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January 16, 2024 19:28
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Demonstration of how to remove the Units table from an NWB file
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "# Removing the Units Table from an NWB file\n", | |
| "\n", | |
| "## Introduction\n", | |
| "\n", | |
| "Removing data from an NWB file is generally NOT recommended. It must be done carefully so as to maintain the validity\n", | |
| "and internal consistency of a file. Think of it like data surgery. To remove some data from an NWB object, you may \n", | |
| "need to create a clone of that NWB object with data removed, and you may need to disconnect NWB objects that you \n", | |
| "do not intend to remove and then reconnect them with appropriate links and references to your cloned NWB object\n", | |
| "with data removed. This procedure should be done with manual inspection at every step. Please consider generating\n", | |
| "a new NWB file from scratch instead of removing data from an NWB file.\n", | |
| "\n", | |
| "Due to how the HDF5 storage format works, opening an NWB file in append mode and deleting or removing data from the file\n", | |
| "will, in general, not physically delete the data from the file. It just removes the data from the index. As a result,\n", | |
| "the file size will not be reduced.\n", | |
| "\n", | |
| "If you want to permanently delete data from the file and reduce the file size, you must create a new file based on the\n", | |
| "original file. You can do this in several ways.\n", | |
| "\n", | |
| "1. Open the NWB file in PyNWB, modify the `NWBFile` object or its children objects in memory, and then \n", | |
| " [export](https://pynwb.readthedocs.io/en/stable/export.html) the modified `NWBFile` object to a new file path. We will\n", | |
| " work through that approach below.\n", | |
| "\n", | |
| "2. Remove (unlink) data from the file using `h5py` or other HDF5 libraries, and then use the \n", | |
| " [h5repack](https://portal.hdfgroup.org/display/HDF5/h5repack) tool from the HDF5 library to create a new file without\n", | |
| " the unlinked data. This method has a key disadvantage in that there are fewer checks that the modified file is \n", | |
| " a valid NWB file. This method will not be described here.\n", | |
| "\n", | |
| "## Download a test NWB file\n", | |
| "\n", | |
| "First, download an example NWB file from DANDI. We will use a 73.2 MB NWB file from Ueli Rutishauser's Lab. \n", | |
| "In your browser:\n", | |
| "\n", | |
| "1. Go to https://dandiarchive.org/dandiset/000004\n", | |
| "2. In the top-right of the page, click Files\n", | |
| "3. Click the first folder \"sub-P10HMH\"\n", | |
| "4. Click the download icon for the first file \"sub-P10HMH_ses-20060901_ecephys+image.nwb\". It may take some\n", | |
| " time to download this file, depending on your internet connection.\n", | |
| "\n", | |
| "## Install PyNWB\n", | |
| "\n", | |
| "Then, you will need to install the latest version of PyNWB from PyPI or conda-forge,\n", | |
| "ideally in a clean virtual environment. Here, let's use `mamba` to create a new conda environment called \"nwb-remove\"\n", | |
| "with `jupyterlab` installed so that we can run this notebook. Then let's use `pip` to install `pynwb` from PyPI.\n", | |
| "\n", | |
| "In a terminal or command prompt with [mambaforge](https://github.com/conda-forge/miniforge#mambaforge) installed, run:\n", | |
| "\n", | |
| "```bash\n", | |
| "mamba create --name nwb-remove --yes jupyterlab\n", | |
| "mamba activate nwb-remove\n", | |
| "pip install pynwb\n", | |
| "```\n", | |
| "\n", | |
| "PyNWB is now installed, so we can use it to open and manipulate the file.\n", | |
| "\n", | |
| "## Open the NWB file\n", | |
| "\n", | |
| "Open this notebook, change the `file_path` variable in the cell below to be the location of your downloaded\n", | |
| "NWB file, and run the cell to read the file into an `NWBFile` object in memory." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 19, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "root pynwb.file.NWBFile at 0x4985526096\n", | |
| "Fields:\n", | |
| " acquisition: {\n", | |
| " events <class 'pynwb.misc.AnnotationSeries'>,\n", | |
| " experiment_ids <class 'pynwb.base.TimeSeries'>\n", | |
| " }\n", | |
| " data_collection: learning: 80, recognition: 81\n", | |
| " devices: {\n", | |
| " Neuralynx-cheetah <class 'pynwb.device.Device'>\n", | |
| " }\n", | |
| " electrode_groups: {\n", | |
