Skip to content

v0.4.5
Compare
Choose a tag to compare
@CodyCBakerPhD CodyCBakerPhD released this 06 Nov 22:50
· 801 commits to main since this release
v0.4.5
c7c40e0
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

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.
Assets 2
Loading