Welcome to np-lims-tk’s documentation!

Indices and tables

Core API

Awesome np-lims-tk is a Python cli/package created with https://github.com/TezRomacH/python-package-template

np_lims_tk.find_files(db_uri: Optional[str] = None, exp_id: Optional[str] = None, wkft: Optional[str] = None, local_path: Optional[str] = None) → List[str]

Finds all files associated with a combination of experiment meta info.

Parameters

  • db_uri – lims database uri

  • exp_id – lims experiment id associated with the files

  • wkft – well known file type name associated with the files you want to find

  • local_path – local filepath of a file you want to find on lims

Returns

A list of filepaths

Note

  • The following combinations of meta info are supported

    • exp_id and wkft

    • local_path

  • A local_path can be prefixed with * but an experiment id will need to be supplied

  • If no db_uri is supplied, will attempt allen_config_auto_discovery

np_lims_tk.get_suffixes() → List[str]

Gets a list of supported filename suffixes.

Returns

list of filename suffixes

np_lims_tk.get_wkft_names() → List[str]

Gets a list of all supported well known file types.

Returns

List of supported well known file types.

Supported Well Known File Types

np_lims_tk.wkft.WKFT_NAMES = ['NewstepConfiguration', 'EcephysReplayStimulus', 'EcephysAreaClassifications', 'SideDlcOutputFile', 'EyeTracking Ellipses', 'RawEyeTrackingVideo', 'RawEyeTrackingVideoMetadata', 'EcephysSurgeryNotes', 'RawFaceTrackingVideoMetadata', 'RawBehaviorTrackingVideoMetadata', 'StimulusPickle', 'EyeDlcOutputFile', 'OptoPickle', 'MappingPickle', 'RawBehaviorTrackingVideo', 'FaceDlcOutputFile', 'EcephysRigSync', 'EcephysPlatformFile', 'RawFaceTrackingVideo', 'EcephysPostStimulusRight', 'EcephysPostInsertionLeft', 'EcephysInsertionLocationImage', 'EcephysPostInsertionRight', 'EcephysPreExperimentRight', 'EcephysPostExperimentLeft', 'EcephysPreInsertionLeft', 'EcephysFiducialImage', 'EcephysPreInsertionRight', 'EcephysBrainSurfaceRight', 'EcephysPostExperimentRight', 'EcephysBrainSurfaceLeft', 'EcephysPostStimulusLeft', 'EcephysPreExperimentLeft', 'EcephysOverlayImage', 'EcephysSortedParams', 'EcephysSortedWhiteningMatInv', 'EcephysSortedTemplates', 'EcephysSortedSpikeClusters', 'EcephysSortedChannelMap', 'EcephysChannelStates', 'EcephysSortedSpikeTimes', 'EcephysSortedProbeInfo', 'EcephysSortedChannelPositions', 'EcephysTemplatesInd', 'EcephysSortedSpikeTemplates', 'EcephysSortedMeanWaveforms', 'EcephysSortedEventTimestamps', 'EcephysSortedSimilarTemplates', 'EcephysSortedLfpTimestamps', 'EcephysSortedMetrics', 'EcephysProbeRawData', 'EcephysSortedLfpContinuous', 'EcephysSortedWhiteningMat', 'EcephysSortedAmplitudes']

Names of well known file types (wkft) on lims

Supported Suffixes

np_lims_tk.local_paths.SUFFIXES = ['_platformD1.json', '.sync', '_surface-image6-right.png', '_surface-image6-left.png', '_surface-image5-left.png', '_surface-image5-right.png', '_surface-image4-left.png', '_surface-image4-right.png', '_surface-image3-right.png', '_surface-image3-left.png', '_surface-image2-right.png', '_surface-image2-left.png', '.overlay.png', '.insertionLocation.png', '.fiducial.png', '_surface-image1-right.png', '_surface-image1-left.png', '.behavior.pkl', '.mapping.pkl', '.areaClassifications.csv', '.behavior.json', '.behavior.mp4', '.eye.json', '.eye.mp4', '.face.json', '.face.mp4', '.motor-locs.csv', '.replay.pkl', '.opto.pkl', '_surgeryNotes.json']

Names of supported suffixes for local_paths.