| " Neuralynx-cheetah-microwires-1 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-13 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-14 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-15 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-16 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-17 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-18 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-19 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-2 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-20 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-22 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-23 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-24 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-3 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-4 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-5 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-6 <class 'pynwb.ecephys.ElectrodeGroup'>,\n", | |
| " Neuralynx-cheetah-microwires-8 <class 'pynwb.ecephys.ElectrodeGroup'>\n", | |
| " }\n", | |
| " electrodes: electrodes <class 'hdmf.common.table.DynamicTable'>\n", | |
| " experiment_description: The data contained within this file describes a new/old recogntion task performed in patients with intractable epilepsy implanted with depth electrodes and Behnke-Fried microwires in the human Medical Temporal Lobe (MTL).\n", | |
| " file_create_date: [datetime.datetime(2020, 5, 26, 19, 8, 23, 826535, tzinfo=tzoffset(None, -25200))]\n", | |
| " identifier: H10_7\n", | |
| " institution: Hunigton Memorial Hospital\n", | |
| " intervals: {\n", | |
| " trials <class 'pynwb.epoch.TimeIntervals'>\n", | |
| " }\n", | |
| " keywords: <StrDataset for HDF5 dataset \"keywords\": shape (7,), type \"|O\">\n", | |
| " lab: Rutishauser\n", | |
| " related_publications: ['Faraut et al. 2018, Scientific Data; Rutishauser et al. 2015, Nat Neurosci;']\n", | |
| " session_description: New/Old recognition task for ID: 7. \n", | |
| " session_start_time: 2006-09-01 00:00:00-07:00\n", | |
| " stimulus: {\n", | |
| " StimulusPresentation <class 'pynwb.image.OpticalSeries'>\n", | |
| " }\n", | |
| " subject: subject pynwb.file.Subject at 0x5245430416\n", | |
| "Fields:\n", | |
| " age: 37\n", | |
| " description: Left Lateral Frontal\n", | |
| " sex: M\n", | |
| " species: Human\n", | |
| " subject_id: P10HMH\n", | |
| "\n", | |
| " timestamps_reference_time: 2006-09-01 00:00:00-07:00\n", | |
| " trials: trials <class 'pynwb.epoch.TimeIntervals'>\n", | |
| " units: units <class 'pynwb.misc.Units'>\n", | |
| "\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "from pynwb import NWBHDF5IO\n", | |
| "\n", | |
| "# CHANGE THIS PATH to the location of the downloaded test NWB file\n", | |
| "file_path = \"/Users/rly/Documents/NWB_Data/dandisets/000004/sub-P10HMH/sub-P10HMH_ses-20060901_ecephys+image.nwb\"\n", | |
| "\n", | |
| "read_io = NWBHDF5IO(file_path, mode=\"r\")\n", | |
| "nwbfile = read_io.read()\n", | |
| "print(nwbfile)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "## Remove the Units table\n", | |
| "\n", | |
| "In this example, we will remove the `Units` table from the file without replacing it. This will still result in a valid\n", | |
| "NWB file because the `Units` table is optional.\n", | |
| "\n", | |
| "First, let's look at the `Units` table in the file. We can see that it has 37 rows (units)." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 20, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>origClusterID</th>\n", | |
| " <th>waveform_mean_encoding</th>\n", | |
| " <th>waveform_mean_recognition</th>\n", | |
| " <th>IsolationDist</th>\n", | |
| " <th>SNR</th>\n", | |
| " <th>waveform_mean_sampling_rate</th>\n", | |
| " <th>spike_times</th>\n", | |
| " <th>electrodes</th>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>id</th>\n", | |
| " <th></th>\n", | |
| " <th></th>\n", | |
| " <th></th>\n", | |
| " <th></th>\n", | |
| " <th></th>\n", | |
| " <th></th>\n", | |
| " <th></th>\n", | |
| " <th></th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>970</td>\n", | |
| " <td>[2.1764968283053565, 2.3406132503530475, 2.453...</td>\n", | |
| " <td>[2.255677148872515, 2.438650365560623, 2.54682...</td>\n", | |
| " <td>54.949626</td>\n", | |
| " <td>2.074611</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4790.086128, 4790.392488, 4790.808088, 4791.1...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>2519</td>\n", | |
| " <td>[1.9953024730819329, 2.146922925948179, 2.2750...</td>\n", | |
| " <td>[1.8679882172094504, 2.0195327093193445, 2.149...</td>\n", | |
| " <td>1301.944632</td>\n", | |
| " <td>1.535590</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4789.163768, 4789.171688, 4790.086128, 4790.7...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>2</th>\n", | |
