CHANGELOG.md

Upcoming

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

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
• Add FacemapInterface, which currently only handles eye tracking PR #752

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

Deprecation

• Removed .get_electrode_table_json() on the BaseRecordingExtractorInterface in favor of GUIDE specific interactions. PR #431

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 (November 30, 2023)

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
• Changed the metadata schema for Fluorescence and DfOverF where the traces metadata can 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
• 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
• Changed default chunking of ImagingExtractorDataChunkIterator to select chunk_shape less than the chunk_mb threshold while keeping the original image size. The default chunk_mb changed to 10MB. PR #667

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 (November 6, 2023)

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

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

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

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

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

Back-compatibility break

• Create 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

• Temporarily disabled filtering for all-zero traces in add_fluorescence_traces as the current implementation is very slow for nearly all zero traces (e.g. suite2p deconvolved traces). PR #527

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.

v0.3.0 (June 7, 2023)

Back-compatibility break

• ExtractorInterface classes now access their extractor with the classmethod cls.get_extractor() instead of the attribute self.Extractor. PR #324
• The spikeextractor_backend option was removed for all RecordingExtractorInterface classes. (PR #324, PR #309]
• The NeuroScopeMultiRecordingExtractor has been removed. If your conversion required this, please submit an issue requesting instructions for how to implement it. PR #309
• The SIPickle interfaces have been removed. PR #309
• The previous conversion option es_key has been moved to the __init__ of all BaseRecordingExtractorInterface classes. It is no longer possible to use this argument in the run_conversion method. PR #318
• Change BaseDataInterface.get_conversion_options_schema from classmethod to object method. PR #353
• Removed utils.json_schema.get_schema_for_NWBFile and moved base metadata schema to external json file. Added constraints to Subject metadata to match DANDI. PR #376
• Duplicate video file paths in the VideoInterface and AudioInterface are no longer silently resolved; please explicitly remove duplicates when initializing the interfaces. PR #403
• Duplicate audio file paths in the AudioInterface are no longer silently resolved; please explicitly remove duplicates when initializing the interfaces. PR #402

