pwspy.dataTypes.PwsMetaData¶
- class pwspy.dataTypes.PwsMetaData(metadata, filePath=None, fileFormat=None, acquisitionDirectory=None)[source]¶
Bases:
pwspy.dataTypes._metadata.MetaDataBase,pwspy.dataTypes._metadata.AnalysisManagerA class that represents the metadata of a PWS acquisition.
- Parameters
metadata (
dict) – The dictionary containing the metadata.
- static decodeHdfMetadata(d)¶
Attempt to extract a dictionary of metadata from an HDF5 dataset.
- Parameters
d (
Dataset) – The h5py.Dataset to load from.- Return type
dict- Returns
A dictionary containing the metadata
- encodeHdfMetadata(d)¶
Save this metadata object as a json string in an HDF5 dataset.
- Parameters
d (
Dataset) – The h5py.Dataset to save the metadata to.- Return type
Dataset
- classmethod fromNano(directory, lock=None, acquisitionDirectory=None)[source]¶
Attempt to load from NanoCytomic .mat file format
- Parameters
directory (
str) – The file path to load the metadata from.- Return type
- Returns
A new instance of PwsMetaData loaded from file
- classmethod fromOldPWS(directory, lock=None, acquisitionDirectory=None)[source]¶
Attempt to load from the old .mat file format.
- Parameters
directory – The file path to load the metadata from.
- Return type
- Returns
A new instance of PwsMetaData loaded from file
- classmethod fromTiff(directory, lock=None, acquisitionDirectory=None)[source]¶
Attempt to load from the standard TIFF file format.
- Parameters
directory – The file path to load the metadata from.
- Return type
- Returns
A new instance of PwsMetaData loaded from file
- getAnalyses()¶
- Return type
List[str]- Returns
A list of the names of analyses that were found.
- classmethod getAnalysesAtPath(path)¶
- Parameters
path (
str) – The path to search for analysis files.- Return type
List[str]- Returns
A list of the names of analyses that were found.
- static getAnalysisResultsClass()[source]¶
- Return type
t_.Type[AbstractHDFAnalysisResults]
- Returns
The class that is used to contain analysis results for this acquisition type.
- getThumbnail()[source]¶
- Return type
ndarray- Returns
An image for quick viewing of the acquisition. No numerical significance.
- loadAnalysis(name)¶
- Parameters
name (str) – The name of the analysis to load.
- Return type
AbstractHDFAnalysisResults
- Returns
A new instance of an AnalysisResults object.
- classmethod loadAny(directory, lock=None, acquisitionDirectory=None)[source]¶
Attempt to load from any file format.
- Parameters
directory – The file path to load the metadata from.
- Return type
- Returns
A new instance of PwsMetaData loaded from file
- metadataToJson(directory)[source]¶
Save the metadata to a JSON file.
- Parameters
directory – The folder path to save the new file to.
- removeAnalysis(name)¶
- Parameters
name (
str) – The name of the analysis to be deleted
- saveAnalysis(analysis, name, overwrite=False)¶
- Parameters
analysis (AbstractHDFAnalysisResults) – An AnalysisResults object to be saved.
name (str) – The name to save the analysis as
overwrite (bool) – If True then any existing file of the same name will be replaced. If False an exception will be raised.
- toDataClass(lock=None)[source]¶
Convert the metadata class to a class that loads the data
- Parameters
lock (
Optional[Lock]) – A Lock object used to synchronize IO in multithreaded and multiprocessing applications.- Return type
- property binning: int¶
The binning setting used by the camera. This is needed in order to properly correct dark counts. This is generally extracted from metadata saved by Micromanager
- Return type
int
- property exposure: float¶
The exposure time of the camera expressed in milliseconds.
- Return type
float
- idTag¶
- property pixelSizeUm: float¶
The pixelSize expressed in microns. This represents the length of each square pixel in object space. Binning has already been accounted for here. This is generally extracted from metadata saved my MicroManager
- Return type
float
- property systemName: str¶
The name of the system this was acquired on. The name is set in the PWS Acquisition Plugin for Micromanager.
- Return type
str
- property time: str¶
The date and time that the acquisition was taken.
- Return type
str