    "### The following code imports and declares functions used for the processing:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "#################################\n",
    "#  Don't modify the code below  #\n",
    "#################################\n",
    "\n",
    "import os\n",
    "import json\n",
    "import numpy as np\n",
    "import intake_io\n",
    "from am_utils.utils import walk_dir\n",
    "from punctatools.lib.convert import load_random_dataset, check_metadata, get_number_of_stacks"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<hr style=\"height:2px;\">\n",
    "\n",
    "## Set up the data and parameters\n",
    "\n",
    "<hr style=\"height:2px;\">\n",
    "\n",
    "### Please provide data paths:\n",
    "\n",
    "`input_dir`: folder with images to be converted\n",
    "\n",
    "`output_dir`: folder to save results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "tags": [
     "parameters"
    ]
   },
   "outputs": [],
   "source": [
    "input_dir = \"../example_data/slices\"\n",
    "output_dir = \"../test_output/stacks\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The following code lists all image files in the input directory:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "30 images were found:\n",
      "['/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z20_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z20_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z20_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z21_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z21_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z21_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z22_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z22_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z22_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z23_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z23_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z23_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z24_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z24_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position1_Z24_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z20_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z20_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z20_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z21_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z21_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z21_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z22_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z22_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z22_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z23_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z23_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z23_C2.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z24_C0.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z24_C1.tif'\n",
      " '/tmp/pycharm_project_989/example_data/slices/sample1_position2_Z24_C2.tif']\n"
     ]
    }
   ],
   "source": [
    "#################################\n",
    "#  Don't modify the code below  #\n",
    "#################################\n",
    "\n",
    "input_dir = os.path.realpath(input_dir)\n",
    "\n",
    "samples = walk_dir(input_dir)\n",
    "\n",
    "print(f'{len(samples)} images were found:')\n",
    "print(np.array(samples))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Please specify codes for channel and z-position:\n",
    "\n",
    "Specify the sequence of characters that precedes the channel and z-position numbering, including the separator (e.g. \"_\") that precedes the channel code.\n",
    "\n",
    "For example, if the image name is \"my_experiment_position1_C0_z001.tif\", the codes should be as follows:\n",
    "\n",
    "`channel_code` = \"_C\"\n",
    "\n",
    "`z_position_code` = \"_z\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "channel_code = \"_C\"\n",
    "z_position_code = \"_Z\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The following code returns the number of stacks that were found\n",
    "\n",
