src/pynwb/create_NWB.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Open namepsace and get exetnsions for multichannel volumetric data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "from pynwb import load_namespaces, get_class\n",
    "from pynwb.file import MultiContainerInterface, NWBContainer\n",
    "import skimage.io as skio\n",
    "from collections.abc import Iterable\n",
    "import numpy as np\n",
    "from pynwb import register_class\n",
    "from hdmf.utils import docval, get_docval, popargs\n",
    "from pynwb.ophys import ImageSeries \n",
    "from pynwb.core import NWBDataInterface\n",
    "from hdmf.common import DynamicTable\n",
    "from hdmf.utils import docval, popargs, get_docval, get_data_shape, popargs_to_dict\n",
    "from pynwb.file import Device\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "from pynwb import NWBFile, TimeSeries, NWBHDF5IO\n",
    "from pynwb.epoch import TimeIntervals\n",
    "from pynwb.file import Subject\n",
    "from pynwb.behavior import SpatialSeries, Position\n",
    "from pynwb.image import ImageSeries\n",
    "from pynwb.ophys import OnePhotonSeries, OpticalChannel, ImageSegmentation, Fluorescence, CorrectedImageStack, MotionCorrection, RoiResponseSeries\n",
    "from datetime import datetime\n",
    "from dateutil import tz\n",
    "import pandas as pd\n",
    "import scipy.io as sio\n",
    "from datetime import datetime, timedelta\n",
    "import tifffile\n",
    "from ndx_multichannel_volume import CElegansSubject, OpticalChannelReferences, OpticalChannelPlus, ImagingVolume, VolumeSegmentation, MultiChannelVolume"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "datapath = os.path.join('/Users', 'danielysprague', 'foco_lab', 'data')"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Creating NWB file for NeuroPAL data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def gen_file(description, identifier, start_date_time, lab, institution, pubs):\n",
    "\n",
    "    nwbfile = NWBFile(\n",
    "        session_description = description,\n",
    "        identifier = identifier,\n",
    "        session_start_time = start_date_time,\n",
    "        lab = lab,\n",
    "        institution = institution,\n",
    "        related_publications = pubs\n",
    "    )\n",
    "\n",
    "    return nwbfile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_im_vol(device, channels, location=\"head\", grid_spacing=[0.3208, 0.3208, 0.75], grid_spacing_unit =\"micrometers\", origin_coords=[0,0,0], origin_coords_unit=\"micrometers\", reference_frame=\"Worm head, left=anterior, bottom=ventral\"):\n",
    "    \n",
    "    # channels should be ordered list of tuples (name, description)\n",
    "\n",
    "    OptChannels = []\n",
    "    OptChanRefData = []\n",
    "    for name, wave in channels:\n",
    "        excite = float(wave.split('-')[0])\n",
    "        emiss_mid = float(wave.split('-')[1])\n",
    "        emiss_range = float(wave.split('-')[2][:-1])\n",
    "        OptChan = OpticalChannelPlus(\n",
    "            name = name,\n",
    "            description = wave,\n",
    "            excitation_lambda = excite,\n",
    "            excitation_range = [excite, excite],\n",
    "            emission_range = [emiss_mid-emiss_range/2, emiss_mid+emiss_range/2],\n",
    "            emission_lambda = emiss_mid\n",
    "        )\n",
    "\n",
    "        OptChannels.append(OptChan)\n",
    "        OptChanRefData.append(wave)\n",
    "\n",
    "    OpticalChannelRefs = OpticalChannelReferences(\n",
    "        name = 'OpticalChannelRefs',\n",
    "        channels = OptChanRefData\n",
    "    )\n",
    "\n",
    "    imaging_vol = ImagingVolume(\n",
    "        name= 'ImagingVolume',\n",
    "        optical_channel_plus = OptChannels,\n",
    "        Order_optical_channels = OpticalChannelRefs,\n",
    "        description = 'NeuroPAL image of C elegan brain',\n",
    "        device = device,\n",
    "        location = location,\n",
    "        grid_spacing = grid_spacing,\n",
    "        grid_spacing_unit = grid_spacing_unit,\n",
    "        origin_coords = origin_coords,\n",
    "        origin_coords_unit = origin_coords_unit,\n",
    "        reference_frame = reference_frame\n",
    "    )\n",
    "\n",
    "    return imaging_vol, OpticalChannelRefs, OptChannels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_vol_seg(imaging_vol, blobs):\n",
    "\n",
    "    vs = VolumeSegmentation(\n",
    "        name = 'VolumeSegmentation',\n",
    "        description = 'Neuron centers for multichannel volumetric image',\n",
    "        imaging_volume = imaging_vol\n",
    "    )\n",
    "\n",
    "    csv = pd.read_csv(blobs)\n",
    "\n",
    "    voxel_mask = []\n",
    "\n",
    "    for i, row in csv.iterrows():\n",
    "        x = row['X']\n",
    "        y = row['Y']\n",
    "        z = row['Z']\n",
    "        ID = row['ID']\n",
    "\n",
    "        voxel_mask.append([np.uint(x),np.uint(y),np.uint(z),1,str(ID)])\n",
    "\n",
    "    vs.add_roi(voxel_mask=voxel_mask)\n",
    "\n",
    "    return vs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_image(data, name, description, imaging_volume, opt_chan_refs, resolution=[0.3208, 0.3208, 0.75], RGBW_channels=[0,1,2,3]):\n",
    "\n",