| " <td>2569</td>\n", | |
| " <td>[-1.0892165502550855, -1.194207382098711, -1.2...</td>\n", | |
| " <td>[-1.2739211957333492, -1.3850635003577056, -1....</td>\n", | |
| " <td>2700.668258</td>\n", | |
| " <td>1.721514</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.484848, 4787.756208, 4788.171848, 4788.3...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>3</th>\n", | |
| " <td>2808</td>\n", | |
| " <td>[3.9792519048004746, 4.225281427560096, 4.4375...</td>\n", | |
| " <td>[4.554116369553418, 4.791653736023812, 4.99612...</td>\n", | |
| " <td>2798.328329</td>\n", | |
| " <td>2.428861</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4790.086128, 4796.592248, 4797.417168, 4798.8...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>4</th>\n", | |
| " <td>3048</td>\n", | |
| " <td>[-7.368623732940135, -7.666343704498384, -7.93...</td>\n", | |
| " <td>[-7.309179748134245, -7.610296381602412, -7.85...</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>3.924017</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.674888, 4787.861608, 4788.101208, 4788.2...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>5</th>\n", | |
| " <td>4126</td>\n", | |
| " <td>[2.3131939714515104, 2.49287475093624, 2.63675...</td>\n", | |
| " <td>[2.2916029270428444, 2.4356759764683518, 2.549...</td>\n", | |
| " <td>3209.140751</td>\n", | |
| " <td>1.817625</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4790.086088, 4794.246448, 4797.826848, 4798.8...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>6</th>\n", | |
| " <td>4245</td>\n", | |
| " <td>[-5.777442084370658, -6.052566885779441, -6.26...</td>\n", | |
| " <td>[-6.394055601868903, -6.6383642870196224, -6.8...</td>\n", | |
| " <td>25.765571</td>\n", | |
| " <td>3.297644</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.630928, 4788.213568, 4788.266488, 4790.6...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>7</th>\n", | |
| " <td>4329</td>\n", | |
| " <td>[-1.9242575810453464, -2.0852046175911347, -2....</td>\n", | |
| " <td>[-1.6547120693159738, -1.782868893659467, -1.8...</td>\n", | |
| " <td>116.662306</td>\n", | |
| " <td>1.637649</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.378728, 4788.789968, 4791.626488, 4791.6...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>8</th>\n", | |
| " <td>2498</td>\n", | |
| " <td>[-2.4713541945868465, -2.6218310636669306, -2....</td>\n", | |
| " <td>[-2.5624289166817404, -2.749951452957572, -2.8...</td>\n", | |
| " <td>1016.161571</td>\n", | |
| " <td>1.558819</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4789.165328, 4789.588288, 4790.794608, 4790.8...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>9</th>\n", | |
| " <td>2530</td>\n", | |
| " <td>[1.8563672622890155, 1.9997108346169516, 2.120...</td>\n", | |
| " <td>[1.9445634547101074, 2.0918185669478353, 2.199...</td>\n", | |
| " <td>780.642771</td>\n", | |
| " <td>1.618448</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.778928, 4788.966848, 4790.086088, 4790.8...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>10</th>\n", | |
| " <td>2088</td>\n", | |
| " <td>[6.047871430730712, 6.375282052804018, 6.73703...</td>\n", | |
| " <td>[5.405554112580891, 5.612333793682148, 5.96803...</td>\n", | |
| " <td>24.444472</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4838.037328, 4842.014248, 4843.459488, 4845.6...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>11</th>\n", | |
| " <td>2095</td>\n", | |
| " <td>[-2.709146247949879, -2.925309328453019, -3.03...</td>\n", | |
| " <td>[-1.9117917689484112, -2.0487637832506564, -2....</td>\n", | |
| " <td>140.162756</td>\n", | |
| " <td>1.684626</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4806.942848, 4806.997728, 4812.365568, 4839.6...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>12</th>\n", | |
| " <td>2332</td>\n", | |
| " <td>[2.823602517191, 2.969629137265953, 3.12642019...</td>\n", | |
| " <td>[3.0355818059511357, 3.198584121564973, 3.3313...</td>\n", | |
| " <td>78.762775</td>\n", | |
| " <td>2.013060</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.393248, 4790.086088, 4790.810608, 4796.5...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>13</th>\n", | |
| " <td>2357</td>\n", | |
| " <td>[1.2274214830606864, 1.3016743035701275, 1.401...</td>\n", | |
| " <td>[1.120015986951992, 1.2023151701844226, 1.2436...</td>\n", | |
| " <td>36.746336</td>\n", | |
| " <td>1.500293</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4793.634568, 4795.696528, 4796.552928, 4800.8...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>14</th>\n", | |
