docs/notebooks/HTML_param_groups.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# HTML Param Groups"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.append(\"..\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/Users/Covitz/CuBIDS/notebooks/testdata'"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# USE THIS BEFORE TESTING!\n",
    "\n",
    "from pathlib import Path\n",
    "import shutil\n",
    "import os\n",
    "#import cubids\n",
    "from bids.layout import parse_file_entities\n",
    "from cubids import CuBIDS\n",
    "from pkg_resources import resource_filename as pkgrf\n",
    "\n",
    "# returns string path to testdata\n",
    "TEST_DATA = pkgrf(\"cubids\", \"testdata\")\n",
    "\n",
    "# should give you the full path\n",
    "tmp_path = Path().resolve()\n",
    "#print(tmp_path)\n",
    "\n",
    "# dest path\n",
    "data_root = tmp_path / \"testdata\"\n",
    "\n",
    "# ensure path does not already exist in cwd\n",
    "if data_root.exists():\n",
    "    shutil.rmtree(str(data_root))\n",
    "\n",
    "# equivalent of command line \"cp\"\n",
    "cwd = shutil.copytree(TEST_DATA, str(data_root))\n",
    "\n",
    "cwd\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "testdata\r\n",
      "testdata/complete\r\n",
      "testdata/complete/sub-01\r\n",
      "testdata/complete/sub-01/ses-phdiff\r\n",
      "testdata/complete/sub-01/ses-phdiff/dwi\r\n",
      "testdata/complete/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval\r\n",
      "testdata/complete/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec\r\n",
      "testdata/complete/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz\r\n",
      "testdata/complete/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.json\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.nii.gz\r\n",
      "testdata/complete/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json\r\n",
      "testdata/complete/sub-01/ses-phdiff/anat\r\n",
      "testdata/complete/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json\r\n",
      "testdata/complete/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz\r\n",
      "testdata/complete/sub-01/ses-phdiff/func\r\n",
      "testdata/complete/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.nii.gz\r\n",
      "testdata/complete/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.json\r\n",
      "testdata/complete/README\r\n",
      "testdata/complete/dataset_description.json\r\n",
      "testdata/complete/sub-02\r\n",
      "testdata/complete/sub-02/ses-phdiff\r\n",
      "testdata/complete/sub-02/ses-phdiff/dwi\r\n",
      "testdata/complete/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.bvec\r\n",
      "testdata/complete/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.nii.gz\r\n",
      "testdata/complete/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.bval\r\n",
      "testdata/complete/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.json\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude1.nii.gz\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_phasediff.json\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude2.json\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_dir-PA_epi.nii.gz\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude2.nii.gz\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude1.json\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_phasediff.nii.gz\r\n",
      "testdata/complete/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_dir-PA_epi.json\r\n",
      "testdata/complete/sub-02/ses-phdiff/anat\r\n",
      "testdata/complete/sub-02/ses-phdiff/anat/sub-02_ses-phdiff_T1w.nii.gz\r\n",
      "testdata/complete/sub-02/ses-phdiff/anat/sub-02_ses-phdiff_T1w.json\r\n",
      "testdata/complete/sub-02/ses-phdiff/func\r\n",
      "testdata/complete/sub-02/ses-phdiff/func/sub-02_ses-phdiff_task-rest_bold.nii.gz\r\n",
      "testdata/complete/sub-02/ses-phdiff/func/sub-02_ses-phdiff_task-rest_bold.json\r\n",
      "testdata/complete/sub-03\r\n",
      "testdata/complete/sub-03/ses-phdiff\r\n",
      "testdata/complete/sub-03/ses-phdiff/dwi\r\n",
      "testdata/complete/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.nii.gz\r\n",
      "testdata/complete/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.json\r\n",
      "testdata/complete/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.bvec\r\n",
      "testdata/complete/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.bval\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude2.nii.gz\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude2.json\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.nii.gz\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude1.nii.gz\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.json\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude1.json\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.json\r\n",
