From f91a0774a8b6f05ef8c89bdfb3a43ae0be0b1cd7 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Tue, 10 Dec 2024 14:21:35 -0600 Subject: [PATCH 1/9] change verbose to false --- .../behavior/lightningpose.rst | 1 - .../recording/openephys.rst | 1 - .../behavior/audio/audiointerface.py | 4 ++-- .../deeplabcut/deeplabcutdatainterface.py | 2 +- .../behavior/fictrac/fictracdatainterface.py | 4 ++-- .../lightningpose/lightningposeconverter.py | 4 ++-- .../lightningposedatainterface.py | 4 ++-- .../behavior/medpc/medpcdatainterface.py | 2 +- .../neuralynx/neuralynx_nvt_interface.py | 4 ++-- .../behavior/sleap/sleapdatainterface.py | 4 ++-- .../alphaomega/alphaomegadatainterface.py | 2 +- .../ecephys/axona/axonadatainterface.py | 2 +- .../ecephys/baselfpextractorinterface.py | 2 +- .../baserecordingextractorinterface.py | 4 ++-- .../ecephys/basesortingextractorinterface.py | 2 +- .../ecephys/biocam/biocamdatainterface.py | 4 ++-- .../blackrock/blackrockdatainterface.py | 6 +++--- .../cellexplorer/cellexplorerdatainterface.py | 8 ++++---- .../ecephys/edf/edfdatainterface.py | 4 ++-- .../ecephys/intan/intandatainterface.py | 4 ++-- .../ecephys/kilosort/kilosortdatainterface.py | 2 +- .../ecephys/maxwell/maxonedatainterface.py | 2 +- .../ecephys/mcsraw/mcsrawdatainterface.py | 2 +- .../ecephys/mearec/mearecdatainterface.py | 4 ++-- .../neuralynx/neuralynxdatainterface.py | 4 ++-- .../neuroscope/neuroscopedatainterface.py | 4 ++-- .../openephys/openephysbinarydatainterface.py | 4 ++-- .../openephys/openephysdatainterface.py | 4 ++-- .../openephys/openephyslegacydatainterface.py | 4 ++-- .../ecephys/phy/phydatainterface.py | 4 ++-- .../ecephys/plexon/plexondatainterface.py | 10 +++++----- .../ecephys/spike2/spike2datainterface.py | 4 ++-- .../spikegadgets/spikegadgetsdatainterface.py | 2 +- .../ecephys/spikeglx/spikeglxdatainterface.py | 4 ++-- .../ecephys/spikeglx/spikeglxnidqinterface.py | 4 ++-- .../ecephys/tdt/tdtdatainterface.py | 4 ++-- .../ophys/baseimagingextractorinterface.py | 2 +- .../ophys/brukertiff/brukertiffconverter.py | 4 ++-- .../brukertiff/brukertiffdatainterface.py | 8 ++++---- .../ophys/caiman/caimandatainterface.py | 2 +- .../ophys/cnmfe/cnmfedatainterface.py | 2 +- .../ophys/extract/extractdatainterface.py | 2 +- .../ophys/hdf5/hdf5datainterface.py | 4 ++-- .../micromanagertiffdatainterface.py | 4 ++-- .../ophys/miniscope/miniscopeconverter.py | 4 ++-- .../ophys/sbx/sbxdatainterface.py | 4 ++-- .../scanimage/scanimageimaginginterfaces.py | 14 ++++++------- .../ophys/suite2p/suite2pdatainterface.py | 2 +- .../tdt_fp/tdtfiberphotometrydatainterface.py | 2 +- .../ophys/tiff/tiffdatainterface.py | 4 ++-- .../text/excel/exceltimeintervalsinterface.py | 4 ++-- .../text/timeintervalsinterface.py | 4 ++-- src/neuroconv/nwbconverter.py | 8 ++++---- .../nwb_helpers/_metadata_and_file_helpers.py | 2 +- .../tools/roiextractors/roiextractors.py | 8 ++++---- .../tools/spikeinterface/spikeinterface.py | 20 +++++++++---------- .../tools/testing/mock_interfaces.py | 4 ++-- tests/test_ecephys/test_ecephys_interfaces.py | 2 +- .../test_temporal_alignment_methods.py | 4 ++-- 59 files changed, 121 insertions(+), 123 deletions(-) diff --git a/docs/conversion_examples_gallery/behavior/lightningpose.rst b/docs/conversion_examples_gallery/behavior/lightningpose.rst index a024a6799..f0b91e804 100644 --- a/docs/conversion_examples_gallery/behavior/lightningpose.rst +++ b/docs/conversion_examples_gallery/behavior/lightningpose.rst @@ -23,7 +23,6 @@ Convert LightningPose pose estimation data to NWB using :py:class:`~neuroconv.da >>> labeled_video_file_path = str(folder_path / "labeled_videos/test_vid_labeled.mp4") >>> converter = LightningPoseConverter(file_path=file_path, original_video_file_path=original_video_file_path, labeled_video_file_path=labeled_video_file_path, verbose=False) - Source data is valid! >>> metadata = converter.get_metadata() >>> # For data provenance we add the time zone information to the conversion >>> session_start_time = metadata["NWBFile"]["session_start_time"] diff --git a/docs/conversion_examples_gallery/recording/openephys.rst b/docs/conversion_examples_gallery/recording/openephys.rst index a5d4e960a..bced73b7f 100644 --- a/docs/conversion_examples_gallery/recording/openephys.rst +++ b/docs/conversion_examples_gallery/recording/openephys.rst @@ -30,4 +30,3 @@ Convert OpenEphys data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys >>> # Choose a path for saving the nwb file and run the conversion >>> nwbfile_path = f"{path_to_save_nwbfile}" # This should be something like: "./saved_file.nwb" >>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata) - NWB file saved at ... diff --git a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py index 6561096b5..b4a934bae 100644 --- a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py +++ b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py @@ -171,7 +171,7 @@ def add_to_nwbfile( write_as: Literal["stimulus", "acquisition"] = "stimulus", iterator_options: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, ): """ Parameters @@ -187,7 +187,7 @@ def add_to_nwbfile( iterator_options : dict, optional Dictionary of options for the SliceableDataChunkIterator. overwrite : bool, default: False - verbose : bool, default: True + verbose : bool, default: False Returns ------- diff --git a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py index 147fcf6ea..8c81a0264 100644 --- a/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py +++ b/src/neuroconv/datainterfaces/behavior/deeplabcut/deeplabcutdatainterface.py @@ -31,7 +31,7 @@ def __init__( file_path: FilePath, config_file_path: Optional[FilePath] = None, subject_name: str = "ind1", - verbose: bool = True, + verbose: bool = False, ): """ Interface for writing DLC's output files to nwb using dlc2nwb. diff --git a/src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py b/src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py index 1d822f919..75e1415dd 100644 --- a/src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py +++ b/src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py @@ -159,7 +159,7 @@ def __init__( file_path: FilePath, radius: Optional[float] = None, configuration_file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, ): """ Interface for writing FicTrac files to nwb. @@ -173,7 +173,7 @@ def __init__( and the units are set to meters. If not provided the units are set to radians. configuration_file_path : FilePath, optional Path to the .txt file with the configuration metadata. Usually called config.txt - verbose : bool, default: True + verbose : bool, default: False controls verbosity. ``True`` by default. """ self.file_path = Path(file_path) diff --git a/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposeconverter.py b/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposeconverter.py index 505aa144d..e25671cc8 100644 --- a/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposeconverter.py +++ b/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposeconverter.py @@ -34,7 +34,7 @@ def __init__( labeled_video_file_path: Optional[FilePath] = None, image_series_original_video_name: Optional[str] = None, image_series_labeled_video_name: Optional[str] = None, - verbose: bool = True, + verbose: bool = False, ): """ The converter for Lightning Pose format to convert the pose estimation data @@ -52,7 +52,7 @@ def __init__( The name of the ImageSeries to add for the original video. image_series_labeled_video_name: string, optional The name of the ImageSeries to add for the labeled video. - verbose : bool, default: True + verbose : bool, default: False controls verbosity. ``True`` by default. """ self.verbose = verbose diff --git a/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposedatainterface.py b/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposedatainterface.py index dbd425b5b..1211c31d1 100644 --- a/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposedatainterface.py +++ b/src/neuroconv/datainterfaces/behavior/lightningpose/lightningposedatainterface.py @@ -64,7 +64,7 @@ def __init__( file_path: FilePath, original_video_file_path: FilePath, labeled_video_file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, ): """ Interface for writing pose estimation data from the Lightning Pose algorithm. @@ -77,7 +77,7 @@ def __init__( Path to the original video file (.mp4). labeled_video_file_path : a string or a path, optional