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View Code? Open in Web Editor NEWNWB extensions for origanizing intracellular electrophysiology metadata
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to_hierarchical_dataframe() DataFrames are too wide and long
Not sure if in your control but I mention this anyway.
to_hierarchical_dataframe() and to_denormalized_dataframe() generate very wide and long DataFrames. To save some space and facilitate visualization, the stimulus, response and electrode columns from intracellular_recordings should contain fewer details.
Define more descriptive names for the tables
We should use descriptive names for the tables that: 1) better communicate the intended use of the tables and 2) avoid overlap with terms used in the community that are ambiguous. Suggested names are:
intracellular_stimuli(new, see #31)intracellular_responses(new, see #31)intracellular_recordings(remain as is)sweeps---rename to--->simultaneous_recordingssweep_sequence---rename to--->sequential_recordingsruns---rename to --->repetitionsconditions---rename to--->experimental_conditions
Also rename the columns
to_hierarchical_dataframe() fails on tables that contain indexed columns
Tested on 279bb2e
MWE:
ir_index = nwbfile.add_intracellular_recording(electrode=electrode,
stimulus=stimulus,
response=response)
# (B) Add a list of sweeps to the sweeps table
sim_rec_table = nwbfile.get_icephys_simultaneous_recordings()
sim_rec_table.add_column('new_metadata',description = 'metadata as array', index= True)
sweep_index = nwbfile.add_icephys_simultaneous_recording(recordings=[ir_index,], new_metadata = [1,2,3])
nwbfile.icephys_simultaneous_recordings.to_hierarchical_dataframe()because of
...
~/miniconda3/envs/nwb/lib/python3.7/site-packages/ndx_icephys_meta/icephys.py in to_hierarchical_dataframe(self, flat_column_index)
192
193 # Construct the pandas dataframe with the hierarchical multi-index
--> 194 multi_index = pd.MultiIndex.from_tuples(index, names=index_names)
195 out_df = pd.DataFrame(data=data, index=multi_index, columns=columns)
196 return out_df
...
TypeError: unhashable type: 'list'to_hierarchical_dataframe not working as intended
In here, syllable_start_time is part of the syllable table, and should have the same level as syllable_start_time, but instead has the same level as the phonemes table. This is a general problem that occurs for the last column of the second-to-last columns in a table hierarchy.
add_intracellular_recording should also accept a stimulus template
add_intracellular_recording should accept for the stimulus argument both a stimulus presentation and a stimulus template.
I think somebody else mentioned this, so I haven't tested it.
Add Stimulus and Reponse tables
As part of the hackathon it was identified that we should add tables for intracellular_stimulus and intracellular_response, which in turn are referenced from the intracellular_recordings table. This is to avoid mixing metadata specific to stimulus and response in the same table.
Add documentation for how to enter time slices using the add_intracellular_recording interface
DynamicTableGrouping type not necessary
We recently decided to make the Sweeps, SweepSequences, Runs, and Conditions types be of type DynamicTable instead of type DynamicTableGrouping in order to allow better naming of the column of DynamicTableRegion objects in each one.
Now the DynamicTableGrouping table has little use. I think anyone who wants to make a custom type for a custom hierarchy would also want to be able to customize the column name. We can provide guidance in a tutorial of how to do this without needing a DynamicTableGrouping type.
Therefore I propose removing the DynamicTableGrouping type.
