From 531077139053367b271fcded04de0cfed478019c Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 3 Jul 2025 10:33:21 -0400 Subject: [PATCH 01/19] just going to use niivue for this --- petdeface/niivue.html | 55 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 petdeface/niivue.html diff --git a/petdeface/niivue.html b/petdeface/niivue.html new file mode 100644 index 0000000..aead905 --- /dev/null +++ b/petdeface/niivue.html @@ -0,0 +1,55 @@ + + + + + NiiVue + + +
sub-01
+
+
+
Original
+ +
+
+
Defaced
+ +
+
+
+ + + 0 +
+ + + \ No newline at end of file From d09c3a83977afeee4e7c84b5a3804ef3d7b54beb Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 3 Jul 2025 12:53:20 -0400 Subject: [PATCH 02/19] dynamically render preview --- petdeface/niivue.html | 143 ++++++++++++++++++++++++---------- petdeface/serve.py | 176 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 279 insertions(+), 40 deletions(-) create mode 100644 petdeface/serve.py diff --git a/petdeface/niivue.html b/petdeface/niivue.html index aead905..542c2cb 100644 --- a/petdeface/niivue.html +++ b/petdeface/niivue.html @@ -5,51 +5,114 @@ NiiVue -
sub-01
-
-
-
Original
- + {% for subject in subjects %} +
+ {{ subject.id }}
-
-
Defaced
- +
+ {% for session in subject.sessions %} +
+
+ {{ session.label }}
+ + {{ session.nifti_path.split('/')[-1] }} + +
+ +
+
+ {% endfor %}
-
-
- - - 0 -
+
+ + + 0 + +
+ {% endfor %} + {% set viewer_configs = [] %} + {% for subject in subjects %} + {% for session in subject.sessions %} + {% set _ = viewer_configs.append({'canvasId': 'gl_' ~ subject.id ~ '_' ~ session.label, 'niftiPath': session.nifti_path}) %} + {% endfor %} + {% endfor %} \ No newline at end of file diff --git a/petdeface/serve.py b/petdeface/serve.py new file mode 100644 index 0000000..70f4d91 --- /dev/null +++ b/petdeface/serve.py @@ -0,0 +1,176 @@ +from flask import Flask, render_template, send_from_directory +import os +import socket +import argparse +import json +from glob import glob + + +def create_app(subjects): + app = Flask(__name__, static_folder="../", template_folder=".") + + @app.route("/") + def index(): + return render_template("niivue.html", subjects=subjects) + + # Serve static files (NIfTI, etc.) from the project root + @app.route("/") + def serve_static(filename): + return send_from_directory( + os.path.abspath(os.path.join(os.path.dirname(__file__), "..")), filename + ) + + return app + + +# Default sample data +sample_subjects = [ + { + "id": "sub-01", + "sessions": [ + { + "label": "Original", + "nifti_path": "data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii", + }, + { + "label": "Defaced", + "nifti_path": "data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii", + }, + ], + }, + { + "id": "sub-02", + "sessions": [ + { + "label": "Original", + "nifti_path": "data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii", + }, + { + "label": "Defaced", + "nifti_path": "data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii", + }, + ], + }, +] + + +def build_subjects_from_datasets(original_dir, defaced_dir): + # Find all NIfTI files in both datasets + orig_files = glob(os.path.join(original_dir, "**", "*.nii*"), recursive=True) + defaced_files = glob(os.path.join(defaced_dir, "**", "*.nii*"), recursive=True) + + # Build a mapping from base filename (without extension) to path + def strip_ext(path): + base = os.path.basename(path) + if base.endswith(".gz"): + base = os.path.splitext(os.path.splitext(base)[0])[0] + else: + base = os.path.splitext(base)[0] + return base + + orig_map = {strip_ext(f): f for f in orig_files} + defaced_map = {strip_ext(f): f for f in defaced_files} + # Find intersection of base names + common_keys = sorted(set(orig_map.keys()) & set(defaced_map.keys())) + subjects = [] + for key in common_keys: + # Try to extract subject/session from path (BIDS-like) + orig_path = orig_map[key] + defaced_path = defaced_map[key] + # Try to get subject id from path + parts = orig_path.split(os.sep) + sub_id = next((p for p in parts if p.startswith("sub-")), key) + session = next((p for p in parts if p.startswith("ses-")), "session") + subjects.append( + { + "id": sub_id, + "sessions": [ + { + "label": "Original", + "nifti_path": os.path.relpath( + orig_path, os.path.dirname(__file__) + ), + }, + { + "label": "Defaced", + "nifti_path": os.path.relpath( + defaced_path, os.path.dirname(__file__) + ), + }, + ], + } + ) + if not subjects: + print("No matching NIfTI files found in both datasets.") + exit(1) + return subjects + + +def run_server(subjects=None): + if subjects is None: + subjects = sample_subjects + app = create_app(subjects) + port = 8000 + while True: + with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: + try: + s.bind(("127.0.0.1", port)) + s.close() + break + except OSError: + port += 1 + print(f"Serving on http://127.0.0.1:{port}") + app.run(debug=True, port=port) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description="Serve NiiVue viewer with dynamic subjects." + ) + parser.add_argument( + "--subject-list", + type=str, + help="Either a path to a JSON file or a JSON string containing the subjects list (mutually exclusive with --original-dataset/--defaced-dataset)", + ) + parser.add_argument( + "--original-dataset", + type=str, + help="Path to the original dataset directory (must be used with --defaced-dataset)", + ) + parser.add_argument( + "--defaced-dataset", + type=str, + help="Path to the defaced dataset directory (must be used with --original-dataset)", + ) + args = parser.parse_args() + + # Mutually exclusive logic + if (args.original_dataset and not args.defaced_dataset) or ( + args.defaced_dataset and not args.original_dataset + ): + print( + "Error: --original-dataset and --defaced-dataset must be provided together." + ) + exit(1) + if args.original_dataset and args.defaced_dataset: + subjects = build_subjects_from_datasets( + args.original_dataset, args.defaced_dataset + ) + elif args.subject_list: + if os.path.isfile(args.subject_list): + with open(args.subject_list, "r") as f: + subjects = json.load(f) + else: + try: + subjects = json.loads(args.subject_list) + except json.JSONDecodeError as e: + print( + f"Error: --subject-list is not a valid file path or JSON string. {e}" + ) + exit(1) + else: + subjects = sample_subjects + + run_server(subjects) + + From 9f033ada2ac43c09a8ab8f39d63e1c1e37ea7f2d Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 14 Jul 2025 13:28:04 -0400 Subject: [PATCH 03/19] serving from across the host file system --- petdeface/niivue.html | 2 +- petdeface/serve.py | 90 +++++++++++++++++++++++++++++++++++++------ 2 files changed, 80 insertions(+), 12 deletions(-) diff --git a/petdeface/niivue.html b/petdeface/niivue.html index 542c2cb..98665bf 100644 --- a/petdeface/niivue.html +++ b/petdeface/niivue.html @@ -15,7 +15,7 @@
{{ session.label }}
- {{ session.nifti_path.split('/')[-1] }} + {{ session.nifti_path.replace('/file', '') if session.nifti_path.startswith('/file') else session.nifti_path }}
diff --git a/petdeface/serve.py b/petdeface/serve.py index 70f4d91..ded8c49 100644 --- a/petdeface/serve.py +++ b/petdeface/serve.py @@ -1,9 +1,10 @@ -from flask import Flask, render_template, send_from_directory +from flask import Flask, render_template, send_from_directory, request, abort import os import socket import argparse import json from glob import glob +from pathlib import Path def create_app(subjects): @@ -11,15 +12,78 @@ def create_app(subjects): @app.route("/") def index(): - return render_template("niivue.html", subjects=subjects) + # Prefix all nifti_paths with /file/ for the new file serving route + modified_subjects = [] + for subject in subjects: + modified_subject = subject.copy() + modified_subject["sessions"] = [] + for session in subject["sessions"]: + modified_session = session.copy() + # Convert filesystem path to URL path + if modified_session["nifti_path"].startswith("/"): + # Absolute path - prefix with /file/ + modified_session["nifti_path"] = ( + f"/file{modified_session['nifti_path']}" + ) + else: + # Relative path - keep as is for backward