NWB_minimalWorkingExample.ipynb

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    "# ----- Import necessary packages -----\n",
    "\n",
    "from datetime import datetime, date\n",
    "import os\n",
    "import numpy as np\n",
    "from uuid import uuid4\n",
    "\n",
    "from pynwb import NWBHDF5IO, NWBFile, TimeSeries\n",
    "from pynwb.file import Subject\n",
    "\n",
    "from pynwb.epoch import TimeIntervals\n",
    "from pynwb.image import ImageSeries\n",
    "\n",
    "from ndx_manoli_meta import AssayMetadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "18da6665",
   "metadata": {},
   "outputs": [],
   "source": [
    "# ------ Set up variables with facts for the NWB file -----\n",
    "\n",
    "# NWB generic metadata\n",
    "GT = 'behavior' # animal genotype\n",
    "sdate = date(2024,3,26) # date of recording session\n",
    "session_description = f'Testing files with new extension.' # description of the recording session\n",
    "experimenter = [ # who ran the experiments\n",
    "        \"Hoglen, Nerissa\",\n",
    "    ]\n",
    "lab='Manoli' # lab ID\n",
    "session_id = 'test1a' # unique identifier for the recording session\n",
    "subj = 'T0001' # animal eartag\n",
    "\n",
    "# Vole lab specific metadata\n",
    "assay = \"partner_preference_test\" # name of assay\n",
    "exclude_flag = False # should the assay be excluded from analyses?\n",
    "duration = 10800.0 # how long the assay ran, in seconds\n",
    "room = 'Platyzilla' # room number or name\n",
    "timeline = 'sensitized' # what behavior timeline -- TODO define set descriptors\n",
    "ethogram = 'mark1' # which ethogram was used to score the behavior video -- TODO define and name ethograms\n",
    "scorer = 'Gina Williams' # who scored the assay\n",
    "timeline_complete = True # does this animal have every assay from the timeline complete and usable\n",
    "colors = np.array([100.0, 100.0, 100.0]) # what color to plot the animal in\n",
    "\n",
    "# Information specific to the assay, in this case PPT\n",
    "ppt = os.path.join('pretend','path') # path to the score file\n",
    "peartag = 'E0001' # partner ear tag\n",
    "seartag = 'E0002' # stranger ear tag\n",
    "pGT = 'mut' # partner genotype\n",
    "sGT = 'WT' # stranger genotype\n",
    "days = 0 # how many days elapsed between pairing and running this assay\n",
    "pChamb = 'right' # which chamber is the partner in (can be any string)\n",
    "PPT_lane = 2 # which lane was the assay run in (expects an integer)\n",
    "\n",
    "# Information about where to put the file\n",
    "fname = 'test_file.nwb'\n",
    "fpath = os.path.join('pretend','write','path')\n",
    "wfullpath = os.path.join(fpath,fname)"
   ]
  },
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       "        <div class='container-wrap'><div class='container-header'><div class='xr-obj-type'><h3>vole_metadata (AssayMetadata)</h3></div></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".assay_type\">assay_type: </span><span class=\"field-value\">partner_preference_test</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".exclude_flag\">exclude_flag: </span><span class=\"field-value\">False</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".duration\">duration: </span><span class=\"field-value\">10800.0</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".room\">room: </span><span class=\"field-value\">Platyzilla</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".timeline\">timeline: </span><span class=\"field-value\">sensitized</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".ethogram\">ethogram: </span><span class=\"field-value\">mark1</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".experimenter\">experimenter: </span><span class=\"field-value\">Gina Williams</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".timeline_complete\">timeline_complete: </span><span class=\"field-value\">True</span></div><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".colors\"><b>colors</b></summary><div style=\"margin-left: 20px;\" class=\"container-fields\">[100. 100. 100.]</div></details><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test\">partner_preference_test: </span><span class=\"field-value\">pretend\\path</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test__partner_ID\">partner_preference_test__partner_ID: </span><span class=\"field-value\">E0001</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test__partner_GT\">partner_preference_test__partner_GT: </span><span class=\"field-value\">mut</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test__days_post_pairing\">partner_preference_test__days_post_pairing: </span><span class=\"field-value\">0</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test__stranger_ID\">partner_preference_test__stranger_ID: </span><span class=\"field-value\">E0002</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test__stranger_GT\">partner_preference_test__stranger_GT: </span><span class=\"field-value\">WT</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test__PPT_lane\">partner_preference_test__PPT_lane: </span><span class=\"field-value\">2</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".partner_preference_test__partner_chamber\">partner_preference_test__partner_chamber: </span><span class=\"field-value\">right</span></div></div>"