    "    image = MultiChannelVolume(\n",
    "        name = name,\n",
    "        Order_optical_channels = opt_chan_refs,\n",
    "        resolution = resolution,\n",
    "        description = description,\n",
    "        RGBW_channels = RGBW_channels,\n",
    "        data = data,\n",
    "        imaging_volume = imaging_volume\n",
    "    )\n",
    "\n",
    "    return image"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "'''\n",
    "Create NWB file from tif file of raw image, neuroPAL software created mat file and csv files of blob locations\n",
    "'''\n",
    "\n",
    "def create_file_FOCO(folder, reference_frame):\n",
    "\n",
    "    worm = folder.split('/')[1]\n",
    "\n",
    "    path = datapath+'/'+folder\n",
    "\n",
    "    for file in os.listdir(path):\n",
    "        if file[-4:] =='.tif':\n",
    "            imfile = path + '/'+file\n",
    "\n",
    "        elif file[-4:] == '.mat' and file[-6:]!= 'ID.mat':\n",
    "            matfile = path + '/'+file\n",
    "\n",
    "        elif file == 'blobs.csv':\n",
    "            blobs = path +'/'+file\n",
    "\n",
    "    data = np.transpose(skio.imread(imfile), (1,0,2,3)) #data should be XYZC\n",
    "    #data = data.astype('uint16')\n",
    "    mat = sio.loadmat(matfile)\n",
    "\n",
    "    scale = np.asarray(mat['info']['scale'][0][0]).flatten()\n",
    "    prefs = np.asarray(mat['prefs']['RGBW'][0][0]).flatten()-1 #subtract 1 to adjust for matlab indexing from 1\n",
    "    \n",
    "    dt = worm.split('-')\n",
    "    session_start = datetime(int(dt[0]),int(dt[1]),int(dt[2]), tzinfo=tz.gettz(\"US/Pacific\"))\n",
    "    \n",
    "    nwbfile = gen_file('Worm head', worm, session_start, 'Kato lab', 'UCSF', \"\")\n",
    "\n",
    "    nwbfile.subject = CElegansSubject(\n",
    "    subject_id = worm,\n",
    "    #age = \"T2H30M\",\n",
    "    #growth_stage_time = pd.Timedelta(hours=2, minutes=30).isoformat(),\n",
    "    date_of_birth = session_start, #currently just using the session start time to bypass the requirement for date of birth\n",
    "    growth_stage = 'YA',\n",
    "    growth_stage_time=pd.Timedelta(hours=2, minutes=30).isoformat(),\n",
    "    cultivation_temp = 20.,\n",
    "    description = dt[3]+'-'+dt[4],\n",
    "    species  =  \"http://purl.obolibrary.org/obo/NCBITaxon_6239\",\n",
    "    sex = \"XX\", #currently just using O for other until support added for other gender specifications\n",
    "    strain = \"OH16230\"\n",
    "    )\n",
    "\n",
    "    device = nwbfile.create_device(\n",
    "    name = \"Microscope\",\n",
    "    description = \"One-photon microscope Weill\",\n",
    "    manufacturer = \"Leica\"\n",
    "    )\n",
    "\n",
    "    channels = [(\"mNeptune 2.5\", \"561-700-75m\"), (\"Tag RFP-T\", \"561-605-70m\"), (\"CyOFP1\", \"488-605-70m\"), (\"GFP-GCaMP\", \"488-525-50m\"), (\"mTagBFP2\", \"405-460-50m\"), (\"mNeptune 2.5 - high excite\", \"639-700-75m\")]\n",
    "    \n",
    "    ImagingVol, OptChannelRefs, OptChannels = create_im_vol(device, channels, location= \"head\", grid_spacing= scale, reference_frame=reference_frame)\n",
    "\n",
    "    vs = create_vol_seg(ImagingVol, blobs)\n",
    "\n",
    "    image= create_image(data, 'NeuroPALImageRaw', worm, ImagingVol, OptChannelRefs, resolution=scale, RGBW_channels=[0,2,4,1])\n",
    "\n",
    "    nwbfile.add_acquisition(image)\n",
    "\n",
    "    neuroPAL_module = nwbfile.create_processing_module(\n",
    "        name = 'NeuroPAL',\n",
    "        description = 'neuroPAL image data and metadata',\n",
    "    )    \n",
    "\n",
    "    processed_im_module = nwbfile.create_processing_module(\n",
    "        name = 'ProcessedImage',\n",
    "        description = 'Pre-processed image. Currently median filtered and histogram matched to original neuroPAL images.'\n",
    "    )\n",
    "\n",
    "    proc_imvol, proc_optchanrefs, proc_optchanplus = create_im_vol(device, [channels[i] for i in [0,2,4,1]], location=\"head\", grid_spacing=scale, reference_frame=reference_frame)\n",
    "\n",
    "    proc_imfile = datapath + '/NP_FOCO_hist_med/'+worm+'/hist_med_image.tif'\n",
    "\n",
    "    proc_data = np.transpose(skio.imread(proc_imfile), (0,3,1,2))\n",
    "    #proc_data = proc_data.astype('uint16')\n",
    "\n",
    "    proc_image = create_image(proc_data, 'Hist_match_med_filt', worm, proc_imvol, proc_optchanrefs, resolution=scale, RGBW_channels=[0,1,2,3])\n",
    "\n",
    "    neuroPAL_module.add(vs)\n",
    "    neuroPAL_module.add(ImagingVol)\n",
    "    neuroPAL_module.add(OptChannelRefs)\n",
    "    neuroPAL_module.add(OptChannels)\n",
    "\n",
    "    processed_im_module.add(proc_image)\n",
    "    processed_im_module.add(proc_optchanrefs)\n",
    "    processed_im_module.add(proc_optchanplus)\n",
    "    processed_im_module.add(proc_imvol)\n",
    "\n",
    "    io = NWBHDF5IO(datapath+'/nwb/'+worm+'.nwb', mode='w')\n",
    "    io.write(nwbfile)\n",
    "    io.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type uint16 is being converted to data type int16 as specified.\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'ImagingVolume/origin_coords': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n"
     ]
    }
   ],
   "source": [