| " <td>2498</td>\n", | |
| " <td>[-2.824695043755286, -3.0307401988082607, -3.1...</td>\n", | |
| " <td>[-3.258529426953644, -3.536159732250002, -3.68...</td>\n", | |
| " <td>1667.376707</td>\n", | |
| " <td>2.048690</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.630928, 4788.266448, 4788.388648, 4788.3...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>15</th>\n", | |
| " <td>2585</td>\n", | |
| " <td>[-0.327877833118743, -0.45845156443332435, -0....</td>\n", | |
| " <td>[0.7860516060137199, 0.7340395697785383, 0.680...</td>\n", | |
| " <td>14.371489</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4790.892688, 4793.726568, 4803.596888, 4805.3...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>16</th>\n", | |
| " <td>2598</td>\n", | |
| " <td>[2.1232642387501732, 2.270659390326574, 2.3742...</td>\n", | |
| " <td>[1.8556815808671219, 2.0242523799238765, 2.115...</td>\n", | |
| " <td>1279.536302</td>\n", | |
| " <td>1.831915</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4790.086088, 4790.790488, 4790.808008, 4791.7...</td>\n", | |
| " <td>x y z imp location filterin...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>17</th>\n", | |
| " <td>2742</td>\n", | |
| " <td>[-1.2245068670748598, -1.4716205507666156, -1....</td>\n", | |
| " <td>[-0.9695218513335611, -1.191220983233553, -1.3...</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>1.805190</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.261848, 4787.301088, 4787.561608, 4787.5...</td>\n", | |
| " <td>x y z imp location filte...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>18</th>\n", | |
| " <td>1413</td>\n", | |
| " <td>[-2.548643607790111, -2.548643607790111, -2.54...</td>\n", | |
| " <td>[-2.5237935325968057, -2.5237935325968057, -2....</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>1.669595</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.366161797764, 4787.3838466140805, 4787.3...</td>\n", | |
| " <td>x y z imp location filte...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>19</th>\n", | |
| " <td>1179</td>\n", | |
| " <td>[-1.2289306492129852, -1.2289306492129852, -1....</td>\n", | |
| " <td>[-0.8136424091326029, -0.8154535142928742, -0....</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>1.013530</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4771.88223744342, 4787.139100252119, 4787.376...</td>\n", | |
| " <td>x y z imp location filte...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>20</th>\n", | |
| " <td>2647</td>\n", | |
| " <td>[0.037290130212203614, 0.011616546233212323, 0...</td>\n", | |
| " <td>[0.5767909527902486, 0.5489105365684017, 0.566...</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>1.100296</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.837768, 4790.566488, 4790.579328, 4790.8...</td>\n", | |
| " <td>x y z imp location filte...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>21</th>\n", | |
| " <td>2468</td>\n", | |
| " <td>[5.2659894782362695, 5.546721850839608, 5.8134...</td>\n", | |
| " <td>[4.857542541911167, 5.147261569552395, 5.31181...</td>\n", | |
| " <td>2967.764983</td>\n", | |
| " <td>2.059100</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4789.521248, 4790.402568, 4792.244968, 4792.5...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>22</th>\n", | |
| " <td>4603</td>\n", | |
| " <td>[4.98627313334537, 5.284474845093591, 5.497782...</td>\n", | |
| " <td>[4.736911863620169, 4.883046649181909, 5.13170...</td>\n", | |
| " <td>140.995186</td>\n", | |
| " <td>1.833047</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.446848, 4790.402568, 4792.244968, 4792.5...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>23</th>\n", | |
| " <td>4648</td>\n", | |
| " <td>[-4.734785929892845, -4.964300116472013, -5.10...</td>\n", | |
| " <td>[-4.913822391802695, -5.129887713095916, -5.28...</td>\n", | |
| " <td>1518.742743</td>\n", | |
| " <td>1.750192</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.802768, 4788.940968, 4789.501928, 4789.5...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>24</th>\n", | |
| " <td>4693</td>\n", | |
| " <td>[1.323939497364863, 1.4111633753647694, 1.5467...</td>\n", | |
| " <td>[1.8068525763401793, 2.051022355545685, 2.1776...</td>\n", | |
| " <td>14.742652</td>\n", | |
| " <td>1.260526</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[5891.409008, 5894.781968, 5904.204008, 5909.6...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>25</th>\n", | |
| " <td>4455</td>\n", | |
| " <td>[-10.287331269184898, -11.208661911067304, -11...</td>\n", | |
