Kuprov: version fragment to 2.13 per IK 2026-08-30

2026-08-30T09:11:33Z

version fragment to 2.13 per IK 2026-08-30

Kuprov: new page for Spinach main f053e432: documents fid2pipe.m from the source header and implementation

2026-08-30T08:03:01Z

new page for Spinach main f053e432: documents fid2pipe.m from the source header and implementation

New page

{{DISPLAYTITLE:fid2pipe.m}} __NOTOC__
Exports phase-sensitive 2D Spinach free induction decays into native NMRPipe time-domain files. The function first points the NMRPipe runtime environment at the installation supplied by the caller: the nmrbin.linux212_64 and com directories are prepended to PATH, the library path is extended with the NMRPipe library directory, and TCLPATH, TCL_LIBRARY, TK_LIBRARY, BLT_LIBRARY, NMRBASE, NMRBIN, and NMRTXT are set; OPENWINHOME is set as well when the openwin directory is present.

Observation frequencies for the two dimensions are computed in MHz from the magnetogyric ratios of the isotopes named in parameters.spins and the magnet field in spin_system.inter.magnet, and the carriers are converted into signed ppm by [[hz2ppm.m]] function. Each of the two components of the free induction decay is then written into a temporary text file, one point per line with the direct-dimension index, the indirect-dimension index, the real part, and the imaginary part, and converted into the NMRPipe format by the txt2pipe.tcl script with complex States acquisition in both dimensions. The temporary text file is deleted after each conversion, and a non-zero exit status from the conversion raises an error carrying the NMRPipe output.

==Syntax==

fid2pipe(spin_system,file_root,fid,parameters,nmrpipe_root)

==Parameters==

spin_system - Spinach spin system structure

file_root - output file name root without shell metacharacters;
the function writes <file_root>_pos.fid and
<file_root>_neg.fid

fid - structure with fid.pos and fid.neg complex matrices;
rows are direct-dimension points, and columns are
indirect-dimension points

parameters - pulse sequence parameters structure with fields
sweep, npoints, offset, and spins

nmrpipe_root - NMRPipe installation root containing com/txt2pipe.tcl
and nmrbin.linux212_64

==Outputs==

this function writes two NMRPipe files

==Notes==
Note: the exported files preserve the two Spinach echo/anti-echo components; recombination is done in the accompanying NMRPipe processing script after the direct-dimension Fourier transform.

parameters.sweep and parameters.offset are ordered [F1 F2], and parameters.npoints is checked against the dimensions of fid.pos and fid.neg: parameters.npoints(1) must equal the number of columns and parameters.npoints(2) the number of rows.

Both file_root and nmrpipe_root are restricted to alphanumeric characters and the /_.- set, and must contain no whitespace, because they are passed to a shell command.

==See also==
[[fid2ascii.m]], [[s2json.m]], [[hz2ppm.m]], [[Import, export, and visualisation]]

''Version 2.11, authors: [[Ilya Kuprov]]''

← Older revision		Revision as of 09:11, 30 August 2026
Line 40:		Line 40:
	[[fid2ascii.m]], [[s2json.m]], [[hz2ppm.m]], [[Import, export, and visualisation]]		[[fid2ascii.m]], [[s2json.m]], [[hz2ppm.m]], [[Import, export, and visualisation]]

−	''Version 2.11, authors: [[Ilya Kuprov]]''	+	''Version 2.13, authors: [[Ilya Kuprov]]''

Fid2pipe.m - Revision history

Kuprov: version fragment to 2.13 per IK 2026-08-30

Kuprov: new page for Spinach main f053e432: documents fid2pipe.m from the source header and implementation