run

#!/bin/bash
set -e
set -x

source environment.sh

FLYWHEEL_BASE=/flywheel/v0
IN=$FLYWHEEL_BASE/input
OUT=$FLYWHEEL_BASE/output
TMP=/tmp

# the following lets output show on stdout and stderr, and also
# redirects them to files that will appear in the output.
# combines http://stackoverflow.com/a/692407 and http://stackoverflow.com/a/11886837
exec > >(tee -i $OUT/stdout.log) 2> >(tee -i $OUT/stderr.log >&2)

cd $TMP

preprocess_nifti() {
  # because the python script is a no-op for things that are
  # correct, we can safely run it on data that has already been fixed.
  RAW=$1
  tmpdir=$(mktemp -d)

  BASENAME=$(basename $RAW)
  FIXED=$tmpdir/$BASENAME
  # fix nifti header issue
  python $FLYWHEEL_BASE/fix_nifti.py $RAW $FIXED

  WITHOUT_EXT="${BASENAME%%.*}"

  # converting input nifti to AFNI
  3dcalc -a $FIXED -prefix $WITHOUT_EXT -expr 'a'
  # XXX make sure WITHOUT_EXT was created?

  echo $WITHOUT_EXT+orig
}

anatomical=$(preprocess_nifti $IN/anatomical/*)
original_functional=$(preprocess_nifti $IN/functional/*)
# This warp target should be in the same space as the anatomical.
# In the future, this might be in the standard space.
warp_target=$IN/warp_target/*

# center to anatomical
@Align_Centers -base $anatomical -dset $original_functional
func=$(@GetAfniPrefix $original_functional)_shft+orig
funcprefix=$(@GetAfniPrefix $func)

# align to anatomical
# XXX removed -giant_move
# XXX does specifying that partial_axial help? XXX untested
align_epi_anat.py -dset2 $func -dset1 $anatomical -dset2to1 -dset2_base 0 \
  -suffix _func2anat -dset1_strip None -dset2_strip None \
  -partial_coverage

# XXX need 3dAllineate?? or is _func2anat enough?

# warp from warp_target to centered functional. This warp uses nearest neighbor
# interpolation, which makes it appropriate for segmentations.
# XXX need to make this into 3dAllineate xxxx
#3dNwarpApply -ainterp NN -short -nwarp \
#   "INV(${funcprefix}_func2anat_mat.aff12.1D)" \
#   -source $warp_target -master $func -prefix __tmp
cat_matvec -ONELINE ${funcprefix}_func2anat_mat.aff12.1D -I \
  > ${funcprefix}_anat2func_mat.aff12.1D
3dAllineate -1Dmatrix_apply ${funcprefix}_anat2func_mat.aff12.1D \
  -base $func -master BASE -source $warp_target -prefix __tmp

funcsegprefix=$(@GetAfniPrefix $original_functional)_seg
# uncenter this back to the original functional space
@Align_Centers -base $original_functional -dset __tmp+orig -no_cp
# change the datum type to byte to save space
# this step also gets rid of the shift transform in the header
3dcalc -a __tmp+orig -expr a -datum byte -nscale -prefix $funcsegprefix
# copy segmentation information from atlas to this native-space
#   segmentation dataset and mark to be shown with integer colormap
3drefit -cmap INT_CMAP $funcsegprefix+orig
3drefit -copytables $warp_target $funcsegprefix+orig

# cleanup tmp files
rm __tmp*

# convert output to nifti
for result in $funcsegprefix+orig.HEAD $original_functional.HEAD; do
  3dAFNItoNIFTI $result
  gzip $(@GetAfniPrefix $result).nii
  mv $(@GetAfniPrefix $result).nii.gz $OUT
done

# copy to output directory
mv *.aff12.1D $OUT