Path to the labeled video file (.mp4). - verbose : bool, default: True + verbose : bool, default: False controls verbosity. ``True`` by default. """ # This import is to assure that the ndx_pose is in the global namespace when an pynwb.io object is created diff --git a/src/neuroconv/datainterfaces/behavior/medpc/medpcdatainterface.py b/src/neuroconv/datainterfaces/behavior/medpc/medpcdatainterface.py index 09f9111d7..04022eba1 100644 --- a/src/neuroconv/datainterfaces/behavior/medpc/medpcdatainterface.py +++ b/src/neuroconv/datainterfaces/behavior/medpc/medpcdatainterface.py @@ -49,7 +49,7 @@ def __init__( start_variable: str, metadata_medpc_name_to_info_dict: dict, aligned_timestamp_names: Optional[list[str]] = None, - verbose: bool = True, + verbose: bool = False, ): """ Initialize MedpcInterface. diff --git a/src/neuroconv/datainterfaces/behavior/neuralynx/neuralynx_nvt_interface.py b/src/neuroconv/datainterfaces/behavior/neuralynx/neuralynx_nvt_interface.py index 213adf731..e118850ae 100644 --- a/src/neuroconv/datainterfaces/behavior/neuralynx/neuralynx_nvt_interface.py +++ b/src/neuroconv/datainterfaces/behavior/neuralynx/neuralynx_nvt_interface.py @@ -22,7 +22,7 @@ class NeuralynxNvtInterface(BaseTemporalAlignmentInterface): info = "Interface for writing Neuralynx position tracking .nvt files to NWB." @validate_call - def __init__(self, file_path: FilePath, verbose: bool = True): + def __init__(self, file_path: FilePath, verbose: bool = False): """ Interface for writing Neuralynx .nvt files to nwb. @@ -30,7 +30,7 @@ def __init__(self, file_path: FilePath, verbose: bool = True): ---------- file_path : FilePath Path to the .nvt file - verbose : bool, default: True + verbose : bool, default: Falsee controls verbosity. """ diff --git a/src/neuroconv/datainterfaces/behavior/sleap/sleapdatainterface.py b/src/neuroconv/datainterfaces/behavior/sleap/sleapdatainterface.py index 713b21c98..90b9b91e1 100644 --- a/src/neuroconv/datainterfaces/behavior/sleap/sleapdatainterface.py +++ b/src/neuroconv/datainterfaces/behavior/sleap/sleapdatainterface.py @@ -32,7 +32,7 @@ def __init__( self, file_path: FilePath, video_file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, frames_per_second: Optional[float] = None, ): """ @@ -42,7 +42,7 @@ def __init__( ---------- file_path : FilePath Path to the .slp file (the output of sleap) - verbose : bool, default: True + verbose : bool, default: Falsee controls verbosity. ``True`` by default. video_file_path : FilePath, optional The file path of the video for extracting timestamps. diff --git a/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py b/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py index 97f89abca..0f4b7bba9 100644 --- a/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py @@ -26,7 +26,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: extractor_kwargs["stream_id"] = self.stream_id return extractor_kwargs - def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, folder_path: DirectoryPath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Load and prepare data for AlphaOmega. diff --git a/src/neuroconv/datainterfaces/ecephys/axona/axonadatainterface.py b/src/neuroconv/datainterfaces/ecephys/axona/axonadatainterface.py index 3c8a1067c..d592f4ee1 100644 --- a/src/neuroconv/datainterfaces/ecephys/axona/axonadatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/axona/axonadatainterface.py @@ -36,7 +36,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: return extractor_kwargs - def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Parameters diff --git a/src/neuroconv/datainterfaces/ecephys/baselfpextractorinterface.py b/src/neuroconv/datainterfaces/ecephys/baselfpextractorinterface.py index af16601bb..79e006c3b 100644 --- a/src/neuroconv/datainterfaces/ecephys/baselfpextractorinterface.py +++ b/src/neuroconv/datainterfaces/ecephys/baselfpextractorinterface.py @@ -15,7 +15,7 @@ class BaseLFPExtractorInterface(BaseRecordingExtractorInterface): "LF", ) - def __init__(self, verbose: bool = True, es_key: str = "ElectricalSeriesLFP", **source_data): + def __init__(self, verbose: bool = False, es_key: str = "ElectricalSeriesLFP", **source_data): super().__init__(verbose=verbose, es_key=es_key, **source_data) def add_to_nwbfile( diff --git a/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py b/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py index 6d0df14c1..623c0b7bc 100644 --- a/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py +++ b/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py @@ -20,11 +20,11 @@ class BaseRecordingExtractorInterface(BaseExtractorInterface): ExtractorModuleName = "spikeinterface.extractors" - def __init__(self, verbose: bool = True, es_key: str = "ElectricalSeries", **source_data): + def __init__(self, verbose: bool = False, es_key: str = "ElectricalSeries", **source_data): """ Parameters ---------- - verbose : bool, default: True + verbose : bool, default: Falsee If True, will print out additional information. es_key : str, default: "ElectricalSeries" The key of this ElectricalSeries in the metadata dictionary. diff --git a/src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py b/src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py index dca2dea5f..1b238e0c6 100644 --- a/src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py +++ b/src/neuroconv/datainterfaces/ecephys/basesortingextractorinterface.py @@ -18,7 +18,7 @@ class BaseSortingExtractorInterface(BaseExtractorInterface): ExtractorModuleName = "spikeinterface.extractors" - def __init__(self, verbose=True, **source_data): + def __init__(self, verbose=False, **source_data): super().__init__(**source_data) self.sorting_extractor = self.get_extractor()(**source_data) self.verbose = verbose diff --git a/src/neuroconv/datainterfaces/ecephys/biocam/biocamdatainterface.py b/src/neuroconv/datainterfaces/ecephys/biocam/biocamdatainterface.py index f12f3a93d..056a8d31f 100644 --- a/src/neuroconv/datainterfaces/ecephys/biocam/biocamdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/biocam/biocamdatainterface.py @@ -20,7 +20,7 @@ def get_source_schema(cls) -> dict: schema["properties"]["file_path"]["description"] = "Path to the .bwr file." return schema - def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Load and prepare data for Biocam. @@ -28,7 +28,7 @@ def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "Ele ---------- file_path : string or Path Path to the .bwr file. - verbose : bool, default: True + verbose : bool, default: False Allows verbose. es_key: str, default: "ElectricalSeries" """ diff --git a/src/neuroconv/datainterfaces/ecephys/blackrock/blackrockdatainterface.py b/src/neuroconv/datainterfaces/ecephys/blackrock/blackrockdatainterface.py index 7e6e499d1..b0a2cbb5d 100644 --- a/src/neuroconv/datainterfaces/ecephys/blackrock/blackrockdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/blackrock/blackrockdatainterface.py @@ -35,7 +35,7 @@ def __init__( self, file_path: FilePath, nsx_override: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): """ @@ -90,7 +90,7 @@ def get_source_schema(cls) -> dict: metadata_schema["properties"]["file_path"].update(description="Path to Blackrock .nev file.") return metadata_schema - def __init__(self, file_path: FilePath, sampling_frequency: Optional[float] = None, verbose: bool = True): + def __init__(self, file_path: FilePath, sampling_frequency: Optional[float] = None, verbose: bool = False): """ Parameters ---------- @@ -100,7 +100,7 @@ def __init__(self, file_path: FilePath, sampling_frequency: Optional[float] = No The sampling frequency for the sorting extractor. When the signal data is available (.ncs) those files will be used to extract the frequency automatically. Otherwise, the sampling frequency needs to be specified for this extractor to be initialized. - verbose : bool, default: True + verbose : bool, default: False Enables verbosity """ super().