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[Bug]: #527
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Hi @jc192015 is the |
@jc192015 Is the data in each VectorIndex column the same length as
|
@jc192015 Can you also post the full stack of the error? |
%%%%%%%%%%% Validation results %%%%%%%%% (base) C:\Windows\System32>nwbinspector D:\Data_share\NWB\ --config dandi The above exception was the direct cause of the following exception: Traceback (most recent call last): %%%%%%%%% Validation ended, look at the last sentence, 'Could not construct TimeIntervals object due to: columns must be the same length' %%%%%%%%% |
Would it be possible to share either this NWB file or alternatively a minimal script that produces a NWB file which also fails the nwbinspector? |
Furthermore, what version of the schema are you currently using? |
How can I share the NWB file with you? |
Is there a more secure way we could communicate? I can share a onedrive link that you can upload your file to but I will need at least an email address to share it with. Either the one you're currently using or a burner one you can use publicly. |
Sent an invite, please check your inbox and spam folder. If you have not received it in a while please let me know and we'll have to figure out another way. |
uploaded. Thank you in advance. |
Try transposing the data provided for the column Note that for QOL reasons, vectors for the most part do not care what dimension they are on so you do not need to change those values in the table. |
After transposing "CueTime" , I got the following outcome. %%%%%%%%%% Validation %%%%%%%%% (base) C:\Windows\System32>nwbinspector D:\Data_share\NWB\ --config dandi NWBInspector Report Summary Timestamp: 2023-07-27 15:20:24.448653-05:00 Found 53 issues over 1 files: 0 PYNWB_VALIDATION0.0 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: root/general/experimenter - 'None' object at location 'general/experimenter' 0.1 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: root/general/related_publications - 'None' object at location 'general/related_publications' 0.2 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: VectorIndex/description - 'None' object at location 'intervals/trials/timeseries_index' 0.3 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: VectorIndex - 'None' object at location 'intervals/trials/timeseries_index' 0.4 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: VectorIndex/description - 'None' object at location 'units/spike_times_index' 0.5 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: VectorIndex - 'None' object at location 'units/spike_times_index' 0.6 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: Units/waveforms/unit - 'None' object at location 'units/waveforms' 0.7 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: Units/waveforms - 'None' object at location 'units/waveforms' 0.8 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: Units/waveforms - 'None' object at location 'units/waveforms' 0.9 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: VectorData/description - 'None' object at location 'units/trials_index' 1 CRITICAL1.10 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit8SS' 1.11 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit8CS' 1.12 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit7SS' 1.13 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit6SS' 1.14 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit5SS' 1.15 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit4SS' 1.16 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit3SS' 1.17 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit2SS' 1.18 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_electrical_series_dims - 'SpikeEventSeries' object at location '/analysis/unit1SS' 1.19 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_subject_age - 'Subject' object at location '/general/subject' 1.20 D:\Data_share\NWB\BAYLORNL23_20190320.nwb and 8 other files: check_dynamic_table_region_data_validity - 'DynamicTableRegion' object with name 'electrodes' 2 BEST_PRACTICE_VIOLATION2.21 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'OptogeneticSeries' object at location '/stimulus/presentation/laser_power' 2.22 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit8SS' 2.23 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit8CS' 2.24 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit7SS' 2.25 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit6SS' 2.26 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit5SS' 2.27 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit4SS' 2.28 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit3SS' 2.29 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit2SS' 2.30 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_resolution - 'SpikeEventSeries' object at location '/analysis/unit1SS' 3 BEST_PRACTICE_SUGGESTION3.31 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_description - 'Device' object at location '/general/devices/laser-473nm (Utralaser)' 3.32 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_description - 'Device' object at location '/general/devices/Cambridge NeuroTech 64ch H2 probe 2x32 shank1:ch1-32 shank2:ch33-64 (Cambridge NeuroTech)' 3.33 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_small_dataset_compression - 'OptogeneticSeries' object at location '/stimulus/presentation/laser_power' 