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@CodyCBakerPhD CodyCBakerPhD released this 26 Sep 22:36
· 3894 commits to main since this release
v0.2.0
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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

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 compresion 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

Contributors

luiztauffer
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