Suggestion: Add super simple example to README
The notebooks are great and well documented; however, I have found it useful to have a barebones almost minimum working demonstration of the new data types. I suggest such an example is added to the bottom of the README. Something like the following:
from datetime import datetime
from dateutil.tz import tzlocal
import numpy as np
from pynwb.icephys import VoltageClampStimulusSeries, VoltageClampSeries
from pynwb import NWBHDF5IO
from ndx_icephys_meta.icephys import ICEphysFile
nwbfile = ICEphysFile(session_description='my first recording',
identifier='EXAMPLE_ID',
session_start_time=datetime.now(tzlocal()))
# Add a device
device = nwbfile.create_device(name='Heka ITC-1600')
# Add an intracellular electrode
electrode = nwbfile.create_ic_electrode(name="elec0",
description='a mock intracellular electrode',
device=device)
# Create an ic-ephys stimulus
stimulus = VoltageClampStimulusSeries(
name="stimulus",
data=[1, 2, 3, 4, 5],
starting_time=123.6,
rate=10e3,
electrode=electrode,
gain=0.02,
sweep_number=15)
# Create an ic-response
response = VoltageClampSeries(
name='response',
data=[0.1, 0.2, 0.3, 0.4, 0.5],
conversion=1e-12,
resolution=np.nan,
starting_time=123.6,
rate=20e3,
electrode=electrode,
gain=0.02,
capacitance_slow=100e-12,
resistance_comp_correction=70.0,
sweep_number=15)
# Add an intracellular recording to the file
nwbfile.add_intracellular_recording(electrode=electrode,
stimulus=stimulus,
response=response)
# Add a list of sweeps to the sweeps table
nwbfile.add_ic_sweep(recordings=[0])
# Add a list of sweep table indices as a sweep sequence
nwbfile.add_ic_sweep_sequence(sweeps=[0])
# Add a list of sweep sequence table indices as a run
nwbfile.add_ic_run(sweep_sequences=[0])
# Add a list of run table indices as a condition
nwbfile.add_ic_condition(runs=[0])
# Write our test file
testpath = "test_icephys_file.h5"
with NWBHDF5IO(testpath, 'w') as io:
io.write(nwbfile)
# Read the data back in
with NWBHDF5IO(testpath, 'r') as io:
infile = io.read()
print(infile)I think the above should run. The downside of including code in the README is that it is not testable and it is quite long, but I think it is helpful for an at-a-glance overview of the extension and its usage nevertheless
API: add_intracellular_recording
nwbfile.add_intracellular_recording(electrode=electrode,
stimulus=stim,
response=resp,
id=sweep_number
)
-
All arguments should be optional, of course skipping all does not make sense.
-
If both stimulus and response are PatchClampSeries they should also both
reference the same electrode and sweep (if not raise an exception). -
It should also raise an error if you mix stimulus and response in a intracellular recording in an erroneous way.
The valid combinations are:
if stimulus == timeseries and response == timeseries:
pass
elif response == VoltageClampSeries:
if stimulus != VoltageClampStimulusSeries:
raise(...)
elif response == CurrentClampSeries:
if stimulus != CurrentClampStimulusSeries:
raise(...)
elif response == IZeroClampSeries:
if stimulus is not None:
raise(...)
else:
raise(...)AttributeError: type object 'HierarchicalDynamicTableMixin' has no attribute '_get_fields'
Using the latest hdmf-dev, this package will run into this error:
...
File "c:\users\luiz\documents\github\nwb-jupyter-widgets\nwbwidgets\view.py", line 9, in <module>
from ndx_icephys_meta.icephys import SweepSequences
File "C:\Users\Luiz\Anaconda3\envs\env_allen\lib\site-packages\ndx_icephys_meta\__init__.py", line 32, in <module>
from .icephys import ICEphysFile, IntracellularRecordings, Sweeps, SweepSequences, Runs, Conditions # noqa E402, F401
File "C:\Users\Luiz\Anaconda3\envs\env_allen\lib\site-packages\ndx_icephys_meta\icephys.py", line 307, in <module>
class Sweeps(DynamicTable, HierarchicalDynamicTableMixin):
File "c:\users\luiz\documents\github\hdmf\src\hdmf\utils.py", line 734, in __init__
func(name, bases, classdict)
File "c:\users\luiz\documents\github\hdmf\src\hdmf\container.py", line 122, in __gather_fields
base_fields = bases[-1]._get_fields() # tuple of field names from base class
AttributeError: type object 'HierarchicalDynamicTableMixin' has no attribute '_get_fields'It looks like ndx-icephys-meta is performing an invalid operation with HierarchicalDynamicTableMixin. The problem only happens with the latest changes in hdmf, I guess this _get_fields was substituted by get_fields_conf
return id when custom id not given as argument
It would be nice if add_intracellular_recording, add_ic_sweep, add_ic_sweep_sequence, add_ic_run, when called without an id (or always), returned the automatically generated id that can be used to populate the ic_sweeps, ic_sweep_sequences, ic_runs, ic_conditions, respectively.
to_denormalized_dataframe() creates weird MultiIndex column ('i', 'd')
Tested on branch add/spec_resp_elec_tables: 607e1ae
Unexpected column i,d appears as a column of the DataFrame generated with to_denormalized_dataframe()
How to reproduce: run the example code including line
sweep_index = nwbfile.add_icephys_simultaneous_recording(recordings=[ir_index, ])
then compare
nwbfile.get_icephys_meta_parent_table().to_hierarchical_dataframe().columns
nwbfile.get_icephys_meta_parent_table().to_denormalized_dataframe().columns
Latest tests fail
Using PyNWB 1.4.0 and HDMF 2.2.0, tests fail:
============================================================== short test summary info ============================================================== FAILED src/pynwb/ndx_icephys_meta/test/test_aligned_dynamic_table_container.py::TestAlignedDynamicTableContainer::test_to_dataframe - AttributeErro...