      "testdata/complete/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.nii.gz\r\n",
      "testdata/complete/sub-03/ses-phdiff/anat\r\n",
      "testdata/complete/sub-03/ses-phdiff/anat/sub-03_ses-phdiff_T1w.json\r\n",
      "testdata/complete/sub-03/ses-phdiff/anat/sub-03_ses-phdiff_T1w.nii.gz\r\n",
      "testdata/complete/sub-03/ses-phdiff/func\r\n",
      "testdata/complete/sub-03/ses-phdiff/func/sub-03_ses-phdiff_task-rest_bold.json\r\n",
      "testdata/complete/sub-03/ses-phdiff/func/sub-03_ses-phdiff_task-rest_bold.nii.gz\r\n",
      "testdata/inconsistent\r\n",
      "testdata/inconsistent/sub-01\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/dwi\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bval\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.bvec\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.nii.gz\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/dwi/sub-01_ses-phdiff_acq-HASC55AP_dwi.json\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.json\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.json\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.nii.gz\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_phasediff.nii.gz\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.json\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude2.nii.gz\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_dir-PA_epi.nii.gz\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/fmap/sub-01_ses-phdiff_acq-v4_magnitude1.json\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/anat\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.json\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/anat/sub-01_ses-phdiff_T1w.nii.gz\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/func\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.nii.gz\r\n",
      "testdata/inconsistent/sub-01/ses-phdiff/func/sub-01_ses-phdiff_task-rest_bold.json\r\n",
      "testdata/inconsistent/README\r\n",
      "testdata/inconsistent/dataset_description.json\r\n",
      "testdata/inconsistent/sub-02\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/dwi\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.bvec\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.nii.gz\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.bval\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.json\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude1.nii.gz\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_phasediff.json\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude2.json\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_dir-PA_epi.nii.gz\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude2.nii.gz\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude1.json\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_phasediff.nii.gz\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/fmap/sub-02_ses-phdiff_dir-PA_epi.json\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/anat\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/anat/sub-02_ses-phdiff_T1w.nii.gz\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/anat/sub-02_ses-phdiff_T1w.json\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/func\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/func/sub-02_ses-phdiff_task-rest_bold.nii.gz\r\n",
      "testdata/inconsistent/sub-02/ses-phdiff/func/sub-02_ses-phdiff_task-rest_bold.json\r\n",
      "testdata/inconsistent/sub-03\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/dwi\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.nii.gz\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.json\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.bvec\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/dwi/sub-03_ses-phdiff_acq-HASC55AP_dwi.bval\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude2.nii.gz\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude2.json\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.nii.gz\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude1.nii.gz\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_dir-PA_epi.json\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_magnitude1.json\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.json\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/fmap/sub-03_ses-phdiff_acq-v4_phasediff.nii.gz\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/anat\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/anat/sub-03_ses-phdiff_T1w.json\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/anat/sub-03_ses-phdiff_T1w.nii.gz\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/func\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/func/sub-03_ses-phdiff_task-rest_bold.json\r\n",
