v0.4.9

v0.4.9 (June 5, 2024)

Deprecations

• Removed stream_id as an argument from IntanRecordingInterface. PR #794
• The usage of compression and compression_opts directly through the neuroconv.tools.spikeinterface submodule are now deprecated - users should refer to the new configure_backend method for a general approach for setting compression. PR #805
• Dropped the testing of Python 3.8 on the CI. Dropped support for Python 3.8 in setup. PR #853
• Deprecated skip_features argument in add_sorting. PR #872
• Deprecate old (v1) iterator from the ecephys pipeline. PR #876

Features

• Added backend control to the make_or_load_nwbfile helper method in neuroconv.tools.nwb_helpers. PR #800
• Released the first official Docker images for the package on the GitHub Container Repository (GHCR). PR #383
• Support "one-file-per-signal" and "one-file-per-channel" mode with IntanRecordingInterface. PR #791
• Added get_default_backend_configuration method to all DataInterface classes. Also added HDF5 backend control to all standalone .run_conversion(...) methods for those interfaces. PR #801
• Added get_default_backend_configuration method to all NWBConverter classes. Also added HDF5 backend control to .run_conversion(...). PR #804
• Released the first official Docker images for the package on the GitHub Container Repository (GHCR). PR #383
• Added ScanImageMultiFileImagingInterface for multi-file (buffered) ScanImage format and changed ScanImageImagingInterface to be routing classes for single and multi-plane imaging. PR #809
• Added a function to generate ogen timestamps and data from onset times and parameters to tools.optogenetics. PR #832
• Added configure_and_write_nwbfile and optimized imports in tools.nwb_helpers module. PR #848
• configure_backend may now apply a BackendConfiguration to equivalent in-memory pynwb.NWBFile objects that have different address in RAM. PR #848
• Add support for doubled ragged arrays in add_units_table. PR #879
• Add support for doubled ragged arrays in add_electrodes. PR #881

Bug fixes

• Remove JSON Schema definitions from the properties field. PR #818
• Fixed writing waveforms directly to file. PR #799
• Avoid in-place modification of the metadata in the VideoInterface and on neo tools. PR #814
• Replaced waveform_extractor.is_extension with waveform_extractor.has_extension. PR #799
• Fixed an issue with set_aligned_starting_time for all SortingInterface's that did not have an initial segment start set (and no recording attached). PR #823
• Fixed a bug with parameterized and pytest-xdist==3.6.1 in the ScanImageImagingInterface tests. PR #829
• Added XX and XO to the base metadata schema. PR #833
• BaseImagingExtractor.add_to_nwbfile() is fixed in the case where metadata is not supplied. PR #849
• Prevent SpikeGLXConverterPipe from setting false properties on the sub-SpikeGLXNIDQInterface. PR #860
• Fixed a bug when adding ragged arrays to the electrode and units table. PR #870
• Fixed a bug where write_recording will call an empty nwbfile when passing a path. PR #877
• Fixed a bug that failed to properly include time alignment information in the output NWB file for objects added from any RecordingInterface in combination with stub_test=True. PR #884
• Fixed a bug that prevented passing nwbfile=None and a backend_configuration to NWBConverter.run_conversion. PR #885

Improvements

• Fixed docstrings related to backend configurations for various methods. PR #822
• Added automatic backend detection when a backend_configuration is passed to an interface or converter. PR #840
• Improve printing of bytes. PR #831
• Support for pathlib in source data schema validation. PR #854
• Use ZoneInfo instead of dateutil.tz in the conversion gallery. PR #858
• Exposed progress_bar_class to ecephys and ophys data iterators. PR #861
• Unified the signatures between add_units, add_sorting and write_sorting. PR #875
• Improved descriptions of all folder and file paths in the source schema, useful for rendering in the GUIDE. PR #886
• Added watermark via source_script field of NWBFile metadata. source_script_file_name is also required to be specified in this case to avoid invalidation. PR #888

Testing

• Add general test for metadata in-place modification by interfaces. PR #815

v0.4.8

v0.4.8 (March 20, 2024)

Bug fixes

• Fixed writing the electrodes field in add_electrical_series when multiple groups are present. PR #784