| " <td>[-7.315705368952566, -7.315705368952566, -7.64...</td>\n", | |
| " <td>43.282241</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4796.851008, 4834.599648, 4919.598208, 4922.9...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>26</th>\n", | |
| " <td>4961</td>\n", | |
| " <td>[5.59877152176297, 5.841501743545079, 6.095332...</td>\n", | |
| " <td>[5.667234047705148, 5.917575835001948, 6.11893...</td>\n", | |
| " <td>24.832714</td>\n", | |
| " <td>1.994933</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.446888, 4790.111968, 4790.402568, 4792.2...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>27</th>\n", | |
| " <td>4528</td>\n", | |
| " <td>[-5.16416672053587, -5.418178478304996, -5.594...</td>\n", | |
| " <td>[-5.457686005836013, -5.7104250391377915, -5.9...</td>\n", | |
| " <td>1841.242825</td>\n", | |
| " <td>2.000195</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.691448, 4787.960208, 4788.980208, 4789.8...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>28</th>\n", | |
| " <td>4564</td>\n", | |
| " <td>[4.703844644646429, 4.937927746210565, 5.08580...</td>\n", | |
| " <td>[4.6658010728239425, 4.892389336217129, 5.0866...</td>\n", | |
| " <td>945.061969</td>\n", | |
| " <td>1.932703</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.446888, 4789.521288, 4790.110208, 4790.1...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>29</th>\n", | |
| " <td>5823</td>\n", | |
| " <td>[5.728572791425566, 5.99580198453578, 6.261548...</td>\n", | |
| " <td>[5.587791510078878, 5.926904930783165, 6.16167...</td>\n", | |
| " <td>15.561102</td>\n", | |
| " <td>2.261887</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4820.443688, 4830.186608, 4908.169368, 4929.4...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>30</th>\n", | |
| " <td>5894</td>\n", | |
| " <td>[-4.73077804512256, -4.898476202058618, -5.008...</td>\n", | |
| " <td>[-4.862234492245103, -5.061440746978259, -5.18...</td>\n", | |
| " <td>1030.742235</td>\n", | |
| " <td>1.508859</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.001408, 4788.331088, 4788.551088, 4789.1...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>31</th>\n", | |
| " <td>5909</td>\n", | |
| " <td>[-0.5586610466677955, -0.7760079182327165, -0....</td>\n", | |
| " <td>[-1.3264553518120181, -1.587127146104324, -1.6...</td>\n", | |
| " <td>13.758655</td>\n", | |
| " <td>1.093016</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4792.823328, 4796.369128, 4797.807928, 4800.7...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>32</th>\n", | |
| " <td>5931</td>\n", | |
| " <td>[0.14249181583647802, 0.3429984839918393, 0.44...</td>\n", | |
| " <td>[-0.3719621633119015, -0.14229420338492527, -0...</td>\n", | |
| " <td>101.993007</td>\n", | |
| " <td>1.244882</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.231848, 4787.324768, 4787.432528, 4787.5...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>33</th>\n", | |
| " <td>5443</td>\n", | |
| " <td>[4.630259191385897, 4.845414865946165, 5.05708...</td>\n", | |
| " <td>[4.907337744643092, 5.138267903502391, 5.39023...</td>\n", | |
| " <td>977.853119</td>\n", | |
| " <td>1.732713</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4789.521288, 4790.402568, 4792.244968, 4792.5...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>34</th>\n", | |
| " <td>5457</td>\n", | |
| " <td>[-4.366063858693557, -4.61496903182344, -4.753...</td>\n", | |
| " <td>[-4.749469479795696, -4.945626544066499, -5.10...</td>\n", | |
| " <td>1697.177504</td>\n", | |
| " <td>1.655575</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.338248, 4789.999368, 4790.423408, 4790.8...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>35</th>\n", | |
| " <td>5459</td>\n", | |
| " <td>[-0.01842692210679583, 0.24097175324993847, 0....</td>\n", | |
| " <td>[-0.48625057679849604, -0.2603314739988116, -0...</td>\n", | |
| " <td>113.440252</td>\n", | |
| " <td>1.295803</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4793.288528, 4793.484768, 4797.003048, 4798.6...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>36</th>\n", | |
| " <td>3846</td>\n", | |
| " <td>[-11.921466457155018, -12.357194465282975, -12...</td>\n", | |
| " <td>[-11.558615043019364, -11.899498264858675, -12...</td>\n", | |
| " <td>19.366741</td>\n", | |
| " <td>3.232238</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4788.976128, 4790.940448, 4792.035488, 4795.1...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>37</th>\n", | |
| " <td>3848</td>\n", | |
| " <td>[-18.184675130569318, -18.917115701981917, -19...</td>\n", | |