compatibility + pass + modified_subject["sessions"].append(modified_session) + modified_subjects.append(modified_subject) + + return render_template("niivue.html", subjects=modified_subjects) # Serve static files (NIfTI, etc.) from the project root @app.route("/") def serve_static(filename): return send_from_directory( - os.path.abspath(os.path.join(os.path.dirname(__file__), "..")), filename + __file__, + filename, + # os.path.dirname(__file__) ) + # New route to serve files from anywhere on the filesystem + @app.route("/file/") + def serve_file(filepath): + """ + Serve files from anywhere on the local filesystem. + URL format: http://localhost:8000/file/path/to/file + Example: http://localhost:8000/file/Users/username/Documents/file.txt + """ + try: + # Convert URL path to filesystem path + # Remove any leading slashes and decode URL encoding + clean_path = filepath.lstrip("/") + + # Security check: prevent directory traversal attacks + if ".." in clean_path or clean_path.startswith("/"): + abort(403, description="Access denied") + + # Convert to absolute path - reconstruct the full path + # The filepath comes from the URL without the leading slash + # So we need to add it back to make it an absolute path + if not clean_path.startswith("/"): + clean_path = "/" + clean_path + + file_path = Path(clean_path) + + # Additional security: ensure the file exists and is readable + if not file_path.exists(): + abort(404, description="File not found") + + if not file_path.is_file(): + abort(400, description="Not a file") + + # Serve the file + return send_from_directory( + directory=str(file_path.parent), + path=file_path.name, + as_attachment=False, + ) + + except Exception as e: + abort(500, description=f"Error serving file: {str(e)}") + return app @@ -81,21 +145,26 @@ def strip_ext(path): parts = orig_path.split(os.sep) sub_id = next((p for p in parts if p.startswith("sub-")), key) session = next((p for p in parts if p.startswith("ses-")), "session") + print(f"defaced_path {defaced_path}") + print(f"os.path.dirname(__file__) {os.path.dirname(__file__)}") + print( + f"os.path.relpath(defaced_path, os.path.dirname(__file__)) {os.path.relpath(defaced_path, os.path.dirname(__file__))}" + ) subjects.append( { "id": sub_id, "sessions": [ { "label": "Original", - "nifti_path": os.path.relpath( - orig_path, os.path.dirname(__file__) - ), + "nifti_path": orig_path, # os.path.relpath( + # orig_path, os.path.dirname(__file__) + # ), }, { "label": "Defaced", - "nifti_path": os.path.relpath( - defaced_path, os.path.dirname(__file__) - ), + "nifti_path": defaced_path, # os.path.relpath( + # defaced_path, os.path.dirname(__file__) + # ), }, ], } @@ -171,6 +240,5 @@ def run_server(subjects=None): else: subjects = sample_subjects + print(subjects) run_server(subjects) - - From bb4b42e43f1a588b5b4af08e662a0e1aaa725560 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Tue, 15 Jul 2025 10:30:55 -0400 Subject: [PATCH 04/19] serves two files next to each other no overlap --- petdeface/niivue.html | 197 +++++++++++++++++++----------------------- petdeface/serve.py | 99 +++++++++++++++++---- 2 files changed, 168 insertions(+), 128 deletions(-) diff --git a/petdeface/niivue.html b/petdeface/niivue.html index 98665bf..dc1fb6b 100644 --- a/petdeface/niivue.html +++ b/petdeface/niivue.html @@ -2,117 +2,94 @@ - NiiVue + NiiVue - Scan Comparisons + - {% for subject in subjects %} -
- {{ subject.id }} -
-
- {% for session in subject.sessions %} -
-
- {{ session.label }}
- - {{ session.nifti_path.replace('/file', '') if session.nifti_path.startswith('/file') else session.nifti_path }} - -
- -
-
- {% endfor %} -
-
- - - 0 - -
- {% endfor %} +
+
NiiVue Viewer
+
Select a scan comparison to view
+
+ +
+ {% for comparison in scan_comparisons %} +
+
{{ comparison.subject_id }}
+
{{ comparison.scan_type.upper() }}
+
Original vs Defaced
+ View Comparison +
+ {% endfor %} +