__init__(file_path=file_path, sampling_frequency=sampling_frequency, verbose=verbose) diff --git a/src/neuroconv/datainterfaces/ecephys/cellexplorer/cellexplorerdatainterface.py b/src/neuroconv/datainterfaces/ecephys/cellexplorer/cellexplorerdatainterface.py index 46e825fb5..d00e47bde 100644 --- a/src/neuroconv/datainterfaces/ecephys/cellexplorer/cellexplorerdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/cellexplorer/cellexplorerdatainterface.py @@ -254,7 +254,7 @@ class CellExplorerRecordingInterface(BaseRecordingExtractorInterface): The folder where the session data is located. It should contain a `{folder.name}.session.mat` file and the binary files `{folder.name}.dat` or `{folder.name}.lfp` for the LFP interface. - verbose : bool, default: True + verbose : bool, default: Falsee Whether to output verbose text. es_key : str, default: "ElectricalSeries" and "ElectricalSeriesLFP" for the LFP interface @@ -294,7 +294,7 @@ def get_source_schema(cls) -> dict: source_schema["properties"]["folder_path"]["description"] = "Folder containing the .session.mat file" return source_schema - def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, folder_path: DirectoryPath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Parameters @@ -382,7 +382,7 @@ class CellExplorerLFPInterface(CellExplorerRecordingInterface): sampling_frequency_key = "srLfp" binary_file_extension = "lfp" - def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str = "ElectricalSeriesLFP"): + def __init__(self, folder_path: DirectoryPath, verbose: bool = False, es_key: str = "ElectricalSeriesLFP"): super().__init__(folder_path, verbose, es_key) def add_to_nwbfile( @@ -425,7 +425,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: return extractor_kwargs - def __init__(self, file_path: FilePath, verbose: bool = True): + def __init__(self, file_path: FilePath, verbose: bool = False): """ Initialize read of Cell Explorer file. diff --git a/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py b/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py index ef169f66f..150aa574b 100644 --- a/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py @@ -37,7 +37,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: def __init__( self, file_path: FilePath, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", channels_to_skip: Optional[list] = None, ): @@ -50,7 +50,7 @@ def __init__( ---------- file_path : str or Path Path to the edf file - verbose : bool, default: True + verbose : bool, default: Falseeeeee Allows verbose. es_key : str, default: "ElectricalSeries" Key for the ElectricalSeries metadata diff --git a/src/neuroconv/datainterfaces/ecephys/intan/intandatainterface.py b/src/neuroconv/datainterfaces/ecephys/intan/intandatainterface.py index 2d7c849f2..d923b2e1e 100644 --- a/src/neuroconv/datainterfaces/ecephys/intan/intandatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/intan/intandatainterface.py @@ -35,7 +35,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: def __init__( self, file_path: FilePath, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ignore_integrity_checks: bool = False, ): @@ -47,7 +47,7 @@ def __init__( file_path : FilePathType Path to either a rhd or a rhs file - verbose : bool, default: True + verbose : bool, default: False Verbose es_key : str, default: "ElectricalSeries" ignore_integrity_checks, bool, default: False. diff --git a/src/neuroconv/datainterfaces/ecephys/kilosort/kilosortdatainterface.py b/src/neuroconv/datainterfaces/ecephys/kilosort/kilosortdatainterface.py index aafde42f0..58fa80169 100644 --- a/src/neuroconv/datainterfaces/ecephys/kilosort/kilosortdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/kilosort/kilosortdatainterface.py @@ -22,7 +22,7 @@ def __init__( self, folder_path: DirectoryPath, keep_good_only: bool = False, - verbose: bool = True, + verbose: bool = False, ): """ Load and prepare sorting data for kilosort diff --git a/src/neuroconv/datainterfaces/ecephys/maxwell/maxonedatainterface.py b/src/neuroconv/datainterfaces/ecephys/maxwell/maxonedatainterface.py index 11902f81b..6351e02b2 100644 --- a/src/neuroconv/datainterfaces/ecephys/maxwell/maxonedatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/maxwell/maxonedatainterface.py @@ -47,7 +47,7 @@ def __init__( file_path: FilePath, hdf5_plugin_path: Optional[DirectoryPath] = None, download_plugin: bool = True, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ) -> None: """ diff --git a/src/neuroconv/datainterfaces/ecephys/mcsraw/mcsrawdatainterface.py b/src/neuroconv/datainterfaces/ecephys/mcsraw/mcsrawdatainterface.py index ff8e82139..d646a4b35 100644 --- a/src/neuroconv/datainterfaces/ecephys/mcsraw/mcsrawdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/mcsraw/mcsrawdatainterface.py @@ -20,7 +20,7 @@ def get_source_schema(cls) -> dict: source_schema["properties"]["file_path"]["description"] = "Path to the .raw file." return source_schema - def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Load and prepare data for MCSRaw. diff --git a/src/neuroconv/datainterfaces/ecephys/mearec/mearecdatainterface.py b/src/neuroconv/datainterfaces/ecephys/mearec/mearecdatainterface.py index 7a82025ca..96a56c130 100644 --- a/src/neuroconv/datainterfaces/ecephys/mearec/mearecdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/mearec/mearecdatainterface.py @@ -23,7 +23,7 @@ def get_source_schema(cls) -> dict: source_schema["properties"]["file_path"]["description"] = "Path to the MEArec .h5 file." return source_schema - def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Load and prepare data for MEArec. @@ -31,7 +31,7 @@ def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "Ele ---------- folder_path : str or Path Path to the MEArec .h5 file. - verbose : bool, default: True + verbose : bool, default: Falsee Allows verbose. es_key : str, default: "ElectricalSeries" """ diff --git a/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py b/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py index 446c06302..49e922f59 100644 --- a/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py @@ -112,7 +112,7 @@ class NeuralynxSortingInterface(BaseSortingExtractorInterface): associated_suffixes = (".nse", ".ntt", ".nse", ".nev") info = "Interface for Neuralynx sorting data." - def __init__(self, folder_path: DirectoryPath, sampling_frequency: Optional[float] = None, verbose: bool = True): + def __init__(self, folder_path: DirectoryPath, sampling_frequency: Optional[float] = None, verbose: bool = False): """_summary_ Parameters @@ -121,7 +121,7 @@ def __init__(self, folder_path: DirectoryPath, sampling_frequency: Optional[floa The path to the folder/directory containing the data files for the session (nse, ntt, nse, nev) sampling_frequency : float, optional If a specific sampling_frequency is desired it can be set with this argument. - verbose : bool, default: True + verbose : bool, default: False Enables verbosity """ diff --git a/src/neuroconv/datainterfaces/ecephys/neuroscope/neuroscopedatainterface.py b/src/neuroconv/datainterfaces/ecephys/neuroscope/neuroscopedatainterface.py index d68532a94..9ed1201ab 100644 --- a/src/neuroconv/datainterfaces/ecephys/neuroscope/neuroscopedatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/neuroscope/neuroscopedatainterface.py @@ -128,7 +128,7 @@ def __init__( file_path: FilePath, gain: Optional[float] = None, xml_file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): """ @@ -271,7 +271,7 @@ def __init__( keep_mua_units: bool = True, exclude_shanks: Optional[list[int]] = None, xml_file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, ): """ Load and prepare spike sorted data and corresponding metadata from the Neuroscope format (.res/.clu files). diff --git a/src/neuroconv/datainterfaces/ecephys/openephys/openephysbinarydatainterface.py b/src/neuroconv/datainterfaces/ecephys/openephys/openephysbinarydatainterface.py index ef67fde40..503faa025 100644 --- a/src/neuroconv/datainterfaces/ecephys/openephys/openephysbinarydatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/openephys/openephysbinarydatainterface.py @@ -43,7 +43,7 @@ def __init__( stream_name: Optional[str] = None, block_index: Optional[int] = None, stub_test: bool = False, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): """ @@ -59,7 +59,7 @@ def __init__( block_index : int, optional, default: None The index of the block to extract from the data. stub_test : bool, default: False - verbose : bool, default: True + verbose : bool, default: Falsee es_key : str, default: "ElectricalSeries" """ from ._openephys_utils import _read_settings_xml diff --git a/src/neuroconv/datainterfaces/ecephys/openephys/openephysdatainterface.py b/src/neuroconv/datainterfaces/ecephys/openephys/openephysdatainterface.py index 81b84c36c..c25cc63ca 100644 --- a/src/neuroconv/datainterfaces/ecephys/openephys/openephysdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/openephys/openephysdatainterface.py @@ -39,7 +39,7 @@ def __new__( folder_path: DirectoryPath, stream_name: Optional[str] = None, block_index: Optional[int] = None, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): """ @@ -58,7 +58,7 @@ def __new__( When channel stream is not available the name of the stream must be specified. block_index : int, optional, default: None The index of the block to extract from the data. - verbose : bool, default: True + verbose : bool, default: False es_key : str, default: "ElectricalSeries" """ super().