FAILED src/pynwb/ndx_icephys_meta/test/test_hierarchical_dynamic_table_mixin.py::TestHierarchicalDynamicTableMixin::test_to_denormalized_dataframe
FAILED src/pynwb/ndx_icephys_meta/test/test_hierarchical_dynamic_table_mixin.py::TestHierarchicalDynamicTableMixin::test_to_denormalized_dataframe_flat_column_index
FAILED src/pynwb/ndx_icephys_meta/test/test_hierarchical_dynamic_table_mixin.py::TestHierarchicalDynamicTableMixin::test_to_hierarchical_dataframe
FAILED src/pynwb/ndx_icephys_meta/test/test_hierarchical_dynamic_table_mixin.py::TestHierarchicalDynamicTableMixin::test_to_hierarchical_dataframe_flat_column_index
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_add_row - ValueError: Shape of passed values is (3,...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_add_row_no_response - ValueError: Shape of passed v...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_add_row_no_stimulus - ValueError: Shape of passed v...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_round_trip_container_no_data - AssertionError: Data...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::ICEphysFileTests::test_add_icephys_meta_full_roundtrip - ValueError: Shape of passed values...
Looks related to conversion to Pandas data frames.
Rename table types to end in Table
@bendichter and I would prefer the convention of having subtypes of DynamicTable end in "Table", similar to how we name descendants of TimeSeries with "Series". See discussion here: NeurodataWithoutBorders/nwb-schema#337 (comment)
To conform with this convention, I suggest changing: IntracellularRecordings, SweepSequences, Runs, and Conditions to IntracellularRecordingsTable, SweepSequencesTable, RunsTable, and ConditionsTable. The 'name' can remain as is, without the 'Table' suffix.
Partial data still added to intracellular_recordings if add_intracellular_recording fails
Additional issue in #66 :
The second add_intracellular_recording, the one causing the issue, still manages to add an additional row (just with the electrode) in the table.
This is not very important (since it fails anyway :) but perhaps it shouldn't happen.
convenience function to get the highest level of the hierarchy
Some experiments might not have a ic_conditions or a ic_runs table. So if one needs to retrieve the whole hierarchy at once (for example with ic_conditions.to_denormalized_dataframe()) they should be able to do it without querying to see if these tables exist in the first place.
performance issue when indexing table
It seems the auto-dereferencing dynamic tables code is struggling with these nested tables. Test data is here. On my computer, after setting up the file read
from pynwb import NWBHDF5IO
fpath = '001_140327B01_EXP_ndx.nwb'
io = NWBHDF5IO(fpath,'r')
nwbfile = io.read()this line:
nwbfile.ic_conditions[0]took 57 seconds to create a 1x1 pandas DataFrame. Is this how the API is intended to be used? I think this is due to the fact that indexing the downstream tables now reads all of that data into memory while creating a pandas DataFrame.
intracellular_recordings: Should store plain TimeSeries
(The current SweepTable implementation suffers from the same issue, see NeurodataWithoutBorders/pynwb#1116).
In ICEphys it is customary to have AD/DA channels which are not associated to an electrode. In MIES and NWBv1/2 we store this channel data as plain timeseries.
And the intracellular_recordings table should therefore also allow to hold plain TimeSeries without an attached electrode.
adding response with no corresponding stimulus
If there is a response, but no stimulus, like in the case of IZeroClamp, how are you supposed to add an entry to the intracellular recordings table? Are rows allows to be added that are missing a stimulus? I tried this and was not able to get it to work. All of the tests that add rows to that table provide both stimulus and response. If this is an intended use-case it should be tested.
Add stimulus_type column to sweep_sequence table
As part of the hackathon this was identified as a required column for the sweep_sequences
id in ic_sweeps not referencing the id in intracellular_recordings
Adding an intracellular recording with a given id and then a sweep with the same id works. But generating the ic_sweeps table raises a IndexError: list index out of range error.
