#! /bin/tcsh -f

#
# check-sliceres-sess
#
# Original Author: Doug Greve
# CVS Revision Info:
#    $Author: nicks $
#    $Date: 2007/01/09 22:41:16 $
#    $Revision: 1.2 $
#
# Copyright (C) 2002-2007,
# The General Hospital Corporation (Boston, MA). 
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-bugs@nmr.mgh.harvard.edu
#



set VERSION = '$Id: check-sliceres-sess,v 1.2 2007/01/09 22:41:16 nicks Exp $';

set inputargs = ($argv);

set fix = 0;
set fsdlist = ();
set PrintHelp = 0;

if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l` 
if($n != 0) then
  set PrintHelp = 1;
  goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l` 
if($n != 0) then
  echo $VERSION
  exit 0;
endif

set PWD = `getpwdcmd`;
if($status) exit 1;

set SessList = `getsesspath $argv`;
if($status || $#SessList == 0) then
  getsesspath $argv 
  exit 1;
endif

goto parse_args;
parse_args_return:

goto check_params;
check_params_return:

foreach sess ($SessList)
  set sessid = `basename $sess`;
  echo "$sessid -----------------------------------"

  foreach fsd ($fsdlist)

    set fsdpath = $sess/$fsd
    if(! -e $fsdpath) then
      echo "INFO: $fsd does not exist for this session, skipping"
      continue;
    endif
    cd $fsdpath;

    set RunList = `getrunlist .`;
    if($#RunList == 0) then
      echo "INFO: no runs found for FSD $fsd, skipping"
      continue;
    endif

    set infodump = $RunList[1]/f-infodump.dat
    if(! -e $infodump) then
      echo "INFO: $infodump does not exist for this FSD, skipping"
      continue;
    endif

    set tmp = `grep dDistFact $infodump`;
    if($#tmp == 0) then
      echo "INFO: no skip factor specified for this data, continuing"
      continue;
    endif

    set distfact = $tmp[3];

    set seqinfo = seq.info
    if(! -e $seqinfo) then
      echo "ERROR: $seqinfo file does not exist, aborting"
      exit;
    endif

    set seqsliceres = `cat $seqinfo | grep slcpixelsize`;
    if($#seqsliceres == 0) then
      echo "ERROR: seq.info file is not formatted properly"
      exit 1;
    endif

  end

end


echo "check-sliceres-sess done"

exit 0

###############################################

############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )

  set flag = $argv[1]; shift;
  
  switch($flag)

   case "-fsd"
      if($#argv < 1) goto arg1err;
      set fsdlist = ($fsdlist $argv[1]); shift;
      breaksw

    case "-verbose":
      set verbose = 1;
      breaksw

    case "-echo":
      set echo = 1;
      breaksw

    case "-debug":
      set verbose = 1;
      set echo = 1;
      breaksw

    case "-g":
    case "-s":
    case "-sf":
    case "-d":
    case "-df":
      shift;
      # ignore getsesspath arguments 
      breaksw

    case "-cwd":
      # ignore getsesspath arguments 
      breaksw

    case "-umask":
      if ( $#argv == 0) goto arg1err;
      umask $1; shift;
      breaksw

    default:
      echo ERROR: Flag $flag unrecognized. 
      echo $cmdline
      exit 1
      breaksw
  endsw

end

goto parse_args_return;
############--------------##################

############--------------##################
check_params:

  if($#fsdlist == 0) then
    set fsdlist = (bold t1epi)
  endif
 
goto check_params_return;
############--------------##################

############--------------##################
arg1err:
  echo "ERROR: flag $flag requires one argument"
  exit 1
############--------------##################

############--------------##################
usage_exit:
  echo ""
  echo "USAGE: check-sliceres-sess"
  echo ""
  echo "Other Arguments (Optional)"
  echo "   -mask mask     : binary mask (fsd/masks/mask)"
  echo "   -hpf  cutoff   : high-pass filter cut off (sec), not with -fit"
  echo "   -meanfit       : fit and remove mean (not with -hpf)"
  echo "   -trendfit      : fit and remove linear trend (not with -hpf)"
  echo ""
  echo "Session Arguments (Required)"
  echo "   -sf sessidfile  ..."
  echo "   -df srchdirfile ..."
  echo "   -s  sessid      ..."
  echo "   -d  srchdir     ..."
  echo ""
  echo "Yet even more options"
  echo "   -help  : help"
  echo "   -debug : print out ridiculous amounts of verbiage"
  echo "   -umask   mask : unix file permission mask"
  echo ""

  if(! $PrintHelp) exit 1;

  echo $VERSION

  cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'

exit 1;


#---- Everything below here is printed out as part of help -----#
BEGINHELP

This will go through each functional subdirectory and check whether
the slice thickness includes the skip.