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      "text/plain": [
       "vole_metadata abc.AssayMetadata at 0x2470293021856\n",
       "Fields:\n",
       "  assay_type: partner_preference_test\n",
       "  colors: [100. 100. 100.]\n",
       "  duration: 10800.0\n",
       "  ethogram: mark1\n",
       "  exclude_flag: False\n",
       "  experimenter: Gina Williams\n",
       "  partner_preference_test: pretend\\path\n",
       "  partner_preference_test__PPT_lane: 2\n",
       "  partner_preference_test__days_post_pairing: 0\n",
       "  partner_preference_test__partner_GT: mut\n",
       "  partner_preference_test__partner_ID: E0001\n",
       "  partner_preference_test__partner_chamber: right\n",
       "  partner_preference_test__stranger_GT: WT\n",
       "  partner_preference_test__stranger_ID: E0002\n",
       "  room: Platyzilla\n",
       "  timeline: sensitized\n",
       "  timeline_complete: True"
      ]
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   "source": [
    "# ----- Code for creating and populating the file -----\n",
    "\n",
    "# Create the NWB file object\n",
    "nwbfile = NWBFile(\n",
    "    session_description=session_description,\n",
    "    identifier = str(uuid4()),\n",
    "    session_start_time = datetime.now(),\n",
    "    lab=lab,\n",
    "    experimenter=experimenter,\n",
    "    session_id = session_id,\n",
    ")\n",
    "\n",
    "# Create session specific subject data object --> goes straight into the file because it is a field of the file\n",
    "nwbfile.subject = Subject(\n",
    "    subject_id = subj,\n",
    "    species = 'Microtus ochrogaster',\n",
    "    sex = 'F',\n",
    "    genotype = 'WT'\n",
    ")\n",
    "\n",
    "# Create lab specific metadata object with the variables defined above\n",
    "meta = AssayMetadata(\n",
    "                        assay_type=assay,\n",
    "                        exclude_flag=exclude_flag,\n",
    "                        duration=duration,\n",
    "                        room=room,\n",
    "                        timeline=timeline,\n",
    "                        ethogram=ethogram,\n",
    "                        experimenter=scorer,\n",
    "                        timeline_complete=timeline_complete,\n",
    "                        colors=colors,\n",
    "                        partner_preference_test=ppt,\n",
    "                        partner_preference_test__partner_ID=peartag,\n",
    "                        partner_preference_test__partner_GT=pGT,\n",
    "                        partner_preference_test__days_post_pairing=days,\n",
    "                        partner_preference_test__stranger_ID=seartag,\n",
    "                        partner_preference_test__stranger_GT=sGT,\n",
    "                        partner_preference_test__PPT_lane = PPT_lane,\n",
    "                        partner_preference_test__partner_chamber = pChamb\n",
    "                        )\n",
    "\n",
    "# Add the test LabMetaDataExtensionExample to the NWBFile\n",
    "nwbfile.add_lab_meta_data(lab_meta_data=meta)\n",
    "\n",
    "# Write the new file object to disk\n",
    "# with NWBHDF5IO(wfullpath, \"w\") as io:\n",
    "    # io.write(nwbfile)"
   ]
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       "        <div class='container-wrap'><div class='container-header'><div class='xr-obj-type'><h3>root (NWBFile)</h3></div></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".session_description\">session_description: </span><span class=\"field-value\">Testing files with new extension.</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".identifier\">identifier: </span><span class=\"field-value\">e09ba12c-2243-4229-b1ac-ee6e7556a5e7</span></div><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".session_start_time\"><b>session_start_time</b></summary><span class=\"field-key\">2024-03-26 14:09:34.402944-07:00</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".timestamps_reference_time\"><b>timestamps_reference_time</b></summary><span class=\"field-key\">2024-03-26 14:09:34.402944-07:00</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".file_create_date\"><b>file_create_date</b></summary><details><summary style=\"display: list-item; margin-left: 20px;\" class=\"container-fields field-key\" title=\".file_create_date[0]\"><b>0</b></summary><span class=\"field-key\">2024-03-26 14:09:34.417114-07:00</span></details></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".experimenter\"><b>experimenter</b></summary><span class=\"field-key\">('Gina Williams',)</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".epoch_tags\"><b>epoch_tags</b></summary><span