Features

• The OpenEphysRecordingInterface is now a wrapper for OpenEphysBinaryRecordingInterface. PR #294
• Swapped the backend for CellExplorerSortingInterface from spikeextactors to spikeinterface. PR #267
• In the conversion YAML, DataInterface classes must now be specified as a dictionary instead of a list. PR #311
• In the conversion YAML, conversion_options can be specified on the global level. PR #312
• The OpenEphysRecordingInterface now redirects to legacy or binary interface depending on the file format. It raises NotImplementedError until the interface for legacy format is added. PR #296
• Added the OpenEphysLegacyRecordingInterface to support Open Ephys legacy format (.continuous files). PR #295
• Added PlexonSortingInterface to support plexon spiking data. PR #316
• Changed SpikeGLXRecordingInterface to accept either the AP or LF bands as file paths. Each will automatically set the correseponding es_key and corresponding metadata for each band or probe. PR #298
• The OpenEphysRecordingInterface redirects to OpenEphysLegacyRecordingInterface for legacy format files instead of raising NotImplementedError. PR #349
• Added a SpikeGLXConverter for easy combination of multiple IMEC and NIDQ data streams. PR #292
• Added an interfaces_by_category lookup table to neuroconv.datainterfaces to make searching for interfaces by modality and format easier. PR #352
• neuroconv.utils.jsonschema.get_schema_from_method_signature can now support the Dict[str, str] typehint, which allows DataInterface.__init__ and .run_conversion to handle dictionary arguments. PR #360
• Added neuroconv.tools.testing.data_interface_mixins module, which contains test suites for different types of DataInterfaces PR #357
• Added keywords to DataInterface classes. PR #375
• Uses open-cv-headless instead of open-cv, making the package lighter PR #387.
• Adds MockRecordingInterface as a general testing mechanism for ecephys interfaces PR #395.
• metadata returned by DataInterface.get_metadata() is now a DeepDict object, making it easier to add and adjust metadata. PR #404.
• The OpenEphysLegacyRecordingInterface is now extracts the session_start_time in get_metadata() from Neo (OpenEphysRawIO) and does not depend on pyopenephys anymore. PR #410
• Added expand_paths. PR #377
• Added basic temporal alignment methods to ecephys, ophys, and icephys DataInterfaces. These are get_timestamps, align_starting_time, align_timestamps, and align_by_interpolation. Added tests that serve as a first demonstration of the intended uses in a variety of cases. PR #237 PR #283 PR #400
• Added basic temporal alignment methods to the SLEAPInterface. Added holistic per-interface, per-method unit testing for ecephys and ophys interfaces. PR #401
• Added expand_paths. PR #377, PR #448
• Added .get_electrode_table_json() to the BaseRecordingExtractorInterface as a convenience helper for the GUIDE project. PR #431
• Added BrukerTiffImagingInterface to support Bruker TIF imaging data. This format consists of individual TIFFs (each file contains a single frame) in OME-TIF format (.ome.tif files) and metadata in XML format (.xml file). PR #390
• Added MicroManagerTiffImagingInterface to support Micro-Manager TIF imaging data. This format consists of multipage TIFFs in OME-TIF format (.ome.tif files) and configuration settings in JSON format ('DisplaySettings.json' file). PR #423
• Added a TemporallyAlignedDataInterface definition for convenience when creating a custom interface for pre-aligned data. PR #434
• Added write_as, units_name, units_description to BaseSortingExtractorInterface run_conversion method to be able to modify them in conversion options. PR #438
• Added basic temporal alignment methods to the VideoInterface. These are align_starting_time is split into align_starting_times (list of times, one per video file) and align_global_starting_time (shift all by a scalar amount). align_by_interpolation is not yet implemented for this interface. PR #283
• Added stream control for the OpenEphysBinaryRecordingInterface. PR #445
• Added the BaseTemporalAlignmentInterface to serve as the new base class for all new temporal alignment methods. PR #442
• Added direct imports for all base classes from the outer level; you may now call from neuroconv import BaseDataInterface, BaseTemporalAlignmentInterface, BaseExtractorInterface. PR #442
• Added basic temporal alignment methods to the AudioInterface. align_starting_time is split into align_starting_times (list of times, one per audio file) and align_global_starting_time (shift all by a scalar amount). align_by_interpolation and other timestamp-based approaches is not yet implemented for this interface. PR #402
• Changed the order of recording properties extraction in NeuroscopeRecordingInterface and NeuroScopeLFPInterface to make them consistent with each other PR #466
• The ScanImageImagingInterface has been updated to read metadata from more recent versions of ScanImage PR #457
• Refactored add_two_photon_series() to add_photon_series() and added photon_series_type optional argument which can be either "OnePhotonSeries" or "TwoPhotonSeries". Changed get_default_ophys_metadata() to add Device and ImagingPlane metadata which are both used by imaging and segmentation. Added photon_series_type to get_nwb_imaging_metadata() to fill metadata for OnePhotonSeries or TwoPhotonSeries. PR #462
• Split align_timestamps and align_starting_times into align_segment_timestamps and align_segment_starting_times for API consistency for multi-segment RecordingInterfaces. PR #463
• Rename align_timestamps and align_segmentt_timestamps into set_aligned_timestamps and set_aligned_segment_timestamps to more clearly indicate their usage and behavior. PR #470

Testing

• The tests for automatic_dandi_upload now follow up-to-date DANDI validation rules for file name conventions. PR #310
• Deactivate MaxOneRecordingInterface metadata tests [PR #371]((#371)
• Integrated the DataInterface testing mixin to the SLEAP Interface. PR #401
• Added holistic per-interface, per-method unit testing for ecephys and ophys interfaces. PR #283
• Live service tests now run in a separate non-required GitHub action. [PR #420]((#420)
• Integrated the DataInterfaceMixin class of tests to the VideoInterface. PR #403
• Add generate_path_expander_demo_ibl and associated test for LocalPathExpander PR #456
• Improved testing of all interface alignment methods via the new TemporalAlignmentMixin class. PR #459

