nmrglue.fileio.varian.read

nmrglue.fileio.varian.read(dir='.', fid_file='fid', procpar_file='procpar', read_blockhead=False, shape=None, torder=None, as_2d=False)

Read Agilent/Varian files in a directory.

Parameters :

dir : str, optional

Directory holding Agilent/Varian data. Default is the current working directory.

fid_file : str, optional

Filename of binary (fid) file in directory.

procpar_file : str, optional

Filename of procpar file in directory.

read_blockhead : bool, optional

True to read blockheader(s) and return then in the Agilent/Varian parameter dictionary. False (default) does not perform this reading.

shape : tuple of ints, optional

Shape of data in binary file. None (default) will attempt to finds this automatically.

torder : {None, ‘r’, ‘o’, ‘f’ or a Python function} , optional

Description of the mapping of traces in the file to the NMR data matrix. None (the default) will attempt to find this automatically which is typically fine for most NMR experiments. See below for additional details.

as_2d : bool, optional

True to return data as a 2D array ignorning the shape and torder parameters.

Returns :

dic : dict

Dictionary of Agilent/Varian parameters.

data : ndarray

Array of NMR data

See also

read_lowmem

Read Agilent/Varian files using mimimal amounts of memory.

write

Write Agilent/Varian files.

Notes

The torder parameter describes how the traces on disk should be re-organized to form the NMR data matrix. In most cases this can be determined automatically by examining the order of phase parameters in the procpar file. This is done if torder is set to None. In some cases it must be explicitly provided. Three common cases are:

Name	Ordering of arrays	torder	Notes
regular	d3, d2, phase2, phase	‘regular’ or ‘r’
opposite	d3, d2, phase, phase2	‘opposite’ or ‘o’
flat	As data exists in file	‘flat’ or ‘f’	Valid for 1D or 2D data

In addition a function which maps indirect dimension index tuples to/from trace numbers as stored on disk can be provided. For reading this function should take 2 arguments: shape, index_tuple and return an integer trace number. For writing this function should again take 2 arguments: shape,trace_number and return the indirect dimension index tuple for the given trace.