ChromatogramExtractorAlgorithm#

class pyopenms.ChromatogramExtractorAlgorithm#

Bases: object

Cython implementation of _ChromatogramExtractorAlgorithm

Original C++ documentation is available here: – Inherits from [‘ProgressLogger’]

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: ChromatogramExtractorAlgorithm) → None

Methods

`__init__`	Overload:
`endProgress`(self)	Ends the progress display
`extractChromatograms`(self, input, output, ...)	Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates
`getLogType`(self)	Returns the type of progress log being used
`nextProgress`(self)	Increment progress by 1 (according to range begin-end)
`setLogType`(self, in_0)	Sets the progress log that should be used.
`setProgress`(self, value)	Sets the current progress
`startProgress`(self, begin, end, label)

endProgress(self) → None#: Ends the progress display

extractChromatograms(self, input: SpectrumAccessOpenMS, output: List[OSChromatogram], extraction_coordinates: List[ExtractionCoordinates], mz_extraction_window: float, ppm: bool, im_extraction_window: float, filter: bytes | str | String) → None#

Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates

Parameters:

input – Input spectral map
output – Output chromatograms (XICs)
extraction_coordinates – Extracts around these coordinates (from rt_start to rt_end in seconds - extracts the whole chromatogram if rt_end - rt_start < 0).
mz_extraction_window – Extracts a window of this size in m/z dimension in Th or ppm (e.g. a window of 50 ppm means an extraction of 25 ppm on either side)
ppm – Whether mz_extraction_window is in ppm or in Th
filter – Which function to apply in m/z space (currently “tophat” only)

getLogType(self) → int#: Returns the type of progress log being used

nextProgress(self) → None#: Increment progress by 1 (according to range begin-end)

setLogType(self, in_0: int) → None#: Sets the progress log that should be used. The default type is NONE!

setProgress(self, value: int) → None#: Sets the current progress

startProgress(self, begin: int, end: int, label: bytes | str | String) → None#