Fixes

• BlackrockRecordingInterface now writes all ElectricalSeries to "acquisition" unless changed using the write_as flag in run_conversion. PR #315
• Excluding Python versions 3.8 and 3.9 for the EdfRecordingInterface on M1 macs due to installation problems. PR #319
• Extend type array condition in get_schema_from_hdmf_class for dataset types (excludes that are DataIO). PR #418
• The base_directory argument to all PathExpander classes can now accept string inputs as well as Path inputs. PR #427
• Fixed the temporal alignment methods for the RecordingInterfaces which has multiple segments. PR #411
• Fixes to the temporal alignment methods for the SortingInterface, both single and multi-segment and recordingless. PR #413
• Fixes to the temporal alignment methods for the certain formats of the RecordingInterface. PR #459
• Fixes the naming of LFP interfaces to be ElectricalSeriesLFP instead of ElectricalSeriesLF. PR #467
• Fixed an issue with incorrect modality-specific extra requirements being associated with certain behavioral formats. PR #469

Documentation and tutorial enhancements

• The instructions to build the documentation were moved to ReadTheDocs. PR #323
• Move testing instructions to ReadTheDocs. PR #320
• Moved NeuroConv catalogue from ReadMe.md to ReadTheDocs. PR #322
• Moved instructions to build the documentation from README.md to ReadTheDocs. PR #323
• Add Spike2RecordingInterface to conversion gallery. PR #338
• Remove authors from module docstrings PR #354
• Add examples for LocalPathExpander usage PR #456
• Add better docstrings to the aux functions of the Neuroscope interface PR #485

Pending deprecation

• Change name from CedRecordingInterface to Spike2RecordingInterface. PR #338

Improvements

• Use Literal in typehints (incompatible with Python<=3.8). PR #340
• BaseDataInterface.get_source_schema modified so it works for .__init__ and .__new__. PR #374

v0.2.4 (February 7, 2023)

Deprecation

• All usages of use_times have been removed from spikeinterface tools and interfaces. The function add_electrical_series now determines whether the timestamps of the spikeinterface recording extractor are uniform or not and automatically stores the data according to best practices PR #40
• Dropped Python 3.7 support. PR #237

Features

• Added a tool for determining rising and falling frames from TTL signals (parse_rising_frames_from_ttl and get_falling_frames_from_ttl). PR #244
• Added the SpikeGLXNIDQInterface for reading data from .nidq.bin files, as well as the ability to parse event times from specific channels via the get_event_starting_times_from_ttl method. Also included a neuroconv.tools.testing.MockSpikeGLXNIDQInterface for testing purposes. PR #247
• Improved handling of writing multiple probes to the same NWB file PR #255

Pending deprecation

• Added DeprecationWarnings to all spikeextractors backends. PR #265
• Added DeprecationWarnings for spikeextractors objects in neuroconv.tools.spikeinterface. PR #266

Fixes

• Temporarily hotfixed the tensorflow dependency after the release of deeplabcut==2.3.0. PR #268
• Fixed cleanup of waveform tests in SI tools. PR #277
• Fixed metadata structure for the CsvTimeIntervalsInterface, which was previously not passed validation in NWBConverters. PR #237
• Added propagation of the load_sync_channel argument for the SpikeGLXNIDQInterface. PR #282
• Fixed the default es_key used by stand-alone write using any RecordingExtractorInterface or LFPExtractorInterface. PR #288
• Fixed the default ExtractorName used to load the spikeinterface extractor of the SpikeGLXLFPInterface. PR #288

Testing

• Re-organized the test_gin_ecephys file by splitting into each sub-modality. PR #282
• Add testing support for Python 3.11. PR #234

v0.2.3

Documentation and tutorial enhancements

• Remove Path(path_to_save_nwbfile).is_file() from each of the gallery pages. PR #177
• Improve docstring for SpikeGLXRecordingInterface. PR #226
• Correct typing of SpikeGLX in conversion gallery. PR #223
• Added tutorial for utilizing YAML metadata in a conversion pipeline. PR #240
• Added page in User Guide for how to use CSVs to specify metadata. PR #241
• Added the BaseDataInterface in the API docs. PR #242
• Fixed typo in styling section. PR #253
• Updated docs on JSON schema. PR #256
• Improved compliance with numpy-style docstring PR #260