Improvements

• Upgraded Pydantic support to >v2.0.0. PR #767
• Absorbed the DatasetInfo model into the DatasetIOConfiguration model. PR #767
• Keyword argument field_name of the DatasetIOConfiguration.from_neurodata_object method has been renamed to dataset_name to be more consistent with its usage. This only affects direct initialization of the model; usage via the BackendConfiguration constructor and its associated helper functions in neuroconv.tools.nwb_helpers is unaffected. PR #767
• Manual construction of a DatasetIOConfiguration now requires the field dataset_name, and will be validated to match the final path of location_in_file. Usage via the automated constructors is unchanged. PR #767
• Enhance get_schema_from_method_signature to extract descriptions from the method docval. PR #771

v0.4.7

v0.4.7 (February 21, 2024)

Deprecation

• Removed .get_electrode_table_json() on the BaseRecordingExtractorInterface in favor of GUIDE specific interactions. PR #431
• Removed the SIPickleRecordingInterface and SIPickleSortingInterface interfaces. PR #757
• Removed the SpikeGLXLFPInterface interface. PR #757

Bug fixes

• LocalPathExpander matches only folder_paths or file_paths if that is indicated in the passed specification. PR #679 and [PR #675](#679
• Fixed depth consideration in partial chunking pattern for the ROI data buffer. PR #677
• Fix mapping between channel names and the electrode table when writing more than one ElectricalSeries to the NWBFile. This fixes an issue when the converter pipeline of SpikeGLXConverterPipe was writing the electrode table region of the NIDQ stream incorrectly. PR #678
• Fix configure_backend when applied to TimeSeries contents that leverage internal links for data or timestamps. PR #732

Features

• Changed the Suite2pSegmentationInterface to support multiple plane segmentation outputs. The interface now has a plane_name and channel_name arguments to determine which plane output and channel trace add to the NWBFile. PR #601
• Added create_path_template and corresponding tests PR #680
• Added tool function configure_datasets for configuring all datasets of an in-memory NWBFile to be backend specific. PR #571
• Added LightningPoseConverter to add pose estimation data and the original and the optional labeled video added as ImageSeries to NWB. PR #633
• Added gain as a required __init__ argument for TdtRecordingInterface. PR #704
• Extract session_start_time from Plexon plx recording file. PR #723

Improvements

• nwbinspector has been removed as a minimal dependency. It becomes an extra (optional) dependency with neuroconv[dandi]. PR #672
• Added a from_nwbfile class method constructor to all BackendConfiguration models. PR #673
• Added compression to FicTracDataInterface. PR #678
• Exposed block_index to all OpenEphys interfaces. PR #695
• Added support for DynamicTable columns in the configure_backend tool function. PR #700
• Refactored ScanImagingInterface to reference ROIExtractors' version of extract_extra_metadata. PR #731
• Added support for Long NHP probe types for the SpikeGLXRecorddingInterfacce. PR #701
• Remove unnecessary duplication of probe setting in SpikeGLXRecordingInterface. PR #696
• Added associated suffixes to all interfaces and converters. PR #734
• Added convenience function get_format_summaries to tools.importing (and exposed at highest level). PR #734

Testing

• RecordingExtractorInterfaceTestMixin now compares either group_name, group or a default value of ElectrodeGroup to the group property in the NWBRecordingExtractor instead of comparing group to group as it was done before PR #736
• TestScanImageImagingInterfaceRecent now checks metadata against new roiextractors implementation PR #741.

v0.4.6

v0.4.6

Back-compatability break

• Changed the metadata schema for Fluorescence and DfOverF where the traces metadata should be provided as a dict instead of a list of dicts. The name of the plane segmentation is used to determine which traces to add to the Fluorescence and DfOverF containers. PR #632

Features

• Added Pydantic data models of BackendConfiguration for both HDF5 and Zarr datasets (container/mapper of all the DatasetConfigurations for a particular file). PR #568
• Modify the filtering of traces to also filter out traces with empty values. PR #649
• Added tool function get_default_dataset_configurations for identifying and collecting all fields of an in-memory NWBFile that could become datasets on disk; and return instances of the Pydantic dataset models filled with default values for chunking/buffering/compression. PR #569
• Added tool function get_default_backend_configuration for conveniently packaging the results of get_default_dataset_configurations into an easy-to-modify mapping from locations of objects within the file to their correseponding dataset configuration options, as well as linking to a specific backend DataIO. PR #570
• Added set_probe() method to BaseRecordingExtractorInterface. PR #639

