pyImagingMSpec.convert package

Submodules

pyImagingMSpec.convert.bruker_sqlite module

pyImagingMSpec.convert.h5 module

pyImagingMSpec.convert.hdf5 module

pyImagingMSpec.convert.hdf5.hdf5_centroids_IMS(input_filename, output_filename)

pyImagingMSpec.convert.hdf5.smooth_spectrum(mzs, intensities, smoothMethod)

pyImagingMSpec.convert.imzml module

pyImagingMSpec.convert.imzml.centroid_imzml(input_filename, output_filename, step=[], apodization=False, w_size=10, min_intensity=1e-05, prevent_duplicate_pixels=False)

:type input_filename string - source file path (must be .imzml) :type output_filename string - output file path (must be .imzml) :type step tuple grid spacing of pixels (if [] the script will try and guess it) :type apodization boolean whether to try and remove FT wiglet artefacts :type w_size window side (m/z bins) for apodization :type min_intensity: float minimum intensity peaks to return during centroiding :type prevent_duplicate_pixels bool if True will only return the first spectrum for pixels with the same coodinates

pyImagingMSpec.convert.sl module

Module contents