Features

• Added AudioInterface for files in WAV format using the add_acoustic_waveform_series utility function from tools/audio to write audio data to NWB. PR #196
• Added the MaxOneRecordingInterface for writing data stored in MaxOne (.raw.h5) format. PR #222
• Added the MCSRawRecordingInterface for writing data stored in MCSRaw (.raw) format. PR #220
• Added the MEArecRecordingInterface for writing data stored in MEArec (structured .h5) format. PR #218
• Added the AlphaOmegaRecordingInterface for writing data stored in AlphaOmega (folder of .mrx) format. PR #212
• Added the PlexonRecordingInterface for writing data stored in Plexon (.plx) format. PR #206
• Added the BiocamRecordingInterface for writing data stored in Biocam (.bwr) format. PR #210
• Added function to add acoustic series as AcousticWaveformSeries object as acquisition or stimulus to NWB. PR #201
• Added new form to the GitHub repo for requesting support for new formats. PR #207
• Simplified the writing of channel_conversion during add_electrical_series if the vector of gains is uniform; in this case, they are now combined into the scalar conversion value. PR #218
• Implement timestamp extraction from videos for the SLEAPInterface PR #238
• Prevented writing of default values for optional columns on the ElectrodeTable. PR #219
• Add interfaces for Excel and Csv time intervals tables. PR #252

Testing

• Added a session_id to the test file for the automatic_dandi_upload helper function. PR #199
• pre-commit version bump. PR #235
• Added a testing sub-module to src and added a method (generate_mock_ttl_signal) for generating synthetic TTL pulses. PR #245

Fixes

• VideoInterface. Only raise a warning if the difference between the rate estimated from timestamps and the fps (frames per seconds) is larger than two decimals. PR #200
• Fixed the bug in a VideoInterface where it would use DataChunkIterator even if the conversion options indicated that it should not. PR #200
• Update usage requirements for HDMF to prevent a buffer overflow issue fixed in hdmf-dev/hdmf#780. PR #195
• Remove the deprecated distutils.version in favor of packaging.version PR #233

v0.2.2

Testing

• Added a set of dev branch gallery tests for PyNWB, HDMF, SI, and NEO. PR #113
• Added tests for the TypeError and ValueError raising for the new starting_frames argument of MovieDataInterface.run_conversion(). PR #113
• Added workflow for automatic detection of CHANGELOG.md updates for PRs. PR #187
• Added support for python 3.10 PR #229

Fixes

• Fixed a new docval typing error that arose in hdmf>3.4.6 versions. PR #113
• Fixed a new input argument issue for starting_frames when using external_file for an ImageSeries in pynwb>2.1.0 versions. PR #113
• Fixed issues regarding interaction between metadata rate values and extractor rate values in tools.roiextractors. PR #159
• Fixed sampling frequency resolution issue when detecting this from timestamps in roiextractors.write_imaging and roiextractors.write_segmentation. PR #159

Documentation and tutorial enhancements

• Added a note in User Guide/DataInterfaces to help installing custom dependencies for users who use Z-shell (zsh). PR #180
• Added MovieInterface example in the conversion gallery. PR #183

Features

• Added ConverterPipe, a class that allows chaining previously initialized interfaces for batch conversion and corresponding tests PR #169
• Added automatic extraction of metadata for NeuralynxRecordingInterface including filtering information for channels, device and recording time information PR #170
• Added stubbing capabilities to timestamp extraction in the MovieInterface avoiding scanning through the whole file when stub_test=True PR #181
• Added a flag include_roi_acceptance to tools.roiextractors.write_segmentation and corresponding interfaces to allow disabling the addition of boolean columns indicating ROI acceptance. PR #193
• Added write_waveforms() function in tools.spikeinterface to write WaveformExtractor objects PR #217

