ReadFids: Read FIDs in Bruker format from a directory
In PepsNMR: Pre-process 1H-NMR FID signals

Description Usage Arguments Details Value Author(s) Examples

Finds all directories of path which contain a valid FID (i.e. contain the files fid, acqu and acqus) and loads them in a matrix.

1	ReadFids(path, l = 1, subdirs = FALSE, dirs.names = FALSE, verbose = FALSE)

`path`	A character string specifying the directory where the FIDs are searched.
`l`	A positive number indicating which line of the title file to use as spectra names.
`subdirs`	If `TRUE`, will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.
`dirs.names`	If `TRUE`, the FID names are recovered from the (sub)directories names, provided one subdirectory corresponds to one FID.
`verbose`	If `"TRUE"`, will print processing information.

The row names are the first line of the file "pdata/1/title" in the directory or the directory name(and subdirectory if subdirs == TRUE) if the title file doesn't exists or the line l is blank. The column names are the time coordinates of the FID. All the FIDs therefore need to have the same length and time interval between points.

Case 1: subdirs = FALSE

DIR1 => 1, 2, 3, ...

Case 2a: subdirs = TRUE

DIR1 => 1 ; DIR2 => 1 ; DIR3 => 1 ; ...

Case 2b: subdirs = TRUE

DIR1 => 1, 2, ... ; DIR2 => 1, 2, ... ; ...

Returns a list with the FIDs and their related information.

Fid_data

The matrix containing the FIDs.

Fid_info

A matrix containing the information about the FIDs. The naming of the row is the same than for Fid_data.

The columns are:

TD: Time domain size
BYTORDA: Determine the endiness of stored data. If 0 -> Little Endian; if 1 -> Big Endian
DIGMOD: Digitization mode
DECIM: Decimation rate of digital filter
DSPFVS: DSP firmware version
SW_h: Sweep width in Hz
SW: Sweep width in ppm
O1: Spectrometer frequency offset
GPRDLY: Group Delay
DT: Dwell time in microseconds

Benoît Legat & Manon Martin

path <-  system.file("extdata", package = "PepsNMRData")
dir(path)

fidList_HS <- ReadFids(file.path(path, "HumanSerum"))
FidData_HS_0 <- fidList_HS[["Fid_data"]]
FidInfo_HS <- fidList_HS[["Fid_info"]]