Fixes

• Fixed GenericDataChunkIterator (in hdmf.py) in the case where the number of dimensions is 1 and the size in bytes is greater than the threshold of 1 GB. PR #638
• Changed np.floor and np.prod usage to math.floor and math.prod in various files. PR #638
• Updated minimal required version of DANDI CLI; updated run_conversion_from_yaml API function and tests to be compatible with naming changes. PR #664

Improvements

• Change metadata extraction library from fparse to parse. PR #654
• The dandi CLI/API is now an optional dependency; it is still required to use the tool function for automated upload as well as the YAML-based NeuroConv CLI. PR #655

v0.4.5

v0.4.5

Back-compatibility break

• The CEDRecordingInterface has now been removed; use the Spike2RecordingInterface instead. PR #602

Features

• Added session_start_time extraction to FicTracDataInterface. PR #598
• Added imaging_plane_name keyword argument to add_imaging_plane function to determine which imaging plane to add from the metadata by name instead of imaging_plane_index.
• Added reference for imaging_plane to default plane segmentation metadata. PR #594
• Changed Compass container for Position container in the FicTracDataInterface. PR #606
• Added option to write units in meters by providing a radius in FicTracDataInterface. PR #606
• Added parent_container keyword argument to add_photon_series that defines whether to add the photon series to acquisition or 'ophys' processing module. PR #587
• Added Pydantic data models of DatasetInfo (immutable summary of core dataset values such as maximum shape and dtype) and DatasetConfiguration for both HDF5 and Zarr datasets (the optional layer that specifies chunk/buffering/compression). PR #567
• Added alignment methods to FicTracDataInterface. PR #607
• Added alignment methods support to MockRecordingInterface PR #611
• Added NeuralynxNvtInterface, which can read position tracking NVT files. PR #580
• Adding radius as a conversion factor in FicTracDataInterface. PR #619
• Coerce FicTracDataInterface original timestamps to start from 0. PR #619
• Added configuration metadata to FicTracDataInterface. PR #618
• Expose number of jobs to automatic_dandi_upload. PR #624
• Added plane_segmentation_name keyword argument to determine which plane segmentation to add from the metadata by name instead of plane_segmentation_index.
  plane_segmentation_name is exposed at BaseSegmentationExtractorInterface.add_to_nwbfile() function to support adding segmentation output from multiple planes. PR #623
• Added SegmentationImages to metadata_schema in BaseSegmentationExtractorInterface to allow for the modification of the name and description of Images container and description of the summary images. PR #622
• Default chunking pattern of RecordingInterfaces now attempts to use as many channels as possible up to 64 total, and fill with as much time as possible up to the chunk_mb. This also required raising the lower HDMF version to 3.11.0 (which introduced 10 MB default chunk sizes). PR #630

Fixes

• Remove starting_time reset to default value (0.0) when adding the rate and updating the photon_series_kwargs or roi_response_series_kwargs, in add_photon_series or add_fluorescence_traces. PR #595
• Changed the date parsing in OpenEphysLegacyRecordingInterface to datetime.strptime with the expected date format explicitly set to "%d-%b-%Y %H%M%S". PR #577
• Pin lower bound HDMF version to 3.10.0. PR #586

Deprecation

• Removed use_times and buffer_size from add_photon_series. PR #600

Testing

• Adds MockImagingInterface as a general testing mechanism for ophys imaging interfaces PR #604.

v0.4.4

v0.4.4

Features

• DeepLabCutInterface now allows using custom timestamps via set_aligned_timestamps method before running conversion. PR #531