Pending deprecation

• Replaced the MovieInterface with VideoInterface and introduced deprecation warnings for the former. PR #74

v0.2.1

Fixes

• Updated BlackrockRecordingInterface to support multi stream file and added gin corresponding gin tests PR #176

v0.2.0

Back-compatability break

• All built-in DataInterfaces are now nested under the neuroconv.datainterfaces import structure - they are no longer available from the outer level. To import a data interface, use the syntax from neuroconv.datainterfaces import <name of interface>. PR #74
• The AxonaRecordingExtractorInterface has been renamed to AxonaRecordingInterface. PR #74
• The AxonaUnitRecordingExtractorInterface has been renamed to AxonaUnitRecordingInterface. PR #74
• The BlackrockRecordingExtractorInterface has been renamed to BlackrockRecordingInterface. PR #74
• The BlackrockSortingExtractorInterface has been renamed to BlackrockSortingInterface. PR #74
• The OpenEphysRecordingExtractorInterface has been renamed to OpenEphysRecordingInterface. PR #74
• The OpenEphysSortingExtractorInterface has been renamed to OpenEphysSortingInterface. PR #74
• The KilosortSortingInterface has been renamed to KiloSortSortingInterface to be more consistent with SpikeInterface. PR #107
• The Neuroscope interfaces have been renamed to NeuroScope to be more consistent with SpikeInterface. PR #107
• The tools.roiextractors.add_epoch functionality has been retired in the newest versions of ROIExtractors. PR #112
• Removed deprecation warnings for save_path argument (which is now nwbfile_path everywhere in the package). PR #124
• Changed default device name for the ecephys pipeline. Device_ecephys -> DeviceEcephys PR #154
• Change names of written electrical series on the ecephys pipeline. ElectricalSeries_raw -> ElectricalSeriesRaw, ElectricalSeries_processed -> ElectricalSeriesProcessed, ElectricalSeries_lfp -> ElectricalSeriesLFP PR #153
• Drop spikeextractor backend support for NeuralynxRecordingInterface PR #174

Fixes

• Prevented the CEDRecordingInterface from writing non-ecephys channel data. PR #37
• Fixed description in write_sorting and in add_units_table to have "neuroconv" in the description. PR #104
• Updated spikeinterface version number to 0.95.1 to fix issue with SpikeGLXInterface probe annotations. The issue is described here. PR #132

Improvements

• Unified the run_conversion method of BaseSegmentationExtractorInterface with that of all the other base interfaces. The method write_segmentation now uses the common make_or_load_nwbfile context manager PR #29
• Coerced the recording extractors with spikeextractors_backend=True to BaseRecording objects for Axona, Blackrock, Openephys, and SpikeGadgets. PR #38
• Added function to add PlaneSegmentation objects to an nwbfile in roiextractors and corresponding unit tests. PR #23
• use_times argument to be deprecated on the ecephys pipeline. The function add_electrical_series now determines whether the timestamps of the spikeinterface recording extractor are uniform or not and automatically stores the data according to best practices PR #40
• Add NWBFile metadata key at the level of the base data interface so it can always be inherited to be available. PR #51.
• Added spikeinterface support to Axona LFP and coerece gin tests for LFP to be spikeinterface objects PR #85
• Added function to add fluorescence traces to an nwbfile in roiextractors and corresponding unit tests. The df over f traces are now added to a DfOverF container instead of the Fluorescence container. The metadata schema has been changed for the BaseSegmentationExtractorInterface to allow metadata for DfOverF, and Flurorescence is now not required in the metadata schema. PR #41
• Improved default values of OpticalChannel object names and other descriptions for Imaging data. PR #88
• Extended the ImagingDataChunkIterator to be compatible with volumetric data. PR #90
• Integrated the ImagingDataChunkIterator with the write_imaging methods. PR #90
• Began work towards making SpikeInterface, SpikeExtractors, and ROIExtractors all non-minimal dependencies. PR #74
• Implemented format-wise and modality-wise extra installation requirements. If there are any requirements to use a module or data interface, these are defined in individual requirements files at the corresponding level of the package. These are in turn easily accessible from the commands pip install neuroconv[format_name]. pip install neuroconv[modality_name] will also install all dependencies necessary to make full use of any interfaces from that modality. PR #100
• Added frame stubbing to the BaseSegmentationExtractorInterface. PR #116
• Added mask_type: str and include_roi_centroids: bool to the add_plane_segmentation helper and write_segmentation functions for the tools.roiextractors submodule. PR #117
• Propagate output_struct_name argument to ExtractSegmentationInterface to match its extractor arguments. PR #128
• Added compression and iteration (with options control) to all Fluorescence traces in write_segmentation. PR #120
• For irregular recordings, timestamps can now be saved along with all traces in write_segmentation. PR #130
• Added mask_type argument to tools.roiextractors.add_plane_segmentation function and all upstream calls. This allows users to request writing not just the image_masks (still the default) but also pixels, voxels or None of the above. PR #119
• utils.json_schema.get_schema_from_method_signature now allows Optional[...] annotation typing and subsequent None values during validation as long as it is still only applied to a simple non-conflicting type (no Optional[Union[..., ...]]). PR #119