    "If executing this cell results in an error, make sure the channel and z-position codes are provided correctly. Note that the codes are case-sensitive.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#################################\n",
    "#  Don't modify the code below  #\n",
    "#################################\n",
    "\n",
    "n = get_number_of_stacks(input_dir, channel_code=channel_code, z_position_code=z_position_code)\n",
    "n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The following code checks image metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The following voxel size was detected:\n",
      "z: None\n",
      "y: 0.11000000110000001\n",
      "x: 0.11000000110000001\n"
     ]
    }
   ],
   "source": [
    "#################################\n",
    "#  Don't modify the code below  #\n",
    "#################################\n",
    "\n",
    "dataset, spacing = check_metadata(input_dir, channel_code=channel_code, z_position_code=z_position_code)\n",
    "print('The following voxel size was detected:')\n",
    "if 'z' in dataset.dims:\n",
    "    dims = ['z', 'y', 'x']\n",
    "else:\n",
    "    dims = ['y', 'x']\n",
    "for s, c in zip(spacing, dims):\n",
    "    print(rf\"{c}: {s}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<hr style=\"height:0.5px;\">\n",
    "\n",
    "### Please specify correct voxel size \n",
    "\n",
    "Specify the correct voxel size (pixel size and z-stepping) in microns if the above values are wrong.\n",
    "\n",
    "Keep `None`, if the value loaded from the metadata is correct."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "z = 0.2\n",
    "y = None\n",
    "x = None"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The following code loads a random stack with correct voxel size"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div><svg style=\"position: absolute; width: 0; height: 0; overflow: hidden\">\n",
       "<defs>\n",
       "<symbol id=\"icon-database\" viewBox=\"0 0 32 32\">\n",
       "<path d=\"M16 0c-8.837 0-16 2.239-16 5v4c0 2.761 7.163 5 16 5s16-2.239 16-5v-4c0-2.761-7.163-5-16-5z\"></path>\n",
       "<path d=\"M16 17c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
       "<path d=\"M16 26c-8.837 0-16-2.239-16-5v6c0 2.761 7.163 5 16 5s16-2.239 16-5v-6c0 2.761-7.163 5-16 5z\"></path>\n",
       "</symbol>\n",
       "<symbol id=\"icon-file-text2\" viewBox=\"0 0 32 32\">\n",
       "<path d=\"M28.681 7.159c-0.694-0.947-1.662-2.053-2.724-3.116s-2.169-2.030-3.116-2.724c-1.612-1.182-2.393-1.319-2.841-1.319h-15.5c-1.378 0-2.5 1.121-2.5 2.5v27c0 1.378 1.122 2.5 2.5 2.5h23c1.378 0 2.5-1.122 2.5-2.5v-19.5c0-0.448-0.137-1.23-1.319-2.841zM24.543 5.457c0.959 0.959 1.712 1.825 2.268 2.543h-4.811v-4.811c0.718 0.556 1.584 1.309 2.543 2.268zM28 29.5c0 0.271-0.229 0.5-0.5 0.5h-23c-0.271 0-0.5-0.229-0.5-0.5v-27c0-0.271 0.229-0.5 0.5-0.5 0 0 15.499-0 15.5 0v7c0 0.552 0.448 1 1 1h7v19.5z\"></path>\n",
       "<path d=\"M23 26h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
       "<path d=\"M23 22h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
       "<path d=\"M23 18h-14c-0.552 0-1-0.448-1-1s0.448-1 1-1h14c0.552 0 1 0.448 1 1s-0.448 1-1 1z\"></path>\n",
       "</symbol>\n",
       "</defs>\n",
       "</svg>\n",
       "<style>/* CSS stylesheet for displaying xarray objects in jupyterlab.\n",
       " *\n",
       " */\n",
       "\n",
       ":root {\n",
       "  --xr-font-color0: var(--jp-content-font-color0, rgba(0, 0, 0, 1));\n",
       "  --xr-font-color2: var(--jp-content-font-color2, rgba(0, 0, 0, 0.54));\n",
       "  --xr-font-color3: var(--jp-content-font-color3, rgba(0, 0, 0, 0.38));\n",
       "  --xr-border-color: var(--jp-border-color2, #e0e0e0);\n",
       "  --xr-disabled-color: var(--jp-layout-color3, #bdbdbd);\n",
       "  --xr-background-color: var(--jp-layout-color0, white);\n",
       "  --xr-background-color-row-even: var(--jp-layout-color1, white);\n",
       "  --xr-background-color-row-odd: var(--jp-layout-color2, #eeeeee);\n",
       "}\n",
       "\n",
       "html[theme=dark],\n",
       "body.vscode-dark {\n",
       "  --xr-font-color0: rgba(255, 255, 255, 1);\n",
