readENVI: Nicolet uses some more keywords in their header file. They...

In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

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

These parameters can be overwritten by giving a list with the respective elements in parameter header.

Description

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.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.

Usage

read.ENVI.Nicolet(file = stop("read.ENVI: file name needed"),
  headerfile = NULL, header = list(), ..., x = NA, y = NA,
  nicolet.correction = FALSE)

read.ENVI(file = stop("read.ENVI: file name needed"), headerfile = NULL,
  header = list(), keys.hdr2data = FALSE, x = 0:1, y = x,
  wavelength = NULL, label = list())

Arguments

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.
...	handed to read.ENVI
x,y	vectors of form c(offset, step size) for the position vectors, see details.
nicolet.correction	see details
keys.hdr2data	determines which fields of the header file should be put into the extra data. Defaults to none. To specify certain entries, give character vectors containing the lowercase names of the header file entries.
wavelength,label	lists that overwrite the respective information from the ENVI header file. These data is then handed to initialize

Details

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:

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.

Value

a hyperSpec object

Author(s)

C. Beleites, testing for the Nicolet files C. Dicko

References

This function was adapted from read.ENVI:

Jarek Tuszynski (2008). caTools: Tools: moving window statistics, GIF, Base64, ROC AUC, etc.. R package version 1.9.

See Also

read.ENVI

textio

hyperSpec documentation built on May 2, 2019, 5:45 p.m.