__new__(cls) diff --git a/src/neuroconv/datainterfaces/ecephys/openephys/openephyslegacydatainterface.py b/src/neuroconv/datainterfaces/ecephys/openephys/openephyslegacydatainterface.py index b3392d2db..e6a8e0d79 100644 --- a/src/neuroconv/datainterfaces/ecephys/openephys/openephyslegacydatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/openephys/openephyslegacydatainterface.py @@ -41,7 +41,7 @@ def __init__( folder_path: DirectoryPath, stream_name: Optional[str] = None, block_index: Optional[int] = None, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): """ @@ -57,7 +57,7 @@ def __init__( The name of the recording stream. block_index : int, optional, default: None The index of the block to extract from the data. - verbose : bool, default: True + verbose : bool, default: Falseee es_key : str, default: "ElectricalSeries" """ available_streams = self.get_stream_names(folder_path=folder_path) diff --git a/src/neuroconv/datainterfaces/ecephys/phy/phydatainterface.py b/src/neuroconv/datainterfaces/ecephys/phy/phydatainterface.py index 157fef2e5..367463f75 100644 --- a/src/neuroconv/datainterfaces/ecephys/phy/phydatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/phy/phydatainterface.py @@ -29,7 +29,7 @@ def __init__( self, folder_path: DirectoryPath, exclude_cluster_groups: Optional[list[str]] = None, - verbose: bool = True, + verbose: bool = False, ): """ Initialize a PhySortingInterface. @@ -40,7 +40,7 @@ def __init__( Path to the output Phy folder (containing the params.py). exclude_cluster_groups : str or list of str, optional Cluster groups to exclude (e.g. "noise" or ["noise", "mua"]). - verbose : bool, default: True + verbose : bool, default: Falsee """ super().__init__(folder_path=folder_path, exclude_cluster_groups=exclude_cluster_groups, verbose=verbose) diff --git a/src/neuroconv/datainterfaces/ecephys/plexon/plexondatainterface.py b/src/neuroconv/datainterfaces/ecephys/plexon/plexondatainterface.py index d1dcc4d45..4d41f5854 100644 --- a/src/neuroconv/datainterfaces/ecephys/plexon/plexondatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/plexon/plexondatainterface.py @@ -28,7 +28,7 @@ def get_source_schema(cls) -> dict: def __init__( self, file_path: FilePath, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", stream_name: str = "WB-Wideband", ): @@ -39,7 +39,7 @@ def __init__( ---------- file_path : str or Path Path to the .plx file. - verbose : bool, default: True + verbose : bool, default: Falsee Allows verbosity. es_key : str, default: "ElectricalSeries" stream_name: str, optional @@ -90,7 +90,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: return extractor_kwargs @validate_call - def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Load and prepare data for Plexon. @@ -98,7 +98,7 @@ def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "Ele ---------- file_path : str or Path Path to the .plx file. - verbose : bool, default: True + verbose : bool, default: False Allows verbosity. es_key : str, default: "ElectricalSeries" """ @@ -148,7 +148,7 @@ def get_source_schema(cls) -> dict: return source_schema @validate_call - def __init__(self, file_path: FilePath, verbose: bool = True): + def __init__(self, file_path: FilePath, verbose: bool = False): """ Load and prepare data for Plexon. diff --git a/src/neuroconv/datainterfaces/ecephys/spike2/spike2datainterface.py b/src/neuroconv/datainterfaces/ecephys/spike2/spike2datainterface.py index bf0ddc860..4fdf4239b 100644 --- a/src/neuroconv/datainterfaces/ecephys/spike2/spike2datainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/spike2/spike2datainterface.py @@ -41,7 +41,7 @@ def get_all_channels_info(cls, file_path: FilePath): return cls.get_extractor().get_all_channels_info(file_path=file_path) @validate_call - def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"): + def __init__(self, file_path: FilePath, verbose: bool = False, es_key: str = "ElectricalSeries"): """ Initialize reading of Spike2 file. @@ -49,7 +49,7 @@ def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "Ele ---------- file_path : FilePathType Path to .smr or .smrx file. - verbose : bool, default: True + verbose : bool, default: False es_key : str, default: "ElectricalSeries" """ _test_sonpy_installation() diff --git a/src/neuroconv/datainterfaces/ecephys/spikegadgets/spikegadgetsdatainterface.py b/src/neuroconv/datainterfaces/ecephys/spikegadgets/spikegadgetsdatainterface.py index b8b483dd0..475572e7b 100644 --- a/src/neuroconv/datainterfaces/ecephys/spikegadgets/spikegadgetsdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/spikegadgets/spikegadgetsdatainterface.py @@ -28,7 +28,7 @@ def __init__( file_path: FilePath, stream_id: str = "trodes", gains: Optional[ArrayType] = None, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): """ diff --git a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py index 00419e036..15135b09f 100644 --- a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py @@ -54,7 +54,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: def __init__( self, file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, es_key: Optional[str] = None, folder_path: Optional[DirectoryPath] = None, stream_id: Optional[str] = None, @@ -69,7 +69,7 @@ def __init__( Examples are 'nidq', 'imec0.ap', 'imec0.lf', 'imec1.ap', 'imec1.lf', etc. file_path : FilePathType Path to .bin file. Point to .ap.bin for SpikeGLXRecordingInterface and .lf.bin for SpikeGLXLFPInterface. - verbose : bool, default: True + verbose : bool, default: False Whether to output verbose text. es_key : str, the key to access the metadata of the ElectricalSeries. """ diff --git a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxnidqinterface.py b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxnidqinterface.py index 1d7079716..75ec20484 100644 --- a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxnidqinterface.py +++ b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxnidqinterface.py @@ -38,7 +38,7 @@ def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict: def __init__( self, file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, load_sync_channel: bool = False, es_key: str = "ElectricalSeriesNIDQ", folder_path: Optional[DirectoryPath] = None, @@ -54,7 +54,7 @@ def __init__( Path to the folder containing the .nidq.bin file. file_path : FilePathType Path to .nidq.bin file. - verbose : bool, default: True + verbose : bool, default: False Whether to output verbose text. load_sync_channel : bool, default: False Whether to load the last channel in the stream, which is typically used for synchronization. diff --git a/src/neuroconv/datainterfaces/ecephys/tdt/tdtdatainterface.py b/src/neuroconv/datainterfaces/ecephys/tdt/tdtdatainterface.py index a46f3e0f8..1dacb355a 100644 --- a/src/neuroconv/datainterfaces/ecephys/tdt/tdtdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/tdt/tdtdatainterface.py @@ -23,7 +23,7 @@ def __init__( folder_path: DirectoryPath, gain: float, stream_id: str = "0", - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): """ @@ -37,7 +37,7 @@ def __init__( Select from multiple streams. gain : float The conversion factor from int16 to microvolts. - verbose : bool, default: True + verbose : bool, default: Falsee Allows verbose. es_key : str, optional diff --git a/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py b/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py index 0019b8bd7..907dd06e8 100644 --- a/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py +++ b/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py @@ -35,7 +35,7 @@ class BaseImagingExtractorInterface(BaseExtractorInterface): def __init__( self, - verbose: bool = True, + verbose: bool = False, photon_series_type: Literal["OnePhotonSeries", "TwoPhotonSeries"] = "TwoPhotonSeries", **source_data, ): diff --git a/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffconverter.py b/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffconverter.py index 2a67da720..ada020a07 100644 --- a/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffconverter.py +++ b/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffconverter.py @@ -50,7 +50,7 @@ def __init__( plane_separation_type: {'contiguous', 'disjoint'} Defines how to write volumetric imaging data. Use 'contiguous' to create the volumetric two photon series, and 'disjoint' to create separate imaging plane and two photon series for each plane. - verbose : bool, default: True + verbose : bool, default: False Controls verbosity. """ self.verbose = verbose @@ -156,7 +156,7 @@ def __init__( ---------- folder_path : DirectoryPath The path to the folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env). - verbose : bool, default: True + verbose : bool, default: False Controls verbosity. """ from roiextractors.extractors.tiffimagingextractors.brukertiffimagingextractor import ( diff --git a/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffdatainterface.py b/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffdatainterface.py index 9742711e1..91156d18b 100644 --- a/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffdatainterface.py @@ -42,7 +42,7 @@ def __init__( self, folder_path: DirectoryPath, stream_name: Optional[str] = None, - verbose: bool = True, + verbose: bool = False, ): """ Initialize reading of TIFF files. @@ -53,7 +53,7 @@ def __init__( The path to the folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env). stream_name : str, optional The name of the recording stream (e.g. 'Ch2'). - verbose : bool, default: True + verbose : bool, default: False """ self.folder_path = folder_path super().__init__( @@ -200,7 +200,7 @@ def __init__( self, folder_path: DirectoryPath, stream_name: Optional[str] = None, - verbose: bool = True, + verbose: bool = False, ): """ Initialize reading of TIFF files. @@ -211,7 +211,7 @@ def __init__( The path to the folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env). stream_name : str, optional The name of the recording stream (e.g. 'Ch2'). - verbose : bool, default: True + verbose : bool, default: False """ super().__init__( folder_path=folder_path, diff --git a/src/neuroconv/datainterfaces/ophys/caiman/caimandatainterface.py b/src/neuroconv/datainterfaces/ophys/caiman/caimandatainterface.py index 386c03d3c..36277903c 100644 --- a/src/neuroconv/datainterfaces/ophys/caiman/caimandatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/caiman/caimandatainterface.py @@ -16,7 +16,7 @@ def get_source_schema(cls) -> dict: source_metadata["properties"]["file_path"]["description"] = "Path to .hdf5 file." return source_metadata - def __init__(self, file_path: FilePath, verbose: bool = True): + def __init__(self, file_path: FilePath, verbose: bool = False): """ Parameters diff --git a/src/neuroconv/datainterfaces/ophys/cnmfe/cnmfedatainterface.py b/src/neuroconv/datainterfaces/ophys/cnmfe/cnmfedatainterface.py index 4ea60c892..5e84aa282 100644 --- a/src/neuroconv/datainterfaces/ophys/cnmfe/cnmfedatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/cnmfe/cnmfedatainterface.py @@ -10,6 +10,6 @@ class CnmfeSegmentationInterface(BaseSegmentationExtractorInterface): associated_suffixes = (".mat",) info = "Interface for constrained non-negative matrix factorization (CNMFE) segmentation." - def __init__(self, file_path: FilePath, verbose: bool = True): + def __init__(self, file_path: FilePath, verbose: bool = False): super().__init__(file_path=file_path) self.verbose = verbose diff --git a/src/neuroconv/datainterfaces/ophys/extract/extractdatainterface.py b/src/neuroconv/datainterfaces/ophys/extract/extractdatainterface.py index 39b3d0a79..3263edbc1 100644 --- a/src/neuroconv/datainterfaces/ophys/extract/extractdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/extract/extractdatainterface.py @@ -17,7 +17,7 @@ def __init__( file_path: FilePath, sampling_frequency: float, output_struct_name: Optional[str] = None, - verbose: bool = True, + verbose: bool = False, ): """ diff --git a/src/neuroconv/datainterfaces/ophys/hdf5/hdf5datainterface.py b/src/neuroconv/datainterfaces/ophys/hdf5/hdf5datainterface.py index 4bb13f86b..c1cfefc95 100644 --- a/src/neuroconv/datainterfaces/ophys/hdf5/hdf5datainterface.py +++ b/src/neuroconv/datainterfaces/ophys/hdf5/hdf5datainterface.py @@ -22,7 +22,7 @@ def __init__( start_time: Optional[float] = None, metadata: Optional[dict] = None, channel_names: Optional[ArrayType] = None, - verbose: bool = True, + verbose: bool = False, photon_series_type: Literal["OnePhotonSeries", "TwoPhotonSeries"] = "TwoPhotonSeries", ): """ @@ -36,7 +36,7 @@ def __init__( start_time : float, optional metadata : dict, optional channel_names : list of str, optional - verbose : bool, default: True + verbose : bool, default: False """ super().__init__( file_path=file_path, diff --git a/src/neuroconv/datainterfaces/ophys/micromanagertiff/micromanagertiffdatainterface.py b/src/neuroconv/datainterfaces/ophys/micromanagertiff/micromanagertiffdatainterface.py index 17cbc95ed..318db0027 100644 --- a/src/neuroconv/datainterfaces/ophys/micromanagertiff/micromanagertiffdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/micromanagertiff/micromanagertiffdatainterface.py @@ -19,7 +19,7 @@ def get_source_schema(cls) -> dict: return source_schema @validate_call - def __init__(self, folder_path: DirectoryPath, verbose: bool = True): + def __init__(self, folder_path: DirectoryPath, verbose: bool = False): """ Data Interface for MicroManagerTiffImagingExtractor. @@ -28,7 +28,7 @@ def __init__(self, folder_path: DirectoryPath, verbose: bool = True): folder_path : FolderPathType The folder path that contains the OME-TIF image files (.ome.tif files) and the 'DisplaySettings' JSON file. - verbose : bool, default: True + verbose : bool, default: False """ super().__init__(folder_path=folder_path) self.verbose = verbose diff --git a/src/neuroconv/datainterfaces/ophys/miniscope/miniscopeconverter.py b/src/neuroconv/datainterfaces/ophys/miniscope/miniscopeconverter.py index d1a0fb701..42f8b0675 100644 --- a/src/neuroconv/datainterfaces/ophys/miniscope/miniscopeconverter.py +++ b/src/neuroconv/datainterfaces/ophys/miniscope/miniscopeconverter.py @@ -24,7 +24,7 @@ def get_source_schema(cls): return source_schema @validate_call - def __init__(self, folder_path: DirectoryPath, verbose: bool = True): + def __init__(self, folder_path: DirectoryPath, verbose: bool = False): """ Initializes the data interfaces for the Miniscope recording and behavioral data stream. @@ -51,7 +51,7 @@ def __init__(self, folder_path: DirectoryPath, verbose: bool = True): ---------- folder_path : FolderPathType The path to the main Miniscope folder. - verbose : bool, default: True + verbose : bool, default: False Controls verbosity. """ self.verbose = verbose diff --git a/src/neuroconv/datainterfaces/ophys/sbx/sbxdatainterface.py b/src/neuroconv/datainterfaces/ophys/sbx/sbxdatainterface.py index 554cc5aba..4e8937082 100644 --- a/src/neuroconv/datainterfaces/ophys/sbx/sbxdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/sbx/sbxdatainterface.py @@ -17,7 +17,7 @@ def __init__( self, file_path: FilePath, sampling_frequency: Optional[float] = None, - verbose: bool = True, + verbose: bool = False, photon_series_type: Literal["OnePhotonSeries", "TwoPhotonSeries"] = "TwoPhotonSeries", ): """ @@ -26,7 +26,7 @@ def __init__( file_path : FilePathType Path to .sbx file. sampling_frequency : float, optional - verbose : bool, default: True + verbose : bool, default: False """ super().