Fixes

• Reorganize timeintervals schema to reside in schemas/ dir to ensure its inclusion in package build. PR #573

v0.4.3

v0.4.3

Fixes

• The sonpy package for the Spike2 interface no longer attempts installation on M1 Macs. PR #563
• Fixed subset_sorting to explicitly cast end_frame to int to avoid SpikeInterface frame slicing edge case. PR #565

v0.4.2

v0.4.2

Fixes

• Exposed es_key argument to users where it was previously omitted on MaxOneRecordingInterface, OpenEphysLegacyRecordingInterface, and OpenEphysRecordingInterface. PR #542
• Added deepcopy for metadata in make_nwbfile_from_metadata. PR #545
• Fixed edge case in subset_sorting where end_frame could exceed recording length. PR #551
• Alter add_electrodes behavior, no error is thrown if a property is present in the metadata but not in the recording extractors. This allows the combination of recording objects that have different properties. PR #558

Features

• Added converters for Bruker TIF format to support multiple streams of imaging data.
  Added BrukerTiffSinglePlaneConverter for single plane imaging data which initializes a BrukerTiffSinglePlaneImagingInterface for each data stream.
  The available data streams can be checked by BrukerTiffSinglePlaneImagingInterface.get_streams(folder_path) method.
  Added BrukerTiffMultiPlaneConverter for volumetric imaging data with plane_separation_type argument that defines
  whether to load the imaging planes as a volume ("contiguous") or separately ("disjoint").
  The available data streams for the defined plane_separation_type can be checked by BrukerTiffMultiPlaneImagingInterface.get_streams(folder_path, plane_separation_type) method.
• Added FicTrac data interface. PR #517

Documentation and tutorial enhancements

• Added FicTrac to the conversion gallery and docs API. PR #560

v0.4.1

v0.4.1

Fixes

• Propagated additional arguments, such as cell_id, from the metadata["Icephys"]["Electrodes"] dictionary used in tools.neo.add_icephys_electrode. PR #538
• Fixed mismatch between expected Electrodes key in tools.neo.add_icephys_electrode and the metadata automatically generated by the AbfInterface. PR #538

v0.4.0

v0.4.0

Back-compatibility break

• Created separate .add_to_nwbfile method for all DataInterfaces. This is effectively the previous .run_conversion method but limited to operations on an in-memory nwbfile: pynwb.NWBFile` object and does not handle any I/O. PR #455

Fixes

• Set gzip compression by default on spikeinterface based interfaces run_conversion. PR #499

Features

• Added stream control with the stream_name argument to the NeuralynxRecordingExtractor. PR #369

• Added a common .temporally_align_data_interfaces method to the NWBConverter class to use as a specification of the protocol for temporally aligning the data interfaces of the converter. PR #362

• Added CellExplorerRecordingInterface for adding data raw and lfp data from the CellExplorer format. CellExplorer's new format contains a basename.session.mat file containing
  rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
  groups, location and brain area #488

• CellExplorerSortingInterface now supports extracting sampling frequency from the new data format. CellExplorer's new format contains a basename.session.mat file containing
  rich metadata including the sorting sampling frequency PR #491 and PR #502

• Added MiniscopeBehaviorInterface for Miniscope behavioral data. The interface uses ndx-miniscope extension to add a Miniscope device with the behavioral camera metadata,
  and an ImageSeries in external mode that is linked to the device. PR #482

  • CellExplorerSortingInterface now supports adding channel metadata to the nwbfile with write_ecephys_metadata=True as a conversion option PR #494

• Added MiniscopeImagingInterface for Miniscope imaging data stream. The interface uses ndx-miniscope extension to add a Miniscope device with the microscope device metadata,
  and the imaging data as OnePhotonSeries. PR #468

• Added MiniscopeConverter for combining the conversion of Miniscope imaging and behavioral data streams. PR #498

Improvements

• Avoid redundant timestamp creation in add_eletrical_series for recording objects without time vector. PR #495

• Avoid modifying the passed metadata structure via deep_dict_update in make_nwbfile_from_metadata. PR #476

Testing

• Added gin test for CellExplorerRecordingInterface. CellExplorer's new format contains a basename.session.mat file containing
  rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
  groups, location and brain area #488.
  • Added gin test for CellExplorerSortingInterface. CellExplorer's new format contains a basename.session.mat file containing
    rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
    groups, location and brain area PR #494.