convert example: bruker2pipe_3d

This example shows how to use nmrglue to convert between the Bruker and NMRPipe file format for a 3D data set. The last block of code lists the differences between this conversion and one performed with bruk2pipe. Note that the direct dimension digital filter is not removed in either conversion.

[source code]

#! /usr/bin/env python

import nmrglue as ng

# read in the varian data (any of the follow lines will work)
dic,data=ng.bruker.read_lowmem("../common_data/3d_bruker")

# Set the parameters (many of these can be found in the procpar file
u = ng.bruker.guess_udic(dic,data)
# Direct Dimension
u[2]['size']     = 768
u[2]['complex']  = True
u[2]['encoding'] = 'direct'
u[2]['sw']       = 11061.947
u[2]['obs']      = 800.134
u[2]['car']      = 4.784*800.134
u[2]['label']    = '1H'

# First indirect dimension
u[1]['size']     = 128
u[1]['complex']  = True
u[1]['encoding'] = 'states'
u[1]['sw']       = 2500.000
u[1]['obs']      = 81.086
u[1]['car']      = 119.787*81.086
u[1]['label']    = '15N'

# Second indirect dimension
u[0]['size']     = 116
u[0]['complex']  = True
u[0]['encoding'] = 'states'
u[0]['sw']       = 5555.556
u[0]['obs']      = 201.204
u[0]['car']      = 55.743*201.204
u[0]['label']    = '13C'


# create the converter object and initilize with varian data
C = ng.convert.converter()
C.from_bruker(dic,data,u)

# create pipe data and then write it out
ng.pipe.write("./data/3d_pipe%03d.fid",*C.to_pipe(),overwrite=True)

# check the conversion against NMRPipe (only check the 5th slice of 3D)
print "Conversion complete, listing differences between files:"
pdic,pdata = ng.pipe.read_lowmem("./data/3d_pipe%03d.fid")
pdic2,pdata2 = ng.pipe.read_lowmem("../common_data/3d_bruker/fid/test%03d.fid")
print ng.misc.pair_similar(pdic,pdata[5],pdic2,pdata2[5],verb=True)