| " <td>[-19.78105764303847, -20.55885124442189, -21.3...</td>\n", | |
| " <td>1306.074987</td>\n", | |
| " <td>5.579544</td>\n", | |
| " <td>[98400.0]</td>\n", | |
| " <td>[4787.666088, 4788.275648, 4788.753248, 4789.2...</td>\n", | |
| " <td>x y z imp location filtering...</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " origClusterID waveform_mean_encoding \\\n", | |
| "id \n", | |
| "0 970 [2.1764968283053565, 2.3406132503530475, 2.453... \n", | |
| "1 2519 [1.9953024730819329, 2.146922925948179, 2.2750... \n", | |
| "2 2569 [-1.0892165502550855, -1.194207382098711, -1.2... \n", | |
| "3 2808 [3.9792519048004746, 4.225281427560096, 4.4375... \n", | |
| "4 3048 [-7.368623732940135, -7.666343704498384, -7.93... \n", | |
| "5 4126 [2.3131939714515104, 2.49287475093624, 2.63675... \n", | |
| "6 4245 [-5.777442084370658, -6.052566885779441, -6.26... \n", | |
| "7 4329 [-1.9242575810453464, -2.0852046175911347, -2.... \n", | |
| "8 2498 [-2.4713541945868465, -2.6218310636669306, -2.... \n", | |
| "9 2530 [1.8563672622890155, 1.9997108346169516, 2.120... \n", | |
| "10 2088 [6.047871430730712, 6.375282052804018, 6.73703... \n", | |
| "11 2095 [-2.709146247949879, -2.925309328453019, -3.03... \n", | |
| "12 2332 [2.823602517191, 2.969629137265953, 3.12642019... \n", | |
| "13 2357 [1.2274214830606864, 1.3016743035701275, 1.401... \n", | |
| "14 2498 [-2.824695043755286, -3.0307401988082607, -3.1... \n", | |
| "15 2585 [-0.327877833118743, -0.45845156443332435, -0.... \n", | |
| "16 2598 [2.1232642387501732, 2.270659390326574, 2.3742... \n", | |
| "17 2742 [-1.2245068670748598, -1.4716205507666156, -1.... \n", | |
| "18 1413 [-2.548643607790111, -2.548643607790111, -2.54... \n", | |
| "19 1179 [-1.2289306492129852, -1.2289306492129852, -1.... \n", | |
| "20 2647 [0.037290130212203614, 0.011616546233212323, 0... \n", | |
| "21 2468 [5.2659894782362695, 5.546721850839608, 5.8134... \n", | |
| "22 4603 [4.98627313334537, 5.284474845093591, 5.497782... \n", | |
| "23 4648 [-4.734785929892845, -4.964300116472013, -5.10... \n", | |
| "24 4693 [1.323939497364863, 1.4111633753647694, 1.5467... \n", | |
| "25 4455 [-10.287331269184898, -11.208661911067304, -11... \n", | |
| "26 4961 [5.59877152176297, 5.841501743545079, 6.095332... \n", | |
| "27 4528 [-5.16416672053587, -5.418178478304996, -5.594... \n", | |
| "28 4564 [4.703844644646429, 4.937927746210565, 5.08580... \n", | |
| "29 5823 [5.728572791425566, 5.99580198453578, 6.261548... \n", | |
| "30 5894 [-4.73077804512256, -4.898476202058618, -5.008... \n", | |
| "31 5909 [-0.5586610466677955, -0.7760079182327165, -0.... \n", | |
| "32 5931 [0.14249181583647802, 0.3429984839918393, 0.44... \n", | |
| "33 5443 [4.630259191385897, 4.845414865946165, 5.05708... \n", | |
| "34 5457 [-4.366063858693557, -4.61496903182344, -4.753... \n", | |
| "35 5459 [-0.01842692210679583, 0.24097175324993847, 0.... \n", | |
| "36 3846 [-11.921466457155018, -12.357194465282975, -12... \n", | |
| "37 3848 [-18.184675130569318, -18.917115701981917, -19... \n", | |
| "\n", | |
| " waveform_mean_recognition IsolationDist \\\n", | |
| "id \n", | |
| "0 [2.255677148872515, 2.438650365560623, 2.54682... 54.949626 \n", | |
| "1 [1.8679882172094504, 2.0195327093193445, 2.149... 1301.944632 \n", | |
| "2 [-1.2739211957333492, -1.3850635003577056, -1.... 2700.668258 \n", | |
| "3 [4.554116369553418, 4.791653736023812, 4.99612... 2798.328329 \n", | |
| "4 [-7.309179748134245, -7.610296381602412, -7.85... NaN \n", | |
| "5 [2.2916029270428444, 2.4356759764683518, 2.549... 3209.140751 \n", | |
| "6 [-6.394055601868903, -6.6383642870196224, -6.8... 25.765571 \n", | |
| "7 [-1.6547120693159738, -1.782868893659467, -1.8... 116.662306 \n", | |
| "8 [-2.5624289166817404, -2.749951452957572, -2.8... 1016.161571 \n", | |
| "9 [1.9445634547101074, 2.0918185669478353, 2.199... 780.642771 \n", | |
| "10 [5.405554112580891, 5.612333793682148, 5.96803... 24.444472 \n", | |
| "11 [-1.9117917689484112, -2.0487637832506564, -2.... 140.162756 \n", | |
| "12 [3.0355818059511357, 3.198584121564973, 3.3313... 78.762775 \n", | |
| "13 [1.120015986951992, 1.2023151701844226, 1.2436... 36.746336 \n", | |
| "14 [-3.258529426953644, -3.536159732250002, -3.68... 1667.376707 \n", | |
| "15 [0.7860516060137199, 0.7340395697785383, 0.680... 14.371489 \n", | |
| "16 [1.8556815808671219, 2.0242523799238765, 2.115... 1279.536302 \n", | |
| "17 [-0.9695218513335611, -1.191220983233553, -1.3... NaN \n", | |
| "18 [-2.5237935325968057, -2.5237935325968057, -2.... NaN \n", | |
| "19 [-0.8136424091326029, -0.8154535142928742, -0.... NaN \n", | |
| "20 [0.5767909527902486, 0.5489105365684017, 0.566... NaN \n", | |
