This function allows ENVI data import as hyperSpec object.
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.
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())
complete name of the binary file
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.
list with the respective information, see details.
handed to read.ENVI
vectors of form c(offset, step size) for the position vectors, see details.
see details
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.
lists that overwrite the respective information
from the ENVI header file. These data is then handed to
initialize
a hyperSpec object
read.ENVI.Nicolet:
Nicolet uses some more keywords in their header file. They are interpreted as follows:
| description | giving the position of the first spectrum |
| z plot titles | wavelength and intensity axis units, comma separated |
These parameters can be overwritten by giving a list with the respective
elements in parameter header.
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.
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 |
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.
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.