__init__( diff --git a/src/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py b/src/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py index c74161e55..4f41c563d 100644 --- a/src/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py +++ b/src/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py @@ -39,7 +39,7 @@ def __new__( channel_name: Optional[str] = None, plane_name: Optional[str] = None, fallback_sampling_frequency: Optional[float] = None, - verbose: bool = True, + verbose: bool = False, ): from roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils import ( extract_extra_metadata, @@ -103,7 +103,7 @@ def __init__( self, file_path: FilePath, fallback_sampling_frequency: Optional[float] = None, - verbose: bool = True, + verbose: bool = False, ): """ DataInterface for reading Tiff files that are generated by ScanImage v3.8. This interface extracts the metadata @@ -186,7 +186,7 @@ def __new__( channel_name: Optional[str] = None, plane_name: Optional[str] = None, extract_all_metadata: bool = False, - verbose: bool = True, + verbose: bool = False, ): from natsort import natsorted from roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils import ( @@ -251,7 +251,7 @@ def __init__( channel_name: Optional[str] = None, image_metadata: Optional[dict] = None, parsed_metadata: Optional[dict] = None, - verbose: bool = True, + verbose: bool = False, ): """ DataInterface for reading multi-file (buffered) TIFF files that are generated by ScanImage. @@ -357,7 +357,7 @@ def __init__( extract_all_metadata: bool = False, image_metadata: Optional[dict] = None, parsed_metadata: Optional[dict] = None, - verbose: bool = True, + verbose: bool = False, ): """ DataInterface for reading multi-file (buffered) TIFF files that are generated by ScanImage. @@ -480,7 +480,7 @@ def __init__( plane_name: Optional[str] = None, image_metadata: Optional[dict] = None, parsed_metadata: Optional[dict] = None, - verbose: bool = True, + verbose: bool = False, ): """ DataInterface for reading multi-file (buffered) TIFF files that are generated by ScanImage. @@ -602,7 +602,7 @@ def __init__( image_metadata: Optional[dict] = None, parsed_metadata: Optional[dict] = None, extract_all_metadata: bool = False, - verbose: bool = True, + verbose: bool = False, ): """ DataInterface for reading multi-file (buffered) TIFF files that are generated by ScanImage. diff --git a/src/neuroconv/datainterfaces/ophys/suite2p/suite2pdatainterface.py b/src/neuroconv/datainterfaces/ophys/suite2p/suite2pdatainterface.py index 056616ce5..c51335bea 100644 --- a/src/neuroconv/datainterfaces/ophys/suite2p/suite2pdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/suite2p/suite2pdatainterface.py @@ -79,7 +79,7 @@ def __init__( channel_name: Optional[str] = None, plane_name: Optional[str] = None, plane_segmentation_name: Optional[str] = None, - verbose: bool = True, + verbose: bool = False, ): """ diff --git a/src/neuroconv/datainterfaces/ophys/tdt_fp/tdtfiberphotometrydatainterface.py b/src/neuroconv/datainterfaces/ophys/tdt_fp/tdtfiberphotometrydatainterface.py index 8b092464e..9b82dbc73 100644 --- a/src/neuroconv/datainterfaces/ophys/tdt_fp/tdtfiberphotometrydatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/tdt_fp/tdtfiberphotometrydatainterface.py @@ -29,7 +29,7 @@ class TDTFiberPhotometryInterface(BaseTemporalAlignmentInterface): associated_suffixes = ("Tbk", "Tdx", "tev", "tin", "tsq") @validate_call - def __init__(self, folder_path: DirectoryPath, verbose: bool = True): + def __init__(self, folder_path: DirectoryPath, verbose: bool = False): """Initialize the TDTFiberPhotometryInterface. Parameters diff --git a/src/neuroconv/datainterfaces/ophys/tiff/tiffdatainterface.py b/src/neuroconv/datainterfaces/ophys/tiff/tiffdatainterface.py index 1eaa3b55e..dce95c9b8 100644 --- a/src/neuroconv/datainterfaces/ophys/tiff/tiffdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/tiff/tiffdatainterface.py @@ -23,7 +23,7 @@ def __init__( self, file_path: FilePath, sampling_frequency: float, - verbose: bool = True, + verbose: bool = False, photon_series_type: Literal["OnePhotonSeries", "TwoPhotonSeries"] = "TwoPhotonSeries", ): """ @@ -33,7 +33,7 @@ def __init__( ---------- file_path : FilePathType sampling_frequency : float - verbose : bool, default: True + verbose : bool, default: False photon_series_type : {'OnePhotonSeries', 'TwoPhotonSeries'}, default: "TwoPhotonSeries" """ super().__init__( diff --git a/src/neuroconv/datainterfaces/text/excel/exceltimeintervalsinterface.py b/src/neuroconv/datainterfaces/text/excel/exceltimeintervalsinterface.py index 92fbbbaa7..313029b9b 100644 --- a/src/neuroconv/datainterfaces/text/excel/exceltimeintervalsinterface.py +++ b/src/neuroconv/datainterfaces/text/excel/exceltimeintervalsinterface.py @@ -18,7 +18,7 @@ def __init__( self, file_path: FilePath, read_kwargs: Optional[dict] = None, - verbose: bool = True, + verbose: bool = False, ): """ Parameters @@ -26,7 +26,7 @@ def __init__( file_path : FilePath read_kwargs : dict, optional Passed to pandas.read_excel() - verbose : bool, default: True + verbose : bool, default: False """ super().__init__(file_path=file_path, read_kwargs=read_kwargs, verbose=verbose) diff --git a/src/neuroconv/datainterfaces/text/timeintervalsinterface.py b/src/neuroconv/datainterfaces/text/timeintervalsinterface.py index 5f5b1107d..40cac7c20 100644 --- a/src/neuroconv/datainterfaces/text/timeintervalsinterface.py +++ b/src/neuroconv/datainterfaces/text/timeintervalsinterface.py @@ -21,14 +21,14 @@ def __init__( self, file_path: FilePath, read_kwargs: Optional[dict] = None, - verbose: bool = True, + verbose: bool = False, ): """ Parameters ---------- file_path : FilePath read_kwargs : dict, optional - verbose : bool, default: True + verbose : bool, default: False """ read_kwargs = read_kwargs or dict() super().__init__(file_path=file_path) diff --git a/src/neuroconv/nwbconverter.py b/src/neuroconv/nwbconverter.py index fe1b09915..16b05a039 100644 --- a/src/neuroconv/nwbconverter.py +++ b/src/neuroconv/nwbconverter.py @@ -61,11 +61,11 @@ def get_source_schema(cls) -> dict: return source_schema @classmethod - def validate_source(cls, source_data: dict[str, dict], verbose: bool = True): + def validate_source(cls, source_data: dict[str, dict], verbose: bool = False): """Validate source_data against Converter source_schema.""" cls._validate_source_data(source_data=source_data, verbose=verbose) - def _validate_source_data(self, source_data: dict[str, dict], verbose: bool = True): + def _validate_source_data(self, source_data: dict[str, dict], verbose: bool = False): # We do this to ensure that python objects are in string format for the JSON schema encoder = _NWBSourceDataEncoder() @@ -77,7 +77,7 @@ def _validate_source_data(self, source_data: dict[str, dict], verbose: bool = Tr print("Source data is valid!") @validate_call - def __init__(self, source_data: dict[str, dict], verbose: bool = True): + def __init__(self, source_data: dict[str, dict], verbose: bool = False): """Validate source_data against source_schema and initialize all data interfaces.""" self.verbose = verbose self._validate_source_data(source_data=source_data, verbose=self.verbose) @@ -301,7 +301,7 @@ def get_source_schema(cls) -> dict: def validate_source(cls): raise NotImplementedError("Source data not available with previously initialized classes.") - def __init__(self, data_interfaces: Union[list[BaseDataInterface], dict[str, BaseDataInterface]], verbose=True): + def __init__(self, data_interfaces: Union[list[BaseDataInterface], dict[str, BaseDataInterface]], verbose=False): self.verbose = verbose if isinstance(data_interfaces, list): # Create unique names for each interface diff --git a/src/neuroconv/tools/nwb_helpers/_metadata_and_file_helpers.py b/src/neuroconv/tools/nwb_helpers/_metadata_and_file_helpers.py index 355c86510..e7473f228 100644 --- a/src/neuroconv/tools/nwb_helpers/_metadata_and_file_helpers.py +++ b/src/neuroconv/tools/nwb_helpers/_metadata_and_file_helpers.py @@ -166,7 +166,7 @@ def make_or_load_nwbfile( metadata: Optional[dict] = None, overwrite: bool = False, backend: Literal["hdf5", "zarr"] = "hdf5", - verbose: bool = True, + verbose: bool = False, ): """ Context for automatically handling decision of write vs. append for writing an NWBFile. diff --git a/src/neuroconv/tools/roiextractors/roiextractors.py b/src/neuroconv/tools/roiextractors/roiextractors.py index 27d3b5f9c..afe58ede6 100644 --- a/src/neuroconv/tools/roiextractors/roiextractors.py +++ b/src/neuroconv/tools/roiextractors/roiextractors.py @@ -753,7 +753,7 @@ def write_imaging( nwbfile: Optional[NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, iterator_type: str = "v2", iterator_options: Optional[dict] = None, photon_series_type: Literal["TwoPhotonSeries", "OnePhotonSeries"] = "TwoPhotonSeries", @@ -792,7 +792,7 @@ def write_imaging_to_nwbfile( nwbfile: Optional[NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, iterator_type: str = "v2", iterator_options: Optional[dict] = None, photon_series_type: Literal["TwoPhotonSeries", "OnePhotonSeries"] = "TwoPhotonSeries", @@ -1904,7 +1904,7 @@ def write_segmentation( nwbfile: Optional[NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, include_background_segmentation: bool = False, include_roi_centroids: bool = True, include_roi_acceptance: bool = True, @@ -1949,7 +1949,7 @@ def write_segmentation_to_nwbfile( nwbfile: Optional[NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, include_background_segmentation: bool = False, include_roi_centroids: bool = True, include_roi_acceptance: bool = True, diff --git a/src/neuroconv/tools/spikeinterface/spikeinterface.py b/src/neuroconv/tools/spikeinterface/spikeinterface.py index fa00d58ed..858d04636 100644 --- a/src/neuroconv/tools/spikeinterface/spikeinterface.py +++ b/src/neuroconv/tools/spikeinterface/spikeinterface.py @@ -1152,7 +1152,7 @@ def write_recording( nwbfile: Optional[pynwb.NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, starting_time: Optional[float] = None, write_as: Optional[str] = "raw", es_key: Optional[str] = None, @@ -1193,7 +1193,7 @@ def write_recording_to_nwbfile( nwbfile: Optional[pynwb.NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, starting_time: Optional[float] = None, write_as: Optional[str] = "raw", es_key: Optional[str] = None, @@ -1256,7 +1256,7 @@ def write_recording_to_nwbfile( properties in the RecordingExtractor object. overwrite : bool, default: False Whether to overwrite the NWBFile if one exists at the nwbfile_path. - verbose : bool, default: True + verbose : bool, default: False If 'nwbfile_path' is specified, informs user after a successful write operation. starting_time : float, optional Sets the starting time of the ElectricalSeries to a manually set value. @@ -1749,7 +1749,7 @@ def write_sorting( nwbfile: Optional[pynwb.NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, unit_ids: Optional[list[Union[str, int]]] = None, property_descriptions: Optional[dict] = None, skip_properties: Optional[list[str]] = None, @@ -1796,7 +1796,7 @@ def write_sorting_to_nwbfile( nwbfile: Optional[pynwb.NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, - verbose: bool = True, + verbose: bool = False, unit_ids: Optional[list[Union[str, int]]] = None, property_descriptions: Optional[dict] = None, skip_properties: Optional[list[str]] = None, @@ -1831,7 +1831,7 @@ def write_sorting_to_nwbfile( overwrite : bool, default: False Whether to overwrite the NWBFile if one exists at the nwbfile_path. The default is False (append mode). - verbose : bool, default: True + verbose : bool, default: False If 'nwbfile_path' is specified, informs user after a successful write operation. unit_ids : list, optional Controls the unit_ids that will be written to the nwb file. If None (default), all @@ -2031,7 +2031,7 @@ def write_sorting_analyzer( metadata: Optional[dict] = None, overwrite: bool = False, recording: Optional[BaseRecording] = None, - verbose: bool = True, + verbose: bool = False, unit_ids: Optional[Union[list[str], list[int]]] = None, write_electrical_series: bool = False, add_electrical_series_kwargs: Optional[dict] = None, @@ -2076,7 +2076,7 @@ def write_sorting_analyzer_to_nwbfile( metadata: Optional[dict] = None, overwrite: bool = False, recording: Optional[BaseRecording] = None, - verbose: bool = True, + verbose: bool = False, unit_ids: Optional[Union[list[str], list[int]]] = None, write_electrical_series: bool = False, add_electrical_series_kwargs: Optional[dict] = None, @@ -2118,7 +2118,7 @@ def write_sorting_analyzer_to_nwbfile( recording : BaseRecording, optional If the sorting_analyzer is 'recordingless', this argument needs to be passed to save electrode info. Otherwise, electrodes info is not added to the nwb file. - verbose : bool, default: True + verbose : bool, default: False If 'nwbfile_path' is specified, informs user after a successful write operation. unit_ids : list, optional Controls the unit_ids that will be written to the nwb file. If None (default), all @@ -2183,7 +2183,7 @@ def write_waveforms( metadata: Optional[dict] = None, overwrite: bool = False, recording: Optional[BaseRecording] = None, - verbose: bool = True, + verbose: bool = False, unit_ids: Optional[list[Union[str, int]]] = None, write_electrical_series: bool = False, add_electrical_series_kwargs: Optional[dict] = None, diff --git a/src/neuroconv/tools/testing/mock_interfaces.py b/src/neuroconv/tools/testing/mock_interfaces.py index 0652284e7..16c1c0676 100644 --- a/src/neuroconv/tools/testing/mock_interfaces.py +++ b/src/neuroconv/tools/testing/mock_interfaces.py @@ -165,7 +165,7 @@ def __init__( sampling_frequency: float = 30_000.0, durations: tuple[float, ...] = (1.0,), seed: int = 0, - verbose: bool = True, + verbose: bool = False, es_key: str = "ElectricalSeries", ): super().__init__( @@ -199,7 +199,7 @@ def __init__( sampling_frequency: float = 30_000.0, durations: tuple[float, ...] = (1.0,), seed: int = 0, - verbose: bool = True, + verbose: bool = False, ): """ Parameters diff --git a/tests/test_ecephys/test_ecephys_interfaces.py b/tests/test_ecephys/test_ecephys_interfaces.py index e036ccb81..18fde6ce5 100644 --- a/tests/test_ecephys/test_ecephys_interfaces.py +++ b/tests/test_ecephys/test_ecephys_interfaces.py @@ -159,7 +159,7 @@ def setUpClass(cls) -> None: class TestSortingInterface(BaseSortingExtractorInterface): ExtractorName = "NumpySorting" - def __init__(self, verbose: bool = True): + def __init__(self, verbose: bool = False): self.sorting_extractor = sorting self.source_data = dict() self.verbose = verbose diff --git a/tests/test_on_data/test_temporal_alignment/test_temporal_alignment_methods.py b/tests/test_on_data/test_temporal_alignment/test_temporal_alignment_methods.py index c8c6bad09..fec1df09e 100644 --- a/tests/test_on_data/test_temporal_alignment/test_temporal_alignment_methods.py +++ b/tests/test_on_data/test_temporal_alignment/test_temporal_alignment_methods.py @@ -356,7 +356,7 @@ def mimic_reading_externally_aligned_timestamps(): class TestAlignmentConverter(NWBConverter): data_interface_classes = dict(Trials=CsvTimeIntervalsInterface, Behavior=MockBehaviorEventInterface) - def __init__(self, source_data: Dict[str, dict], verbose: bool = True): + def __init__(self, source_data: Dict[str, dict], verbose: bool = False): super().__init__(source_data=source_data, verbose=verbose) unaligned_trial_start_timestamps = self.data_interface_objects["Trials"].get_timestamps( @@ -504,7 +504,7 @@ class TestAlignmentConverter(NWBConverter): NIDQ=MockSpikeGLXNIDQInterface, Trials=CsvTimeIntervalsInterface, Behavior=MockBehaviorEventInterface ) - def __init__(self, source_data: Dict[str, dict], verbose: bool = True): + def __init__(self, source_data: Dict[str, dict], verbose: bool = False): super().__init__(source_data=source_data, verbose=verbose) inferred_aligned_trial_start_time = self.data_interface_objects["NIDQ"].get_event_times_from_ttl( From 6147f843ac875de8d501ae16b6426503727fd22a Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Tue, 10 Dec 2024 15:14:07 -0600 Subject: [PATCH 2/9] fix tests --- .../ecephys/alphaomega/alphaomegadatainterface.py | 2 +- .../test_utils/test_get_json_schema_from_method_signature.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py b/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py index 0f4b7bba9..0a9bd80c8 100644 --- a/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/alphaomega/alphaomegadatainterface.py @@ -36,7 +36,7 @@ def __init__(self, folder_path: DirectoryPath, verbose: bool = False, es_key: st Path to the folder of .mpx files. verbose: boolean Allows verbose. - Default is True. + Default is False. es_key: str, default: "ElectricalSeries" """ super().__init__(folder_path=folder_path, verbose=verbose, es_key=es_key) diff --git a/tests/test_minimal/test_utils/test_get_json_schema_from_method_signature.py b/tests/test_minimal/test_utils/test_get_json_schema_from_method_signature.py index e6fe27e16..497ea3af7 100644 --- a/tests/test_minimal/test_utils/test_get_json_schema_from_method_signature.py +++ b/tests/test_minimal/test_utils/test_get_json_schema_from_method_signature.py @@ -213,7 +213,7 @@ def test_get_json_schema_from_example_data_interface(): "type": "string", "description": "Path to the folder of .mpx files.", }, - "verbose": {"default": True, "type": "boolean", "description": "Allows verbose.\nDefault is True."}, + "verbose": {"default": False, "type": "boolean", "description": "Allows verbose.\nDefault is False."