#! /bin/csh -f

#
# dicom-rename
#
#
#
# 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
#
#


set VERSION = 'dicom-rename dev';
set inputargs = ($argv);
set PrintHelp = 0;

set OutBase = ();
set InFileList = ();

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

source $FREESURFER_HOME/sources.csh

goto parse_args;
parse_args_return:
goto check_params;
check_params_return:

set OutDir = `dirname $OutBase`;
mkdir -p $OutDir
if($status) then
  echo "ERROR: creating $OutDir"
  exit 1;
endif

echo "Checking $#InFileList files"

@ ndicoms = 0;
foreach InFile ($InFileList)

  set filetype = `mri_probedicom --i $InFile --d filetype`;
  if($status) then
    echo "ERROR: $filetype"
    exit 1;
  endif
  if($filetype == "notdicom") continue;
  @ ndicoms = $ndicoms + 1;

  set seriesno = `mri_probedicom --i $InFile --t 20 11`;
  if($status) then
    echo "ERROR: $seriesno"
    exit 1;
  endif

  set imageno = `mri_probedicom --i $InFile --t 20 13`;
  if($status) then
    echo "ERROR: $imageno"
    exit 1;
  endif

  set seriesnopad = `printf "%03d" $seriesno`
  set imagenopad  = `printf "%05d" $imageno`

  set OutFile = $OutBase-$seriesnopad-$imagenopad.dcm

  echo $ndicoms $InFile $OutFile
  cp $InFile $OutFile

end

echo "Copied $ndicoms dicom files"
echo "dicom-rename done"

exit 0

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

  set flag = $argv[1]; shift;

  switch($flag)

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

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

    default:
      set InFileList = ($InFileList $flag)
      breaksw
  endsw

end

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

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

  if($#OutBase == 0) then
    echo "ERROR: must spec an output base"
    exit 1;
  endif

  if($#InFileList == 0) then
    echo "ERROR: no input files specified"
    exit 1;
  endif

goto check_params_return;
############--------------##################

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

############--------------##################
arg2err:
  echo "ERROR: flag $flag requires two arguments"
  exit 1
############--------------##################

############--------------##################
usage_exit:
  echo "USAGE: dicom-rename"
  echo ""
  echo "Copies dicom file(s) to new path with more meaningful names"
  echo ""
  echo " --o outbase"
  echo ""
  echo "   --version    : print version and exit"
  echo "   --help       : print help and exit"
  echo ""

  if($PrintHelp) \
  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

Renames (actually copies) input dicom files to a new name that
takes the form outbase-SSS-IIIII.dcm. The output can be used
with dcmdir-info-mgh.

Example:

dicom-rename dicomdir/* --o mydicoms/bert

This will find all the dicoms in dicomdir/*, and rename them to
mydicoms/bert-SSS-IIIII.dcm, where SSS is the series number (dicom tag
20,11) and IIIII is the image number (dicom tag 20,13). The series
number and image number are padded with zeros to make them 3 or 5
digits long. Note: does not actually rename the dicom file; it just
copies it to a new name (ie, it will not delete the input file(s)).

It is ok if input files are not dicom. The script will only use the
files in the list that are dicom.

This script is especially useful when copying data from a Siemens CD
where the file names are often uninterpretable.


See also cp-dicom, dcmdir-info-mgh, mri_probedicom, unpacksdcmdir