readENVI: read.ENVI.Nicolet

Description

Nicolet uses some more keywords in their header file. read.ENVI.Nicolet therefore appends "description", "z plot titles", and "pixel size" to keys.hdr2log before calling read.ENVI. They are then interpreted as follows: ll{ description giving the position of the first spectrum z plot titles wavelength and intensity axis units, comma separated pixel size interpreted as x and y step size }

Usage

read.ENVI.Nicolet(..., x=NA, y=NA, log=list(), keys.hdr2log=TRUE,
    nicolet.correction=FALSE)
read.ENVI(file=stop("read.ENVI: file name needed"), headerfile=NULL,
    header=list(), keys.hdr2data=FALSE, keys.hdr2log=TRUE, x=0:1, y=x,
    wavelength=NULL, label=list(), log=list())

Arguments

nicolet.correction

see details

...

handed to read.ENVI

file

complete name of the binary file

headerfile

name of the ASCII header file. If NULL, the name of the header file is guessed by looking for a second file with the same basename but different suffix as file.

header

list with the respective information, see details.

x,y

vectors of form c(offset, step size) for the position vectors, see details.

wavelength,label,log

lists that overwrite the respective information from the ENVI header file. These data is then handed to initialize

keys.hdr2data,keys.hdr2log

determine which fields of the header file should be put into the extra data and which are to be stored in long.description$header in the hyperSpec object's log. Defaults to putting all header information into the log, and none as extra data.

Value

read.ENVI: a hyperSpec object

Details

read.ENVI.Nicolet: The values in header line description seem to be microns while the pixel size seems to be in microns. If nicolet.correction is true, the pixel size values (i.e. the step sizes) are multiplied by 1000.

read.ENVI: read.ENVI.Nicolet should be a good starting point for writing custom wrappers for read.ENVI that take into account your manufacturer's special entries in the header file.

ENVI data usually consists of two files, an ASCII header and a binary data file. The header contains all information necessary for correctly reading the binary file.

I experienced missing header files (or rather: header files without any contents) produced by Bruker Opus' ENVI export.

In this case the necessary information can be given as a list in parameter header instead. The elements of header are then:

lll{ header$ values meaning samples integer no of columns / spectra in x direction lines integer no of lines / spectra in y direction bands integer no of wavelengths / data points per spectrum `data type` format of the binary file 1 1 byte unsigned integer 2 2 byte signed integer 3 4 byte signed integer 4 4 byte float 5 8 byte double 9 16 (2 x 8) byte complex double 12 2 byte unsigned integer `header offset` integer number of bytes to skip before binary data starts interleave directions of the data cube "BSQ" band sequential (indexing: [sample, line, band]) "BIL" band interleave by line (indexing: [sample, line, band]) "BIP" band interleave by pixel (indexing: [band, line, sample]) `byte order` 0 or "little" little endian 1 or "big" big endian "swap" swap byte order }

Some more information that is not provided by the ENVI files may be given:

Wavelength axis and axis labels in the respective parameters. For more information, see initialize.

The spatial information is by default a sequence from 0 to header$samples - 1 and header$lines - 1, respectively. x and y give offset of the first spectrum and step size.

Thus, the object's $x colum is: (0 : header$samples - 1) * x [2] + x [1]. The $y colum is calculated analogously.

References

This function was adapted from read.ENVI: