mni works on at least 1 subject

Author: bendhouseart

petdeface/__init__.py

@@ -0,0 +1,73 @@
+"""
+PET Deface - A nipype PET and MR defacing pipeline for BIDS datasets.
+
+This package provides tools for defacing PET and MR images using FreeSurfer's MiDeFace.
+"""
+
+import sys
+from pathlib import Path
+
+# Add the package directory to sys.path when running as script
+if __name__ == "__main__" or (
+    len(sys.argv) > 0 and sys.argv[0].endswith("petdeface.py")
+):
+    # Running as script - add current directory to path
+    package_dir = Path(__file__).parent
+    if str(package_dir) not in sys.path:
+        sys.path.insert(0, str(package_dir))
+
+# Import main components
+try:
+    from .petdeface import PetDeface, deface, cli, main
+    from .mideface import ApplyMideface, Mideface
+    from .pet import WeightedAverage
+    from .qa import run_qa
+    from .utils import run_validator
+    from .noanat import copy_default_anat_to_subject, remove_default_anat
+except ImportError:
+    # Fallback for when running as script
+    try:
+        from petdeface import PetDeface, deface, cli, main
+        from mideface import ApplyMideface, Mideface
+        from pet import WeightedAverage
+        from qa import run_qa
+        from utils import run_validator
+        from noanat import copy_default_anat_to_subject, remove_default_anat
+    except ImportError:
+        # Last resort - import from current directory
+        import os
+
+        sys.path.insert(0, os.path.dirname(__file__))
+        from petdeface import PetDeface, deface, cli, main
+        from mideface import ApplyMideface, Mideface
+        from pet import WeightedAverage
+        from qa import run_qa
+        from utils import run_validator
+        from noanat import copy_default_anat_to_subject, remove_default_anat
+
+# Version info
+try:
+    from importlib.metadata import version
+
+    __version__ = version("petdeface")
+except ImportError:
+    __version__ = "unknown"
+
+__bids_version__ = "1.8.0"
+
+# Main exports
+__all__ = [
+    "PetDeface",
+    "deface",
+    "cli",
+    "main",
+    "ApplyMideface",
+    "Mideface",
+    "WeightedAverage",
+    "run_qa",
+    "run_validator",
+    "copy_default_anat_to_subject",
+    "remove_default_anat",
+    "__version__",
+    "__bids_version__",
+]

petdeface/noanat.py

@@ -1,4 +1,5 @@
 """Functionality for handling cases where anatomical images are not available."""
+
 import nibabel
 import numpy
 import shutil
@@ -318,17 +319,19 @@ def remove_default_anat(
             remaining_files = set(anat_dir.iterdir()) - set(created_files)
             if not remaining_files:
                 created_dirs.append(anat_dir)
-
-    # Remove the files
-    for file_path in created_files:
-        if file_path.exists():
-            file_path.unlink()
-            print(f"Removed file: {file_path}")
-
-    # Remove the directories (only if they're empty)
-    for dir_path in created_dirs:
-        if dir_path.exists() and not any(dir_path.iterdir()):
-            dir_path.rmdir()
-            print(f"Removed directory: {dir_path}")
-
-    print("Cleanup completed successfully")
+    if os.getenv("PETDEFACE_DEBUG", "").lower() != "true":
+        # Remove the files
+        for file_path in created_files:
+            if file_path.exists():
+                file_path.unlink()
+                print(f"Removed file: {file_path}")
+
+        # Remove the directories (only if they're empty)
+        for dir_path in created_dirs:
+            if dir_path.exists() and not any(dir_path.iterdir()):
+                dir_path.rmdir()
+                print(f"Removed directory: {dir_path}")
+
+        print("Cleanup completed successfully")
+    else:
+        print("PETDEFACE_DEBUG=true, leaving template T1w's in place")

petdeface/petdeface.py

@@ -26,16 +26,34 @@
 from importlib.metadata import version
 
 
-try:
-    from mideface import ApplyMideface
-    from mideface import Mideface
+# Import local modules - handle both script and module execution
+import sys
+import os
+from pathlib import Path
+
+# Determine if we're running as a script (including through debugger)
+is_script = (
+    __name__ == "__main__"
+    or len(sys.argv) > 0
+    and sys.argv[0].endswith("petdeface.py")
+    or "debugpy" in sys.modules
+)
+
+if is_script:
+    # Running as script - add current directory to path for local imports
+    current_dir = Path(__file__).parent
+    if str(current_dir) not in sys.path:
+        sys.path.insert(0, str(current_dir))
+
+    # Import using absolute imports (script mode)
+    from mideface import ApplyMideface, Mideface
     from pet import WeightedAverage
     from qa import run_qa
     from utils import run_validator
     from noanat import copy_default_anat_to_subject, remove_default_anat
-except ModuleNotFoundError:
-    from .mideface import ApplyMideface
-    from .mideface import Mideface
+else:
+    # Running as module - use relative imports
+    from .mideface import ApplyMideface, Mideface
     from .pet import WeightedAverage
     from .qa import run_qa
     from .utils import run_validator
@@ -1321,23 +1339,12 @@ def main():  # noqa: max-complexity: 12
 
         try:
             # Determine the defaced directory based on placement
-            if args.placement == "adjacent":
-                defaced_dir = args.bids_dir.parent / f"{args.bids_dir.name}_defaced"
-            elif args.placement == "inplace":
-                defaced_dir = args.bids_dir
-            elif args.placement == "derivatives":
-                defaced_dir = args.bids_dir / "derivatives" / "petdeface"
-            else:
-                defaced_dir = (
-                    args.output_dir
-                    if args.output_dir
-                    else args.bids_dir / "derivatives" / "petdeface"
-                )
 
