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
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