3.34 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_small_dataset_compression - 'SpikeEventSeries' object at location '/analysis/unit8SS' 3.35 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_small_dataset_compression - 'SpikeEventSeries' object at location '/analysis/unit6SS' 3.36 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_experimenter_form - 'NWBFile' object at location '/' 3.37 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_doi_publications - 'NWBFile' object at location '/' 3.38 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_column_binary_capability - 'TimeIntervals' object with name 'trials' 3.39 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_column_binary_capability - 'TimeIntervals' object with name 'trials' 3.40 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_column_binary_capability - 'TimeIntervals' object with name 'trials' 3.41 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_column_binary_capability - 'TimeIntervals' object with name 'trials' 3.42 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_column_binary_capability - 'TimeIntervals' object with name 'trials' 3.43 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_column_binary_capability - 'TimeIntervals' object with name 'trials' 3.44 D:\Data_share\NWB\BAYLORNL23_20190320.nwb: check_column_binary_capability - 'TimeIntervals' object with name 'trials' %%%%%%%%%%%% CRITICAL label appears %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%% Fake upload %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% (base) C:\Windows\System32\000572>dandi organize D:\Data_share\NWB\ -f dry |
After transposing the data related to "unitXXX, " I got the following outcome. %%%%%%%%%%%% Validation %%%%%%%%%%%%%%%%%%%%% (base) C:\Windows\System32>nwbinspector D:\Data_share\NWB\ --config dandi The above exception was the direct cause of the following exception: Traceback (most recent call last): %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Fake update %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% (base) C:\Windows\System32\000572>dandi organize D:\Data_share\NWB\ -f dry |
@jc192015 Is this dataset already on DANDI or are you trying to upload it do DANDI? As far as I can tell, the Spike Event Series shapes look right but I'll need to investigate this further. The error you're getting is also a bug in pynwb. |
Yes, I am struggling to upload nwbs to DANDI. |
I see, I will need to warn you that DANDIsets need to be at least schema version 2.1 or higher. The file you've created is still version 2.0b, you will most likely need to adapt the script to at least schema version 2.1. This may also impact why the nwbinspector is failing your file. |
Note we are still looking at it, the error still indicates an shape error which I have not been able to validate. |
I don't know how to modify the following code to meet MatNWB 2.6.0 requirment. That is why I am still using 2.0b. trials_epoch = types.core.TimeIntervals(... |
I believe the main change for |
@jc192015 my suggestion would be to at least upgrade the schema to 2.1.0 using the MAtNWB version that you have. I then recommend working with the file using the newest release of MatNWB since that supports all schema versions after 2.1.0 (the MatNWB version only specifies the most recent supported schema). |
I generated a new nwb file using MatNWB 2.6.0.2. But I got an error message indicating that "Could not construct Units object due to: columns must be the same length." But I have checked the "Units" . The length of "id", "soike_times_index", and "waveforms" are the same. I uploaded related files "BAYLORNL23_20190320-2.6.0.2.nwb" and "Message for file made on 20230728_NL23_20190320-2.6.0.2.txt" to the onedrive that you invited me yesterday for your reference. |
I generated a new nwb file using MatNWB 2.6.0.2. But I got an error message indicating that "Could not construct Units object due to: columns must be the same length." But I have checked the "Units" . The length of "id", "soike_times_index", and "waveforms" are the same. I uploaded related files "BAYLORNL23_20190320-2.6.0.2.nwb" and "Message for file made on 20230728_NL23_20190320-2.6.0.2.txt" to the onedrive that you invited me yesterday for your reference.
Thank you.
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From: Lawrence ***@***.***>
Sent: Friday, July 28, 2023 8:46 AM
To: NeurodataWithoutBorders/matnwb ***@***.***>
Cc: Chen, Jian ***@***.***>; Mention ***@***.***>
Subject: Re: [NeurodataWithoutBorders/matnwb] [Bug]: (Issue #527)
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@jc192015<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jc192015&d=DwMCaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=9Gl8TqypehHm7acAeymJOA&m=WHIWfYJMF-7hJZ-OnHdY2XVs4ma8v-2Cb4Pw6HIR-kSBprrPkHnsapM944FEydb2&s=AKbimVc1M1HqHygNNMa6kKkzy0rS6hsK6bIQMUn6LFo&e=> my suggestion would be to at least upgrade the schema to 2.1.0 using the MAtNWB version that you have. I then recommend working with the file using the newest release of MatNWB since that supports all schema versions after 2.1.0 (the MatNWB version only specifies the most recent supported schema).
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There is a column called |
When adding trails_index as VectorIndex to type.core.Units (2.6.0), I got the following error message:
Unrecognized method, property, or field 'vectorindex' for class 'types.core.Units'.
