import2Dspectra {ChemoSpec2D}

Import 2D Spectroscopic Data

Description

This function imports a single file (for instance, a csv) containing a 2D spectroscopic data set. The current version handles various types of ASCII text files as well as a few other types. This function is called by files2Spectra2DObject and is exported and documented to assist in developing new format codes.

Usage

import2Dspectra(file, fmt, nF2, debug = 0, ...)

Arguments

file

Character string giving the path to a file containing a 2D spectrum.

fmt

Character string giving the format code to use. Details below.

nF2

Integer giving the number of data points in the F2 (x) dimension. Note: If any dimension is zero-filled you may need to study the acquistion details to get the correct value for this argument. This may be vendor-dependent.

debug

Integer. Applies to fmt = "dx" only. See readJDX for details.

...

Arguments to be passed to read.table, or readJDX. For read.table, You MUST supply values for sep, dec and header consistent with your file structure, unless they are the same as the defaults for read.table.

Value

A list with 3 elements:

• A matrix of the z values. The no. of columns = nF2 and the no. of rows follows from the size of the imported data.

• A vector giving the F2 (x) values.

• A vector giving the F1 (y) values.

Format Codes for Plain-Text ASCII Files

ASCII format codes are constructed in two parts separated by a hyphen. Three or more columns are expected. The first part gives the order of the columns in the file, e.g. F2F1R means the first column has the F2 values, the second column has the F1 values and the third the real-valued intensities. The second part of the format code relates to the order of the rows, i.e. which column varies fastest and in what direction. These codes are best understood in relation to how the data is stored internally in a matrix. The internal matrix is organized exactly as the data appears on the screen, with F2 decreasing left-to-right, and F1 increasing top-to-bottom. There are many possible formats (only those listed are implemented, please e-mail for help creating additional combinations):

• "F2F1R-F2decF1dec" Columns in the file are F2 (x), F1 (y), real. Both F2 and F1 are decreasing. Last row is first in the file. This format is used at least some of the time by nmrPipe.

• fmt = "F1F2RI-F1decF2dec2" Columns in the file are F1 (y), F2 (x), real and imaginary (imaginary data will be skipped). F1 is held at a fixed value while F2 decreases. F1 starts high and decreases, so last row is first in the file. There are two sets of data in the file: The data after FT'ing along F2 only, and the data after FT'ing along both dimensions. The "2" in the format name means we are taking the second data set. This format is used by JEOL when exporting to "generic ascii". Argument nF2 is ignored with this format as the value is sought from the corresponding *.hdr file. Doing so also allows one to import files with slightly different F1 and or F2, but for this to be successful you will need to 1) set allowSloppy = TRUE in the call to files2Spectra2DObject and 2) harmonize the dimensions manually after initial import.

Other Format Codes

Here are some other format codes you can use:

• "SimpleM". Imports matrices composed of z values. The F2 and F1 values are created from the dimension of the matrix. After import, you will have to manually convert the F2 and F1 values to ppm. You may also have to transpose the matrices, or perhaps invert the order of the rows or columns. Imported via read.table.

• "Btotxt". This format imports Bruker data written to a file using the Bruker "totxt" command. Tested with TopSpin 4.0.7. This format is read via readLines and thus the ... argument does not apply.

• "dx". This format imports files written in the JCAMP-DX format, via package readJDX.

Author(s)

Bryan A. Hanson, DePauw University.