    "create_file_FOCO('NP_FOCO_cropped/2021-12-03-w00-NP1', reference_frame = 'origin = anterior, dorsal, left')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-01-22-w04-NP1', reference_frame = 'origin = posterior, dorsal, left')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-02-11-w03-NP1', reference_frame = 'origin = posterior, dorsal, left')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-02-12-w00-NP1', reference_frame = 'origin = posterior, ventral, right')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-02-12-w01-NP1', reference_frame = 'origin = posterior, ventral, right')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-02-22-w04-NP1', reference_frame = 'origin = anterior, ventral left; slightly rotated')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-03-05-w00-NP1', reference_frame = 'origin = posterior, ventral, right')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-04-01-w00-NP1', reference_frame = 'origin = anterior, dorsal, left')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-04-26-w00-NP1', reference_frame = 'origin = posterior, dorsal, left; slightly rotated')\n",
    "create_file_FOCO('NP_FOCO_cropped/2022-04-26-w01-NP1', reference_frame = 'origin = posterior, ventral, right')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/resolution': Value with data type int64 is being converted to data type float64 (min specification: float32).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n",
      "/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:260: DtypeConversionWarning: Spec 'MultiChannelVolume/data': Value with data type float64 is being converted to data type int64 (min specification: int16).\n",
      "  warnings.warn(full_warning_msg, DtypeConversionWarning)\n"
     ]
    },
    {
     "ename": "BuildError",
     "evalue": "OpticalChannelRefs (OpticalChannelRefs): could not convert 'channels' for OpticalChannelReferences 'OpticalChannelRefs'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:995\u001b[0m, in \u001b[0;36mObjectMapper.__add_datasets\u001b[0;34m(self, builder, datasets, container, build_manager, source, export)\u001b[0m\n\u001b[1;32m    994\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[0;32m--> 995\u001b[0m     data, dtype \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mconvert_dtype(spec, attr_value)\n\u001b[1;32m    996\u001b[0m \u001b[39mexcept\u001b[39;00m \u001b[39mException\u001b[39;00m \u001b[39mas\u001b[39;00m ex:\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:201\u001b[0m, in \u001b[0;36mObjectMapper.convert_dtype\u001b[0;34m(cls, spec, value, spec_dtype)\u001b[0m\n\u001b[1;32m    200\u001b[0m     spec_dtype \u001b[39m=\u001b[39m spec\u001b[39m.\u001b[39mdtype\n\u001b[0;32m--> 201\u001b[0m ret, ret_dtype \u001b[39m=\u001b[39m \u001b[39mcls\u001b[39;49m\u001b[39m.\u001b[39;49m__check_edgecases(spec, value, spec_dtype)\n\u001b[1;32m    202\u001b[0m \u001b[39mif\u001b[39;00m ret \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39mor\u001b[39;00m ret_dtype \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:319\u001b[0m, in \u001b[0;36mObjectMapper.__check_edgecases\u001b[0;34m(cls, spec, value, spec_dtype)\u001b[0m\n\u001b[1;32m    318\u001b[0m     msg \u001b[39m=\u001b[39m \u001b[39m\"\u001b[39m\u001b[39mgot RefSpec for value of type \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m\"\u001b[39m \u001b[39m%\u001b[39m \u001b[39mtype\u001b[39m(value)\n\u001b[0;32m--> 319\u001b[0m     \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(msg)\n\u001b[1;32m    320\u001b[0m \u001b[39mreturn\u001b[39;00m value, spec_dtype\n",
      "\u001b[0;31mValueError\u001b[0m: got RefSpec for value of type <class 'list'>",
      "\nThe above exception was the direct cause of the following exception:\n",
      "\u001b[0;31mBuildError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[9], line 70\u001b[0m\n\u001b[1;32m     67\u001b[0m neuroPAL_module\u001b[39m.\u001b[39madd(OpticalChannelRefs)\n\u001b[1;32m     69\u001b[0m io \u001b[39m=\u001b[39m NWBHDF5IO(datapath\u001b[39m+\u001b[39m\u001b[39m'\u001b[39m\u001b[39m/nwb/\u001b[39m\u001b[39m'\u001b[39m\u001b[39m+\u001b[39m\u001b[39m'\u001b[39m\u001b[39mtest+\u001b[39m\u001b[39m'\u001b[39m\u001b[39m+\u001b[39m\u001b[39m'\u001b[39m\u001b[39m.nwb\u001b[39m\u001b[39m'\u001b[39m, mode\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mw\u001b[39m\u001b[39m'\u001b[39m)\n\u001b[0;32m---> 70\u001b[0m io\u001b[39m.\u001b[39;49mwrite(nwbfile)\n\u001b[1;32m     71\u001b[0m io\u001b[39m.\u001b[39mclose()\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/backends/hdf5/h5tools.py:360\u001b[0m, in \u001b[0;36mHDF5IO.write\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    355\u001b[0m     \u001b[39mraise\u001b[39;00m UnsupportedOperation((\u001b[39m\"\u001b[39m\u001b[39mCannot write to file \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m in mode \u001b[39m\u001b[39m'\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m. \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    356\u001b[0m                                 \u001b[39m\"\u001b[39m\u001b[39mPlease use mode \u001b[39m\u001b[39m'\u001b[39m\u001b[39mr+\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39mw\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39mw-\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39mx\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, or \u001b[39m\u001b[39m'\u001b[39m\u001b[39ma\u001b[39m\u001b[39m'\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m    357\u001b[0m                                \u001b[39m%\u001b[39m (\u001b[39mself\u001b[39m\u001b[39m.