      "testdata/inconsistent/sub-03/ses-phdiff/func/sub-03_ses-phdiff_task-rest_bold.nii.gz\r\n"
     ]
    }
   ],
   "source": [
    "! find testdata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'a': [0, 2], 'b': [1, 3], 'c': [4], 'd': [5]}\n",
      "{'subject': '01', 'session': 'phdiff', 'acquisition': 'v4', 'suffix': 'magnitude1', 'datatype': 'fmap', 'extension': '.json'}\n",
      "acquisition-v4_datatype-fmap_extension-.json_session-phdiff_subject-01_suffix-magnitude1\n",
      "Entities:  {'acquisition': 'v4', 'datatype': 'fmap', 'extension': '.json', 'session': 'phdiff', 'subject': '01', 'suffix': 'magnitude1'}\n",
      "F_2_K:  acquisition-v4_datatype-fmap_extension-.json_session-phdiff_subject-01_suffix-magnitude1\n"
     ]
    }
   ],
   "source": [
    "# TEST BED FOR HTML THING\n",
    "\n",
    "\n",
    "\n",
    "# ISSUE! Grouping by char!\n",
    "\n",
    "#param_group = cubids_obj.get_param_groups(key_group)\n",
    "# print(key_group)\n",
    "# #print(param_group)\n",
    "\n",
    "NON_KEY_ENTITIES = set([\"subject\", \"session\", \"extension\"])\n",
    "\n",
    "def key_group_to_entities(key_group):\n",
    "    return dict([group.split(\"-\") for group in key_group.split(\"_\")])\n",
    "\n",
    "\n",
    "def entities_to_key_group(entities):\n",
    "    group_keys = sorted(entities.keys())\n",
    "    return \"_\".join(\n",
    "         [\"{}-{}\".format(key, entities[key]) for key in group_keys])\n",
    "\n",
    "def file_to_entities(filename):\n",
    "    entities = parse_file_entities(str(filename))\n",
    "    return entities\n",
    "\n",
    "def file_to_key_group(filename):\n",
    "    entities = parse_file_entities(str(filename))\n",
    "    keys = entities_to_key_group(entities)\n",
    "    return keys\n",
    "\n",
    "def key_group_to_entities(key_group):\n",
    "    return dict([group.split(\"-\") for group in key_group.split(\"_\")])\n",
    "\n",
    "def get_file_params(files):\n",
    "    \"\"\"Finds a list of *parameter groups* from a list of files.\n",
    "\n",
    "    Parameters:\n",
    "    -----------\n",
    "\n",
    "    files : list\n",
    "        List of file names\n",
    "\n",
    "    Returns:\n",
    "    --------\n",
    "\n",
    "    files_params : dictionary\n",
    "        A dictionary of filename, param_dict pairs\n",
    "\n",
    "    For each file in `files`, find critical parameters for metadata. Then find\n",
    "    unique sets of these critical parameters.\n",
    "    \"\"\"\n",
    "\n",
    "    # # DICTIONARY OF FILENAME, DICT_PARAMS\n",
    "    files_params = {}\n",
    "    for path in files:\n",
    "        metadata = self.layout.get_metadata(path)\n",
    "        wanted_keys = metadata.keys() & IMAGING_PARAMS\n",
    "        example_data = {key: metadata[key] for key in wanted_keys}\n",
    "\n",
    "        # Expand slice timing to multiple columns\n",
    "        SliceTime = example_data.get('SliceTiming')\n",
    "        if SliceTime:\n",
    "            # round each slice time to one place after the decimal\n",
    "            for i in range(len(SliceTime)):\n",
    "                SliceTime[i] = round(SliceTime[i], 1)\n",
    "            example_data.update(\n",
    "                {\"SliceTime%03d\" % SliceNum: time for\n",
    "                SliceNum, time in enumerate(SliceTime)})\n",
    "            del example_data['SliceTiming']\n",
    "\n",
    "        # ADD TO THE DICTIONARY\n",
    "        files_params[path] = example_data\n",
    "\n",
    "    return files_params\n",
    "\n",
    "\n",
    "#def get_param_groups(key_group, path):\n",
    "#    key_entities = key_group_to_entities(key_group)\n",
    "#    path = Path(path)\n",
    "#    matching_files = path.layout.get(return_type=\"file\", scope=\"self\",\n",
    "#                                     **key_entities)\n",
    "#    return _get_param_groups(matching_files)\n",
    "\n",
    "\n",
    "\n",
    "filename = \"/Users/Covitz/CuBIDS/cubids/testdata/complete/sub-01/ses-phdiff/fmap/sub-02_ses-phdiff_acq-v4_magnitude1.json\"\n",
    "path = \"/Users/Covitz/CuBIDS/cubids/testdata/complete/\"\n",
    "ret_entities = file_to_entities(filename)\n",
    "print(ret_entities)\n",
    "key_group = entities_to_key_group(ret_entities)\n",
    "print(key_group)\n",
    "\n",
    "entities = key_group_to_entities(key_group)\n",
    "print(\"Entities: \", entities)\n",