- {% set viewer_configs = [] %} - {% for subject in subjects %} - {% for session in subject.sessions %} - {% set _ = viewer_configs.append({'canvasId': 'gl_' ~ subject.id ~ '_' ~ session.label, 'niftiPath': session.nifti_path}) %} - {% endfor %} - {% endfor %} - \ No newline at end of file diff --git a/petdeface/serve.py b/petdeface/serve.py index ded8c49..6d14425 100644 --- a/petdeface/serve.py +++ b/petdeface/serve.py @@ -12,26 +12,89 @@ def create_app(subjects): @app.route("/") def index(): - # Prefix all nifti_paths with /file/ for the new file serving route - modified_subjects = [] + # Create a list of all scan comparisons + scan_comparisons = [] for subject in subjects: - modified_subject = subject.copy() - modified_subject["sessions"] = [] + # Group sessions by scan type (anat, pet, defacemask) + scan_groups = {} for session in subject["sessions"]: - modified_session = session.copy() - # Convert filesystem path to URL path - if modified_session["nifti_path"].startswith("/"): - # Absolute path - prefix with /file/ - modified_session["nifti_path"] = ( - f"/file{modified_session['nifti_path']}" - ) - else: - # Relative path - keep as is for backward compatibility - pass - modified_subject["sessions"].append(modified_session) - modified_subjects.append(modified_subject) - - return render_template("niivue.html", subjects=modified_subjects) + # Extract scan type from path + path_parts = session["nifti_path"].split("/") + scan_type = "unknown" + if "anat" in path_parts: + scan_type = "anat" + elif "pet" in path_parts: + scan_type = "pet" + elif "defacemask" in path_parts: + scan_type = "defacemask" + + if scan_type not in scan_groups: + scan_groups[scan_type] = [] + scan_groups[scan_type].append(session) + + # Create a comparison for each scan type + for scan_type, sessions in scan_groups.items(): + if len(sessions) == 2: # Original and Defaced + comparison = { + "subject_id": subject["id"], + "scan_type": scan_type, + "sessions": sessions, + } + scan_comparisons.append(comparison) + + # Prefix all nifti_paths with /file/ (only if not already prefixed) + for comparison in scan_comparisons: + for session in comparison["sessions"]: + # Remove any existing /file/ prefix first, then add it back + if session["nifti_path"].startswith("/file/"): + session["nifti_path"] = session["nifti_path"][6:] # Remove /file/ + if session["nifti_path"].startswith("/"): + session["nifti_path"] = f"/file{session['nifti_path']}" + + return render_template("niivue.html", scan_comparisons=scan_comparisons) + + @app.route("/scan//") + def scan_page(subject_id, scan_type): + """Serve a single scan comparison page""" + # Find the specific scan comparison + target_comparison = None + for subject in subjects: + if subject["id"] == subject_id: + # Find sessions for this scan type + sessions = [] + for session in subject["sessions"]: + path_parts = session["nifti_path"].split("/") + current_scan_type = "unknown" + if "anat" in path_parts: + current_scan_type = "anat" + elif "pet" in path_parts: + current_scan_type = "pet" + elif "defacemask" in path_parts: + current_scan_type = "defacemask" + + if current_scan_type == scan_type: + sessions.append(session) + + if len(sessions) == 2: # Original and Defaced + target_comparison = { + "subject_id": subject_id, + "scan_type": scan_type, + "sessions": sessions, + } + break + + if not target_comparison: + abort(404, description="Scan comparison not found") + + # Prefix nifti_paths with /file/ (only if not already prefixed) + for session in target_comparison["sessions"]: + # Remove any existing /file/ prefix first, then add it back + if session["nifti_path"].startswith("/file/"): + session["nifti_path"] = session["nifti_path"][6:] # Remove /file/ + if session["nifti_path"].startswith("/"): + session["nifti_path"] = f"/file{session['nifti_path']}" + + return render_template("scan.html", comparison=target_comparison) # Serve static files (NIfTI, etc.) from the project root @app.route("/") From 5a0e918afb72cdf624d4df8013e528720fa3ac59 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Tue, 15 Jul 2025 11:02:22 -0400 Subject: [PATCH 05/19] comparison works for sure --- petdeface/serve.