This function supervises the entire import process. Not all official formats are supported, see the vignettes. Prior to release, this package is checked against a very large number of files in the author's collection. However, the JCAMP-DX standard allows many variations and it is difficult to anticipate all permutations. Error messages will generally let you know what's going on. If you have a file that you feel should be supported but gives an error, please file an issue at Github and share the file.
Character. The file name to import.
Logical. "Stop on Failed Check"
The default is
Integer. The level of debug reporting desired. For those options giving
a lot of output, you may wish to consider directing the output via
In cases where an error is about to stop execution, you get additional information regardless of
A list, as follows:
The first element is a data frame summarizing the pieces of the imported file.
The second element is the file metadata.
The third element is a integer vector giving the comment lines found (exclusive of the metdata, which typically contains many comments).
Additional elements contain the extracted data as follows:
If the file contains multiple spectra (not currently supported), there will be one data frame for each spectrum.
If the file contains the real and imaginary parts of a 1D NMR spectrum, there will be two data frames, one containing the real portion and the other the imaginary portion.
If the file contains one non-NMR spectrum, a single data frame will be returned.
In all cases above, the data frame has
In the case of 2D NMR data, additional list elements are returned including the F2 frequency values, the F1 frequency values, and a matrix containing the 2D data.
The examples make use of data files included with the package. File
is an IR spectrum of Smart Balance Original spread (a butter substitute). The
spectrum is presented in transmission format, and was recorded on a ThermoFisher
instrument. The file uses AFFN compression, and was written
with the JCAMP-DX 5.01 standard. Note that even though the Y-axis was recorded in
percent transmission, in the JDX file it is stored on [0...1].
PCRF.jdx is a 1H NMR
spectrum of a hexane extract of a reduced fat potato chip. The spectrum was
recorded on a JEOL instrument. The file uses SQZ DIF DUP compression, and was written
with the JCAMP-DX 6.00 standard.
PCRF_line265.jdx has a deliberate error in it.
isasspc1.jdx is a 2D NMR file recorded on a JEOL GX 400 instrument.
The file is freely available at http://www.jcamp-dx.org/.
MiniDIFDUP.JDX is a small demonstration file, used in the vignettes to
illustrate the decompression process. It is derived from a freely available file.
Internally, this package uses a tolerance factor when comparing values during certain checks.
This is desirable because the original values in the files
are text strings of varying lengths which get converted to numerical values by
values in the file, such as FIRSTY, are stored with low precision, and the computation of the
value to be compared occurs with much greater precision. In these cases the check can fail
even when the tolerance is pretty loose. In these cases one might consider setting
SOFC = FALSE to allow the calculation to proceed. If you do this, be certain to check
the results carefully as described under
The standard requires a "Y Value Check" when in DIF mode. Extra Y values have been appended to each line to use in the check, and the last Y value on a line must equal the first Y value on the next line IFF one is in DIF mode. After a successful check, the extra Y value must be removed. In actual practice, some vendors, at least some of the time, seem to differ as to the definition of "being in DIF mode". In turn, this determines how the Y value check should proceed.
The standard says "When, and only when, the last ordinate of a line is in DIF form ... The first ordinate of the next line ... is always an actual value, equal to the last calculated ordinate of the previous line". See section 5.8.3 of the 1988 publication.
Taking this definition literally, the Y value check (and removal of the extra value), should occur when one sees e.g. ... DIF DIF DIF (end of line). Let's call this "literal DIF". A literal DIF is easy to detect and act on.
In other cases, something like ... DIF DUP DUP (end of line) is considered to be in DIF mode for Y value check purposes. In these cases we have look backwards to see if we are in DIF mode. Let's call this "relayed DIF".
However, some vendors may treat ... DIF DUP DUP (end of line) as not in DIF mode, and hence one should not do the Y value check and not remove any values, since this vendor would not have added an extra Y value.
In addition to these three possibilities,
readJDX through versions 0.3.xx used a different
definition, namely if there were any DIF entries anywhere on the line, then DIF mode was
assumed and the Y value check carried out. This worked for many files, but not all.
In the 0.4.xx series,
readJDX detects both the literal and relayed definitions and
tries to keep moving forward as much as possible.
readJDX is not particularly fast. Priority has been given to assuring correct answers,
helpful debugging messages and understandable code.
browseVignettes("readJDX") for background information,
references, supported formats, and details about the roles of each function.
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# IR spectrum sbo <- system.file("extdata", "SBO.jdx", package = "readJDX") chk <- readJDX(sbo) plot(chk[]$x, chk[]$y / 100, type = "l", main = "Original Smart Balance Spread", xlab = "wavenumber", ylab = "Percent Transmission" ) # 1H NMR spectrum pcrf <- system.file("extdata", "PCRF.jdx", package = "readJDX") chk <- readJDX(pcrf) plot(chk[]$x, chk[]$y, type = "l", main = "Reduced Fat Potato Chip Extract", xlab = "ppm", ylab = "Intensity" ) # Capturing processing for troubleshooting mdd <- system.file("extdata", "MiniDIFDUP.JDX", package = "readJDX") tf <- tempfile(pattern = "Troubleshooting", fileext = "txt") chk <- readJDX(mdd, debug = 6) sinkall() # close the file connection file.show(tf) # 2D HETCORR spectrum ## Not run: nmr2d <- system.file("extdata", "isasspc1.dx", package = "readJDX") chk <- readJDX(nmr2d) contour(chk$Matrix, drawlabels = FALSE) # default contours not optimal ## End(Not run) ## Not run: # Line 265 has an N -> G error. Try with various levels of debug. # Even with debug = 0 you get useful diagnostic info. problem <- system.file("extdata", "PCRF_line265.jdx", package = "readJDX") chk <- readJDX(problem) ## End(Not run)
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