       "  --xr-font-color2: rgba(255, 255, 255, 0.54);\n",
       "  --xr-font-color3: rgba(255, 255, 255, 0.38);\n",
       "  --xr-border-color: #1F1F1F;\n",
       "  --xr-disabled-color: #515151;\n",
       "  --xr-background-color: #111111;\n",
       "  --xr-background-color-row-even: #111111;\n",
       "  --xr-background-color-row-odd: #313131;\n",
       "}\n",
       "\n",
       ".xr-wrap {\n",
       "  display: block !important;\n",
       "  min-width: 300px;\n",
       "  max-width: 700px;\n",
       "}\n",
       "\n",
       ".xr-text-repr-fallback {\n",
       "  /* fallback to plain text repr when CSS is not injected (untrusted notebook) */\n",
       "  display: none;\n",
       "}\n",
       "\n",
       ".xr-header {\n",
       "  padding-top: 6px;\n",
       "  padding-bottom: 6px;\n",
       "  margin-bottom: 4px;\n",
       "  border-bottom: solid 1px var(--xr-border-color);\n",
       "}\n",
       "\n",
       ".xr-header > div,\n",
       ".xr-header > ul {\n",
       "  display: inline;\n",
       "  margin-top: 0;\n",
       "  margin-bottom: 0;\n",
       "}\n",
       "\n",
       ".xr-obj-type,\n",
       ".xr-array-name {\n",
       "  margin-left: 2px;\n",
       "  margin-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-obj-type {\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-sections {\n",
       "  padding-left: 0 !important;\n",
       "  display: grid;\n",
       "  grid-template-columns: 150px auto auto 1fr 20px 20px;\n",
       "}\n",
       "\n",
       ".xr-section-item {\n",
       "  display: contents;\n",
       "}\n",
       "\n",
       ".xr-section-item input {\n",
       "  display: none;\n",
       "}\n",
       "\n",
       ".xr-section-item input + label {\n",
       "  color: var(--xr-disabled-color);\n",
       "}\n",
       "\n",
       ".xr-section-item input:enabled + label {\n",
       "  cursor: pointer;\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-section-item input:enabled + label:hover {\n",
       "  color: var(--xr-font-color0);\n",
       "}\n",
       "\n",
       ".xr-section-summary {\n",
       "  grid-column: 1;\n",
       "  color: var(--xr-font-color2);\n",
       "  font-weight: 500;\n",
       "}\n",
       "\n",
       ".xr-section-summary > span {\n",
       "  display: inline-block;\n",
       "  padding-left: 0.5em;\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:disabled + label {\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-section-summary-in + label:before {\n",
       "  display: inline-block;\n",
       "  content: '►';\n",
       "  font-size: 11px;\n",
       "  width: 15px;\n",
       "  text-align: center;\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:disabled + label:before {\n",
       "  color: var(--xr-disabled-color);\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:checked + label:before {\n",
       "  content: '▼';\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:checked + label > span {\n",
       "  display: none;\n",
       "}\n",
       "\n",
       ".xr-section-summary,\n",
       ".xr-section-inline-details {\n",
       "  padding-top: 4px;\n",
       "  padding-bottom: 4px;\n",
       "}\n",
       "\n",
       ".xr-section-inline-details {\n",
       "  grid-column: 2 / -1;\n",
       "}\n",
       "\n",
       ".xr-section-details {\n",
       "  display: none;\n",
       "  grid-column: 1 / -1;\n",
       "  margin-bottom: 5px;\n",
       "}\n",
       "\n",
       ".xr-section-summary-in:checked ~ .xr-section-details {\n",
       "  display: contents;\n",
       "}\n",
       "\n",
       ".xr-array-wrap {\n",
       "  grid-column: 1 / -1;\n",
       "  display: grid;\n",
       "  grid-template-columns: 20px auto;\n",
       "}\n",
       "\n",
       ".xr-array-wrap > label {\n",
       "  grid-column: 1;\n",
       "  vertical-align: top;\n",
       "}\n",
       "\n",
       ".xr-preview {\n",
       "  color: var(--xr-font-color3);\n",
       "}\n",
       "\n",
       ".xr-array-preview,\n",
       ".xr-array-data {\n",
       "  padding: 0 5px !important;\n",
       "  grid-column: 2;\n",
