syntactical changes to scripts

Author: Arshitha

src/dsst_defacing_wf.py

@@ -65,6 +65,13 @@ def compress_to_gz(input_file, output_file):
                 f_output.writelines(f_input)
 
 
+def copy_over_sidecar(scan_filepath, input_anat_dir, output_anat_dir):
+    prefix = '_'.join([i for i in re.split('_|\.', scan_filepath.name) if i not in ['defaced', 'nii', 'gz']])
+    filename = prefix + '.json'
+    json_sidecar = input_anat_dir / filename
+    shutil.copy2(json_sidecar, output_anat_dir / filename)
+
+
 def reorganize_into_bids(input_dir, defacing_outputs, mapping_dict, no_clean):
     # make afni_intermediate_files for each session within anat dir
     for anat_dir in defacing_outputs.rglob('anat'):
@@ -86,10 +93,15 @@ def reorganize_into_bids(input_dir, defacing_outputs, mapping_dict, no_clean):
                 gz_file = anat_dir / Path(primary_t1).name
                 compress_to_gz(nii_filepath, gz_file)
 
+                # copy over corresponding json sidecar
+                copy_over_sidecar(Path(primary_t1), input_dir / anat_dir.relative_to(defacing_outputs), anat_dir)
+
             elif nii_filepath.name.endswith('_defaced.nii.gz'):
                 new_filename = '_'.join(nii_filepath.name.split('_')[:-1]) + '.nii.gz'
                 shutil.copy2(nii_filepath, str(anat_dir / new_filename))
 
+                copy_over_sidecar(nii_filepath, input_dir / anat_dir.relative_to(defacing_outputs), anat_dir)
+
         # move QC images and afni intermediate files to a new directory
         intermediate_files_dir = anat_dir / 'afni_intermediate_files'
         intermediate_files_dir.mkdir(parents=True, exist_ok=True)
@@ -118,7 +130,9 @@ def create_vqc_id_list(vqc_dir):
 
 def vqcdeface_prep(input_dir, defacing_output_dir):
     vqcdeface_dir = defacing_output_dir.parent / 'visualqc_prep' / 'vqcdeface'
-    for defaced_img in defacing_output_dir.rglob('*.nii.gz'):
+    interested_files = [f for f in defacing_output_dir.rglob('*.nii.gz') if
+                        'afni_intermediate_files' not in str(f).split('/')]
+    for defaced_img in interested_files:
         # please kill me now ughhh
         entities = defaced_img.name.split('.')[0].split('_')
         vqcd_subj_dir = vqcdeface_dir / f"{'/'.join(entities)}"

src/generate_mappings.py

@@ -42,7 +42,7 @@ def primary_scans_qc_prep(mapping_dict, visualqc_prep):
     :return str vqc_t1_mri_cmd: A visualqc T1 MRI command string.
     """
 
-    interested_keys = ('primary_t1', 'others')
+    interested_keys = ['primary_t1', 'others']
     primaries = []
     for subjid in mapping_dict.keys():
 

src/register.py

@@ -32,10 +32,10 @@ def preprocess_facemask(fmask_path, logfile_obj):
 
 
 def get_intermediate_filenames(outdir, prefix):
-    mat = f"{outdir.joinpath(prefix)}_reg.mat"
-    reg_out = f"{outdir.joinpath('registered.nii.gz')}"
-    mask = f"{outdir.joinpath(prefix)}_mask.nii.gz"
-    defaced_out = f"{outdir.joinpath(prefix)}_defaced.nii.gz"
+    mat = f"{outdir / prefix}_reg.mat"
+    reg_out = f"{outdir / prefix}_registered.nii.gz"
+    mask = f"{outdir / prefix}_mask.nii.gz"
+    defaced_out = f"{outdir / prefix}_defaced.nii.gz"
     return mat, reg_out, mask, defaced_out
 
 
@@ -58,13 +58,14 @@ def register_to_primary_scan(subj_dir, afni_workdir, primary_scan, other_scans_l
 
         matrix, reg_out, other_mask, other_defaced = get_intermediate_filenames(other_outdir, other_prefix)
 
-        mkdir_cmd = f"mkdir -p {other_outdir}; cp {other} {other_outdir.joinpath('original.nii.gz')}"
+        other_outdir.mkdir(parents=True, exist_ok=True)
+        cp_cmd = f"cp {other} {other_outdir.joinpath('original.nii.gz')}"
 
         flirt_cmd = f"flirt -dof 6 -cost mutualinfo -searchcost mutualinfo -in {primary_scan} "f"-ref {other} -omat {matrix} -out {reg_out}"
 
         # t1 mask can be found in the afni work directory
         applyxfm_cmd = f"flirt -interp nearestneighbour -applyxfm -init {matrix} "f"-in {t1_mask} -ref {other} -out {other_mask}"
 
         mask_cmd = f"fslmaths {other} -mas {other_mask} {other_defaced}"
-        full_cmd = " ; ".join(["module load fsl", mkdir_cmd, flirt_cmd, applyxfm_cmd, mask_cmd]) + '\n'
+        full_cmd = " ; ".join(["module load fsl", cp_cmd, flirt_cmd, applyxfm_cmd, mask_cmd]) + '\n'
         run_command(full_cmd, log_fileobj)