#! /bin/tcsh -f
#
# Name: minc2seqinfo
#
# Purpose: extracts the relevent information for the seq.info file
#          that is part of the Sessions Database.
#
# The seq.info file has a tag-value following format.
# Example, for a data set with 16 slices, each slice 64x64, with 100 TRs,
# TR = 2 seconds, slice thickness of 5 mm, pixel size of 3.125
# collected with a sequence called ep2d_fid_ts_20b2604, then the
# seq.info file is shown below.  The order is actually unimportant. If there
# is no temporal dimension, then there would be no "ntrs" and "TR" fields.
#
# ------ cut here -------
# sequencename     ep2d_fid_ts_20b2604
# nrows            64
# ncols            64
# nslcs            16
# rowpixelsize     3.125
# colpixelsize     3.125
# slcpixelsize     5.000
# ntrs             100
# TR               2.0
# ------ cut here -------
#
# Original Author: Doug Greve
#
# Copyright © 2021 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

if($#argv != 1  && $#argv != 2  ) then
  echo "Usage: minc2seqinfo mincfile <seqinfofile>"
  exit 1;
endif

set TR   = ();
set ntrs = ();

set mnc     = $argv[1];

if(! -e $mnc) then
  echo "ERROR: $mnc does not exist"
  exit 1;
endif

### Get the name of the sequnce ###
set seq  = `mincinfo -attvalue acquisition:scanning_sequence $mnc`;
set seq  = `basename $seq`;

## Get the names of the dimensions ##
set dimnames = `mincinfo -dimnames $mnc`;

## If the first dimension is time, then extract the relevant
## information and remove it from the list of dimension names
if($dimnames[1] == time) then
  set TR   = `mincinfo -attvalue  time:step $mnc`;
  set ntrs = `mincinfo -dimlength time      $mnc`;
  shift dimnames;
endif

## Get the number and size of each dimension
## vdim:  nslices, nrows, ncols
## vsize: slice thicknes, row thickness, col thickness
set vdim  = ();
set vsize = ();
foreach dim ($dimnames)
  set n = `mincinfo -dimlength $dim      $mnc`;
  set d = `mincinfo -attvalue  $dim\:step $mnc`;
  set d = `echo "sqrt($d*$d)" | bc -l`; # absolute value
  set vdim  = ($vdim  $n);
  set vsize = ($vsize $d);
end

if($#argv == 2) then
  # send to  seq.info file specified on command-line #
  set seqinfo = $argv[2];
  set seqinfodir  = `dirname  $seqinfo`;
  mkdir -p $seqinfodir
  rm -f $seqinfo
  echo "sequencename $seq"      >> $seqinfo
  echo "nrows        $vdim[2]"  >> $seqinfo
  echo "ncols        $vdim[3]"  >> $seqinfo
  echo "nslcs        $vdim[1]"  >> $seqinfo
  echo "rowpixelsize $vsize[2]" >> $seqinfo
  echo "colpixelsize $vsize[3]" >> $seqinfo
  echo "slcpixelsize $vsize[1]" >> $seqinfo
  if($#TR != 0) then
    echo "ntrs         $ntrs"   >> $seqinfo
    echo "TR           $TR"     >> $seqinfo
  endif
else
  # no seq.info file specified, print to stdout #
  echo "sequencename $seq"
  echo "nrows        $vdim[2]"
  echo "ncols        $vdim[3]"
  echo "nslcs        $vdim[1]"
  echo "rowpixelsize $vsize[2]"
  echo "colpixelsize $vsize[3]"
  echo "slcpixelsize $vsize[1]"
  if($#TR != 0) then
    echo "ntrs         $ntrs"
    echo "TR           $TR"
  endif
endif

exit 0