{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Downloading ConWhAt Atlases"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Import the fetcher function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "from conwhat.utils.fetchers import fetch_conwhat_atlas\n",
    "import glob"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define the output directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "atlas_dir = '/scratch/hpc3230/Data/conwhat_atlases'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define which atlas to grab"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "atlas_name = 'CWL2k8Sc33Vol3d100s_v01'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Break a leg"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "removing existing folder\n",
      "\n",
      "\n",
      "duplicate file detected - removing...\n",
      "rm CWL2k8Sc33Vol3d100s_v01.zip\n",
      "\n",
      "\n",
      "downloading data_file CWL2k8Sc33Vol3d100s_v01.zip...\n",
      "wget https://www.nitrc.org/frs/download.php/10381/CWL2k8Sc33Vol3d100s_v01.zip\n",
      "\n",
      "\n",
      "unzipping file...\n",
      "unzip CWL2k8Sc33Vol3d100s_v01.zip\n",
      "\n",
      "\n",
      "finished unzipping.\n"
     ]
    }
   ],
   "source": [
    "fetch_conwhat_atlas(atlas_name,atlas_dir,remove_existing=True);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The zipped and unzipped atlas folders are now there in the top-level atlas directory;"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01.zip',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/README.md']"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "glob.glob(atlas_dir + '/*')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The .zip file can be optionally removed automatically if desired. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "volumetric atlas folders contain a small number of fairly small .txt files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/region_mapping_fsav_rh.txt',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/weights.txt',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/mappings.txt',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/region_labels.txt',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/bounding_boxes.txt',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/hemispheres.txt',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/cortex.txt',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/region_mapping_fsav_lh.txt']"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "glob.glob('%s/%s/*.txt' %(atlas_dir,atlas_name))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "...and a larger number of nifti images; one for each atlas structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_7-64_norm.nii.gz',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_23-30_norm.nii.gz',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_65-69_norm.nii.gz',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_55-70_norm.nii.gz',\n",
       " '/scratch/hpc3230/Data/conwhat_atlases/CWL2k8Sc33Vol3d100s_v01/vismap_grp_28-64_norm.nii.gz']"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "glob.glob('%s/%s/*.nii.gz' %(atlas_dir,atlas_name))[:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2445"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(glob.glob('%s/%s/*.nii.gz' %(atlas_dir,atlas_name)))"
   ]
  }
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