nexusLIMS.extractors.plugins.tofwerk_pfib

Tofwerk fibTOF pFIB-ToF-SIMS HDF5 extractor plugin.

Module Contents

Classes

TofwerkPfibExtractor

Extractor for Tofwerk fibTOF pFIB-ToF-SIMS HDF5 files.

API

class nexusLIMS.extractors.plugins.tofwerk_pfib.TofwerkPfibExtractor

Extractor for Tofwerk fibTOF pFIB-ToF-SIMS HDF5 files.

Handles both raw files (no PeakData/PeakData) and opened/processed files (has PeakData/PeakData with integrated peak intensities). Performs content sniffing to confirm the file is a Tofwerk fibTOF FIB-SIMS acquisition before attempting extraction.

name

‘tofwerk_pfib_extractor’

priority

150

supported_extensions

Type: typing.ClassVar

supports(context: ExtractionContext) → bool

Check if this extractor supports the given file.

Performs content sniffing to verify this is a Tofwerk fibTOF FIB-SIMS HDF5 file by checking for the presence of FullSpectra/SumSpectrum, FIBParams, FIBImages, and the TofDAQ Version root attribute.

Parameters:

context – The extraction context containing file information

Returns:

True if this appears to be a Tofwerk fibTOF FIB-SIMS HDF5 file

Return type:

bool

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

Extract metadata from a Tofwerk fibTOF pFIB-ToF-SIMS HDF5 file.

Parameters:

context – The extraction context containing file information

Returns:

List containing one metadata dict with nx_meta key

Return type:

list[dict]