tools/filetree_example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from examplecode.example import DirectoryTree"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "```Text\n",
      "├─ sub-01_part-mag_T1w.nii.gz \n",
      "├─ sub-01_part-mag_T1w.json \n",
      "├─ sub-01_part-phase_T1w.nii.gz   comments can be added here\n",
      "└─ sub-01_part-phase_T1w.json         but padding them could be optimized\n",
      "```\n",
      "\n"
     ]
    }
   ],
   "source": [
    "directory_list =  {\n",
    "                \"sub-01_part-mag_T1w.nii.gz\" : \"\", # leave this value empty for files\n",
    "                \"sub-01_part-mag_T1w.json\" : \"\",\n",
    "                \"sub-01_part-phase_T1w.nii.gz\" : \"  comments can be added here\",\n",
    "                \"sub-01_part-phase_T1w.json\" : \"        but padding them could be optimized\",\n",
    "}\n",
    "\n",
    "tree = DirectoryTree(directory_list)\n",
    "text = tree.generate()\n",
    "print(text)      "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "```Text\n",
      "├─ sub-01\\\n",
      "│  ├─ sub-01_part-mag_T1w.nii.gz \n",
      "│  ├─ sub-01_part-mag_T1w.json \n",
      "│  ├─ sub-01_part-phase_T1w.nii.gz \n",
      "│  └─ sub-01_part-phase_T1w.json \n",
      "└─ sub-02\\\n",
      "   └─ sub-02_part-mag_T1w.nii.gz \n",
      "```\n",
      "\n"
     ]
    }
   ],
   "source": [
    "directory_dict =  {\n",
    "                    \"sub-01\": { # use nested dictionaries to represent directories\n",
    "                        \"sub-01_part-mag_T1w.nii.gz\" : \"\",\n",
    "                        \"sub-01_part-mag_T1w.json\" : \"\",\n",
    "                        \"sub-01_part-phase_T1w.nii.gz\" : \"\",\n",
    "                        \"sub-01_part-phase_T1w.json\" : \"\",\n",
    "                    },\n",
    "                    \"sub-02\": {\n",
    "                        \"sub-02_part-mag_T1w.nii.gz\" : \"\",\n",
    "                    }\n",
    "                    }\n",
    "\n",
    "tree = DirectoryTree(directory_dict)\n",
    "text = tree.generate()\n",
    "print(text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "```Text\n",
      "└─ sub-01\\\n",
      "   └─ anat\\\n",
      "      ├─ sub-01_part-mag_T1w.nii.gz \n",
      "      ├─ sub-01_part-mag_T1w.json \n",
      "      ├─ sub-01_part-phase_T1w.nii.gz \n",
      "      └─ sub-01_part-phase_T1w.json \n",
      "```\n",
      "\n"
     ]
    }
   ],
   "source": [
    "nested_directory_dict =  {\n",
    "                        \"sub-01\" : {\n",
    "                            \"anat\": { # you can represent subdirectories by nesting directories\n",
    "                                \"sub-01_part-mag_T1w.nii.gz\" : \"\",\n",
    "                                \"sub-01_part-mag_T1w.json\" : \"\",\n",
    "                                \"sub-01_part-phase_T1w.nii.gz\" : \"\",\n",
    "                                \"sub-01_part-phase_T1w.json\" : \"\",\n",
    "                            }\n",
    "                        }\n",
    "                        }\n",
    "                        \n",
    "tree = DirectoryTree(nested_directory_dict)\n",
    "text = tree.generate()\n",
    "print(text)                        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "```Text\n",
      "└─ my_processed_data\\\n",
      "   ├─ code\\\n",
      "   │  ├─ processing_pipeline-1.0.0.img \n",
      "   │  ├─ hpc_submitter.sh \n",
      "   │  └─ ... \n",
      "   ├─ sourcedata\\\n",
      "   │  ├─ sub-01\\\n",
      "   │  ├─ sub-02\\\n",
      "   │  └─ ... \n",
      "   ├─ sub-01\\\n",
      "   ├─ sub-02\\\n",
      "   └─ ... \n",
      "```\n",
      "\n"
     ]
    }
   ],
   "source": [
    "directory = {  \n",
    "            \"my_processed_data\": {\n",
    "                \"code\":{\n",
    "                    \"processing_pipeline-1.0.0.img\" : \"\",\n",
    "                    \"hpc_submitter.sh\" : \"\",\n",
    "                    \"...\" : \"\",\n",
