diff --git a/CHANGELOG.md b/CHANGELOG.md index ba0e4068f..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. @@ -22,8 +24,9 @@ Small fixes should be here. # v0.6.6 (December 20, 2024) -## 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) * 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) 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/docs/conversion_examples_gallery/recording/spikeglx.rst b/docs/conversion_examples_gallery/recording/spikeglx.rst index 0bc67fc1d..e6ff6bf03 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 diff --git a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py index 6561096b5..ec2920432 100644 --- a/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py +++ b/src/neuroconv/datainterfaces/behavior/audio/audiointerface.py @@ -170,8 +170,6 @@ def add_to_nwbfile( stub_frames: int = 1000, write_as: Literal["stimulus", "acquisition"] = "stimulus", iterator_options: Optional[dict] = None, - overwrite: bool = False, - verbose: bool = True, ): """ Parameters @@ -186,8 +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: True 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 62edaf140..07a06227b 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 d519dc71a..17c2cfc03 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..0a9bd80c8 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. @@ -36,7 +36,7 @@ def __init__(self, folder_path: DirectoryPath, verbose: bool = True, es_key: str 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/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 c9df3ba52..1b7b18119 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: False 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 8eeb59324..0b44318e2 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 bc9f9b51b..811aab81a 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 9ffeb78a2..ebd921117 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 d87c8f0bd..cdb80c28d 100644 --- a/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/neuralynx/neuralynxdatainterface.py @@ -116,7 +116,7 @@ def __init__( self, folder_path: DirectoryPath, sampling_frequency: Optional[float] = None, - verbose: bool = True, + verbose: bool = False, stream_id: Optional[str] = None, ): """_summary_ @@ -127,7 +127,7 @@ def __init__( 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 stream_id: str, optional Used by Spikeinterface and neo to calculate the t_start, if not provided and the stream is unique 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 e375ec351..9cc39798b 100644 --- a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py +++ b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxdatainterface.py @@ -55,7 +55,7 @@ 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, @@ -70,7 +70,7 @@ def __init__( Examples are '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 4c7e5a6d9..eae58421f 100644 --- a/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxnidqinterface.py +++ b/src/neuroconv/datainterfaces/ecephys/spikeglx/spikeglxnidqinterface.py @@ -35,7 +35,7 @@ def get_source_schema(cls) -> dict: def __init__( self, file_path: Optional[FilePath] = None, - verbose: bool = True, + verbose: bool = False, load_sync_channel: Optional[bool] = None, es_key: str = "ElectricalSeriesNIDQ", folder_path: Optional[DirectoryPath] = None, @@ -51,7 +51,7 @@ 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. es_key : str, default: "ElectricalSeriesNIDQ" """ 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 04407a3d4..08cd31125 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 1fc854b81..81c17474d 100644 --- a/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffconverter.py +++ b/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffconverter.py @@ -51,7 +51,7 @@ 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 @@ -190,7 +190,7 @@ 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 f7e7bee1b..ea1d1e4ba 100644 --- a/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/brukertiff/brukertiffdatainterface.py @@ -60,7 +60,7 @@ def __init__( self, folder_path: DirectoryPath, stream_name: Optional[str] = None, - verbose: bool = True, + verbose: bool = False, ): """ Initialize reading of TIFF files. @@ -71,7 +71,7 @@ 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__( @@ -233,7 +233,7 @@ def __init__( self, folder_path: DirectoryPath, stream_name: Optional[str] = None, - verbose: bool = True, + verbose: bool = False, ): """ Initialize reading of TIFF files. @@ -244,7 +244,7 @@ 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 802645139..9ab1f460f 100644 --- a/src/neuroconv/datainterfaces/ophys/caiman/caimandatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/caiman/caimandatainterface.py @@ -17,7 +17,7 @@ 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 5373b7004..8484920cd 100644 --- a/src/neuroconv/datainterfaces/ophys/micromanagertiff/micromanagertiffdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/micromanagertiff/micromanagertiffdatainterface.py @@ -20,7 +20,7 @@ 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. @@ -29,7 +29,7 @@ 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 59424d7a5..75b72d06a 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 49e556d06..fc259cad2 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 7d9d7003b..b004b8ee0 100644 --- a/src/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py +++ b/src/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py @@ -40,7 +40,7 @@ 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, @@ -104,7 +104,7 @@ 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 @@ -189,7 +189,7 @@ 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 ( @@ -254,7 +254,7 @@ 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. @@ -361,7 +361,7 @@ 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. @@ -485,7 +485,7 @@ 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. @@ -608,7 +608,7 @@ 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 8a3f876c2..a2a8e876c 100644 --- a/src/neuroconv/datainterfaces/ophys/suite2p/suite2pdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/suite2p/suite2pdatainterface.py @@ -80,7 +80,7 @@ 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 0c6b90aea..bef262cab 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 ce98561de..5c83f0c72 100644 --- a/src/neuroconv/datainterfaces/ophys/tiff/tiffdatainterface.py +++ b/src/neuroconv/datainterfaces/ophys/tiff/tiffdatainterface.py @@ -24,7 +24,7 @@ def __init__( self, file_path: FilePath, sampling_frequency: float, - verbose: bool = True, + verbose: bool = False, photon_series_type: Literal["OnePhotonSeries", "TwoPhotonSeries"] = "TwoPhotonSeries", ): """ @@ -34,7 +34,7 @@ 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 a1de63a07..2520a1236 100644 --- a/src/neuroconv/datainterfaces/text/timeintervalsinterface.py +++ b/src/neuroconv/datainterfaces/text/timeintervalsinterface.py @@ -21,7 +21,7 @@ def __init__( self, file_path: FilePath, read_kwargs: Optional[dict] = None, - verbose: bool = True, + verbose: bool = False, ): """ Initialize the TimeIntervalsInterface. @@ -32,8 +32,7 @@ def __init__( The path to the file containing time intervals data. read_kwargs : dict, optional Additional arguments for reading the file, by default None. - verbose : bool, optional - If True, provides verbose output, by 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 ff066ad6b..1aa68bb4d 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) @@ -312,7 +312,7 @@ 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 d31e6032c..8e0f89226 100644 --- a/src/neuroconv/tools/spikeinterface/spikeinterface.py +++ b/src/neuroconv/tools/spikeinterface/spikeinterface.py @@ -1162,7 +1162,7 @@ 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, @@ -1203,7 +1203,7 @@ 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, @@ -1266,7 +1266,7 @@ 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. @@ -1759,7 +1759,7 @@ 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, @@ -1806,7 +1806,7 @@ 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, @@ -1841,7 +1841,7 @@ 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 @@ -2041,7 +2041,7 @@ 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, @@ -2086,7 +2086,7 @@ 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, @@ -2128,7 +2128,7 @@ 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 @@ -2193,7 +2193,7 @@ 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 38cc750ab..903036083 100644 --- a/src/neuroconv/tools/testing/mock_interfaces.py +++ b/src/neuroconv/tools/testing/mock_interfaces.py @@ -208,7 +208,7 @@ 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__( @@ -245,7 +245,7 @@ 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_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"], 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 081cd172d..7f7927b00 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 @@ -355,7 +355,7 @@ 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( @@ -503,7 +503,7 @@ 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(