#! /bin/tcsh

# fixup_mni_paths
#
# The MNI tools, when originally compiled and installed, hard-code
# the perl path into several files.  This is problematic if the
# MNI tools are moved to another system, and the perl path is
# different.
#
# If the MNI tools built on one system are moved to another, then
# this script patches the files with the correct perl path.
#
# if MY_PERL is set to a path to perl, it will use that instead of
# trying to determine the default path.  this is useful when
# needing to over-ride the default path.
#
# Original Author: Nick Schmansky
#
# 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 echo=1

if (! $?MY_PERL) then
    setenv MY_PERL `which perl`
    if ($status) then
        echo "You do not seem to have perl on your system!"
        echo "The MNI tools require perl."
        exit 1
    endif
endif
echo "Using perl '$MY_PERL'"

# MINC_BIN_DIR is defined by $FREESURFER_HOME/FreeSurferEnv.csh
if (! $?MINC_BIN_DIR) then
    echo "MINC_BIN_DIR is not defined!"
    echo "Type 'source $FREESURFER_HOME/SetUpFreeSurfer.csh' to set this,"
    echo "where FREESURFER_HOME is set to your Freesurfer installation path,"
    echo "or set MINC_BIN_DIR to your MINC toolkit /bin path."
    exit 1
else if (! -e $MINC_BIN_DIR) then
    echo "MINC_BIN_DIR '$MINC_BIN_DIR' does not exist!"
    exit 1
endif

cd $MINC_BIN_DIR

setenv SEDFLAGS1 "s,/usr/pubsw/bin/perl,${MY_PERL},g"
setenv SEDFLAGS2 "s,/usr/local/bin/perl,${MY_PERL},g"
echo $SEDFLAGS1 >sedfile1
echo $SEDFLAGS2 >sedfile2

# this is included to fixup older MINC toolkit installations:
setenv MINC_HOME_DIR `echo $MINC_BIN_DIR | sed - -e s/'\/'bin//`
setenv SEDFLAGS3 "s,/usr/pubsw/packages/mni/1.0.4,${MINC_HOME_DIR},g"
echo $SEDFLAGS3 >sedfile3
setenv SEDFLAGS4 "s,/usr/pubsw/packages/mni/current,${MINC_HOME_DIR},g"
echo $SEDFLAGS4 >sedfile4

# these are the files that contain the hard-coded paths in need of fixup:
set MNI_FILES = ( autocrop field2imp imp2field make_template mritoself mritotal nu_correct nu_estimate nu_estimate_np_and_em nu_evaluate resample_labels sharpen_volume xfmtool )

foreach file ($MNI_FILES)
    echo "Patching $file...(original file saved to $file.old)"
    mv $file $file.old
    sed -f sedfile1 $file.old > $file.1
    sed -f sedfile2 $file.1 > $file.2
    sed -f sedfile3 $file.2 > $file.3
    sed -f sedfile4 $file.3 > $file
    chmod a+x $file
    if (-e $file.1) rm -f $file.1
    if (-e $file.2) rm -f $file.2
    if (-e $file.3) rm -f $file.3
end
rm -f sedfile1 sedfile2 sedfile3 sedfile4
echo "done."

echo "Here are the changes:"
foreach file ($MNI_FILES)
    echo "diff $file $file.old"
    diff $file $file.old
end
echo "done."
echo "Note: not all systems will require a patch,"
echo "and may not show any differences."

echo "Now a test of the MNI tool 'nu_correct'..."
rehash
nu_correct
echo "A version number and usage message should have been displayed."