Note though that, if a sweep with index 0 is added, generating the table works just fine.
MWE:
nwbfile.add_intracellular_recording(electrode=electrode,
stimulus=stimulus,
response=response,
id=10)
nwbfile.add_ic_sweep(recordings=[10], id=12) # replace 10 with 0 to fix
nwbfile.ic_sweeps.to_dataframe()
Avoid using `ic` as abbreviation for icephys
Please don't use the ic abbreviation for icephys as in icephys ic means CurrentClamp. I think icephys is better.
error when add_intracellular_recording called only with electrode and stimulus
In section 3.1 in the icephys tutorial adding an intracellular recording with just a stimulus or a response doesn't seem to work as intended:
A recording may optionally also consist of just an electrode and stimulus or electrode and response, but at least one of stimulus or response are required.
MWE:
rowindex = nwbfile.add_intracellular_recording(electrode=electrode,
stimulus=stimulus,
id=10)
error
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-7-9493f38a37ac> in <module>
1 rowindex = nwbfile.add_intracellular_recording(electrode=electrode,
2 stimulus=stimulus,
----> 3 id=10)
~/miniconda3/envs/nwb_latest/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
451
452 if is_method:
--> 453 return func(args[0], **parsed['args'])
454 else:
455 return func(**parsed['args'])
~/miniconda3/envs/nwb_latest/lib/python3.7/site-packages/ndx_icephys_meta/icephys.py in add_intracellular_recording(self, **kwargs)
679 if stimulus.name not in self.stimulus:
680 self.add_stimulus(stimulus, use_sweep_table=False)
--> 681 if response.name not in self.acquisition:
682 self.add_acquisition(response, use_sweep_table=False)
683 if electrode.name not in self.ic_electrodes:
AttributeError: 'NoneType' object has no attribute 'name'
HierarchicalDynamicTableMixin.to_hierarchical_dataframe fails on empty hcol target table
Feature request: a key to map the nwbfile_in.stimulus to intracellular_recordings[n]["stimuli"]
Hi, thanks for the great work first of all!
I think it would be easier for the end users to have a key to map the nwbfile_in.stimulus to intracellular_recordings[n]["stimuli"] in the intracellular_recordings[n]["stimuli"] table.
A column with the name of the stimulus dataset in the intracellular_recordings table would be nice to have.
What do you think?
validation fails
Following the documentation at https://pynwb.readthedocs.io/en/stable/validation.html :
Similar to NeurodataWithoutBorders/pynwb#1058
The validation below fails:
python -m pynwb.validate file_with_extension.nwb
to_denonormalized_table not working as intended
Using the README here, using the latest dev branch. The column names in the last table are mangled:
Generalize Runs/Conditions tables
It would be nicer to be able to define the meaning of tables which index Sweeps/SweepSequence tables on the go and don't have them hard coded.
Use case:
- In MIES we have two different sweep sequences (repeated acquisition (RA) cycles and stimset cycle IDs). None of them fits into Runs.
- In addition we also store quality control results (true/false/not done) per sweep and per RA cycle. It would therefore be nice to have one table for storing all quality control results.
Profile read/write performance of the extension
ICEphysFileTests.test_add_icephys_meta_full_roundtrip has code to add profiling for writing and reading a file that can be enabled by removing the corresponding line comments. The read performance seems reasonable, but it appears that for write HDMF currently may do a large number of recursions, that slow down performance. It would be good investigate why this occurs. It is unclear whether this is specific to the extension (maybe something with the ObjectMappers) or whether this is a general issue in HDMF.
42486451 function calls (40629931 primitive calls) in 21.592 seconds
Ordered by: cumulative time
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add custom column to table before adding rows
The same issue as here: NeurodataWithoutBorders/pynwb#1071
This is my workaround. It's copied from the code I shared with you:
SweepSeq += 1
args = {'sweeps': Sweeps,'id': SweepSeq}
# If column added, then the new column is mandatory
if addedNewColSwSeq:
args['repetition'] = repetition
row_id = nwbfile.add_ic_sweep_sequence(**args)
CurrentClampStimulusSeries and VoltageClampSeries combined in add_intracellular_recording
In the notebook provided as example at https://github.com/oruebel/ndx-icephys-meta/blob/master/src/pynwb/examples/icephys_meta_to_pandas.ipynb, CurrentClampStimulusSeries and VoltageClampSeries are added as stimulus and response in the intracellular_recordings table (Section 3. Construct our Intracellular Electrophysiolgy Metadata tables, paragraph Add intracelluar recordings).