}, "es_key": {"default": "ElectricalSeries", "type": "string"}, }, "required": ["folder_path"], From 28ad43e5a6e2fa465b5dbaec2f4399858fe97fe7 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Wed, 11 Dec 2024 08:21:55 -0600 Subject: [PATCH 3/9] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 728123253..2ac0740a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ ## Improvements * Use mixing tests for ecephy's mocks [PR #1136](https://github.com/catalystneuro/neuroconv/pull/1136) * Use pytest format for dandi tests to avoid window permission error on teardown [PR #1151](https://github.com/catalystneuro/neuroconv/pull/1151) +* Interfaces and converters now have `verbose=False` by default [PR #1153](https://github.com/catalystneuro/neuroconv/pull/1153) # v0.6.5 (November 1, 2024) From 354c87f2844e8f3a5daca0d3228ac84c3ada282a Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Wed, 11 Dec 2024 15:53:16 -0600 Subject: [PATCH 4/9] docs and merge --- CHANGELOG.md | 8 ++------ docs/conversion_examples_gallery/recording/spikeglx.rst | 1 - 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47e9bd8d8..c1f51a402 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,9 @@ # v0.6.6 (Upcoming) -## Deprecations +## Deprecations and Changes * Removed use of `jsonschema.RefResolver` as it will be deprecated from the jsonschema library [PR #1133](https://github.com/catalystneuro/neuroconv/pull/1133) * Completely removed compression settings from most places[PR #1126](https://github.com/catalystneuro/neuroconv/pull/1126) +* Interfaces and converters now have `verbose=False` by default [PR #1153](https://github.com/catalystneuro/neuroconv/pull/1153) ## Bug Fixes * datetime objects now can be validated as conversion options [#1139](https://github.com/catalystneuro/neuroconv/pull/1126) @@ -11,7 +12,6 @@ * `SpikeGLXConverterPipe` converter now accepts multi-probe structures with multi-trigger and does not assume a specific folder structure [#1150](https://github.com/catalystneuro/neuroconv/pull/1150) * `SpikeGLXNIDQInterface` is no longer written as an ElectricalSeries [#1152](https://github.com/catalystneuro/neuroconv/pull/1152) - ## Features * Propagate the `unit_electrode_indices` argument from the spikeinterface tools to `BaseSortingExtractorInterface`. This allows users to map units to the electrode table when adding sorting data [PR #1124](https://github.com/catalystneuro/neuroconv/pull/1124) * Imaging interfaces have a new conversion option `always_write_timestamps` that can be used to force writing timestamps even if neuroconv's heuristics indicates regular sampling rate [PR #1125](https://github.com/catalystneuro/neuroconv/pull/1125) @@ -22,13 +22,9 @@ * YAML specification files now accepts an outer keyword `upload_to_dandiset="< six-digit ID >"` to automatically upload the produced NWB files to the DANDI archive [PR #1089](https://github.com/catalystneuro/neuroconv/pull/1089) *`SpikeGLXNIDQInterface` now handdles digital demuxed channels (`XD0`) [#1152](https://github.com/catalystneuro/neuroconv/pull/1152) - - - ## Improvements * Use mixing tests for ecephy's mocks [PR #1136](https://github.com/catalystneuro/neuroconv/pull/1136) * Use pytest format for dandi tests to avoid window permission error on teardown [PR #1151](https://github.com/catalystneuro/neuroconv/pull/1151) -* Interfaces and converters now have `verbose=False` by default [PR #1153](https://github.com/catalystneuro/neuroconv/pull/1153) # v0.6.5 (November 1, 2024) diff --git a/docs/conversion_examples_gallery/recording/spikeglx.rst b/docs/conversion_examples_gallery/recording/spikeglx.rst index 97b23bac9..484f2b1ab 100644 --- a/docs/conversion_examples_gallery/recording/spikeglx.rst +++ b/docs/conversion_examples_gallery/recording/spikeglx.rst @@ -24,7 +24,6 @@ We can easily convert all data stored in the native SpikeGLX folder structure to >>> >>> folder_path = f"{ECEPHY_DATA_PATH}/spikeglx/Noise4Sam_g0" >>> converter = SpikeGLXConverterPipe(folder_path=folder_path) - Source data is valid! >>> # Extract what metadata we can from the source files >>> metadata = converter.get_metadata() >>> # For data provenance we add the time zone information to the conversion From d234021cda9679fbb58fab3fbad9e5da1eca21ed Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Fri, 20 Dec 2024 11:03:19 -0600 Subject: [PATCH 5/9] Update src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py Co-authored-by: Paul Adkisson --- .../datainterfaces/ecephys/baserecordingextractorinterface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py b/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py index 623c0b7bc..b7b00e4d0 100644 --- a/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py +++ b/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py @@ -24,7 +24,7 @@ def __init__(self, verbose: bool = False, es_key: str = "ElectricalSeries", **so """ Parameters ---------- - verbose : bool, default: Falsee + verbose : bool, default: False If True, will print out additional information. es_key : str, default: "ElectricalSeries" The key of this ElectricalSeries in the metadata dictionary. From e9fb902346c7bee92d8e87b25cc75c927784a93e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 20 Dec 2024 17:05:38 +0000 Subject: [PATCH 6/9] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py b/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py index 24c2934bc..cdb80c28d 100644 --- a/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py @@ -112,7 +112,6 @@ class NeuralynxSortingInterface(BaseSortingExtractorInterface): associated_suffixes = (".nse", ".ntt", ".nse", ".nev") info = "Interface for Neuralynx sorting data." - def __init__( self, folder_path: DirectoryPath, From 7b17c9eb32059d95fd0390fe5482e37d8792dc76 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Fri, 20 Dec 2024 11:19:11 -0600 Subject: [PATCH 7/9] Paul comment about audio interface --- src/neuroconv/datainterfaces/behavior/audio/audiointerface.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py index b4a934bae..792c1f045 100644 --- a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py +++ b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py @@ -171,7 +171,6 @@ def add_to_nwbfile( write_as: Literal["stimulus", "acquisition"] = "stimulus", iterator_options: Optional[dict] = None, overwrite: bool = False, - verbose: bool = False, ): """ Parameters From 987ab0197fafa75f8c08134e7ce7c459a41fedcb Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Fri, 20 Dec 2024 11:19:42 -0600 Subject: [PATCH 8/9] stuff --- src/neuroconv/datainterfaces/behavior/audio/audiointerface.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py index 792c1f045..ec2920432 100644 --- a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py +++ b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py @@ -170,7 +170,6 @@ def add_to_nwbfile( stub_frames: int = 1000, write_as: Literal["stimulus", "acquisition"] = "stimulus", iterator_options: Optional[dict] = None, - overwrite: bool = False, ): """ Parameters @@ -185,8 +184,6 @@ def add_to_nwbfile( "stimulus" or as "acquisition". iterator_options : dict, optional Dictionary of options for the SliceableDataChunkIterator. - overwrite : bool, default: False - verbose : bool, default: False Returns ------- From 2c3b466155008e14c09fe03be8fcd2278341f24b Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Fri, 20 Dec 2024 13:04:51 -0600 Subject: [PATCH 9/9] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e7d8fb5de..70cb1589c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ ## Features ## Improvements +* Interfaces and converters now have `verbose=False` by default [PR #1153](https://github.com/catalystneuro/neuroconv/pull/1153) + # v0.6.9 (Upcoming) Small fixes should be here. @@ -25,7 +27,6 @@ Small fixes should be here. ## Deprecations and Changes * Removed use of `jsonschema.RefResolver` as it will be deprecated from the jsonschema library [PR #1133](https://github.com/catalystneuro/neuroconv/pull/1133) * Completely removed compression settings from most places[PR #1126](https://github.com/catalystneuro/neuroconv/pull/1126) -* Interfaces and converters now have `verbose=False` by default [PR #1153](https://github.com/catalystneuro/neuroconv/pull/1153) * Completely removed compression settings from most places [PR #1126](https://github.com/catalystneuro/neuroconv/pull/1126) * Soft deprecation for `file_path` as an argument of `SpikeGLXNIDQInterface` and `SpikeGLXRecordingInterface` [PR #1155](https://github.com/catalystneuro/neuroconv/pull/1155) * `starting_time` in RecordingInterfaces has given a soft deprecation in favor of time alignment methods [PR #1158](https://github.com/catalystneuro/neuroconv/pull/1158)