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/petdeface/serve.py b/petdeface/serve.py index 6d14425..6432517 100644 --- a/petdeface/serve.py +++ b/petdeface/serve.py @@ -86,12 +86,11 @@ def scan_page(subject_id, scan_type): if not target_comparison: abort(404, description="Scan comparison not found") - # Prefix nifti_paths with /file/ (only if not already prefixed) + # Prefix nifti_paths with /file/ for session in target_comparison["sessions"]: - # Remove any existing /file/ prefix first, then add it back - if session["nifti_path"].startswith("/file/"): - session["nifti_path"] = session["nifti_path"][6:] # Remove /file/ - if session["nifti_path"].startswith("/"): + if session["nifti_path"].startswith("/") and not session[ + "nifti_path" + ].startswith("/file/"): session["nifti_path"] = f"/file{session['nifti_path']}" return render_template("scan.html", comparison=target_comparison) From db020133104f153e0fa1f49d219db4f2b8a99c75 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Tue, 15 Jul 2025 11:30:23 -0400 Subject: [PATCH 06/19] scan niivue preview added to full report --- petdeface/qa.py | 188 ++++++++++++++++++++++++++++++++- petdeface/scan.html | 234 +++++++++++++++++++++++++++++++++++++++++ petdeface/serve.py | 87 +++++++++------ petdeface/subject.html | 226 +++++++++++++++++++++++++++++++++++++++ 4 files changed, 698 insertions(+), 37 deletions(-) create mode 100644 petdeface/scan.html create mode 100644 petdeface/subject.html diff --git a/petdeface/qa.py b/petdeface/qa.py index 4c21f5f..6216cef 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -466,6 +466,7 @@ def create_comparison_html( size="compact", orig_path=None, defaced_path=None, + flask_port=8000, ): """Create HTML comparison page for a subject using nilearn ortho views.""" @@ -737,8 +738,33 @@ def create_comparison_html(
""" - html_content += """ + # Determine scan type from file paths + scan_type = "pet" + if orig_path and "anat" in orig_path: + scan_type = "anat" + elif orig_path and "defacemask" in orig_path: + scan_type = "defacemask" + + # Create NiiVue URL + niivue_url = f"http://localhost:{flask_port}/scan/{subject_id}/{scan_type}" + + html_content += f"""
+ + 🔄 View in NiiVue (Interactive 3D) + +
← Back to Index
@@ -753,7 +779,7 @@ def create_comparison_html( return comparison_file -def process_subject(subject, output_dir, size="compact"): +def process_subject(subject, output_dir, size="compact", flask_port=8000): """Process a single subject (for parallel processing).""" print(f"Processing {subject['id']}...") try: @@ -766,6 +792,7 @@ def process_subject(subject, output_dir, size="compact"): size, subject["orig_path"], subject["defaced_path"], + flask_port, ) print(f" Completed: {subject['id']}") return comparison_file @@ -848,7 +875,9 @@ def get_unique_key(file_path): return subjects -def create_side_by_side_index_html(subjects, output_dir, size="compact"): +def create_side_by_side_index_html( + subjects, output_dir, size="compact", flask_port=8000 +): """Create index page for side-by-side comparisons.""" comparisons_html = "" @@ -863,6 +892,16 @@ def create_side_by_side_index_html(subjects, output_dir, size="compact"): orig_png = f"images/original_{subject_id}.png" defaced_png = f"images/defaced_{subject_id}.png" + # Determine scan type from file paths + scan_type = "pet" + if "anat" in orig_basename: + scan_type = "anat" + elif "defacemask" in orig_basename: + scan_type = "defacemask" + + # Create NiiVue URL + niivue_url = f"http://localhost:{flask_port}/scan/{subject_id}/{scan_type}" + comparisons_html += f"""

{subject_id}

@@ -876,6 +915,22 @@ def create_side_by_side_index_html(subjects, output_dir, size="compact"): Defaced: {defaced_basename}
+
+ + 🔄 View in NiiVue (Interactive 3D) + +