Not only this is not ideal for a tutorial, because it's creating confusion, but add_intracellular_recording should actually raise an exception if incompatible classes are stored together. (I think they are incompatible...)
Storing data from multiple electrodes?
@rightbower asks, can these new hierarchical tables be used to store data from multiple electrodes in the same experiment? If not, what is the recommended strategy for storing such data?
Extract complex VectorData to its own type: TimeSeriesRef
The IntracellularStimuliTable and IntracellularResponsesTable types both have a dataset:
- name: stimulus
neurodata_type_inc: VectorData
dtype:
- name: idx_start
dtype: int32
doc: Start index into the TimeSeries 'data' and 'timestamp' datasets of the
referenced TimeSeries. The first dimension of those arrays is always time.
- name: count
dtype: int32
doc: Number of data samples available in this time series, during this epoch
- name: timeseries
dtype:
target_type: TimeSeries
reftype: object
doc: The TimeSeries that this index applies to
doc: Column storing the reference to the recorded stimulus for the recording
(rows)Aside from the name and docstring, this is the same as the definition for the 'timeseries' column of the TimeIntervals table. Since this exact structure would now be used three times in the schema, I think this should be its own type named something like TimeSeriesRef or TimeSeriesColumn and included in the table, e.g.:
- name: stimulus
neurodata_type_inc: TimeSeriesRef
doc: Column storing the reference to the recorded stimulus for the recording
(rows)Add ic prefix to ICEphysFile functions and properties
In the ICEphysFile type the properties and functions specific to the icephys metadata structure should include the ic prefix to prevent name collisions later on and to make the context clear. E.g., ICEphysFile.conditions should be renamed to ICEphysFile.ic_conditions, ICEphysFile.add_condition to ICEphysFile.add_ic_condition etc. This will require changes to the fields, functions and init function of ICEphysFile as well as update of ObjectMapper and tests. Per discussion with @rly
Tests fail
With the dev branch of PyNWB and HDMF, I get the following test errors:
============================================================== short test summary info ============================================================== FAILED src/pynwb/ndx_icephys_meta/test/test_aligned_dynamic_table_container.py::TestAlignedDynamicTableContainer::test_round_trip_container - Excep...
FAILED src/pynwb/ndx_icephys_meta/test/test_aligned_dynamic_table_container.py::TestAlignedDynamicTableContainer::test_to_dataframe - AttributeErro...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_add_row - Exception: Container 'intracellular_recor...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_add_row_no_response - Exception: Container 'intrace...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_add_row_no_stimulus - Exception: Container 'intrace...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_basic_write - Exception: Container 'intracellular_r...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_round_trip_container_no_data - Exception: Container...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::IntracellularRecordingsTableTests::test_write_with_stimulus_template - Exception: Container...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::SimultaneousRecordingsTableTests::test_basic_write - Exception: Container 'intracellular_re...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::SequentialRecordingsTableTests::test_basic_write - Exception: Container 'intracellular_reco...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::RepetitionsTableTests::test_basic_write - Exception: Container 'intracellular_recordings' (...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::ExperimentalConditionsTableTests::test_basic_write - Exception: Container 'intracellular_re...
FAILED src/pynwb/ndx_icephys_meta/test/test_icephys.py::ICEphysFileTests::test_add_icephys_meta_full_roundtrip - Exception: Container 'intracellula...
===================================================== 13 failed, 58 passed, 1 skipped in 28.71s =====================================================
There are several different errors:
ValueError: Must supply 'columns' if specifying 'colnames'
AttributeError: 'Int64Index' object has no attribute 'data'
AttributeError: 'IntracellularRecordingsTable' object has no attribute 'electrodes'
error on the README script when used with h5py>=3.1.0
It raises this error when used with h5py 3.1.0 or 3.2.0.
TypeError: No conversion path for dtype: dtype('<U9')
It may be due to the h5py 3.0.0 update.
compression of new tables
These tables can potentially be large and repetitive.
Will there be a way to apply H5DataIO on them for compression?
Enrico reports some significant differences in size between a) a NWB file in which each acquisition and stimulation datasets have been wrapped for compression with H5DataIO and b) a NWB file simply archived with gzip.