       "}\n",
       "\n",
       ".xr-array-data,\n",
       ".xr-array-in:checked ~ .xr-array-preview {\n",
       "  display: none;\n",
       "}\n",
       "\n",
       ".xr-array-in:checked ~ .xr-array-data,\n",
       ".xr-array-preview {\n",
       "  display: inline-block;\n",
       "}\n",
       "\n",
       ".xr-dim-list {\n",
       "  display: inline-block !important;\n",
       "  list-style: none;\n",
       "  padding: 0 !important;\n",
       "  margin: 0;\n",
       "}\n",
       "\n",
       ".xr-dim-list li {\n",
       "  display: inline-block;\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "}\n",
       "\n",
       ".xr-dim-list:before {\n",
       "  content: '(';\n",
       "}\n",
       "\n",
       ".xr-dim-list:after {\n",
       "  content: ')';\n",
       "}\n",
       "\n",
       ".xr-dim-list li:not(:last-child):after {\n",
       "  content: ',';\n",
       "  padding-right: 5px;\n",
       "}\n",
       "\n",
       ".xr-has-index {\n",
       "  font-weight: bold;\n",
       "}\n",
       "\n",
       ".xr-var-list,\n",
       ".xr-var-item {\n",
       "  display: contents;\n",
       "}\n",
       "\n",
       ".xr-var-item > div,\n",
       ".xr-var-item label,\n",
       ".xr-var-item > .xr-var-name span {\n",
       "  background-color: var(--xr-background-color-row-even);\n",
       "  margin-bottom: 0;\n",
       "}\n",
       "\n",
       ".xr-var-item > .xr-var-name:hover span {\n",
       "  padding-right: 5px;\n",
       "}\n",
       "\n",
       ".xr-var-list > li:nth-child(odd) > div,\n",
       ".xr-var-list > li:nth-child(odd) > label,\n",
       ".xr-var-list > li:nth-child(odd) > .xr-var-name span {\n",
       "  background-color: var(--xr-background-color-row-odd);\n",
       "}\n",
       "\n",
       ".xr-var-name {\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-var-dims {\n",
       "  grid-column: 2;\n",
       "}\n",
       "\n",
       ".xr-var-dtype {\n",
       "  grid-column: 3;\n",
       "  text-align: right;\n",
       "  color: var(--xr-font-color2);\n",
       "}\n",
       "\n",
       ".xr-var-preview {\n",
       "  grid-column: 4;\n",
       "}\n",
       "\n",
       ".xr-var-name,\n",
       ".xr-var-dims,\n",
       ".xr-var-dtype,\n",
       ".xr-preview,\n",
       ".xr-attrs dt {\n",
       "  white-space: nowrap;\n",
       "  overflow: hidden;\n",
       "  text-overflow: ellipsis;\n",
       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-var-name:hover,\n",
       ".xr-var-dims:hover,\n",
       ".xr-var-dtype:hover,\n",
       ".xr-attrs dt:hover {\n",
       "  overflow: visible;\n",
       "  width: auto;\n",
       "  z-index: 1;\n",
       "}\n",
       "\n",
       ".xr-var-attrs,\n",
       ".xr-var-data {\n",
       "  display: none;\n",
       "  background-color: var(--xr-background-color) !important;\n",
       "  padding-bottom: 5px !important;\n",
       "}\n",
       "\n",
       ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n",
       ".xr-var-data-in:checked ~ .xr-var-data {\n",
       "  display: block;\n",
       "}\n",
       "\n",
       ".xr-var-data > table {\n",
       "  float: right;\n",
       "}\n",
       "\n",
       ".xr-var-name span,\n",
       ".xr-var-data,\n",
       ".xr-attrs {\n",
       "  padding-left: 25px !important;\n",
       "}\n",
       "\n",
       ".xr-attrs,\n",
       ".xr-var-attrs,\n",
       ".xr-var-data {\n",
       "  grid-column: 1 / -1;\n",
       "}\n",
       "\n",
       "dl.xr-attrs {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  display: grid;\n",
       "  grid-template-columns: 125px auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt,\n",
       ".xr-attrs dd {\n",
       "  padding: 0;\n",
       "  margin: 0;\n",
       "  float: left;\n",
       "  padding-right: 10px;\n",
       "  width: auto;\n",
       "}\n",
       "\n",
       ".xr-attrs dt {\n",
       "  font-weight: normal;\n",
       "  grid-column: 1;\n",
       "}\n",
       "\n",
       ".xr-attrs dt:hover span {\n",
       "  display: inline-block;\n",
       "  background: var(--xr-background-color);\n",
       "  padding-right: 10px;\n",