Error in convertTrials4jia (line 643)
nwb.units.vectorindex.set('trials_index', trials_idx);
That is why I avoided to add trials_index to Units.
Do I need to remove trials" from Units?
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Sent: Friday, July 28, 2023 10:09 AM
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Subject: Re: [NeurodataWithoutBorders/matnwb] [Bug]: (Issue #527)
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There is a column called trials in the Units table. If it is supposed to be there you will need a VectorIndex named trials_index with 9 elements. We do have trials-specific tables so my assumption is that it's not supposed to be there and should perhaps be in the intervals_trials table or elsewhere.
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In |
Could you please tell me how to add trials_index to the vectordata property in the Units table?
The following is the original code for initializing units, trials, and trials_index and adding trials and trials_index to units.
nwb.units = types.core.Units('colnames',...
{'spike_times', 'trials', 'trials_index', 'waveforms'},...
'description', 'Analysed Spike Events');
unitTrials = types.hdmf_common.VectorData(...
'description', 'A large group of trial IDs for each unit',...
'data', []);
trials_idx = types.hdmf_common.VectorIndex(...
'data', [],...
'target', types.untyped.ObjectView('/units/trials'));
nwb.units.vectorindex.set('trials_index', trials_idx);
nwb.units.vectordata.set('trials', unitTrials);
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Sent: Friday, July 28, 2023 10:25 AM
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Subject: Re: [NeurodataWithoutBorders/matnwb] [Bug]: (Issue #527)
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In 2.6.0 all VectorIndex objects are valid VectorData objects so you should add trials_index to the vectordata property in the Units table instead. In fact, this should be done for all VectorIndex objects created in the script.
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Try this: nwb.units = types.core.Units('colnames',...
{'spike_times', 'trials', 'waveforms'},...
'description', 'Analysed Spike Events');
unitTrials = types.hdmf_common.VectorData(...
'description', 'A large group of trial IDs for each unit',...
'data', []);
trials_idx = types.hdmf_common.VectorIndex(...
'data', [],...
'target', types.untyped.ObjectView('/units/trials'));
nwb.units.vectordata.set('trials_index', trials_idx);
nwb.units.vectordata.set('trials', unitTrials); Also note that you should remove any vector index columns from |
I modified the code, used nwbRead to validate the output nwb, and got message "Unrecognized field name "internal". Is there still something wrong with units?
nwbRead('C:\Users\hi2ch\Desktop\nwb\out\BAYLORNL23_20190320.nwb')
ans =
NwbFile with properties:
nwb_version: '2.6.0'
file_create_date: [1×1 types.untyped.DataStub]
identifier: 'BAYLORNL23_20190320'
session_description: 'Animal `BAYLORNL23` on Session `20190320`'
session_start_time: 2019-03-20T09:59:31.000000-05:00
timestamps_reference_time: 2019-03-20T09:59:31.000000-05:00
acquisition: [0×1 types.untyped.Set]
analysis: [9×1 types.untyped.Set]
general: [0×1 types.untyped.Set]
general_data_collection: 'extracellularDataType: sorted spike times, spike waveform snipets, spike band voltage traces↵cellType: Identified PC, others↵identificationMethod: SS and CS spike waveforms and cross-correlogram, spike waveforms↵amplifierRolloff: ↵spikeSorting: manual:matclust↵ADunit: 14 bits'
general_devices: [2×1 types.untyped.Set]
general_experiment_description: 'experimentType: behavior, extracellular, photostim↵referenceAtlas: Allen Reference Atlas↵task_keyword: detection, discrimination, lick Left lick Right, delay, somatosensory, motor, response, reward'
general_experimenter: [1×1 types.untyped.DataStub]
general_extracellular_ephys: [1×1 types.untyped.Set]
general_extracellular_ephys_electrodes: [1×1 types.hdmf_common.DynamicTable]
general_institution: 'Baylor College of Medicine, Houston, TX 77030'
general_intracellular_ephys: [0×1 types.untyped.Set]
general_intracellular_ephys_experimental_conditions: []
general_intracellular_ephys_filtering: []
general_intracellular_ephys_intracellular_recordings: []
general_intracellular_ephys_repetitions: []
general_intracellular_ephys_sequential_recordings: []
general_intracellular_ephys_simultaneous_recordings: []
general_intracellular_ephys_sweep_table: []
general_keywords: [1×1 types.untyped.DataStub]
general_lab: 'Nuo Li'
general_notes: []
general_optogenetics: [1×1 types.untyped.Set]
general_optophysiology: [0×1 types.untyped.Set]
general_pharmacology: []
general_protocol: 'IACUC'
general_related_publications: [1×1 types.untyped.DataStub]
general_session_id: '20190320'
general_slices: []
general_source_script: 'convertTrials4jia'
general_source_script_file_name: 'convertTrials4jia.m'
general_stimulus: 'photostim'
general_subject: [1×1 types.core.Subject]
general_surgery: 'Mice were prepared for photoinhibition and electrophysiology with a clear-skull cap and a headpost. The scalp and periosteum over the dorsal surface of the skull were removed. A layer of cyanoacrylate adhesive (Krazy glue, Elmer's Products Inc.) was directly applied to the intact skull. A custom made headpost was placed on the skull with its posterior edge aligned with the suture lambda and cemented in place with clear dental acrylic (Lang Dental Jet Repair Acrylic; 1223-clear). A thin layer of clear dental acrylic was applied over the cyanoacrylate adhesive covering the entire exposed skull, followed by a thin layer of clear nail polish (Electron Microscopy Sciences, 72180).'
