#!/bin/tcsh

@global_parse `basename $0` "$*" ; if ($status) exit 0

set version   = "1.0";  set rev_dat   = "Feb 22, 2024"
# + script to do deobliquing while preserving the coord origin
#
# ----------------------------------------------------------------

set this_prog = "adjunct_deob_around_origin"
set prog_abbr = "adfo"
#set tpname    = "${this_prog:gas///}"
set here      = $PWD

# ----------------------- set defaults --------------------------

set input   = ""
set prefix  = ""

set odir    = $here
set opref   = ""
set wdir    = ""

set obl_meth  = "-oblique_recenter"

set do_ow     = ""                      # def: don't overwrite output
set DO_CLEAN  = 1                       # def: rm working dir

# ------------------- process options, a la rr ----------------------

if ( $#argv == 0 ) goto SHOW_HELP

set ac = 1
while ( $ac <= $#argv )
    # terminal options
    if ( ("$argv[$ac]" == "-h" ) || ("$argv[$ac]" == "-help" )) then
        goto SHOW_HELP
    endif
    if ( "$argv[$ac]" == "-ver" ) then
        goto SHOW_VERSION
    endif

    if ( "$argv[$ac]" == '-echo' ) then
        set echo

    # --------- required

    else if ( "$argv[$ac]" == "-input" ) then
        if ( $ac >= $#argv ) goto FAIL_MISSING_ARG
        @ ac += 1
        set input = "$argv[$ac]"

    else if ( "$argv[$ac]" == "-prefix" ) then
        if ( $ac >= $#argv ) goto FAIL_MISSING_ARG
        @ ac += 1
        set prefix = "$argv[$ac]"
        set opref  = `basename "$argv[$ac]"`
        set odir   = `dirname  "$argv[$ac]"`

    # --------- opt

    else if ( "$argv[$ac]" == "-workdir" ) then
        if ( $ac >= $#argv ) goto FAIL_MISSING_ARG
        @ ac += 1
        set wdir = "$argv[$ac]"

        set tf = `python -c "print('/' in '${wdir}')"`
        if ( "${tf}" == "True" ) then
            echo "** ERROR: '-workdir ..' is a name only, no '/' allowed\n"
            goto BAD_EXIT
        endif

    # can choose any of 3drefit's deobliquing styles
    else if ( "$argv[$ac]" == "-oblique_origin" ) then
        set obl_meth = "$argv[$ac]"
    else if ( "$argv[$ac]" == "-oblique_recenter" ) then
        set obl_meth = "$argv[$ac]"
    else if ( "$argv[$ac]" == "-oblique_recenter_raw" ) then
        set obl_meth = "$argv[$ac]"

    else if ( "$argv[$ac]" == "-overwrite" ) then
        set do_ow = "-overwrite"

    else if ( "$argv[$ac]" == "-no_clean" ) then
        set DO_CLEAN = 0
        
    else
        echo "\n\n** ERROR: unexpected option #$ac = '$argv[$ac]'\n\n"
        goto BAD_EXIT
        
    endif
    @ ac += 1
end

# =======================================================================
# ======================== ** Verify + setup ** =========================
# =======================================================================

if ( "${prefix}" == "" ) then
    echo "** ERROR: need to provide output name with '-prefix ..'"
    goto BAD_EXIT
endif

if ( "${input}" == "" ) then
    echo "** ERROR: need to provide input dataset with '-input ..'"
    goto BAD_EXIT
endif

# -----------------------------------------------------------------------
# Check obliquity and av_space

# Is the dset oblique? If not, just copy and exit
set is_obl = `3dinfo -is_oblique "${input}"`

if ( "${is_obl}" == "0" ) then
    echo "++ Input dset is not oblique: just copying with 3dcopy."
    3dcopy ${do_ow} "${input}" "${prefix}"

    if ( $status ) then
        echo "** ERROR: will not overwrite existing file"
        goto BAD_EXIT
    endif

    goto DONE_MSG
endif

# This should always be "+orig", but sometimes there are header issues
# (like [qs]form_code stuff
set avsp = `3dinfo -av_space "${input}"`

if ( "${avsp}" != "+orig" ) then
    echo "+* WARN: input dataset is *not* in orig space."
    echo "   That is surprising that it would have obliquity, then."
endif
# -----------------------------------------------------------------------