| "21 [4.857542541911167, 5.147261569552395, 5.31181... 2967.764983 \n", | |
| "22 [4.736911863620169, 4.883046649181909, 5.13170... 140.995186 \n", | |
| "23 [-4.913822391802695, -5.129887713095916, -5.28... 1518.742743 \n", | |
| "24 [1.8068525763401793, 2.051022355545685, 2.1776... 14.742652 \n", | |
| "25 [-7.315705368952566, -7.315705368952566, -7.64... 43.282241 \n", | |
| "26 [5.667234047705148, 5.917575835001948, 6.11893... 24.832714 \n", | |
| "27 [-5.457686005836013, -5.7104250391377915, -5.9... 1841.242825 \n", | |
| "28 [4.6658010728239425, 4.892389336217129, 5.0866... 945.061969 \n", | |
| "29 [5.587791510078878, 5.926904930783165, 6.16167... 15.561102 \n", | |
| "30 [-4.862234492245103, -5.061440746978259, -5.18... 1030.742235 \n", | |
| "31 [-1.3264553518120181, -1.587127146104324, -1.6... 13.758655 \n", | |
| "32 [-0.3719621633119015, -0.14229420338492527, -0... 101.993007 \n", | |
| "33 [4.907337744643092, 5.138267903502391, 5.39023... 977.853119 \n", | |
| "34 [-4.749469479795696, -4.945626544066499, -5.10... 1697.177504 \n", | |
| "35 [-0.48625057679849604, -0.2603314739988116, -0... 113.440252 \n", | |
| "36 [-11.558615043019364, -11.899498264858675, -12... 19.366741 \n", | |
| "37 [-19.78105764303847, -20.55885124442189, -21.3... 1306.074987 \n", | |
| "\n", | |
| " SNR waveform_mean_sampling_rate \\\n", | |
| "id \n", | |
| "0 2.074611 [98400.0] \n", | |
| "1 1.535590 [98400.0] \n", | |
| "2 1.721514 [98400.0] \n", | |
| "3 2.428861 [98400.0] \n", | |
| "4 3.924017 [98400.0] \n", | |
| "5 1.817625 [98400.0] \n", | |
| "6 3.297644 [98400.0] \n", | |
| "7 1.637649 [98400.0] \n", | |
| "8 1.558819 [98400.0] \n", | |
| "9 1.618448 [98400.0] \n", | |
| "10 NaN [98400.0] \n", | |
| "11 1.684626 [98400.0] \n", | |
| "12 2.013060 [98400.0] \n", | |
| "13 1.500293 [98400.0] \n", | |
| "14 2.048690 [98400.0] \n", | |
| "15 NaN [98400.0] \n", | |
| "16 1.831915 [98400.0] \n", | |
| "17 1.805190 [98400.0] \n", | |
| "18 1.669595 [98400.0] \n", | |
| "19 1.013530 [98400.0] \n", | |
| "20 1.100296 [98400.0] \n", | |
| "21 2.059100 [98400.0] \n", | |
| "22 1.833047 [98400.0] \n", | |
| "23 1.750192 [98400.0] \n", | |
| "24 1.260526 [98400.0] \n", | |
| "25 NaN [98400.0] \n", | |
| "26 1.994933 [98400.0] \n", | |
| "27 2.000195 [98400.0] \n", | |
| "28 1.932703 [98400.0] \n", | |
| "29 2.261887 [98400.0] \n", | |
| "30 1.508859 [98400.0] \n", | |
| "31 1.093016 [98400.0] \n", | |
| "32 1.244882 [98400.0] \n", | |
| "33 1.732713 [98400.0] \n", | |
| "34 1.655575 [98400.0] \n", | |
| "35 1.295803 [98400.0] \n", | |
| "36 3.232238 [98400.0] \n", | |
| "37 5.579544 [98400.0] \n", | |
| "\n", | |
| " spike_times \\\n", | |
| "id \n", | |
| "0 [4790.086128, 4790.392488, 4790.808088, 4791.1... \n", | |
| "1 [4789.163768, 4789.171688, 4790.086128, 4790.7... \n", | |
| "2 [4787.484848, 4787.756208, 4788.171848, 4788.3... \n", | |
| "3 [4790.086128, 4796.592248, 4797.417168, 4798.8... \n", | |
| "4 [4787.674888, 4787.861608, 4788.101208, 4788.2... \n", | |
| "5 [4790.086088, 4794.246448, 4797.826848, 4798.8... \n", | |
| "6 [4787.630928, 4788.213568, 4788.266488, 4790.6... \n", | |
| "7 [4788.378728, 4788.789968, 4791.626488, 4791.6... \n", | |
| "8 [4789.165328, 4789.588288, 4790.794608, 4790.8... \n", | |
| "9 [4788.778928, 4788.966848, 4790.086088, 4790.8... \n", | |
| "10 [4838.037328, 4842.014248, 4843.459488, 4845.6... \n", | |
| "11 [4806.942848, 4806.997728, 4812.365568, 4839.6... \n", | |
| "12 [4788.393248, 4790.086088, 4790.810608, 4796.5... \n", | |
| "13 [4793.634568, 4795.696528, 4796.552928, 4800.8... \n", | |
| "14 [4787.630928, 4788.266448, 4788.388648, 4788.3... \n", | |
| "15 [4790.892688, 4793.726568, 4803.596888, 4805.3... \n", | |
| "16 [4790.086088, 4790.790488, 4790.808008, 4791.7... \n", | |
| "17 [4787.261848, 4787.301088, 4787.561608, 4787.5... \n", | |
| "18 [4787.366161797764, 4787.3838466140805, 4787.3... \n", | |
| "19 [4771.88223744342, 4787.139100252119, 4787.376... \n", | |
| "20 [4788.837768, 4790.566488, 4790.579328, 4790.8... \n", | |
| "21 [4789.521248, 4790.402568, 4792.244968, 4792.5... \n", | |
| "22 [4787.446848, 4790.402568, 4792.244968, 4792.5... \n", | |
| "23 [4788.802768, 4788.940968, 4789.501928, 4789.5... \n", | |
| "24 [5891.409008, 5894.781968, 5904.204008, 5909.6... \n", | |
| "25 [4796.851008, 4834.599648, 4919.598208, 4922.9... \n", | |
| "26 [4787.446888, 4790.111968, 4790.402568, 4792.2... \n", | |
| "27 [4787.691448, 4787.960208, 4788.980208, 4789.8... \n", | |
| "28 [4787.446888, 4789.521288, 4790.110208, 4790.1... \n", | |
| "29 [4820.443688, 4830.186608, 4908.169368, 4929.4... \n", | |