general_virus: []
intervals: [0×1 types.untyped.Set]
intervals_epochs: []
intervals_invalid_times: []
intervals_trials: [1×1 types.core.TimeIntervals]
processing: [0×1 types.untyped.Set]
scratch: [0×1 types.untyped.Set]
stimulus_presentation: [2×1 types.untyped.Set]
stimulus_templates: [0×1 types.untyped.Set]
units: [1×1 types.core.Units]
Unrecognized field name "internal".
…________________________________
From: Lawrence ***@***.***>
Sent: Friday, July 28, 2023 10:50 AM
To: NeurodataWithoutBorders/matnwb ***@***.***>
Cc: Chen, Jian ***@***.***>; Mention ***@***.***>
Subject: Re: [NeurodataWithoutBorders/matnwb] [Bug]: (Issue #527)
***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
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Try this:
nwb.units = types.core.Units('colnames',...
{'spike_times', 'trials', 'waveforms'},...
'description', 'Analysed Spike Events');
unitTrials = types.hdmf_common.VectorData(...
'description', 'A large group of trial IDs for each unit',...
'data', []);
trials_idx = types.hdmf_common.VectorIndex(...
'data', [],...
'target', types.untyped.ObjectView('/units/trials'));
nwb.units.vectordata.set('trials_index', trials_idx);
nwb.units.vectordata.set('trials', unitTrials);
Also note that you should remove any vector index columns from colnames. They, along with the vectordata they are referencing, consitute a single column in the Units table (and all Dynamic Table objects).
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It looks like the file is displayed properly so I don't think so. Could you share that exported file in onedrive I can confirm if that's true or not? |
BAYLORNL23_20190320-2.6.0.2.new.nwb has been uploaded. Thank you so much.
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Subject: Re: [NeurodataWithoutBorders/matnwb] [Bug]: (Issue #527)
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It looks like the file is displayed properly so I don't think so. Could you share that exported file in onedrive I can confirm if that's true or not?
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I don't have any issues reading this file. That error that you're seeing might be from either the script or some other thing you've set up to run after reading the file. |
Running the validation, the "Critical" label is still there. I uploaded "Messages for_BAYLORNL23_20190320-2.6.0.2.new.txt" for your reference.
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I don't have any issues reading this file. That error that you're seeing might be from either the script or some other thing you've set up to run after reading the file.
