hyperspy.io_plugins.emd module

class hyperspy.io_plugins.emd.EMD(signals=None, user=None, microscope=None, sample=None, comments=None)

Bases: object

Class for storing electron microscopy datasets.

The EMD class can hold an arbitrary amount of datasets in the signals dictionary. These are saved as HyperSpy Signal instances. Global metadata are saved in four dictionaries (user, microscope, sample, comments). To print relevant information about the EMD instance use the log_info() function. EMD instances can be loaded from and saved to emd-files, an hdf5 standard developed at Lawrence Berkeley National Lab (https://emdatasets.com/).

signals

Dictionary which contains all datasets as Signal instances.

Type

dictionary

user

Dictionary which contains user related metadata.

Type

dictionary

microscope

Dictionary which contains microscope related metadata.

Type

dictionary

sample

Dictionary which contains sample related metadata.

Type

dictionary

comments

Dictionary which contains additional commentary metadata.

Type

dictionary

add_signal(signal, name=None, metadata=None)

Add a HyperSpy signal to the EMD instance and make sure all metadata is present.

Parameters

• signal (Signal) – HyperSpy signal which should be added to the EMD instance.

• name (string, optional) – Name of the (used as a key for the signals dictionary). If not specified, signal.metadata.General.title will be used. If this is an empty string, both name and signal title are set to ‘dataset’ per default. If specified, name overwrites the signal title.

• metadata (dictionary) – Dictionary which holds signal specific metadata which will be added to the signal.

Returns

Return type

None

Notes

This is the preferred way to add signals to the EMD instance. Directly adding to the signals dictionary is possible but does not make sure all metadata are correct. This method is also called in the standard constructor on all entries in the signals dictionary!

classmethod load_from_emd(filename, lazy=False, dataset_name=None)

Construct EMD object from an emd-file.

Parameters

• filename (string) – The name of the emd-file from which to load the signals. Standard format is ‘*.emd’.

• False (bool, optional) – If False (default) loads data to memory. If True, enables loading only if requested.

• dataset_name (string or iterable, optional) – Only add dataset with specific name. Note, this has to be the full group path in the file. For example `/experimental/science_data’. If the dataset is not found, an IOError with the possible datasets will be raised. Several names can be specified in the form of a list.

Returns

emd – A EMD object containing the loaded signals.

Return type

EMD

log_info()

( all relevant information about the EMD instance.

save_to_emd(filename='datacollection.emd')

Save EMD data in a file with emd(hdf5)-format.

Parameters

filename (string, optional) – The name of the emd-file in which to store the signals. The default is ‘datacollection.emd’.

Returns

Return type

None

hyperspy.io_plugins.emd.EMD_VERSION = '0.2'

class hyperspy.io_plugins.emd.FeiEMDReader(filename, select_type=None, first_frame=0, last_frame=None, sum_frames=True, sum_EDS_detectors=True, rebin_energy=1, SI_dtype=None, load_SI_image_stack=False, lazy=False)

Bases: object

Class for reading FEI electron microscopy datasets.

The FeiEMDReader reads EMD files saved by the FEI Velox software package.

dictionaries

List of dictionaries which are passed to the file_reader.

Type

list

im_type

String specifying whether the data is an image, spectrum or spectrum image.

Type

string

class hyperspy.io_plugins.emd.FeiSpectrumStream(stream_group, reader)

Bases: object

Read spectrum image stored in FEI’s stream format

Once initialized, the instance of this class supports numpy style indexing and slicing of the data stored in the stream format.

get_pixelsize_offset_unit()

property shape

stream_to_array(stream_data, spectrum_image=None)

Convert stream to array.

Parameters

• stream_data (array) –

• spectrum_image (array or None) – If array, the data from the stream are added to the array. Otherwise it creates a new array and returns it.

stream_to_sparse_array(stream_data)

Convert stream in sparse array

Parameters

stream_data (array) –

hyperspy.io_plugins.emd.calculate_chunks(shape, dtype, chunk_size_mb=100)

Calculate chunks to get target chunk size.

The chunks are optimized for C-order reading speed.

Parameters

• shape (tuple of ints) – The shape of the array

• dtype (string or numpy dtype) – The dtype of the array

• chunk_size_mb (int) – The maximum size of the resulting chunks in MB. The default is 100MB as reccommended by the dask documentation.

hyperspy.io_plugins.emd.default_extension = 0

hyperspy.io_plugins.emd.description = 'Read data from Berkeleys EMD files.'

hyperspy.io_plugins.emd.fei_check(filename)

Function to check if the EMD file is an FEI file.

Parameters

filename (string) – The name of the emd-file from which to load the signals. Standard format is ‘*.emd’.

Returns

Return type

Boolean

hyperspy.io_plugins.emd.file_extensions = ('emd', 'EMD')

hyperspy.io_plugins.emd.file_reader(filename, log_info=False, lazy=False, **kwds)

hyperspy.io_plugins.emd.file_writer(filename, signal, signal_metadata=None, user=None, microscope=None, sample=None, comments=None, **kwds)

hyperspy.io_plugins.emd.format_name = 'Electron Microscopy Data (EMD)'

hyperspy.io_plugins.emd.full_support = False

hyperspy.io_plugins.emd.reads_images = True

hyperspy.io_plugins.emd.reads_spectrum = True

hyperspy.io_plugins.emd.reads_spectrum_image = True

hyperspy.io_plugins.emd.writes = True