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[WIP] Fix and update commit #1279

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[WIP] Fix and update commit #1279

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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ dependencies = [
"deepdiff>=8.1,<8.7",
"dipy==1.11.*",
"dmri-amico==2.1.*",
"dmri-commit==2.3.*",
"dmri-commit==2.4.*",
"docopt==0.6.*",
"dvc==3.59.*",
"formulaic==0.5.*",
Expand Down
13 changes: 5 additions & 8 deletions src/scilpy/cli/scil_tractogram_commit.py
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Expand Up @@ -234,12 +234,11 @@ def _save_results(args, tmp_dir, ext, in_hdf5_file, offsets_list, sub_dir,

# Simplifying output for streamlines and cleaning output directory
streamline_weights = np.loadtxt(os.path.join(commit_results_dir,
'streamline_weights.txt'))

'streamline_weights.txt'))
# Loading the tractogram (we never did yet! Only sent the filename to
# commit). Reminder. If input was a hdf5, we have changed
# args.in_tractogram to our tmp_tractogram saved in tmp_dir.
if ext == '.trk' and args.reference is None:
if ext in ['.trk', '.h5'] and args.reference is None:
args.reference = 'same'
logging.debug('Loading tractogram from {} with reference {}.'
.format(args.in_tractogram, args.reference))
Expand All @@ -261,7 +260,7 @@ def _save_results(args, tmp_dir, ext, in_hdf5_file, offsets_list, sub_dir,
'tot_commit_w'
# Reload is needed because of COMMIT handling its file by itself
sft.data_per_streamline[dps_key] = streamline_weights
sft.data_per_streamline[dps_key_tot] = streamline_weights * length_list
sft.data_per_streamline[dps_key_tot] = np.squeeze(streamline_weights) * length_list

if args.keep_whole_tractogram:
output_filename = os.path.join(out_dir, 'tractogram.trk')
Expand Down Expand Up @@ -391,7 +390,6 @@ def main():

# Prepare tmp dir for all our intermediate files
tmp_dir = tempfile.TemporaryDirectory()

# === Loading ===
dwi_img = nib.load(args.in_dwi)

Expand Down Expand Up @@ -443,8 +441,7 @@ def main():

# Preparation for fitting
commit.core.setup()
mit = commit.Evaluation('.', '.')

mit = commit.Evaluation('.', '.', dictionary_path=tmp_dir.name)
# FIX for very small values during HCP processing
# (based on order of magnitude of signal)
data = dwi_img.get_fdata(dtype=np.float32)
Expand Down Expand Up @@ -476,7 +473,7 @@ def main():
return
mit.load_kernels()
use_mask = args.in_tracking_mask is not None
mit.load_dictionary(tmp_dir.name, use_all_voxels_in_mask=use_mask)
mit.load_dictionary(None, use_all_voxels_in_mask=use_mask)
mit.set_threads(args.nbr_processes)
mit.set_verbose(False)

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