ImzMLWriter

pyimzml.ImzMLWriter module

class pyimzml.ImzMLWriter.ImzMLWriter(output_filename, mz_dtype=<class 'numpy.float64'>, intensity_dtype=<class 'numpy.float32'>, mode='auto', spec_type='centroid', scan_direction='top_down', line_scan_direction='line_left_right', scan_pattern='one_way', scan_type='horizontal_line', mz_compression=<pyimzml.compression.NoCompression object>, intensity_compression=<pyimzml.compression.NoCompression object>, polarity=None)

Create an imzML+ibd file.

Parameters

• output_filename – is used to make the base name by removing the extension (if any). two files will be made by adding “.ibd” and “.imzML” to the base name

• intensity_dtype – The numpy data type to use for saving intensity values

• mz_dtype – The numpy data type to use for saving mz array values

• mode –

  • “continuous” mode will save the first mz array only

  • ”processed” mode save every mz array separately

  • ”auto” mode writes only mz arrays that have not already been written

• intensity_compression – How to compress the intensity data before saving must be an instance of NoCompression or ZlibCompression

• mz_compression – How to compress the mz array data before saving

addSpectrum(mzs, intensities, coords, userParams=[])

Add a mass spectrum to the file.

Parameters

• mz – mz array

• intensities – intensity array

• coords –

  • 2-tuple of x and y position OR

  • 3-tuple of x, y, and z position

  note some applications want coords to be 1-indexed

close()

Writes the XML file and closes all files. Will be called automatically if with-pattern is used.

finish()

alias of close()

pyimzml.compression module

This module holds adapters for compressing an ImzML file’s binary data, currently only usable with ImzMLWriter.

class pyimzml.compression.NoCompression

No compression.

compress(bytes)

decompress(bytes)

name = 'no compression'

rounding(data)

class pyimzml.compression.ZlibCompression(round_amt=None)

Zlib compression with optional rounding of values. Rounding helps the compression, but is lossy.

Parameters

round_amt – Number of digits after comma. None means no rounding.

compress(bytes)

decompress(bytes)

name = 'zlib compression'

rounding(data)