    "                },\n",
    "                \"sourcedata\": {\n",
    "                    \"sub-01\" : {}, # use empty dictionaries to represent directories without specifying their content\n",
    "                    \"sub-02\" : {},\n",
    "                    \"...\" : \"\",\n",
    "                },\n",
    "                \"sub-01\" : {},\n",
    "                \"sub-02\" : {},\n",
    "                \"...\" : \"\"\n",
    "                }\n",
    "            }\n",
    "\n",
    "tree = DirectoryTree(directory)\n",
    "text = tree.generate()\n",
    "print(text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "```Text\n",
      "├─ dataset_description.json \n",
      "├─ sub-01\\\n",
      "│  ├─ sessions.tsv \n",
      "│  ├─ ses-01\\\n",
      "│  │  └─ anat\\\n",
      "│  │     ├─ sub-01_part-mag_T1w.nii.gz \n",
      "│  │     ├─ sub-01_part-mag_T1w.json \n",
      "│  │     ├─ sub-01_part-phase_T1w.nii.gz \n",
      "│  │     └─ sub-01_part-phase_T1w.json \n",
      "│  └─ scans.tsv \n",
      "└─ ses-02\\\n",
      "   └─ func\\\n",
      "      └─ sub-01_bold.nii.gz \n",
      "```\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# you can also represent files and directories on the same level\n",
    "\n",
    "directory = {\n",
    "            \"dataset_description.json\" : \"\",\n",
    "            \"sub-01\" : {\n",
    "                \"sessions.tsv\" : \"\",\n",
    "                \"ses-01\" : {\n",
    "                    \"anat\" : {\n",
    "                        \"sub-01_part-mag_T1w.nii.gz\" : \"\",\n",
    "                        \"sub-01_part-mag_T1w.json\" : \"\",\n",
    "                        \"sub-01_part-phase_T1w.nii.gz\" : \"\",\n",
    "                        \"sub-01_part-phase_T1w.json\" : \"\",\n",
    "                        }\n",
    "                    },\n",
    "                    \"scans.tsv\": \"\",\n",
    "                },\n",
    "                \"ses-02\": {\n",
    "                    \"func\": {\n",
    "                        \"sub-01_bold.nii.gz\" : \"\",\n",
    "                    }\n",
    "                }\n",
    "            }\n",
    "\n",
    "tree = DirectoryTree(directory)\n",
    "text = tree.generate()\n",
    "print(text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "```Text\n",
      "└─ sub-<label>\\\n",
      "   └─ [ses-<label>]\\\n",
      "      └─ motion\\\n",
      "         ├─ sub-<label>[_ses-<label>]_task-<label>[_tracksys-<label>]_motion.tsv \n",
      "         ├─ sub-<label>[_ses-<label>]_task-<label>_motion.json \n",
      "         ├─ sub-<label>[_ses-<label>]_task-<label>_channels.tsv \n",
      "         ├─ sub-<label>[_ses-<label>]_task-<label>_coordsystem.json \n",
      "         ├─ sub-<label>[_ses-<label>]_task-<label>_events.tsv \n",
      "         └─ sub-<label>[_ses-<label>]_task-<label>_events.json \n",
      "```\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# BIDS motion example recording data\n",
    "\n",
    "directory = {\n",
    "            \"sub-<label>\" : {\n",
    "                \"[ses-<label>]\" : {\n",
    "                    \"motion\" : {\n",
    "                        \"sub-<label>[_ses-<label>]_task-<label>[_tracksys-<label>]_motion.tsv\" : \"\",\n",
    "                        \"sub-<label>[_ses-<label>]_task-<label>_motion.json\" : \"\",\n",
    "                        \"sub-<label>[_ses-<label>]_task-<label>_channels.tsv\" : \"\",\n",
    "                        \"sub-<label>[_ses-<label>]_task-<label>_coordsystem.json\" : \"\",\n",
    "                        \"sub-<label>[_ses-<label>]_task-<label>_events.tsv\" : \"\",\n",
    "                        \"sub-<label>[_ses-<label>]_task-<label>_events.json\" : \"\",\n",
    "                        }\n",
    "                    }\n",
    "                }\n",
    "            }\n",
    "\n",
    "tree = DirectoryTree(directory)\n",
    "text = tree.generate()\n",
    "print(text)\n"
   ]
  }
 ],
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