\u001b[39msource, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__mode))\n\u001b[1;32m    359\u001b[0m cache_spec \u001b[39m=\u001b[39m popargs(\u001b[39m'\u001b[39m\u001b[39mcache_spec\u001b[39m\u001b[39m'\u001b[39m, kwargs)\n\u001b[0;32m--> 360\u001b[0m \u001b[39msuper\u001b[39;49m()\u001b[39m.\u001b[39;49mwrite(\u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mkwargs)\n\u001b[1;32m    361\u001b[0m \u001b[39mif\u001b[39;00m cache_spec:\n\u001b[1;32m    362\u001b[0m     \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__cache_spec()\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/backends/io.py:53\u001b[0m, in \u001b[0;36mHDMFIO.write\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m     51\u001b[0m \u001b[39m\u001b[39m\u001b[39m\"\"\"Write a container to the IO source.\"\"\"\u001b[39;00m\n\u001b[1;32m     52\u001b[0m container \u001b[39m=\u001b[39m popargs(\u001b[39m'\u001b[39m\u001b[39mcontainer\u001b[39m\u001b[39m'\u001b[39m, kwargs)\n\u001b[0;32m---> 53\u001b[0m f_builder \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__manager\u001b[39m.\u001b[39;49mbuild(container, source\u001b[39m=\u001b[39;49m\u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__source, root\u001b[39m=\u001b[39;49m\u001b[39mTrue\u001b[39;49;00m)\n\u001b[1;32m     54\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mwrite_builder(f_builder, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/manager.py:171\u001b[0m, in \u001b[0;36mBuildManager.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    167\u001b[0m             \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mCannot change container_source once set: \u001b[39m\u001b[39m'\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m.\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m\"\u001b[39m\n\u001b[1;32m    168\u001b[0m                              \u001b[39m%\u001b[39m (container\u001b[39m.\u001b[39mname, container\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__module__\u001b[39m,\n\u001b[1;32m    169\u001b[0m                                 container\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__name__\u001b[39m))\n\u001b[1;32m    170\u001b[0m \u001b[39m# NOTE: if exporting, then existing cached builder will be ignored and overridden with new build result\u001b[39;00m\n\u001b[0;32m--> 171\u001b[0m result \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__type_map\u001b[39m.\u001b[39;49mbuild(container, \u001b[39mself\u001b[39;49m, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec_ext, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m    172\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mprebuilt(container, result)\n\u001b[1;32m    173\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__active_prebuilt(result)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/manager.py:770\u001b[0m, in \u001b[0;36mTypeMap.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    768\u001b[0m \u001b[39mif\u001b[39;00m manager \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m    769\u001b[0m     manager \u001b[39m=\u001b[39m BuildManager(\u001b[39mself\u001b[39m)\n\u001b[0;32m--> 770\u001b[0m builder \u001b[39m=\u001b[39m obj_mapper\u001b[39m.\u001b[39;49mbuild(container, manager, builder\u001b[39m=\u001b[39;49mbuilder, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec_ext, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m    772\u001b[0m \u001b[39m# add additional attributes (namespace, data_type, object_id) to builder\u001b[39;00m\n\u001b[1;32m    773\u001b[0m namespace, data_type \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mget_container_ns_dt(container)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:706\u001b[0m, in \u001b[0;36mObjectMapper.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    704\u001b[0m         builder \u001b[39m=\u001b[39m GroupBuilder(name, parent\u001b[39m=\u001b[39mparent, source\u001b[39m=\u001b[39msource)\n\u001b[1;32m    705\u001b[0m     \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_datasets(builder, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__spec\u001b[39m.\u001b[39mdatasets, container, manager, source, export)\n\u001b[0;32m--> 706\u001b[0m     \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__add_groups(builder, \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__spec\u001b[39m.\u001b[39;49mgroups, container, manager, source, export)\n\u001b[1;32m    707\u001b[0m     \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_links(builder, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__spec\u001b[39m.\u001b[39mlinks, container, manager, source, export)\n\u001b[1;32m    708\u001b[0m \u001b[39melse\u001b[39;00m:\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:1027\u001b[0m, in \u001b[0;36mObjectMapper.__add_groups\u001b[0;34m(self, builder, groups, container, build_manager, source, export)\u001b[0m\n\u001b[1;32m   1025\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_datasets(sub_builder, spec\u001b[39m.