       "}\n",
       "\n",
       ".xr-attrs dd {\n",
       "  grid-column: 2;\n",
       "  white-space: pre-wrap;\n",
       "  word-break: break-all;\n",
       "}\n",
       "\n",
       ".xr-icon-database,\n",
       ".xr-icon-file-text2 {\n",
       "  display: inline-block;\n",
       "  vertical-align: middle;\n",
       "  width: 1em;\n",
       "  height: 1.5em !important;\n",
       "  stroke-width: 0;\n",
       "  stroke: currentColor;\n",
       "  fill: currentColor;\n",
       "}\n",
       "</style><pre class='xr-text-repr-fallback'>&lt;xarray.Dataset&gt;\n",
       "Dimensions:  (y: 326, x: 326, z: 5, c: 3)\n",
       "Coordinates:\n",
       "  * y        (y) float64 0.0 0.11 0.22 0.33 0.44 ... 35.42 35.53 35.64 35.75\n",
       "  * x        (x) float64 0.0 0.11 0.22 0.33 0.44 ... 35.42 35.53 35.64 35.75\n",
       "  * z        (z) float64 0.0 0.2 0.4 0.6 0.8\n",
       "Dimensions without coordinates: c\n",
       "Data variables:\n",
       "    image    (c, z, y, x) uint16 105 106 103 110 106 113 ... 101 102 100 102 100\n",
       "Attributes:\n",
       "    metadata:  {&#x27;spacing_units&#x27;: {&#x27;x&#x27;: &#x27;µm&#x27;, &#x27;y&#x27;: &#x27;µm&#x27;, &#x27;z&#x27;: &#x27;µm&#x27;}}</pre><div class='xr-wrap' style='display:none'><div class='xr-header'><div class='xr-obj-type'>xarray.Dataset</div></div><ul class='xr-sections'><li class='xr-section-item'><input id='section-8902e51d-903e-49b4-a284-d3091695dfbd' class='xr-section-summary-in' type='checkbox' disabled ><label for='section-8902e51d-903e-49b4-a284-d3091695dfbd' class='xr-section-summary'  title='Expand/collapse section'>Dimensions:</label><div class='xr-section-inline-details'><ul class='xr-dim-list'><li><span class='xr-has-index'>y</span>: 326</li><li><span class='xr-has-index'>x</span>: 326</li><li><span class='xr-has-index'>z</span>: 5</li><li><span>c</span>: 3</li></ul></div><div class='xr-section-details'></div></li><li class='xr-section-item'><input id='section-eff74773-c6b1-4b58-ab73-1cdf67ff94d5' class='xr-section-summary-in' type='checkbox'  checked><label for='section-eff74773-c6b1-4b58-ab73-1cdf67ff94d5' class='xr-section-summary' >Coordinates: <span>(3)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>y</span></div><div class='xr-var-dims'>(y)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.0 0.11 0.22 ... 35.53 35.64 35.75</div><input id='attrs-5a901f45-3986-4949-bfd8-207b897e1f08' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-5a901f45-3986-4949-bfd8-207b897e1f08' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-0fddf719-f453-463a-bbde-a1f8fb60c1a0' class='xr-var-data-in' type='checkbox'><label for='data-0fddf719-f453-463a-bbde-a1f8fb60c1a0' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0.  ,  0.11,  0.22, ..., 35.53, 35.64, 35.75])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>x</span></div><div class='xr-var-dims'>(x)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.0 0.11 0.22 ... 35.53 35.64 35.75</div><input id='attrs-b738c6c1-e3d6-4a3d-83b6-3f5998f28ce1' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-b738c6c1-e3d6-4a3d-83b6-3f5998f28ce1' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-d1cd1562-c67e-48f3-b66f-2f4e95e1d04e' class='xr-var-data-in' type='checkbox'><label for='data-d1cd1562-c67e-48f3-b66f-2f4e95e1d04e' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([ 0.  ,  0.11,  0.22, ..., 35.53, 35.64, 35.75])</pre></div></li><li class='xr-var-item'><div class='xr-var-name'><span class='xr-has-index'>z</span></div><div class='xr-var-dims'>(z)</div><div class='xr-var-dtype'>float64</div><div class='xr-var-preview xr-preview'>0.0 0.2 0.4 0.6 0.8</div><input id='attrs-dce96a75-a825-4a43-8481-50aaef076b68' class='xr-var-attrs-in' type='checkbox' disabled><label for='attrs-dce96a75-a825-4a43-8481-50aaef076b68' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-ac8977cc-562d-4347-bd9f-612bcedccd97' class='xr-var-data-in' type='checkbox'><label for='data-ac8977cc-562d-4347-bd9f-612bcedccd97' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'></dl></div><div class='xr-var-data'><pre>array([0. , 0.2, 0.4, 0.6, 0.8])</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-00c40a7b-c85d-4f31-8f35-7481f91db8a9' class='xr-section-summary-in' type='checkbox'  checked><label for='section-00c40a7b-c85d-4f31-8f35-7481f91db8a9' class='xr-section-summary' >Data variables: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><ul class='xr-var-list'><li class='xr-var-item'><div class='xr-var-name'><span>image</span></div><div class='xr-var-dims'>(c, z, y, x)</div><div class='xr-var-dtype'>uint16</div><div class='xr-var-preview xr-preview'>105 106 103 110 ... 