""" @@ -1188,6 +1243,104 @@ def create_gif_index_html(subjects, output_dir, size="compact"): return index_file +def launch_flask_server(subjects, port, output_dir): + """ + Launch Flask server with the averaged PET files from QA preprocessing. + + Args: + subjects: List of preprocessed subjects with averaged file paths + port: Port to run Flask server on + output_dir: Output directory containing temp_3d_images + + Returns: + subprocess.Popen: Flask server process + """ + import subprocess + import sys + import json + import tempfile + + # Convert subjects to the format expected by serve.py + flask_subjects = [] + for subject in subjects: + # Determine scan type from the original file path or basename + orig_basename = os.path.basename(subject["orig_path"]) + scan_type = "pet" # default + + # Check if it's anatomical or defacemask + if "T1w" in orig_basename or "anat" in orig_basename: + scan_type = "anat" + elif "defacemask" in orig_basename: + scan_type = "defacemask" + + flask_subjects.append( + { + "id": subject["id"], + "scan_type": scan_type, # Add scan type to the subject object + "sessions": [ + { + "label": "Original", + "nifti_path": subject["orig_path"], # Use actual file path + }, + { + "label": "Defaced", + "nifti_path": subject["defaced_path"], # Use actual file path + }, + ], + } + ) + + # Create a temporary JSON file with the subjects data + subjects_file = os.path.join(output_dir, "flask_subjects.json") + with open(subjects_file, "w") as f: + json.dump(flask_subjects, f, indent=2) + + # Launch Flask server using serve.py + serve_script = os.path.join(os.path.dirname(__file__), "serve.py") + + # Check if serve.py exists + if not os.path.exists(serve_script): + print(f"Warning: serve.py not found at {serve_script}") + print("Flask server will not be launched.") + return None + + try: + # Launch Flask server in background + cmd = [ + sys.executable, + serve_script, + "--subject-list", + subjects_file, + "--port", + str(port), + ] + + # Start the Flask server process + process = subprocess.Popen( + cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True + ) + + # Give it a moment to start + import time + + time.sleep(2) + + # Check if process is still running + if process.poll() is None: + print(f"Flask server started successfully on port {port}") + return process + else: + stdout, stderr = process.communicate() + print(f"Failed to start Flask server:") + print(f"STDOUT: {stdout}") + print(f"STDERR: {stderr}") + return None + + except Exception as e: + print(f"Error launching Flask server: {e}") + return None + + def run_qa( faced_dir, defaced_dir, @@ -1196,6 +1349,8 @@ def run_qa( n_jobs=None, size="compact", open_browser=False, + flask_port=8000, + launch_flask=True, ): """ Run QA report generation programmatically. @@ -1269,6 +1424,7 @@ def run_qa( process_subject, output_dir=output_dir, size=size, + flask_port=flask_port, ) # Process all subjects in parallel @@ -1282,7 +1438,7 @@ def run_qa( # Create both HTML files side_by_side_file = create_side_by_side_index_html( - preprocessed_subjects, output_dir, size + preprocessed_subjects, output_dir, size, flask_port ) animated_file = create_gif_index_html(preprocessed_subjects, output_dir, size) @@ -1398,6 +1554,16 @@ def run_qa( print(f"\nAll files generated in: {output_dir}") print(f"Open index.html in your browser to view comparisons") + # Launch Flask server with averaged files if requested + flask_process = None + if launch_flask: + print(f"\nLaunching Flask NiiVue server on port {flask_port}...") + flask_process = launch_flask_server( + preprocessed_subjects, flask_port, output_dir + ) + print(f"Flask server started at: http://localhost:{flask_port}") + print(f"NiiVue links in the QA report will now work!") + return { "output_dir": output_dir, "side_by_side_file": side_by_side_file, @@ -1406,6 +1572,7 @@ def run_qa( "command_file": command_file, "subjects_processed": len(successful), "total_subjects": len(preprocessed_subjects), + "flask_process": flask_process, } @@ -1445,6 +1612,17 @@ def main(): default="compact", help="Image size: 'compact' for closer together or 'full' for entire page width", ) + parser.add_argument( + "--flask-port", + type=int, + default=8000, + help="Port for Flask NiiVue server (default: 8000)", + ) + parser.add_argument( + "--no-flask", + action="store_true", + help="Do not launch Flask server (default: launches Flask server)", + ) args = parser.parse_args() return run_qa( @@ -1455,6 +1633,8 @@ def main(): n_jobs=args.n_jobs, size=args.size, open_browser=args.open_browser, + flask_port=args.flask_port, + launch_flask=not args.no_flask, ) diff --git a/petdeface/scan.html b/petdeface/scan.html new file mode 100644 index 0000000..3a92950 --- /dev/null +++ b/petdeface/scan.html @@ -0,0 +1,234 @@ + + + + + NiiVue - {{ comparison.subject_id }} {{ comparison.scan_type.upper() }} + + + +