\u001b[39mdatasets, container, build_manager, source, export)\n\u001b[1;32m   1026\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_links(sub_builder, spec\u001b[39m.\u001b[39mlinks, container, build_manager, source, export)\n\u001b[0;32m-> 1027\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__add_groups(sub_builder, spec\u001b[39m.\u001b[39;49mgroups, container, build_manager, source, export)\n\u001b[1;32m   1028\u001b[0m empty \u001b[39m=\u001b[39m sub_builder\u001b[39m.\u001b[39mis_empty()\n\u001b[1;32m   1029\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mnot\u001b[39;00m empty \u001b[39mor\u001b[39;00m (empty \u001b[39mand\u001b[39;00m spec\u001b[39m.\u001b[39mrequired):\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:1040\u001b[0m, in \u001b[0;36mObjectMapper.__add_groups\u001b[0;34m(self, builder, groups, container, build_manager, source, export)\u001b[0m\n\u001b[1;32m   1038\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__check_quantity(attr_value, spec, container)\n\u001b[1;32m   1039\u001b[0m \u001b[39mif\u001b[39;00m attr_value \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[0;32m-> 1040\u001b[0m     \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__add_containers(builder, spec, attr_value, build_manager, source, container, export)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:1098\u001b[0m, in \u001b[0;36mObjectMapper.__add_containers\u001b[0;34m(self, builder, spec, value, build_manager, source, parent_container, export)\u001b[0m\n\u001b[1;32m   1096\u001b[0m \u001b[39melif\u001b[39;00m \u001b[39misinstance\u001b[39m(value, \u001b[39mlist\u001b[39m):\n\u001b[1;32m   1097\u001b[0m     \u001b[39mfor\u001b[39;00m container \u001b[39min\u001b[39;00m value:\n\u001b[0;32m-> 1098\u001b[0m         \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__add_containers(builder, spec, container, build_manager, source, parent_container, export)\n\u001b[1;32m   1099\u001b[0m \u001b[39melse\u001b[39;00m:  \u001b[39m# pragma: no cover\u001b[39;00m\n\u001b[1;32m   1100\u001b[0m     msg \u001b[39m=\u001b[39m (\u001b[39m\"\u001b[39m\u001b[39mReceived \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m, expected AbstractContainer or a list of AbstractContainers.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m   1101\u001b[0m            \u001b[39m%\u001b[39m value\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__name__\u001b[39m)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:1060\u001b[0m, in \u001b[0;36mObjectMapper.__add_containers\u001b[0;34m(self, builder, spec, value, build_manager, source, parent_container, export)\u001b[0m\n\u001b[1;32m   1058\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mlogger\u001b[39m.\u001b[39mdebug(\u001b[39m\"\u001b[39m\u001b[39m    Building newly instantiated \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m \u001b[39m\u001b[39m'\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m\"\u001b[39m \u001b[39m%\u001b[39m (value\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__name__\u001b[39m, value\u001b[39m.\u001b[39mname))\n\u001b[1;32m   1059\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39misinstance\u001b[39m(spec, BaseStorageSpec):\n\u001b[0;32m-> 1060\u001b[0m     new_builder \u001b[39m=\u001b[39m build_manager\u001b[39m.\u001b[39;49mbuild(value, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m   1061\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[1;32m   1062\u001b[0m     new_builder \u001b[39m=\u001b[39m build_manager\u001b[39m.\u001b[39mbuild(value, source\u001b[39m=\u001b[39msource, export\u001b[39m=\u001b[39mexport)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/manager.py:171\u001b[0m, in \u001b[0;36mBuildManager.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    167\u001b[0m             \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mCannot change container_source once set: \u001b[39m\u001b[39m'\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m.\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m\"\u001b[39m\n\u001b[1;32m    168\u001b[0m                              \u001b[39m%\u001b[39m (container\u001b[39m.\u001b[39mname, container\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__module__\u001b[39m,\n\u001b[1;32m    169\u001b[0m                                 container\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__name__\u001b[39m))\n\u001b[1;32m    170\u001b[0m \u001b[39m# NOTE: if exporting, then existing cached builder will be ignored and overridden with new build result\u001b[39;00m\n\u001b[0;32m--> 171\u001b[0m result \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__type_map\u001b[39m.\u001b[39;49mbuild(container, \u001b[39mself\u001b[39;49m, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec_ext, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m    172\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mprebuilt(container, result)\n\u001b[1;32m    173\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__active_prebuilt(result)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/manager.py:770\u001b[0m, in \u001b[0;36mTypeMap.