             # Run QA
             qa_result = run_qa(
                 faced_dir=str(args.bids_dir),
-                defaced_dir=str(defaced_dir),
+                defaced_dir=str(args.output_dir),
+                output_dir=str(args.bids_dir / "derivatives" / "petdeface" / "qa"),
                 subject=(
                     " ".join(args.participant_label) if args.participant_label else None
                 ),

petdeface/qa.py

@@ -2,6 +2,7 @@
 import os
 import tempfile
 import shutil
+import sys
 from glob import glob
 import nilearn
 from nilearn import plotting
@@ -17,15 +18,36 @@
 import seaborn as sns
 from PIL import Image, ImageDraw
 from nipype import Workflow, Node
-from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT
 from tempfile import TemporaryDirectory
 from pathlib import Path
 
+# Handle imports for both script and module execution (including debugger)
+is_script = (
+    __name__ == "__main__"
+    or len(sys.argv) > 0
+    and sys.argv[0].endswith("qa.py")
+    or "debugpy" in sys.modules
+)
+
+if is_script:
+    # Running as script - add current directory to path for local imports
+    current_dir = Path(__file__).parent
+    if str(current_dir) not in sys.path:
+        sys.path.insert(0, str(current_dir))
+
+# Import nireports - this should work in both script and module mode
+from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT
+
 
 def preprocess_single_subject(s, output_dir):
     """Preprocess a single subject's images (for parallel processing)."""
     temp_dir = os.path.join(output_dir, "temp_3d_images")
 
+    # Debug: Print what files we're processing
+    print(f"Preprocessing subject {s['id']}:")
+    print(f"  Original: {s['orig_path']}")
+    print(f"  Defaced: {s['defaced_path']}")
+
     # Extract BIDS suffix from original path to preserve meaningful naming
     orig_basename = os.path.basename(s["orig_path"])
     defaced_basename = os.path.basename(s["defaced_path"])
@@ -484,7 +506,13 @@ def create_comparison_html(
         ("original", orig_img, orig_basename, "hot"),  # Colored for original
         ("defaced", defaced_img, defaced_basename, "gray"),  # Grey for defaced
     ]:
-        # save image to temp folder for later loading
+        # Debug: Print what we're processing
+        print(f"Processing {label} image: {basename}")
+        print(f"  Image shape: {img.shape}")
+        print(f"  Image data type: {img.get_data_dtype()}")
+        print(
+            f"  Image min/max: {img.get_fdata().min():.3f}/{img.get_fdata().max():.3f}"
+        )
 
         # Create single sagittal slice using matplotlib directly
         img_data = img.get_fdata()
@@ -819,6 +847,13 @@ def get_unique_key(file_path):
     defaced_map = {get_unique_key(f): f for f in defaced_files}
     common_keys = sorted(set(orig_map.keys()) & set(defaced_map.keys()))
 
+    # Debug: Print what files are being found
+    print(f"Found {len(orig_files)} files in original directory")
+    print(f"Found {len(defaced_files)} files in defaced directory")
+    print(f"Found {len(common_keys)} common files")
+    for key in common_keys:
+        print(f"  {key}: {orig_map[key]} -> {defaced_map[key]}")
+
     subjects = []
     for key in common_keys:
         orig_path = orig_map[key]
@@ -833,19 +868,40 @@ def get_unique_key(file_path):
         else:
             subject_id = sub_id
 
+        # Check if this is a T1w file (prioritize T1w over PET)
+        is_t1w = "T1w" in orig_path or "T1w" in defaced_path
+
         subjects.append(
             {
                 "id": subject_id,
                 "orig_path": orig_path,
                 "defaced_path": defaced_path,
+                "is_t1w": is_t1w,
             }
         )
 
-    if not subjects:
+    # Sort subjects to prioritize T1w files over PET files
+    subjects.sort(key=lambda x: (not x["is_t1w"], x["id"]))
+
+    # For each subject, only keep the T1w file if available, otherwise keep the first file
+    filtered_subjects = []
+    seen_subjects = set()
+
+    for subject in subjects:
+        subject_id = subject["id"]
+        if subject_id not in seen_subjects:
+            filtered_subjects.append(subject)
+            seen_subjects.add(subject_id)
+        elif subject["is_t1w"]:
+            # Replace the existing entry with the T1w version
+            filtered_subjects = [s for s in filtered_subjects if s["id"] != subject_id]
+            filtered_subjects.append(subject)
+
+    if not filtered_subjects:
         print("No matching NIfTI files found in both datasets.")
         exit(1)
 
-    return subjects
+    return filtered_subjects
 
 
 def create_side_by_side_index_html(subjects, output_dir, size="compact"):