Documentation and tutorial enhancements:

• Unified the documentation of NeuroConv structure in the User Guide readthedocs. PR #39
• Added package for viewing source code in the neuroconv documentation PR #62
• Added Contributing guide for the Developer section of readthedocs. PR #73
• Added style guide to the readthedocs PR #28
• Added ABF data conversion tutorial @luiztauffer PR #89
• Added Icephys API documentation @luiztauffer PR #103
• Added Blackrock sorting conversion gallery example PR #134
• Extended the User Guide Get metadata section in DataInterfaces with a demonstration for loading metadata from YAML. PR #144
• Fixed a redundancy in PR #144 and API links. PR #154
• Added SLEAP conversion gallery example PR #161

Features

• Added conversion interface for Neuralynx sorting data together with gin data test and a conversion example in the gallery. PR #58
• Added conversion interface for DeepLabCut data together with gin data test and a conversion example in the gallery. PR #24
• Allow writing of offsets to ElectricalSeries objects from SpikeInterface (requires PyNWB>=2.1.0). PR #37
• Added conversion interface for EDF (European Data Format) data together with corresponding unit tests and a conversion example in the gallery. PR #45
• Created ImagingExtractorDataChunkIterator, a data chunk iterator for ImagingExtractor objects. PR #54
• Added support for writing spikeinterface recording extractor with multiple segments and corresponding unit test PR #67
• Added spikeinterface support to the Axona data interface PR #61
• Added new util function get_package for safely attempting to attempt a package import and informatively notifying the user of how to perform the installation otherwise. PR #74
• All built-in DataInterfaces now load their external dependencies on-demand at time of object initialization instead of on package or interface import. PR #74
• Adde spikeinterface support for Blackrock sorting interfacePR #134
• Added conversion interface for TDT recording data together with gin data test. PR #135
• Added conversion interface for SLEAP pose estimation data together with gin test for data. PR #160

Testing

• Added unittests for correctly writing the scaling factors to the nwbfile in the add_electrical_series function of the spikeinterface module. PR #37
• Added unittest for compression options in the add_electrical_series function of the spikeinterface module. PR #64
• Added unittests for chunking in the add_electrical_series function of the spikeinterface module. PR #84
• Tests are now organized according to modality-wise lazy installations. PR #100

v0.1.1

Fixes

• Fixed the behavior of the file_paths usage in the MovieInterface when run via the YAML conversion specification. PR #33

Improvements

• Added function to add ImagingPlane objects to an nwbfile in roiextractors and corresponding unit tests. PR #19
• Added function to add summary images from a SegmentationExtractor object to an nwbfile in the roiextractors module and corresponding unit tests PR #22
• Small improvements on ABFInterface @luiztauffer PR #89

Features

• Add non-iterative writing capabilities to add_electrical_series. PR #32

Testing

• Added unittests for the write_as functionality in the add_electrical_series of the spikeinterface module. PR #32

v0.1.0

• The first release of NeuroConv.