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    768\u001b[0m \u001b[39mif\u001b[39;00m manager \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m    769\u001b[0m     manager \u001b[39m=\u001b[39m BuildManager(\u001b[39mself\u001b[39m)\n\u001b[0;32m--> 770\u001b[0m builder \u001b[39m=\u001b[39m obj_mapper\u001b[39m.\u001b[39;49mbuild(container, manager, builder\u001b[39m=\u001b[39;49mbuilder, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec_ext, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m    772\u001b[0m \u001b[39m# add additional attributes (namespace, data_type, object_id) to builder\u001b[39;00m\n\u001b[1;32m    773\u001b[0m namespace, data_type \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mget_container_ns_dt(container)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:706\u001b[0m, in \u001b[0;36mObjectMapper.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    704\u001b[0m         builder \u001b[39m=\u001b[39m GroupBuilder(name, parent\u001b[39m=\u001b[39mparent, source\u001b[39m=\u001b[39msource)\n\u001b[1;32m    705\u001b[0m     \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_datasets(builder, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__spec\u001b[39m.\u001b[39mdatasets, container, manager, source, export)\n\u001b[0;32m--> 706\u001b[0m     \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__add_groups(builder, \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__spec\u001b[39m.\u001b[39;49mgroups, container, manager, source, export)\n\u001b[1;32m    707\u001b[0m     \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_links(builder, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__spec\u001b[39m.\u001b[39mlinks, container, manager, source, export)\n\u001b[1;32m    708\u001b[0m \u001b[39melse\u001b[39;00m:\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:1040\u001b[0m, in \u001b[0;36mObjectMapper.__add_groups\u001b[0;34m(self, builder, groups, container, build_manager, source, export)\u001b[0m\n\u001b[1;32m   1038\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__check_quantity(attr_value, spec, container)\n\u001b[1;32m   1039\u001b[0m \u001b[39mif\u001b[39;00m attr_value \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[0;32m-> 1040\u001b[0m     \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__add_containers(builder, spec, attr_value, build_manager, source, container, export)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:1060\u001b[0m, in \u001b[0;36mObjectMapper.__add_containers\u001b[0;34m(self, builder, spec, value, build_manager, source, parent_container, export)\u001b[0m\n\u001b[1;32m   1058\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mlogger\u001b[39m.\u001b[39mdebug(\u001b[39m\"\u001b[39m\u001b[39m    Building newly instantiated \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m \u001b[39m\u001b[39m'\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m\"\u001b[39m \u001b[39m%\u001b[39m (value\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__name__\u001b[39m, value\u001b[39m.\u001b[39mname))\n\u001b[1;32m   1059\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39misinstance\u001b[39m(spec, BaseStorageSpec):\n\u001b[0;32m-> 1060\u001b[0m     new_builder \u001b[39m=\u001b[39m build_manager\u001b[39m.\u001b[39;49mbuild(value, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m   1061\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[1;32m   1062\u001b[0m     new_builder \u001b[39m=\u001b[39m build_manager\u001b[39m.\u001b[39mbuild(value, source\u001b[39m=\u001b[39msource, export\u001b[39m=\u001b[39mexport)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/manager.py:171\u001b[0m, in \u001b[0;36mBuildManager.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    167\u001b[0m             \u001b[39mraise\u001b[39;00m \u001b[39mValueError\u001b[39;00m(\u001b[39m\"\u001b[39m\u001b[39mCannot change container_source once set: \u001b[39m\u001b[39m'\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m.\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m\"\u001b[39m\n\u001b[1;32m    168\u001b[0m                              \u001b[39m%\u001b[39m (container\u001b[39m.\u001b[39mname, container\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__module__\u001b[39m,\n\u001b[1;32m    169\u001b[0m                                 container\u001b[39m.\u001b[39m\u001b[39m__class__\u001b[39m\u001b[39m.\u001b[39m\u001b[39m__name__\u001b[39m))\n\u001b[1;32m    170\u001b[0m \u001b[39m# NOTE: if exporting, then existing cached builder will be ignored and overridden with new build result\u001b[39;00m\n\u001b[0;32m--> 171\u001b[0m result \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__type_map\u001b[39m.\u001b[39;49mbuild(container, \u001b[39mself\u001b[39;49m, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec_ext, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m    172\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mprebuilt(container, result)\n\u001b[1;32m    173\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__active_prebuilt(result)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/manager.py:770\u001b[0m, in \u001b[0;36mTypeMap.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    768\u001b[0m \u001b[39mif\u001b[39;00m manager \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m    769\u001b[0m     manager \u001b[39m=\u001b[39m BuildManager(\u001b[39mself\u001b[39m)\n\u001b[0;32m--> 770\u001b[0m builder \u001b[39m=\u001b[39m obj_mapper\u001b[39m.