+ ← Back to All Comparisons +
{{ comparison.subject_id }}
+
{{ comparison.scan_type.upper() }}
+
+ +
+ {% for session in comparison.sessions %} +
+
{{ session.label }}
+
+ {{ session.nifti_path.replace('/file', '') if session.nifti_path.startswith('/file') else session.nifti_path }} +
+ +
+ {% endfor %} +
+ +
+
+ + + 0 +
+ +
+ + + + \ No newline at end of file diff --git a/petdeface/serve.py b/petdeface/serve.py index 6432517..e85af69 100644 --- a/petdeface/serve.py +++ b/petdeface/serve.py @@ -60,28 +60,39 @@ def scan_page(subject_id, scan_type): target_comparison = None for subject in subjects: if subject["id"] == subject_id: - # Find sessions for this scan type - sessions = [] - for session in subject["sessions"]: - path_parts = session["nifti_path"].split("/") - current_scan_type = "unknown" - if "anat" in path_parts: - current_scan_type = "anat" - elif "pet" in path_parts: - current_scan_type = "pet" - elif "defacemask" in path_parts: - current_scan_type = "defacemask" - - if current_scan_type == scan_type: - sessions.append(session) - - if len(sessions) == 2: # Original and Defaced - target_comparison = { - "subject_id": subject_id, - "scan_type": scan_type, - "sessions": sessions, - } - break + # Check if this subject has the requested scan type + if "scan_type" in subject and subject["scan_type"] == scan_type: + # Use the sessions directly if scan type matches + if len(subject["sessions"]) == 2: # Original and Defaced + target_comparison = { + "subject_id": subject_id, + "scan_type": scan_type, + "sessions": subject["sessions"], + } + break + else: + # Fallback to path-based detection for backward compatibility + sessions = [] + for session in subject["sessions"]: + path_parts = session["nifti_path"].split("/") + current_scan_type = "unknown" + if "anat" in path_parts: + current_scan_type = "anat" + elif "pet" in path_parts: + current_scan_type = "pet" + elif "defacemask" in path_parts: + current_scan_type = "defacemask" + + if current_scan_type == scan_type: + sessions.append(session) + + if len(sessions) == 2: # Original and Defaced + target_comparison = { + "subject_id": subject_id, + "scan_type": scan_type, + "sessions": sessions, + } + break if not target_comparison: abort(404, description="Scan comparison not found") @@ -237,19 +248,23 @@ def strip_ext(path): return subjects -def run_server(subjects=None): +def run_server(subjects=None, port=None): if subjects is None: subjects = sample_subjects app = create_app(subjects) - port = 8000 - while True: - with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: - try: - s.bind(("127.0.0.1", port)) - s.close() - break - except OSError: - port += 1 + + # If no port specified, find an available port + if port is None: + port = 8000 + while True: + with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: + try: + s.bind(("127.0.0.1", port)) + s.close() + break + except OSError: + port += 1 + print(f"Serving on http://127.0.0.1:{port}") app.run(debug=True, port=port) @@ -273,6 +288,12 @@ def run_server(subjects=None): type=str, help="Path to the defaced dataset directory (must be used with --original-dataset)", ) + parser.add_argument( + "--port", + type=int, + default=8000, + help="Port to run the Flask server on (default: 8000)", + ) args = parser.parse_args() # Mutually exclusive logic @@ -303,4 +324,4 @@ def run_server(subjects=None): subjects = sample_subjects print(subjects) - run_server(subjects) + run_server(subjects, args.port) diff --git a/petdeface/subject.html b/petdeface/subject.html new file mode 100644 index 0000000..6485566 --- /dev/null +++ b/petdeface/subject.html @@ -0,0 +1,226 @@ + + + + + NiiVue - {{ subject.id }} + + + +