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Oh that's interesting. I guess the second dimension is now the one that is checked for valid spike event series. Can you transpose the spike event series data? If you did before generating this file then undo that transpose. |
If undoing the transpose, I got the following:
hdmf.build.errors.ConstructError: (root/analysis/unit1SS GroupBuilder {'attributes': {'comments': 'cellType: PCSimpleSpikes', 'description': 'single unit1SS with cell type information and approximate depth', 'help': 'Snapshots of spike events from data.', 'namespace': 'core', 'neurodata_type': 'SpikeEventSeries'}, 'groups': {}, 'datasets': {'control': root/analysis/unit1SS/control DatasetBuilder {'attributes': {}, 'data': <Closed HDF5 dataset>}, 'control_description': root/analysis/unit1SS/control_description DatasetBuilder {'attributes': {}, 'data': <Closed HDF5 dataset>}, 'data': root/analysis/unit1SS/data DatasetBuilder {'attributes': {'conversion': 1.0, 'resolution': 0.0, 'unit': 'volt'}, 'data': <Closed HDF5 dataset>}, 'electrodes': root/analysis/unit1SS/electrodes DatasetBuilder {'attributes': {'description': 'Electrodes involved with these spike events', 'help': 'a subset (i.e. slice or region) of a DynamicTable', 'namespace': 'core', 'neurodata_type': 'DynamicTableRegion', 'table': root/general/extracellular_ephys/electrodes GroupBuilder {'attributes': {'colnames': array(['x', 'y', 'z', 'imp', 'location', 'filtering', 'group',
'group_name'], dtype=object), 'description': 'Electrodes', 'help': 'A column-centric table', 'namespace': 'core', 'neurodata_type': 'DynamicTable'}, 'groups': {}, 'datasets': {'filtering': root/general/extracellular_ephys/electrodes/filtering DatasetBuilder {'attributes': {'description': 'description of hardware filtering', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <Closed HDF5 dataset>}, 'group': root/general/extracellular_ephys/electrodes/group DatasetBuilder {'attributes': {'description': 'a reference to the ElectrodeGroup this electrode is a part of', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <hdmf.backends.hdf5.h5_utils.BuilderH5ReferenceDataset object at 0x0000026EF93A3AC0>}, 'group_name': root/general/extracellular_ephys/electrodes/group_name DatasetBuilder {'attributes': {'description': 'the name of the ElectrodeGroup this electrode is a part of', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <Closed HDF5 dataset>}, 'id': root/general/extracellular_ephys/electrodes/id DatasetBuilder {'attributes': {'help': 'unique identifiers for a list of elements', 'namespace': 'core', 'neurodata_type': 'ElementIdentifiers'}, 'data': <Closed HDF5 dataset>}, 'imp': root/general/extracellular_ephys/electrodes/imp DatasetBuilder {'attributes': {'description': 'the impedance of the channel', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <Closed HDF5 dataset>}, 'location': root/general/extracellular_ephys/electrodes/location DatasetBuilder {'attributes': {'description': 'the location of channel within the subject e.g. brain region', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <Closed HDF5 dataset>}, 'x': root/general/extracellular_ephys/electrodes/x DatasetBuilder {'attributes': {'description': 'the x coordinate of the channel location', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <Closed HDF5 dataset>}, 'y': root/general/extracellular_ephys/electrodes/y DatasetBuilder {'attributes': {'description': 'the y coordinate of the channel location', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <Closed HDF5 dataset>}, 'z': root/general/extracellular_ephys/electrodes/z DatasetBuilder {'attributes': {'description': 'the z coordinate of the channel location', 'help': 'Values for a list of elements', 'namespace': 'core', 'neurodata_type': 'VectorData'}, 'data': <Closed HDF5 dataset>}}, 'links': {}}}, 'data': <Closed HDF5 dataset>}, 'timestamps': root/analysis/unit1SS/timestamps DatasetBuilder {'attributes': {'interval': 1, 'unit': 'second'}, 'data': <Closed HDF5 dataset>}}, 'links': {}}, 'Could not construct SpikeEventSeries object due to: Must provide the same number of timestamps and spike events')
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Sent: Friday, July 28, 2023 11:47 AM
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Oh that's interesting. I guess the second dimension is now the one that is checked for valid spike event series. Can you transpose the spike event series data? If you did before generating this file then undo that transpose.
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Very strange. Could you share this version with the onedrive so we can take a look at it? |
BAYLORNL23_20190320-2.6.0.2.newWT.nwb has been uploaded. Thank you.
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Subject: Re: [NeurodataWithoutBorders/matnwb] [Bug]: (Issue #527)
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Very strange. Could you share this version with the onedrive so we can take a look at it?
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@jc192015 I have opened a new issue here for discussion regarding this error: NeurodataWithoutBorders/pynwb#1746 Hopefully this is easily resolvable. |
What happened?
When running NWB validation for a created nwb file, I got the following error message indicating that "Could not construct TimeIntervals object due to: columns must be the same length. " I checked the length of columns (all elements in 'colnames' ) are the same. Could you please let me know how to fix that?
Thank you in advance for your time.
Steps to Reproduce
Error Message
'Could not construct TimeIntervals object due to: columns must be the same length'
Operating System
Windows
Matlab Version
R2023a
Code of Conduct
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