OnDiscImzMLExperiment#

class pyopenms.OnDiscImzMLExperiment(*args, **kwargs)#

Bases: object

Random-access on-disc reader for imzML (.imzML + .ibd), analogous to OnDiscMSExperiment for indexed mzML.

__init__(self) → None#

Attributes

`close`	Close the companion .ibd file and release on-disc resources
`extractIonImage`	Overloaded function.
`getGeometry`	Return the shared 2D MSImagingGeometry (0-based pixel grid + (x,y)->spectrum index), built lazily from the index
`getImzMLMeta`	Return dataset-level ImzMLMeta parsed during open()
`getIndex`	Return ImzMLSpectrumIndex entry without reading .ibd peak data
`getNrSpectra`
`getSpectrum`
`getSpectrumAtCoord`
`gridHeight`
`gridWidth`
`isOpen`
`open`	Open imzML index and companion .ibd file
`size`

close#: Close the companion .ibd file and release on-disc resources

extractIonImage#

Overloaded function.

extractIonImage(self, mz: float, tolerance_ppm: float) -> pyopenms._pyopenms_experiment.IonImage

Extract a single-mass ion image over the whole dataset by summing intensities in [mz - dm, mz + dm] (dm = mz * tolerance_ppm * 1e-6), decoding each pixel from the .ibd on demand

extractIonImage(self, mz: float, tolerance_ppm: float, region_id: int) -> pyopenms._pyopenms_experiment.IonImage

Extract a single-mass ion image restricted to one region, decoding each pixel from the .ibd on demand

getGeometry#: Return the shared 2D MSImagingGeometry (0-based pixel grid + (x,y)->spectrum index), built lazily from the index

getImzMLMeta#: Return dataset-level ImzMLMeta parsed during open()

getIndex#: Return ImzMLSpectrumIndex entry without reading .ibd peak data

getNrSpectra#

getSpectrum#

getSpectrumAtCoord#

gridHeight#

gridWidth#

isOpen#

open#: Open imzML index and companion .ibd file

size#