\u001b[39;49mbuild(container, manager, builder\u001b[39m=\u001b[39;49mbuilder, source\u001b[39m=\u001b[39;49msource, spec_ext\u001b[39m=\u001b[39;49mspec_ext, export\u001b[39m=\u001b[39;49mexport)\n\u001b[1;32m    772\u001b[0m \u001b[39m# add additional attributes (namespace, data_type, object_id) to builder\u001b[39;00m\n\u001b[1;32m    773\u001b[0m namespace, data_type \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mget_container_ns_dt(container)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/utils.py:645\u001b[0m, in \u001b[0;36mdocval.<locals>.dec.<locals>.func_call\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    643\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mfunc_call\u001b[39m(\u001b[39m*\u001b[39margs, \u001b[39m*\u001b[39m\u001b[39m*\u001b[39mkwargs):\n\u001b[1;32m    644\u001b[0m     pargs \u001b[39m=\u001b[39m _check_args(args, kwargs)\n\u001b[0;32m--> 645\u001b[0m     \u001b[39mreturn\u001b[39;00m func(args[\u001b[39m0\u001b[39;49m], \u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49mpargs)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:705\u001b[0m, in \u001b[0;36mObjectMapper.build\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m    703\u001b[0m \u001b[39mif\u001b[39;00m builder \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m    704\u001b[0m     builder \u001b[39m=\u001b[39m GroupBuilder(name, parent\u001b[39m=\u001b[39mparent, source\u001b[39m=\u001b[39msource)\n\u001b[0;32m--> 705\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__add_datasets(builder, \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m__spec\u001b[39m.\u001b[39;49mdatasets, container, manager, source, export)\n\u001b[1;32m    706\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_groups(builder, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__spec\u001b[39m.\u001b[39mgroups, container, manager, source, export)\n\u001b[1;32m    707\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__add_links(builder, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m__spec\u001b[39m.\u001b[39mlinks, container, manager, source, export)\n",
      "File \u001b[0;32m/Applications/anaconda3/envs/eats-worm/lib/python3.11/site-packages/hdmf/build/objectmapper.py:999\u001b[0m, in \u001b[0;36mObjectMapper.__add_datasets\u001b[0;34m(self, builder, datasets, container, build_manager, source, export)\u001b[0m\n\u001b[1;32m    997\u001b[0m     msg \u001b[39m=\u001b[39m \u001b[39m'\u001b[39m\u001b[39mcould not convert \u001b[39m\u001b[39m\\'\u001b[39;00m\u001b[39m%s\u001b[39;00m\u001b[39m\\'\u001b[39;00m\u001b[39m for \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m \u001b[39m\u001b[39m\\'\u001b[39;00m\u001b[39m%s\u001b[39;00m\u001b[39m\\'\u001b[39;00m\u001b[39m'\u001b[39m\n\u001b[1;32m    998\u001b[0m     msg \u001b[39m=\u001b[39m msg \u001b[39m%\u001b[39m (spec\u001b[39m.\u001b[39mname, \u001b[39mtype\u001b[39m(container)\u001b[39m.\u001b[39m\u001b[39m__name__\u001b[39m, container\u001b[39m.\u001b[39mname)\n\u001b[0;32m--> 999\u001b[0m     \u001b[39mraise\u001b[39;00m BuildError(builder, msg) \u001b[39mfrom\u001b[39;00m \u001b[39mex\u001b[39;00m\n\u001b[1;32m   1000\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mlogger\u001b[39m.\u001b[39mdebug(\u001b[39m\"\u001b[39m\u001b[39m        Adding untyped dataset for spec name \u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m and adding attributes\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m   1001\u001b[0m                   \u001b[39m%\u001b[39m \u001b[39mrepr\u001b[39m(spec\u001b[39m.\u001b[39mname))\n\u001b[1;32m   1002\u001b[0m sub_builder \u001b[39m=\u001b[39m DatasetBuilder(spec\u001b[39m.\u001b[39mname, data, parent\u001b[39m=\u001b[39mbuilder, source\u001b[39m=\u001b[39msource, dtype\u001b[39m=\u001b[39mdtype)\n",
      "\u001b[0;31mBuildError\u001b[0m: OpticalChannelRefs (OpticalChannelRefs): could not convert 'channels' for OpticalChannelReferences 'OpticalChannelRefs'"
     ]
    }
   ],
   "source": [
    "nwbfile = gen_file('Worm head', 'worm', datetime.today() , 'Kato lab', 'UCSF', \"\") \n",
    "\n",
    "channels = [(\"mNeptune 2.5\", \"561-700-75m\"), (\"Tag RFP-T\", \"561-605-70m\"), (\"CyOFP1\", \"488-605-70m\"), (\"GFP-GCaMP\", \"488-525-50m\"), (\"mTagBFP2\", \"405-460-50m\"), (\"mNeptune 2.5 - high excite\", \"639-700-75m\")]\n",
    "\n",
    "device = nwbfile.create_device(\n",
    "    name = \"Microscope\",\n",
    "    description = \"One-photon microscope Weill\",\n",
    "    manufacturer = \"Leica\"\n",
    "    )\n",
    "\n",
    "OptChannels = []\n",
    "OptChanRefData = []\n",
    "for name, wave in channels:\n",
    "    excite = float(wave.split('-')[0])\n",
    "    emiss_mid = float(wave.split('-')[1])\n",
    "    emiss_range = float(wave.split('-')[2][:-1])\n",
    "    OptChan = OpticalChannelPlus(\n",
    "        name = name,\n",
    "        description = wave,\n",
    "        excitation_lambda = excite,\n",
    "        excitation_range = [excite, excite],\n",
    "        emission_range = [emiss_mid-emiss_range/2, emiss_mid+emiss_range/2],\n",
    "        emission_lambda = emiss_mid\n",
    "    )\n",
    "\n",
