`nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview`#

HyperSpy-based preview generator for microscopy data files.

Module Contents#

Classes#

HyperSpyPreviewGenerator

Preview generator for files that can be loaded with HyperSpy.

Functions#

`add_annotation_markers`	Add annotation markers from a DM3/DM4 file to a HyperSpy signal.
`sig_to_thumbnail`	Generate a preview thumbnail from an arbitrary HyperSpy signal.

Data#

SPECTRUM_IMAGE_LOGO

Logo background to use for a spectrum image preview

API#

nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.SPECTRUM_IMAGE_LOGO#: Logo background to use for a spectrum image preview

nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.add_annotation_markers(s)[source]#

Add annotation markers from a DM3/DM4 file to a HyperSpy signal.

Read annotations from a signal originating from DigitalMicrograph and convert the ones (that we can) into HyperSpy 2.0+ markers for plotting. Uses the modern hs.plot.markers API instead of the deprecated dict2marker.

Parameters:: s (hyperspy.signal.BaseSignal (or subclass)) – The HyperSpy signal for which a thumbnail should be generated

nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.sig_to_thumbnail(s, out_path: Path, dpi: int = 92)[source]#

Generate a preview thumbnail from an arbitrary HyperSpy signal.

For a 2D signal, the signal from the first navigation position is used (most likely the top- and left-most position. For a 1D signal (i.e. a spectrum or spectrum image), the output depends on the number of navigation dimensions:

0: Image of spectrum
1: Image of linescan (a la DigitalMicrograph)
2: Image of spectra sampled from navigation space
2+: As for 2 dimensions

Parameters:

s (hyperspy.signal.BaseSignal (or subclass)) – The HyperSpy signal for which a thumbnail should be generated
out_path – A path to the desired thumbnail filename. All formats supported by savefig() can be used.
dpi (int) – The “dots per inch” resolution for the outputted figure

Returns:

f – Handle to a matplotlib Figure

Return type:

matplotlib.figure.Figure

Notes:

This method heavily utilizes HyperSpy’s existing plotting functions to figure out how to best display the image

class nexusLIMS.extractors.plugins.preview_generators.hyperspy_preview.HyperSpyPreviewGenerator[source]#

Preview generator for files that can be loaded with HyperSpy.

This generator handles preview generation for scientific data files that HyperSpy can load, including dm3, dm4, ser, and other formats. It uses the sig_to_thumbnail function to create previews.

name#: ‘hyperspy_preview’

priority#: 100

supported_extensions#: Type: typing.ClassVar

supports(context: ExtractionContext) → bool[source]#

Check if this generator supports the given file.

Parameters:: context – The extraction context containing file information
Returns:: True if file extension is supported by HyperSpy
Return type:: bool

generate(context: ExtractionContext, output_path: Path) → bool[source]#

Generate a thumbnail preview using HyperSpy.

Parameters:

context – The extraction context containing file information
output_path – Path where the preview image should be saved

Returns:

True if preview was successfully generated, False otherwise