102 100 102 100</div><input id='attrs-f5de5e70-0e1b-4b93-bfe3-bf9c0cefec38' class='xr-var-attrs-in' type='checkbox' ><label for='attrs-f5de5e70-0e1b-4b93-bfe3-bf9c0cefec38' title='Show/Hide attributes'><svg class='icon xr-icon-file-text2'><use xlink:href='#icon-file-text2'></use></svg></label><input id='data-1d4fe79e-0e7f-4374-a397-1d38cf8a2ce9' class='xr-var-data-in' type='checkbox'><label for='data-1d4fe79e-0e7f-4374-a397-1d38cf8a2ce9' title='Show/Hide data repr'><svg class='icon xr-icon-database'><use xlink:href='#icon-database'></use></svg></label><div class='xr-var-attrs'><dl class='xr-attrs'><dt><span>metadata :</span></dt><dd>{&#x27;spacing&#x27;: {&#x27;y&#x27;: 0.11000000110000001, &#x27;x&#x27;: 0.11000000110000001, &#x27;z&#x27;: 0.2}, &#x27;original_shape&#x27;: (2, 3, 5, 326, 326), &#x27;original_axes&#x27;: &#x27;iczyx&#x27;, &#x27;axes&#x27;: &#x27;iczyx&#x27;, &#x27;spacing_units&#x27;: {&#x27;x&#x27;: &#x27;µm&#x27;, &#x27;y&#x27;: &#x27;µm&#x27;, &#x27;z&#x27;: &#x27;µm&#x27;}, &#x27;coords&#x27;: {&#x27;i&#x27;: [&#x27;/sample1_position1&#x27;, &#x27;/sample1_position2&#x27;]}, &#x27;fileheader&#x27;: {&#x27;dtype&#x27;: dtype(&#x27;uint16&#x27;), &#x27;shape&#x27;: (326, 326), &#x27;npartitions&#x27;: 1, &#x27;metadata&#x27;: {&#x27;original_shape&#x27;: (326, 326), &#x27;original_axes&#x27;: &#x27;yx&#x27;, &#x27;axes&#x27;: &#x27;yx&#x27;, &#x27;spacing&#x27;: {&#x27;y&#x27;: 0.11000000110000001, &#x27;x&#x27;: 0.11000000110000001, &#x27;z&#x27;: 0.2}, &#x27;spacing_units&#x27;: {&#x27;x&#x27;: &#x27;µm&#x27;, &#x27;y&#x27;: &#x27;µm&#x27;}, &#x27;fileheader&#x27;: {&#x27;imagej&#x27;: {&#x27;ImageJ&#x27;: &#x27;1.53f&#x27;, &#x27;unit&#x27;: &#x27;\\\\u00B5m&#x27;, &#x27;min&#x27;: 79.0, &#x27;max&#x27;: 2019.0, &#x27;Info&#x27;: &#x27;05282021_GFPNHX9_HOXWT - Position 1_XY_Z20_T0_C0.tif\\nSoftware: SlideBook\\nDateTime: 2021:05:28 09:40:35\\n&#x27;}}}}}</dd><dt><span>uri :</span></dt><dd>/tmp/pycharm_project_989/example_data/slices</dd></dl></div><div class='xr-var-data'><pre>array([[[[105, 106, 103, ..., 137, 138, 138],\n",
       "         [113, 106, 103, ..., 155, 141, 150],\n",
       "         [107, 105, 111, ..., 150, 152, 147],\n",
       "         ...,\n",
       "         [101, 105, 103, ..., 180, 152, 147],\n",
       "         [101, 106, 107, ..., 154, 172, 164],\n",
       "         [104, 103, 103, ..., 176, 156, 159]],\n",
       "\n",
       "        [[109, 102, 105, ..., 141, 141, 138],\n",
       "         [112, 110, 105, ..., 151, 141, 137],\n",
       "         [110, 100, 105, ..., 143, 150, 140],\n",
       "         ...,\n",
       "         [103, 103, 107, ..., 170, 166, 165],\n",
       "         [103, 102,  98, ..., 154, 174, 168],\n",
       "         [102, 101, 105, ..., 175, 172, 169]],\n",
       "\n",
       "        [[103,  99, 104, ..., 142, 139, 146],\n",
       "         [110, 106, 108, ..., 140, 152, 145],\n",
       "         [105, 104, 109, ..., 152, 144, 154],\n",
       "         ...,\n",
       "...\n",
       "         ...,\n",
       "         [101,  98, 100, ...,  98, 101, 101],\n",
       "         [ 99,  98, 102, ...,  99, 102, 104],\n",
       "         [101, 100, 101, ..., 104, 104, 102]],\n",
       "\n",
       "        [[101, 103, 100, ..., 100, 100, 101],\n",
       "         [101, 104, 102, ...,  99, 103, 101],\n",
       "         [101, 102, 100, ..., 102,  99, 103],\n",
       "         ...,\n",
       "         [104, 100, 101, ..., 102, 104, 100],\n",
       "         [104, 105,  99, ..., 100, 101, 102],\n",
       "         [102,  98,  99, ...,  99, 101,  99]],\n",