    "    OptChannels.append(OptChan)\n",
    "    OptChanRefData.append(wave)\n",
    "\n",
    "OpticalChannelRefs = OpticalChannelReferences(\n",
    "        name = 'OpticalChannelRefs',\n",
    "        channels = OptChannels\n",
    "    )\n",
    "\n",
    "imaging_vol = ImagingVolume(\n",
    "        name= 'ImagingVolume',\n",
    "        optical_channel_plus = OptChannels,\n",
    "        Order_optical_channels = OpticalChannelRefs,\n",
    "        description = 'NeuroPAL image of C elegan brain',\n",
    "        device = device,\n",
    "        location = 'test',\n",
    "        grid_spacing = [0.75,0.75,0.75],\n",
    "        grid_spacing_unit = 'meters',\n",
    "        origin_coords = [0,0,0],\n",
    "        origin_coords_unit = 'meters',\n",
    "        reference_frame = 'reference'\n",
    "    )\n",
    "\n",
    "image = MultiChannelVolume(\n",
    "    name = 'test',\n",
    "    Order_optical_channels = OpticalChannelRefs,\n",
    "    resolution = [1,1,1],\n",
    "    description = 'test',\n",
    "    RGBW_channels = [0,1,2,3],\n",
    "    data = np.ones((100,100,100,100)),\n",
    "    imaging_volume = imaging_vol\n",
    ")\n",
    "\n",
    "nwbfile.add_acquisition(image)\n",
    "\n",
    "neuroPAL_module = nwbfile.create_processing_module(\n",
    "    name = 'NeuroPAL',\n",
    "    description = 'neuroPAL image data and metadata',\n",
    ")    \n",
    "\n",
    "neuroPAL_module.add(imaging_vol)\n",
    "neuroPAL_module.add(OptChannels)\n",
    "neuroPAL_module.add(OpticalChannelRefs)\n",
    "\n",
    "io = NWBHDF5IO(datapath+'/nwb/'+'test+'+'.nwb', mode='w')\n",
    "io.write(nwbfile)\n",
    "io.close()"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Read NWB files and recreate relevant files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "with NWBHDF5IO(datapath+\"/nwb/2022-02-12-w01-NP1.nwb\", mode='r', load_namespaces=True) as io:\n",
    "    read_nwbfile = io.read()\n",
    "    subject = read_nwbfile.subject #get the metadata about the experiment subject\n",
    "    growth_stage = subject.growth_stage\n",
    "    growth_time = subject.growth_stage_time\n",
    "    image = read_nwbfile.acquisition['NeuroPALImageRaw'].data[:] #get the neuroPAL image as a np array\n",
    "    resolution = read_nwbfile.acquisition['NeuroPALImageRaw'].resolution[:] #get the resolution of the image in um/pixels\n",
    "    channels = read_nwbfile.acquisition['NeuroPALImageRaw'].RGBW_channels[:] #get which channels of the image correspond to which RGBW pseudocolors\n",
    "    seg = read_nwbfile.processing['NeuroPAL']['VolumeSegmentation'].voxel_mask[:] #get the locations of neuron centers\n",
    "    im_vol = read_nwbfile.processing['NeuroPAL']['ImagingVolume'] #get the metadata associated with the imaging acquisition\n",
    "    optchans = read_nwbfile.processing['NeuroPAL']['ImagingVolume'].optical_channel_plus[:] #get information about all of the optical channels used in acquisition\n",
    "    chan_refs = read_nwbfile.processing['NeuroPAL']['OpticalChannelRefs'].channels[:] #get the order of the optical channels in the image\n",
    "    proc_image = read_nwbfile.processing['ProcessedImage']['Hist_match_med_filt'].data[:] #get the pre-processed image\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "YA\n"
     ]
    }
   ],
   "source": [
    "print(growth_time)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "'''\n",
    "Recreate blobs.csv from vol_seg\n",
    "'''\n",
    "\n",
    "blobs = pd.DataFrame.from_records(seg, columns=['X', 'Y','Z','weight', 'ID'])\n",
    "blobs = blobs.drop(['weight'], axis=1)\n",
    "blobs = blobs.replace('nan', '', regex=True)\n",
    "blobs.to_csv(datapath+'/nwb/test.csv')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(45, 6, 240, 1000)\n"
     ]
    }
   ],
   "source": [
    "'''\n",
    "Recreate original image from acquisition raw image\n",
    "'''\n",
    "print(image.shape)\n",
    "\n",
    "#im = np.transpose(image,(2,3,1,0)) #have to flip some of the axes to align with how FIJI reads tiff images\n",
    "#image = image.astype('uint16')\n",
    "#print(im.dtype)\n",
    "#print(im.shape)\n",
    "\n",
    "tifffile.imwrite(datapath + '/nwb/test.tif', image, imagej = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(45, 4, 240, 1000)\n",
      "uint16\n"
     ]
    },
    {
     "ename": "",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31mThe Kernel crashed while executing code in the the current cell or a previous cell. Please review the code in the cell(s) to identify a possible cause of the failure. Click <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. View Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
     ]
    }
   ],
   "source": [
    "'''\n",
    "Recreate histogram matched image from processed data\n",
    "'''\n",
    "\n",
    "print(proc_image.shape)\n",
    "\n",
    "#im = np.transpose(proc_image, (3,0,2,1)) #have to flip some of the axes to align with how FIJI reads tiff images\n",
    "#proc_image = proc_image.astype('uint16')\n",
    "print(proc_image.dtype)\n",
    "\n",
    "tifffile.imwrite(datapath + '/nwb/test_proc.tif', proc_image, imagej = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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