    "\n",
    "key_groups = file_to_key_group(filename)\n",
    "print(\"F_2_K: \", key_groups)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['acquisition-HASC55AP_datatype-dwi_suffix-dwi',\n",
       " 'acquisition-v4_datatype-fmap_fmap-magnitude1_suffix-magnitude1',\n",
       " 'acquisition-v4_datatype-fmap_fmap-magnitude2_suffix-magnitude2',\n",
       " 'acquisition-v4_datatype-fmap_fmap-phasediff_suffix-phasediff',\n",
       " 'datatype-anat_suffix-T1w',\n",
       " 'datatype-fmap_direction-PA_fmap-epi_suffix-epi',\n",
       " 'datatype-func_suffix-bold_task-rest']"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "\n",
    "# IMPORT SET TRACE\n",
    "# assert 0, debug\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "cubids_obj = CuBIDS(\"/Users/Covitz/CuBIDS/cubids/testdata/complete/\")\n",
    "key_group = cubids_obj.get_key_groups()\n",
    "key_group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: pybids in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (0.12.1)\n",
      "Requirement already satisfied: pandas>=0.23 in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (from pybids) (1.1.3)\n",
      "Requirement already satisfied: scipy in /Users/Covitz/.local/lib/python3.8/site-packages (from pybids) (1.5.2)\n",
      "Requirement already satisfied: sqlalchemy in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (from pybids) (1.3.19)\n",
      "Requirement already satisfied: bids-validator in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (from pybids) (1.5.6)\n",
      "Requirement already satisfied: patsy in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (from pybids) (0.5.1)\n",
      "Requirement already satisfied: numpy in /Users/Covitz/.local/lib/python3.8/site-packages (from pybids) (1.19.2)\n",
      "Requirement already satisfied: num2words in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (from pybids) (0.5.10)\n",
      "Requirement already satisfied: nibabel>=2.1 in /Users/Covitz/.local/lib/python3.8/site-packages (from pybids) (3.1.1)\n",
      "Requirement already satisfied: click in /Users/Covitz/.local/lib/python3.8/site-packages (from pybids) (7.1.2)\n",
      "Requirement already satisfied: pytz>=2017.2 in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (from pandas>=0.23->pybids) (2020.1)\n",
      "Requirement already satisfied: python-dateutil>=2.7.3 in /Users/Covitz/.local/lib/python3.8/site-packages (from pandas>=0.23->pybids) (2.8.1)\n",
      "Requirement already satisfied: six in /Users/Covitz/.local/lib/python3.8/site-packages (from patsy->pybids) (1.15.0)\n",
      "Requirement already satisfied: docopt>=0.6.2 in /Applications/miniconda3/envs/cubids/lib/python3.8/site-packages (from num2words->pybids) (0.6.2)\n",
      "Requirement already satisfied: packaging>=14.3 in /Users/Covitz/.local/lib/python3.8/site-packages (from nibabel>=2.1->pybids) (20.4)\n",
      "Requirement already satisfied: pyparsing>=2.0.2 in /Users/Covitz/.local/lib/python3.8/site-packages (from packaging>=14.3->nibabel>=2.1->pybids) (2.4.7)\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pathlib\n",
    "\n",
    "# @Params\n",
    "# - path: a string containing the path to the bids directory inside which we want to change files\n",
    "# @Returns\n",
    "# - HTML report of acquisitions and their parameter groups\n",
    "\n",
    "\n",
    "# WHERE DO WE FIND THE ACQUISITION TYPE?\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "def _entities_to_key_group(entities):\n",
    "    group_keys = sorted(entities.keys() - NON_KEY_ENTITIES)\n",
    "    return \"_\".join(\n",
    "        [\"{}-{}\".format(key, entities[key]) for key in group_keys])\n",
    "\n",
    "\n",
    "def _file_to_key_group(filename):\n",
    "    entities = parse_file_entities(str(filename))\n",
    "    return _entities_to_key_group(entities)\n",
    "\n",
    "\n",
    "def html_groups(bids_dir):\n",
    "    # get key groups using cubids.get_key_groups\n",
    "    # use key_group_to_entities to get entities\n",
    "    # get param groups for each entity\n",
    "\n",
    "\n",
    "    # initialize dictionary of acquisition types\n",
    "    d_acts = {}\n",
    "    for path in pathlib.Path(path_to_dir).iterdir():\n",
    "        if path.is_file():\n",
    "            ext = path.suffix\n",
    "            # check if the file is a .json file\n",
    "            if ext == \".json\":\n",
    "                # parse keys\n",
    "                d_keys = parse_file_entities(path)\n",
    "\n",
    "\n",
    "\n",
    "                # create html file\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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