SciFiReaders.readers.microscopy.em.tem.emd_reader.EMDReader

class SciFiReaders.readers.microscopy.em.tem.emd_reader.EMDReader(file_path: str, sum_frames: bool = False, no_eds: bool = False, eds_stream: bool = False)

Bases: Reader

Creates an instance of EMDReader which can read one or more HDF5 datasets formatted in the FEI Velox style EDM file

We can read Images, and SpectrumStreams (SpectrumImages and Spectra). Please note that all original metadata are retained in each sidpy dataset.

Parameters:

file_path (str) – Path to a HDF5 file

Returns:

datasets – dictionary of sidpy.Datasets

Return type:

dict

Initialize an EMDReader instance.

Parameters:

• file_path (str) – Path to the HDF5 (.emd) file to be read.

• sum_frames (bool, optional) – If True, sum all frames in the dataset. Defaults to False.

• no_eds (bool, optional) – If True, disables EDS (Energy Dispersive Spectroscopy)

• False. (data handling. Defaults to)

_h5_file

The opened HDF5 file object.

Type:

h5py.File

datasets

Dictionary to store dataset references.

Type:

dict

channel_number

The current channel number (default is 0).

Type:

int

key

Formatted string key for the current channel.

Type:

str

data_array

Array to hold data from the file.

Type:

ndarray or None

metadata

Metadata extracted from the file.

Type:

dict or None

label_dict

Dictionary for label mapping.

Type:

dict

no_eds

Indicates if EDS data handling is disabled.

Type:

bool

sum_frames

Indicates if frames should be summed.

Type:

bool

number_of_frames

Number of frames in the dataset (default is 1).

Type:

int

Methods

can_read	Checks whether or not this Reader can read the provided file
close	Close the h5 file.
extract_crucial_metadata	Extract some crucial metadata from the original metadata.
get_data	Get the image data and metadata from the file.
get_eds	Get the EDS data from the file.
get_eds_spectrum	Get the EDS spectrum.
get_image	Get the image data.
read	Reads all available datasets in FEI Velox style hdf5 files with .edm

can_read()

Checks whether or not this Reader can read the provided file

Returns:

True if this Reader can read the provided file Else, False

Return type:

bool

close()

Close the h5 file.

extract_crucial_metadata(key)

Extract some crucial metadata from the original metadata.

get_data(image_key)

Get the image data and metadata from the file.

get_eds(eds_stream=False)

Get the EDS data from the file.

get_eds_spectrum() → ndarray

Get the EDS spectrum.

get_image()

Get the image data.

read(eds_stream: bool = False, bin_xy: int = 2)

Reads all available datasets in FEI Velox style hdf5 files with .edm

Parameters:

• eds_stream (boolean) – switch to return spectrum image (default - False) or original spectrum stream (True)

• bin_xy (int) – binning factor for EDS spectrum size reduction

Returns:

datasets – Datasets present in the provided file

Return type:

list of sidpy.Dataset objects