# make workdir name, if nec
if ( "${wdir}" == "" ) then
    set tmp_code = `3dnewid -fun11`  # should be essentially unique hash
    set wdir     = __workdir_${prog_abbr}_${tmp_code}
endif

# check output directory, use input one if nothing given
if ( ! -e "${odir}" ) then
    echo "++ Making new output directory: ${odir}"
    \mkdir -p "${odir}"
endif

# make the working directory
if ( ! -e "${odir}/${wdir}" ) then
    echo "++ Making working directory: ${odir}/${wdir}"
    \mkdir -p "${odir}/${wdir}"
else
    echo "+* WARNING:  Somehow found a premade working directory (?):"
    echo "      ${odir}/${wdir}"
endif

echo "++ Oblique method in 3drefit is: ${obl_meth}"

# =======================================================================
# =========================== ** Main work ** ===========================
# =======================================================================

# copy dset: *must* be to BRIK/HEAD format
3dcopy   "${input}"         "${odir}/${wdir}/tmp"

# move to working directory
cd "${odir}/${wdir}"

# do the deobliquing stuff
3drefit  ${obl_meth}        tmp${avsp}
3drefit  -deoblique         tmp${avsp}

# done, copy back up 
3dcopy ${do_ow} tmp${avsp}  "../${opref}"

if ( $status ) then
    echo "** ERROR: will not overwrite existing file"
    goto BAD_EXIT
endif

# ---------------------------------------------------------------------

# move out of wdir to the odir
cd ..

if ( $DO_CLEAN == 1 ) then
    echo "++ Clean working dir"
    \rm -rf ${wdir}
else
    echo "++ NOT removing temporary axialization working dir: ${wdir}"
endif

DONE_MSG: 

cat <<EOF

++ DONE. See the output:
   ${prefix}

EOF

goto GOOD_EXIT

# ========================================================================
# ========================================================================

SHOW_HELP:
cat << EOF
-------------------------------------------------------------------------

Overview ~1~

This is a simple program to wrap around the 3drefit functionality to 
remove obliquity from a dataset whilst preserving its origin.

In many cases, this is very useful to run on oblique anatomicals
before processing.

ver  = ${version}
auth = PA Taylor, RC Reynolds (SSCC, NIMH, NIH)
-------------------------------------------------------------------------

Options ~1~

-input                 : (req) input volumetric dataset name
-prefix                : (req) output dataset name
-oblique_origin        : style of preserving origin, via 3drefit (def)
-oblique_recenter      : style of preserving origin, via 3drefit (def)
-oblique_recenter_raw  : style of preserving origin, via 3drefit (def)
-workdir               : working directory name (just name, no path;
                         will be subdirectory of the output location)
-overwrite             : when writing output, overwrite any preexisting
                         dataset (def: do not overwrite)
-no_clean              : when done, do not remove temporary working
                         directory (def: do remove woroking directory
-echo                  : run very verbosely (with 'set echo' on)
-ver                   : display program version
-help                  : show help
-hview                 : show help in text editor

-------------------------------------------------------------------------

Examples ~1~

1) Basic usage:
     adjunct_deob_around_origin                       \
         -input   sub-001_T1w.nii.gz                  \
         -prefix  sub-001_T1w_DEOB.nii.gz

2) Different origin-preservation choice:
     adjunct_deob_around_origin                       \
         -oblique_recenter_raw                        \
         -input   sub-001_T1w.nii.gz                  \
         -prefix  sub-001_T1w_DEOB.nii.gz

EOF

# ----------------------------------------------------------------------

goto GOOD_EXIT

SHOW_VERSION:
    echo "version  $version (${rev_dat})"
    goto GOOD_EXIT

FAIL_MISSING_ARG:
    echo "** ERROR: Missing an argument after option flag: '$argv[$ac]'"
    goto BAD_EXIT

BAD_EXIT:
    exit 1

GOOD_EXIT:
    exit 0