pwspy.dataTypes.DynMetaData¶
- class pwspy.dataTypes.DynMetaData(metadata, filePath=None, fileFormat=None, acquisitionDirectory=None)[source]¶
Bases:
pwspy.dataTypes._metadata.MetaDataBase,pwspy.dataTypes._metadata.AnalysisManagerA class that represents the metadata of a Dynamics acquisition.
- class FileFormats(value)[source]¶
Bases:
enum.EnumAn enumerator identifying the types of file formats that this class can be loaded from.
- 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 fromOldPWS(directory, lock=None, acquisitionDirectory=None)[source]¶
Loads old dynamics cubes which were saved the same as old pws cubes. a raw binary file with some metadata saved in random .mat files. Does not support automatic detection of binning, pixel size, camera dark counts, system name.
- Parameters
directory (
str) – The path to the folder containing the data files load the metadata from.- Return type
- Returns
A new instance of DynMetaData.
- classmethod fromTiff(directory, lock=None, acquisitionDirectory=None)[source]¶
- Parameters
directory – The path to the folder containing the data files load the metadata from.
- Return type
- Returns
A new instance of DynMetaData 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 the image used for quick viewing of the acquisition. Has no numeric significance.
- Return type
ndarray
- loadAnalysis(name)¶
- Parameters
name (str) – The name of the analysis to load.
- Return type
AbstractHDFAnalysisResults
- Returns
A new instance of an AnalysisResults object.
- 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]¶
- Parameters
lock (mp.Lock) – A multiprocessing lock that can prevent help us synchronize demands on the hard drive when loading many files in parallel. Probably not needed.
- Returns
The data object associated with this metadata object.
- Return type
pwsdtmd.DynCube
- 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
- property idTag: str¶
Returns: str: A unique string identifying this acquisition.
- Return type
str
- 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
- property times: Tuple[float, ...]¶
A sequence indicatin the time associated with each 2D slice of the 3rd axis of the data array
- Return type
Tuple[float,...]
- property wavelength: int¶
The wavelength that this acquisition was acquired at.
- Return type
int