read-spc: Import for Thermo Galactic's spc file format These functions...

In specmine: Metabolomics and Spectral Data Analysis and Mining

Description

Import for Thermo Galactic's spc file format These functions allow to import .spc files.

Usage

read_spc_nosubhdr(filename, keys.hdr2data = c("fexper", "fres", "fsource"),
  keys.hdr2log = c("fdate", "fpeakpt"), keys.log2data = FALSE,
  keys.log2log = TRUE, log.txt = TRUE, log.bin = FALSE,
  log.disk = FALSE, hdr = list(), nosubhdr = TRUE, no.object = FALSE)

Arguments

filename	The complete file name of the .spc file.
keys.hdr2data, keys.hdr2log, keys.log2data, keys.log2log	character vectors with the names of parameters in the .spc file's log block (log2xxx) or header (hdr2xxx) that should go into the extra data (yyy2data) or into the long.description field of the returned hyperSpec object's log (yyy2log). All header fields specified in the .spc file format specification (see below) are imported and can be referred to by their de-capitalized names.
log.txt	Should the text part of the .spc file's log block be read?
log.bin, log.disk	Should the normal and on-disk binary parts of the .spc file's log block be read? If so, they will be put as raw vectors into the hyperSpec object's log.
hdr	A list with fileheader fields that overwrite the settings of actual file's header. Use with care, and look into the source code for detailed insight on the elements of this list.
nosubhdr	Boolean value to decide if the header should be read or not. Default to TRUE.
no.object	If TRUE, a list with wavelengths, spectra, labels, log and data are returned instead of a hyperSpec object. This parameter will likely be subject to change in future - use with care.

Value

If the file contains multiple spectra with individual wavelength axes, read.spc returns a list of hyperSpec objects. Otherwise the result is a hyperSpec object.

read.spc.KaiserMap returns a hyperSpec object with data columns x, y, and z containing the stage position as recorded in the .spc files' log.

Note

Only a restricted set of test files was available for development. Particularly, the w-planes feature could not be tested.

If you have .spc files that cannot be read with these function, don't hesitate to contact the package maintainer with your code patch or asking advice.

Author(s)

C. Beleites

See Also

textio

specmine documentation built on Sept. 21, 2021, 5:06 p.m.