       "\n",
       "        [[103,  97,  99, ..., 101, 103, 100],\n",
       "         [100, 103, 100, ..., 102, 104, 102],\n",
       "         [ 96, 102,  99, ..., 102,  98,  99],\n",
       "         ...,\n",
       "         [104, 100, 101, ..., 101, 101, 104],\n",
       "         [100,  99, 101, ..., 100, 100, 103],\n",
       "         [105, 102, 101, ..., 100, 102, 100]]]], dtype=uint16)</pre></div></li></ul></div></li><li class='xr-section-item'><input id='section-99b9c39a-c4df-44c0-8160-a213bd3745fb' class='xr-section-summary-in' type='checkbox'  checked><label for='section-99b9c39a-c4df-44c0-8160-a213bd3745fb' class='xr-section-summary' >Attributes: <span>(1)</span></label><div class='xr-section-inline-details'></div><div class='xr-section-details'><dl class='xr-attrs'><dt><span>metadata :</span></dt><dd>{&#x27;spacing_units&#x27;: {&#x27;x&#x27;: &#x27;µm&#x27;, &#x27;y&#x27;: &#x27;µm&#x27;, &#x27;z&#x27;: &#x27;µm&#x27;}}</dd></dl></div></li></ul></div></div>"
      ],
      "text/plain": [
       "<xarray.Dataset>\n",
       "Dimensions:  (y: 326, x: 326, z: 5, c: 3)\n",
       "Coordinates:\n",
       "  * y        (y) float64 0.0 0.11 0.22 0.33 0.44 ... 35.42 35.53 35.64 35.75\n",
       "  * x        (x) float64 0.0 0.11 0.22 0.33 0.44 ... 35.42 35.53 35.64 35.75\n",
       "  * z        (z) float64 0.0 0.2 0.4 0.6 0.8\n",
       "Dimensions without coordinates: c\n",
       "Data variables:\n",
       "    image    (c, z, y, x) uint16 105 106 103 110 106 113 ... 101 102 100 102 100\n",
       "Attributes:\n",
       "    metadata:  {'spacing_units': {'x': 'µm', 'y': 'µm', 'z': 'µm'}}"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#################################\n",
    "#  Don't modify the code below  #\n",
    "#################################\n",
    "\n",
    "if 'z' in dataset.dims:\n",
    "    spacing = [z, y, x]\n",
    "else:\n",
    "    spacing = [y, x]\n",
    "dataset = load_random_dataset(input_dir, channel_code=channel_code, \n",
    "                              z_position_code=z_position_code, spacing=spacing)\n",
    "dataset"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<hr style=\"height:2px;\">\n",
    "\n",
    "## Run the full processing\n",
    "\n",
    "The parameters set up in this notebook will be used to convert images in batch.\n",
    "\n",
    "<hr style=\"height:2px;\">\n",
    "\n",
    "### Please provide the file name to save the parameters\n",
    "\n",
    "If only a filename is provided, the parameter file will be saved in the same directory with this notebook. Provide the full path to save the parameters to a different directory.\n",
    "\n",
    "Default is `parameters_conversion.json`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "parameter_file = 'parameters_conversion.json'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### The following code saves the parameters\n",
    "\n",
    "To run the full processing, run the notebook [run_images_to_stack.ipynb](run_images_to_stack.ipynb) with the parameter file specified here. \n",
    "\n",
    "Alternatively run the [run_images_to_stack.py](../scripts/run_images_to_stack.py) script:\n",
    "\n",
    "``python run_images_to_stack.py -p <parameter file> -j <number of parallel processes> -i <input directory> -o <output directory>``"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#################################\n",
    "#  Don't modify the code below  #\n",
    "#################################\n",
    "\n",
    "spacing = list(intake_io.get_spacing(dataset))\n",
    "\n",
    "params = dict(\n",
    "    input_dir=os.path.realpath(input_dir),\n",
    "    output_dir=os.path.realpath(output_dir),\n",
    "    spacing=spacing,\n",
    "    channel_code=channel_code,\n",
    "    z_position_code=z_position_code\n",
    ")\n",
    "\n",
    "with open(parameter_file, 'w') as f:\n",
    "    json.dump(params, f, indent=4)\n",
    "    \n",
    "params"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python [conda env:punctatools]",
   "language": "python",
   "name": "conda-env-punctatools-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}