Prevent binding of stimuli, responses and electrodes metadata dictionaries to external variables
If a dictionary is passed to one of the stimulus_, response_, electrode_metadata arguments, the dictionary is changed with some internal tuples after the call to add_intracellular_recording:
Example from icephys_meta_simple_example.ipynb:
nwbfile.intracellular_recordings.add_column(
name='voltage_threshold',
data=[0.1, 0.12, 0.13],
description='Just and example filter on the electrode',
category='electrodes') # Just added a PR with this line
em = {}
em['voltage_threshold'] = 2
em
# outputs: {'voltage_threshold': 2}
nwbfile.add_intracellular_recording(electrode=electrode,
stimulus=stimulus, response=response, recording_tag='B', electrode_metadata = em)
em
# outputs:
# {'voltage_threshold': 2,
# 'electrode': elec0 pynwb.icephys.IntracellularElectrode at 0x4538476176
# Fields:
# description: a mock intracellular electrode
# device: Heka ITC-1600 pynwb.device.Device at 0x4538475536}The issue probably comes from these lines: x = popargs('x_metadata', kwargs).
I am not sure if this is intended but it's surely unexpected.
'table' attribute should be on 'recordings' dataset not 'recordings_index' dataset?
ndx-icephys-meta/src/spec/create_extension_spec.py
Lines 101 to 109 in 57833ea
In the Sweeps type, the 'recordings' dataset is of type DynamicTableRegion which contains the 'table' attribute that should be overridden with a target table.
Same for the SweepSequences, Runs, and Conditions types.
Category tables require metadata even if stimulus/object is missing
The stimuli table (IntracellularStimuliTable) (and co.) requires stimulus_metadata to be passed even if the stimulus argument itself is None.
I understand why this is happening, but it doesn't seem like an expected behavior.
Example from README identical until line (A):
ir_table = nwbfile.get_intracellular_recordings()
ir_table.add_column('new_column', 'Stimulus special column', category='stimuli')
meta = {}
meta['new_column'] = 2
ir_index = nwbfile.add_intracellular_recording(electrode=electrode,
stimulus=stimulus,
response=response,
stimulus_metadata = meta)
# All going fine until here
ir_index = nwbfile.add_intracellular_recording(electrode=electrode,
response=response)Error:
ValueError: row data keys don't match available columns
you supplied 0 extra keys: set()
and were missing 1 keys: {'new_column'}Add unit tests for HierarchicalDynamicTableMixin
#13 added the HierarchicalDynamicTableMixin class. This is currently only tested in the example Jupyter notebooks but not yet via dedicated unit tests. We should add tests for this class.
Add stimulus_type metadata table
The metadata structure for describing stimulus types should be further refined. One proposal for this has been to add a separatestimulus_types stable which in turn should be referenced from the the sweep_sequences (aka, sequential_recording) table. Having the stimulus_types as a separate table would have the added advantage that the table can be reused across experiments.
Deprecate NWBFile.general.intracellular_ephys.filtering
Deprecate the general NWBFile.general.intracellular_ephys.filtering string dataset in favor of the filtering string dataset on IntracellularElectrode, which already exists.
add_intracellular_recording raises ValueError: row data keys don't match available columns
After the last updates, I am not able to add_intracellular_recordings anymore:
For example in https://github.com/oruebel/ndx-icephys-meta/blob/master/src/pynwb/examples/icephys_meta_simple_example.ipynb
nwbfile.add_intracellular_recording(electrode=electrode, stimulus, response, 10)
raises a ValueError. Full error is pasted at the end.
ValueError: row data keys don't match available columns
you supplied 1 extra keys: {'enforce_unique_id'}
and were missing 0 keys: set()
Is any of these packages at the wrong version?
