Expand description
This library provides a means of accessing mass spectrometry and mass spectrometry imaging data stored in either the .mzML or .imzML data formats.
let parser = ImzMLReader::from_path(“/path/to/data.imzML”).unwrap();
for error in parser.errors() { println!(“{:?}”, error); }
let imzml: ImzML<_> = parser.into();
imzml.ion_image(772.573, 100.0);
Re-exports
pub use self::imzml::ImzML;pub use self::imzml::ImzMLReader;pub use mzml::mzml::MzML;pub use mzml::MzMLReader;pub use self::mzml::mzml::*;Modules
Error handling
ImzML file parsing (relies heavily on
mzml)MzML file parsing
Parsing ontologies stored in the OBO format
Validating .mzML and .imzML files
Structs
Represents an tag.
BinaryDataArray represents the tag and captures information required to read and parse the stored binary data.
Represents a tag.
Iterator over a
ChromatogramList returning all chromatograms in the listRepresents a list of
ChromatogramsProvides a single interface to compressed data, decompressing the data on
read() if necessaryCoordinate describes the pixel location of a spectrum/scan
Enables access to data stored in
data_location. The data could be compressed and/or encoded
and stored with various different types. This information is captured in the data_descriptionRepresents a tag.
Represents a tag.
Represents a list of
PrecursorsRepresents a tag.
Represents a tag.
Iterator over a
ScanList returning each Scan in turn.Represents a list of
ScansRepresents a tag.
Represents a list of
ScanWindowsRepresents a tag.
Represents a list of
SelectedIonsSpectrum captures both binary data and metadata associated with a mass spectrum.
Provide ability to access a spectrum (contains
DataAccess for both m/z and intensity arrays)SpectrumAccessIterator provides an iterator over a spectrum
Iterator over a
SpectrumList returning all spectra in the listRepresents a list of
SpectrumRepresents a tag.
WritableSpectrum contains information required to be able to write out a spectrum to imzML.
Enums
The type of data being stored (e.g. m/z values, intensities)
The type used to store binary data (e.g. m/zs or intensities)
Possible means of compressing binary data stored in (i)mzML
Polarity used to acquire the spectrum
Spectrum mode
ScanLocation describes how ImzMLWriter should deal with a particular scan.
Either ignore it, or store it with the specified coordinate.
Represents a reference to a
SpectrumType of spectrum acquired
Constants
Accession in OBO for 32-bit float
Accession in OBO for 64-bit float
Accession in OBO for binary data type
Accession for a centroided spectrum
Accession in OBO for compression (parent term)
Accession in OBO for external array length
Accession in OBO for external data
Accession in OBO for external encoded length
Accession in OBO for external offset
Accession in OBO for intensity array
Accession for MS1 spectrum
Accession in OBO for m/z array
Accession for negative polarity scan
Accession for no combination of spectra
Accession in OBO for no compression
Accession for pixel position in x direction
Accession for pixel position in y direction
Accession for pixel position in z direction
Accession for positive polarity scan
Accession for a profile spectrum
Accession for parent term describing polarity
Accession for parent term describing spectrum representation
Accession in OBO for Zlib compression