#! /bin/sh

#  Processing script for the Rowland NMR Toolkit
#  The script processes data along all dimensions
#  with generic processing parameters
#  For more customized processing scripts use the script
#  generator at http://sbtools.uchc.edu/nmr
#  NOTE: When using the sbtools script generator 
#  copy and paste the contents of the sbtools.input 
#  file directly into the script generator to quickly and accurately
#  fill out the form page with relevant parameters


section -c 4096 1024
echo 'Creating a parameter file for Bruker format and importing data'
if [ -e ser.par ]; then rm ser.par; fi
if [ -e ser.dat ]; then mv ser.dat ser.dat.orig; fi
if [ -e ser ]; then cp ser ser.dat; else echo 'file ser does not exit! Exiting!'; exit 1; fi
echo 'Format   big-endian   int-32' >> ser.par
echo 'DOM   t1   t2' >> ser.par
echo 'N		150 C	1024 C' >> ser.par
echo 'SW	14085.1048	11160.7143' >> ser.par
echo 'SF	  201.2074	  800.1899' >> ser.par
echo 'PPM	   41.7315	    4.7638' >> ser.par
echo 'QUAD	STATES-TPPI	STATES' >> ser.par
echo 'LAYOUT  T1:300 T2:2048' >> ser.par
rnmrtk LOAD ser.dat
rnmrtk SEEPAR
rm ser.dat

echo 'Saving time domain data'
rnmrtk << EOF
DIM t2
COM 'Take the complex conjugate to reverse acquisition dimension'
CONJ
COM 'Eliminating intial points in Bruker digital filtered data'
SHRINK 953 72
SAVE time_2d.sec
EOF

echo 'Starting t2 fourier transformation of 2D data set'
rnmrtk << EOF
DIM t2
BC 12.5
GM 20.0 20.0
ZEROFILL 2048
FFT 0.5
PHASE 144.000 0.0
REALPART
SAVE F2_PROC.sec
SEEPAR
EOF

section -d
section -c 2048 1024
echo 'Starting t1 Fourier transformation of 2D data set w/o LP'
rnmrtk << EOF
LOAD F3_PROC.sec
DIM t1
ZEROFILL 512
FFT 0.50
PHASE 0.0 0.0
REALPART
SEEPAR
EOF

echo 'Saving data in Rowland NMRToolkit format as hsqcetgpsi.sec and '
echo 'NMRPipe format as .ft2'
echo 'If the files exist they will be overwritten!'
rnmrtk << EOF
SAVE hsqcetgpsi.sec
PUTNMRPIPE hsqcetgpsi.ft2 f3 f2
EOF

echo 'Removing shared memory section'
section -d

echo 'Cleaning up intermediate files'
rm time_3d.sec time_3d.par F3_PROC.sec F3_PROC.par