| "30 [4788.001408, 4788.331088, 4788.551088, 4789.1... \n", | |
| "31 [4792.823328, 4796.369128, 4797.807928, 4800.7... \n", | |
| "32 [4787.231848, 4787.324768, 4787.432528, 4787.5... \n", | |
| "33 [4789.521288, 4790.402568, 4792.244968, 4792.5... \n", | |
| "34 [4788.338248, 4789.999368, 4790.423408, 4790.8... \n", | |
| "35 [4793.288528, 4793.484768, 4797.003048, 4798.6... \n", | |
| "36 [4788.976128, 4790.940448, 4792.035488, 4795.1... \n", | |
| "37 [4787.666088, 4788.275648, 4788.753248, 4789.2... \n", | |
| "\n", | |
| " electrodes \n", | |
| "id \n", | |
| "0 x y z imp location filterin... \n", | |
| "1 x y z imp location filterin... \n", | |
| "2 x y z imp location filterin... \n", | |
| "3 x y z imp location filterin... \n", | |
| "4 x y z imp location filterin... \n", | |
| "5 x y z imp location filterin... \n", | |
| "6 x y z imp location filterin... \n", | |
| "7 x y z imp location filterin... \n", | |
| "8 x y z imp location filterin... \n", | |
| "9 x y z imp location filterin... \n", | |
| "10 x y z imp location filterin... \n", | |
| "11 x y z imp location filterin... \n", | |
| "12 x y z imp location filterin... \n", | |
| "13 x y z imp location filterin... \n", | |
| "14 x y z imp location filterin... \n", | |
| "15 x y z imp location filterin... \n", | |
| "16 x y z imp location filterin... \n", | |
| "17 x y z imp location filte... \n", | |
| "18 x y z imp location filte... \n", | |
| "19 x y z imp location filte... \n", | |
| "20 x y z imp location filte... \n", | |
| "21 x y z imp location filtering... \n", | |
| "22 x y z imp location filtering... \n", | |
| "23 x y z imp location filtering... \n", | |
| "24 x y z imp location filtering... \n", | |
| "25 x y z imp location filtering... \n", | |
| "26 x y z imp location filtering... \n", | |
| "27 x y z imp location filtering... \n", | |
| "28 x y z imp location filtering... \n", | |
| "29 x y z imp location filtering... \n", | |
| "30 x y z imp location filtering... \n", | |
| "31 x y z imp location filtering... \n", | |
| "32 x y z imp location filtering... \n", | |
| "33 x y z imp location filtering... \n", | |
| "34 x y z imp location filtering... \n", | |
| "35 x y z imp location filtering... \n", | |
| "36 x y z imp location filtering... \n", | |
| "37 x y z imp location filtering... " | |
| ] | |
| }, | |
| "execution_count": 20, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "nwbfile.units.to_dataframe()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 21, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# unlink the Units table from its parent container, NWBFile\n", | |
| "nwbfile.units.reset_parent()\n", | |
| "\n", | |
| "# remove the Units table from the NWBFile fields\n", | |
| "# this is a temporary hack to get around the fact that nwbfile.units is a special attribute of NWBFile\n", | |
| "nwbfile.fields[\"units\"] = None\n", | |
| "\n", | |
| "# now, NWBFile.units is None\n", | |
| "nwbfile.units" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 22, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# finally, create a new IO object for exporting the modified in-memory NWBFile object\n", | |
| "# to a new file path\n", | |
| "export_path = \"./trimmed_nwbfile.nwb\"\n", | |
| "with NWBHDF5IO(export_path, mode=\"w\") as export_io:\n", | |
| " export_io.export(src_io=read_io, nwbfile=nwbfile)\n", | |
| "\n", | |
| "read_io.close()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": {}, | |
| "source": [ | |
| "Let's verify that our new file is valid and does not have a `Units` table." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 23, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "Validation errors: []\n", | |
| "None\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "from pynwb import validate\n", | |
| "\n", | |
| "with NWBHDF5IO(export_path, mode=\"r\") as read_export_io:\n", | |
| " errors = validate(read_export_io)\n", | |
| " print(\"Validation errors:\", errors) # this should be an empty list\n", | |
| "\n", | |
| " read_nwbfile = read_export_io.read()\n", | |
| " print(read_nwbfile.units)\n" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "test", | |
| "language": "python", | |
| "name": "python3" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": { | |
| "name": "ipython", | |
| "version": 3 | |
| }, | |
| "file_extension": ".py", | |
| "mimetype": "text/x-python", | |
| "name": "python", | |
| "nbconvert_exporter": "python", | |
| "pygments_lexer": "ipython3", | |
| "version": "3.11.7" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2 | |
| } |
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