h5py 2.10.0 pypi_0 pypi
hdmf 1.3.3 pypi_0 pypi
ndx-icephys-meta 0.1.0 dev_0 <develop>
numpy 1.17.3 pypi_0 pypi
nwb-docutils 0.3.1 pypi_0 pypi
pandas 0.25.2 pypi_0 pypi
pynwb 1.1.2 pypi_0 pypi
python 3.7.4 h265db76_1
ruamel-yaml 0.16.5 pypi_0 pypi
ruamel-yaml-clib 0.2.0 pypi_0 pypi
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-5-6537f1a1d799> in <module>
2 stimulus=stimulus,
3 response=response,
----> 4 id=10)
~/miniconda3/envs/ndx/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
436 raise_from(ExceptionType(msg), None)
437
--> 438 return func(self, **parsed['args'])
439 else:
440 def func_call(*args, **kwargs):
/nfs4/bbp.epfl.ch/user/username/private/git/ndx-icephys-meta/src/pynwb/ndx_icephys_meta/icephys.py in add_intracellular_recording(self, **kwargs)
482 self._check_intracellular_recordings()
483 # Add the recoding to the intracellular_recordings table
--> 484 call_docval_func(self.intracellular_recordings.add_recording, kwargs)
485
486 def _check_ic_sweeps(self):
~/miniconda3/envs/ndx/lib/python3.7/site-packages/hdmf/utils.py in call_docval_func(func, kwargs)
325 def call_docval_func(func, kwargs):
326 fargs, fkwargs = fmt_docval_args(func, kwargs)
--> 327 return func(*fargs, **fkwargs)
328
329
~/miniconda3/envs/ndx/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
436 raise_from(ExceptionType(msg), None)
437
--> 438 return func(self, **parsed['args'])
439 else:
440 def func_call(*args, **kwargs):
/nfs4/bbp.epfl.ch/user/username/private/git/ndx-icephys-meta/src/pynwb/ndx_icephys_meta/icephys.py in add_recording(self, **kwargs)
114 'response': (response_start_index, response_index_count, response)}
115 row_kwargs.update(kwargs)
--> 116 return super(IntracellularRecordings, self).add_row(enforce_unique_id=True, **row_kwargs)
117
118
~/miniconda3/envs/ndx/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
436 raise_from(ExceptionType(msg), None)
437
--> 438 return func(self, **parsed['args'])
439 else:
440 def func_call(*args, **kwargs):
~/miniconda3/envs/ndx/lib/python3.7/site-packages/hdmf/common/table.py in add_row(self, **kwargs)
325 'row data keys don\'t match available columns',
326 'you supplied {} extra keys: {}'.format(len(extra_columns), extra_columns),
--> 327 'and were missing {} keys: {}'.format(len(missing_columns), missing_columns)
328 ])
329 )
ValueError: row data keys don't match available columns
you supplied 1 extra keys: {'enforce_unique_id'}
and were missing 0 keys: set()
sql-like "unique index" for the id column
intracellular_recordings, ic_sweeps, ic_sweep_sequences, ic_runs tables allow insertions of rows with the same id.
I think id should be unique.
MWE:
nwbfile.add_ic_sweep(recordings=[0], id=12)
nwbfile.add_ic_sweep(recordings=[0], id=12)
nwbfile.ic_sweeps.to_dataframe()
Make all tables AlignedDynamicTables
The Conditions, Repeat, SequentialRecording, SimultaneousRecording tables should also be AlignedDynamicTables to make it easier to extend them later on add metadata specific to sub-categories to the table.
Validation error in example file
After resolving the validation error in #21 , another validation error appears: the 'colnames' attribute of /general/intracellular_ephys/intracellular_recordings/ is empty which raises an IndexError.
I raised this issue in hdmf-dev/hdmf#317
Example notebooks should use either current clamp or voltage clamp
The example notebooks add a CurrentClampStimulusSeries and a VoltageClampSeries as stimulus and response to the NWBFile. These types are semantically incompatible. The CurrentClampStimulusSeries should be paired with a CurrentClampSeries and a VoltageClampStimulusSeries should be paired with a VoltageClampSeries.
I don't know if there are any exceptions to this rule (besides when a response is recorded without a stimulus and perhaps vice versa). If there are no exceptions, then perhaps the API should raise an error (or at least a warning) if incompatible types are passed into the new sweep table. At the very least, the example notebooks should use the typical use case.
Remove nested type definition specifications
The type definition of IntracellularRecordingsTable includes the type definitions for IntracellularElectrodesTable, IntracellularStimuliTable, and IntracellularResponsesTable. I understand that these three types are meant to be used only within the IntracellularRecordingsTable, but these types can still technically be used elsewhere, and if these types are defined outside of IntracellularRecordingsTable, it would be easier to parse the schema and avoid edge cases that arise from having nested type definitions.
I suggest moving the specifications for these types to the root level of the extension and using neurodata_type_inc to include them in the IntracellularElectrodesTable type.
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