class=\"field-key\">set()</span></details><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".session_id\">session_id: </span><span class=\"field-value\">test1a</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab\">lab: </span><span class=\"field-value\">Manoli</span></div><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".subject\"><b>subject</b></summary><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.age__reference\">age__reference: </span><span class=\"field-value\">birth</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.genotype\">genotype: </span><span class=\"field-value\">WT</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.sex\">sex: </span><span class=\"field-value\">F</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.species\">species: </span><span class=\"field-value\">Microtus ochrogaster</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.subject_id\">subject_id: </span><span class=\"field-value\">T0001</span></div></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".lab_meta_data\"><b>lab_meta_data</b></summary><details><summary style=\"display: list-item; margin-left: 20px;\" class=\"container-fields field-key\" title=\".lab_meta_data['vole_metadata']\"><b>vole_metadata</b></summary><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].assay_type\">assay_type: </span><span class=\"field-value\">partner_preference_test</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].exclude_flag\">exclude_flag: </span><span class=\"field-value\">False</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].duration\">duration: </span><span class=\"field-value\">10800.0</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].room\">room: </span><span class=\"field-value\">Platyzilla</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].timeline\">timeline: </span><span class=\"field-value\">sensitized</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].ethogram\">ethogram: </span><span class=\"field-value\">mark1</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].experimenter\">experimenter: </span><span class=\"field-value\">Gina Williams</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].timeline_complete\">timeline_complete: </span><span class=\"field-value\">True</span></div><details><summary style=\"display: list-item; margin-left: 40px;\" class=\"container-fields field-key\" title=\".lab_meta_data['vole_metadata'].colors\"><b>colors</b></summary><div style=\"margin-left: 60px;\" class=\"container-fields\">[100. 100. 100.]</div></details><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test\">partner_preference_test: </span><span class=\"field-value\">pretend\\path</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test__partner_ID\">partner_preference_test__partner_ID: </span><span class=\"field-value\">E0001</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test__partner_GT\">partner_preference_test__partner_GT: </span><span class=\"field-value\">mut</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test__days_post_pairing\">partner_preference_test__days_post_pairing: </span><span class=\"field-value\">0</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test__stranger_ID\">partner_preference_test__stranger_ID: </span><span class=\"field-value\">E0002</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test__stranger_GT\">partner_preference_test__stranger_GT: </span><span class=\"field-value\">WT</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test__PPT_lane\">partner_preference_test__PPT_lane: </span><span class=\"field-value\">2</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab_meta_data['vole_metadata'].partner_preference_test__partner_chamber\">partner_preference_test__partner_chamber: </span><span class=\"field-value\">right</span></div></details></details></div>"
      ],
      "text/plain": [
       "root pynwb.file.NWBFile at 0x2770995710512\n",
       "Fields:\n",
       "  experimenter: ['Gina Williams']\n",
       "  file_create_date: [datetime.datetime(2024, 3, 26, 14, 9, 34, 417114, tzinfo=tzlocal())]\n",
       "  identifier: e09ba12c-2243-4229-b1ac-ee6e7556a5e7\n",
       "  lab: Manoli\n",
       "  lab_meta_data: {\n",
       "    vole_metadata <class 'abc.AssayMetadata'>\n",
       "  }\n",
       "  session_description: Testing files with new extension.\n",
       "  session_id: test1a\n",
       "  session_start_time: 2024-03-26 14:09:34.402944-07:00\n",
       "  subject: subject pynwb.file.Subject at 0x2770995711664\n",
       "Fields:\n",
       "  age__reference: birth\n",
       "  genotype: WT\n",
       "  sex: F\n",
       "  species: Microtus ochrogaster\n",
       "  subject_id: T0001\n",
       "\n",
       "  timestamps_reference_time: 2024-03-26 14:09:34.402944-07:00"
      ]
     },
     "execution_count": 13,
     "metadata": {},
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   ],
   "source": [
    "# ----- Have a look at the file structure -----\n",
    "nwbfile"
   ]
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