separating generate 3D renders function from defacing pipeline

Author: Arshitha

src/dsst_defacing_wf.py

@@ -56,17 +56,6 @@ def get_sess_dirs(subj_dir_path, mapping_dict):
     return sess_dirs
 
 
-def generate_3d_renders(defaced_img, render_outdir):
-    rotations = [(45, 5, 10), (-45, 5, 10)]
-    for idx, rot in enumerate(rotations):
-        yaw, pitch, roll = rot[0], rot[1], rot[2]
-        outfile = render_outdir.joinpath('defaced_render_' + str(idx) + '.png')
-        fsleyes_render_cmd = f"export TMP_DISPLAY=`echo $DISPLAY`; unset DISPLAY; module unload fsl; fsleyes render --scene 3d -rot {yaw} {pitch} {roll} --outfile {outfile} {defaced_img} -dr 20 250 -in spline -bf 0.3 -r 100 -ns 500; export DISPLAY=`echo $TMP_DISPLAY`"
-        print(fsleyes_render_cmd)
-        run_command(fsleyes_render_cmd)
-        print(f"Has the render been created? {outfile.exists()}")
-
-
 def create_defacing_id_list(qc_dir):
     rel_paths_to_orig = [re.sub('/orig.nii.gz', '', str(o.relative_to(qc_dir))) for o in qc_dir.rglob('orig.nii.gz')]
     with open(qc_dir / 'defacing_id_list.txt', 'w') as f:
@@ -85,8 +74,6 @@ def vqcdeface_prep(input_dir, defacing_output_dir):
         defaced_link = vqcd_subj_dir / 'defaced.nii.gz'
         if not defaced_link.exists():
             defaced_link.symlink_to(defaced_img)
-        generate_3d_renders(defaced_img, vqcd_subj_dir)
-
         img = list(input_dir.rglob(defaced_img.name))[0]
         img_link = vqcd_subj_dir / 'orig.nii.gz'
         if not img_link.exists(): img_link.symlink_to(img)

src/generate_renders.py

@@ -0,0 +1,50 @@
+#!/usr/local/bin/python3
+"""
+Generates 3D renders of defaced images using FSLeyes. More info on FSLeyes can be found\
+ https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/install.html#install-from-conda-forge-recommended
+"""
+import argparse
+import subprocess
+from pathlib import Path
+
+
+def get_args():
+    parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter, description=__doc__)
+
+    parser.add_argument('-o', '--output', type=Path, action='store', dest='outdir', metavar='OUTPUT_DIR',
+                        default=Path('.'), help="Path to defacing outputs directory.")
+
+    return parser.parse_args()
+
+
+def run_command(cmdstr):
+    """Runs the given command str as shell subprocess. If logfile object is provided, then the stdout and stderr of the
+    subprocess is written to the log file.
+    :param str cmdstr: A shell command formatted as a string variable.
+    :param io.TextIOWrapper logfile: optional, File object to log the stdout and stderr of the subprocess.
+    """
+    p = subprocess.run(cmdstr, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, encoding='utf8', shell=True)
+    print(p.stdout)
+
+
+def generate_3d_renders(defaced_img, render_outdir):
+    rotations = [(45, 5, 10), (-45, 5, 10)]
+    for idx, rot in enumerate(rotations):
+        yaw, pitch, roll = rot[0], rot[1], rot[2]
+        outfile = render_outdir.joinpath('defaced_render_99' + str(idx) + '.png')
+        fsleyes_render_cmd = f"export TMP_DISPLAY=$DISPLAY; unset DISPLAY; fsleyes render --scene 3d -rot {yaw} {pitch} {roll} --outfile {outfile} {defaced_img} -dr 20 250 -in spline -bf 0.3 -r 100 -ns 500; export DISPLAY=$TMP_DISPLAY"
+        print(fsleyes_render_cmd)
+        run_command(fsleyes_render_cmd)
+        print(f"Has the render been created? {outfile.exists()}")
+
+
+def main():
+    args = get_args()
+    defaced_imgs = list(args.outdir.rglob('defaced.nii.gz'))
+    for img in defaced_imgs:
+        generate_3d_renders(img, img.parent)
+    # print(defaced_imgs)
+
+
+if __name__ == "__main__":
+    main()