nexusLIMS.extractors.plugins.digital_micrograph

Digital Micrograph (.dm3/.dm4) extractor plugin.

Module Contents

Classes

DM3Extractor

Extractor for Gatan DigitalMicrograph files (.dm3 and .dm4).

Functions

get_dm3_metadata	Get metadata from a dm3 or dm4 file.
get_pre_path	Get the appropriate pre-path in the metadata tag structure for a given signal.
parse_dm3_microscope_info	Parse the “microscope info” metadata.
parse_dm3_eels_info	Parse EELS information from the metadata.
parse_dm3_eds_info	Parse EDS information from the dm3 metadata.
parse_dm3_spectrum_image_info	Parse “spectrum image” information from the metadata.
process_tecnai_microscope_info	Process the Microscope_Info metadata string into a dictionary of key-value pairs.

API

class nexusLIMS.extractors.plugins.digital_micrograph.DM3Extractor

Extractor for Gatan DigitalMicrograph files (.dm3 and .dm4).

This extractor handles metadata extraction from files saved by Gatan’s DigitalMicrograph software, commonly used on FEI/Thermo and JEOL TEMs.

name

‘dm3_extractor’

priority

100

supported_extensions

Type: typing.ClassVar

supports(context: ExtractionContext) → bool

Check if this extractor supports the given file.

Parameters:

context – The extraction context containing file information

Returns:

True if file extension is .dm3 or .dm4

Return type:

bool

extract(context: ExtractionContext) → dict[str, Any] | list[dict[str, Any]]

Extract metadata from a DM3/DM4 file.

Parameters:

context – The extraction context containing file information

Returns:

For DM3/DM4 files: Always returns a list of metadata dicts. Each dict contains ‘nx_meta’ with NexusLIMS-specific metadata. Single-signal files return a 1-element list for consistency. If the file cannot be opened, returns basic metadata as a single dict (following the standard extractor contract for error cases).

Return type:

list[dict] or dict

nexusLIMS.extractors.plugins.digital_micrograph.get_dm3_metadata(filename: Path, instrument=None)

Get metadata from a dm3 or dm4 file.

Returns the metadata from a .dm3 file saved by Digital Micrograph, with some non-relevant information stripped out. Instrument-specific metadata parsing is handled by instrument profiles (see nexusLIMS.extractors.plugins.profiles).

Parameters:

• filename (str) – path to a .dm3 file saved by Gatan’s Digital Micrograph

• instrument (Instrument, optional) – The instrument object (used for timezone info). Instrument-specific parsing is now handled via profiles, not this parameter.

Returns:

metadata – List of extracted metadata dicts, one per signal. If None, the file could not be opened.

Return type:

list[dict] or None

nexusLIMS.extractors.plugins.digital_micrograph.get_pre_path(mdict: Dict) → List[str]

Get the appropriate pre-path in the metadata tag structure for a given signal.

Get the path into a dictionary where the important DigitalMicrograph metadata is expected to be found. If the .dm3/.dm4 file contains a stack of images, the important metadata for NexusLIMS is not at its usual place and is instead under a plan info tag, so this method will determine if the stack metadata is present and return the correct path.

Parameters:

mdict (dict) – A metadata dictionary as returned by get_dm3_metadata()

Returns:

• A list containing the subsequent keys that need to be traversed to

• get to the point in the mdict where the important metadata is stored

nexusLIMS.extractors.plugins.digital_micrograph.parse_dm3_microscope_info(mdict)

Parse the “microscope info” metadata.

Parse the “important” metadata that is saved at specific places within the DM3 tag structure into a consistent place in the metadata dictionary returned by get_dm3_metadata(). Specifically looks at the “Microscope Info”, “Session Info”, and “Meta Data” nodes (these are not present on every microscope).

Parameters:

mdict (dict) – A metadata dictionary as returned by get_dm3_metadata()

Returns:

mdict – The same metadata dictionary with some values added under the root-level nx_meta key

Return type:

dict

nexusLIMS.extractors.plugins.digital_micrograph.parse_dm3_eels_info(mdict)

Parse EELS information from the metadata.

Parses metadata from the DigitalMicrograph tag structure that concerns any EELS acquisition or spectrometer settings, placing it in an EELS dictionary underneath the root-level nx_meta node.

Parameters:

mdict (dict) – A metadata dictionary as returned by get_dm3_metadata()

Returns:

mdict – The metadata dict with all the “EELS-specific” metadata added under nx_meta

Return type:

dict

nexusLIMS.extractors.plugins.digital_micrograph.parse_dm3_eds_info(mdict)

Parse EDS information from the dm3 metadata.

Parses metadata from the DigitalMicrograph tag structure that concerns any EDS acquisition or spectrometer settings, placing it in an EDS dictionary underneath the root-level nx_meta node. Metadata values that are commonly incorrect or may be placeholders are specified in a list under the nx_meta.warnings node.

Parameters:

mdict (dict) – A metadata dictionary as returned by get_dm3_metadata()

Returns:

mdict – The metadata dictionary with all the “EDS-specific” metadata added as sub-node under the nx_meta root level dictionary

Return type:

dict

nexusLIMS.extractors.plugins.digital_micrograph.parse_dm3_spectrum_image_info(mdict)

Parse “spectrum image” information from the metadata.

Parses metadata that concerns any spectrum imaging information (the “SI” tag) and places it in a “Spectrum Imaging” dictionary underneath the root-level nx_meta node. Metadata values that are commonly incorrect or may be placeholders are specified in a list under the nx_meta.warnings node.

Parameters:

mdict (dict) – A metadata dictionary as returned by get_dm3_metadata()

Returns:

mdict – The metadata dictionary with all the “EDS-specific” metadata added as sub-node under the nx_meta root level dictionary

Return type:

dict

nexusLIMS.extractors.plugins.digital_micrograph.process_tecnai_microscope_info(microscope_info, delimiter='\u2028')

Process the Microscope_Info metadata string into a dictionary of key-value pairs.

This method is only relevant for FEI Titan TEMs that write additional metadata into a unicode-delimited string at a certain place in the DM3 tag structure

Parameters:

• microscope_info (str) – The string of data obtained from the Tecnai.Microscope_Info leaf of the metadata

• delimiter (str) – The value (a unicode string) used to split the microscope_info string.

Returns:

info_dict – The information contained in the string, in a more easily-digestible form.

Return type:

dict