+ ← Back to All Subjects +
{{ subject.id }}
+
+ +
+ {% for session in subject.sessions %} +
+
{{ session.label }}
+
+ {{ session.nifti_path.replace('/file', '') if session.nifti_path.startswith('/file') else session.nifti_path }} +
+ +
+ {% endfor %} +
+ +
+
+ + + 0 +
+ +
+ + + + \ No newline at end of file From 2036f81fbb84d455e0f90034b62d0cae9ff573ea Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Wed, 16 Jul 2025 12:11:39 -0400 Subject: [PATCH 07/19] creates reports, but the logic between comparing and datasets is tortured --- petdeface/petdeface.py | 1 + petdeface/qa.py | 208 ++++++++++++++++++++++++++++---- petdeface/serve.py | 10 +- petdeface/templates/niivue.html | 99 +++++++++++++++ petdeface/templates/viewer.html | 20 +++ 5 files changed, 304 insertions(+), 34 deletions(-) create mode 100644 petdeface/templates/niivue.html create mode 100644 petdeface/templates/viewer.html diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index ab5aa07..a91f8ac 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -1293,6 +1293,7 @@ def main(): # noqa: max-complexity: 12 " ".join(args.participant_label) if args.participant_label else None ), open_browser=args.open_browser, + defacing_method="default" ) print("\n" + "=" * 60) diff --git a/petdeface/qa.py b/petdeface/qa.py index 6216cef..a9e8448 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -1,5 +1,6 @@ import argparse import os +import re import tempfile import shutil from glob import glob @@ -16,7 +17,9 @@ from functools import partial import seaborn as sns from PIL import Image, ImageDraw +from petutils.petutils import collect_anat_and_pet from nipype import Workflow, Node +from nipype.interfaces.freesurfer import ApplyVolTransform from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT from tempfile import TemporaryDirectory from pathlib import Path @@ -70,6 +73,7 @@ def extract_bids_name(basename): "defaced_path": defaced_3d_path, # Update to 3D path "orig_img": orig_img, # Keep loaded image for direct use "defaced_img": defaced_img, # Keep loaded image for direct use + "registration_file": s.get("registration_file"), } print(f" Preprocessed {s['id']}") @@ -101,51 +105,130 @@ def preprocess_images(subjects: dict, output_dir, n_jobs=None): return preprocessed_subjects +def _extract_bids_parts(orig_path, subject_id): + """Extract subject and session parts from BIDS path.""" + path_parts = orig_path.split(os.sep) + subject_part = next((p for p in path_parts if p.startswith("sub-")), subject_id) + session_part = next((p for p in path_parts if p.startswith("ses-")), "") + return subject_part, session_part + + +def _create_valid_node_name(prefix, subject_part, session_part): + """Create a valid node name from BIDS parts.""" + if session_part: + return f"{prefix}_{subject_part}_{session_part}".replace("-", "_") + else: + return f"{prefix}_{subject_part}".replace("-", "_") + + def generate_simple_before_and_after(preprocessed_subjects: dict, output_dir): if not output_dir: output_dir = TemporaryDirectory() - wf = Workflow( - name="simple_before_after_report", base_dir=Path(output_dir) / "images/" - ) + # Create a unique workflow name to avoid conflicts + workflow_name = f"simple_before_after_report" - # Create a list to store all nodes - nodes = [] + wf = Workflow(name=workflow_name, base_dir=Path(output_dir) / "images/") + + # Create a list to store nodes that need to be added manually (not connected) + unconnected_nodes = [] + # node_counter = 0 # Add counter to ensure unique names + # seen_hashes = set() # Track which hashes we've already processed for s in preprocessed_subjects: - # only run this on the T1w images for now - if "T1w" in s["orig_path"]: - o_path = Path(s["orig_path"]) - # Create a valid node name by replacing invalid characters but preserving session info - # Use the full path to ensure uniqueness - path_parts = s["orig_path"].split(os.sep) - subject_part = next( - (p for p in path_parts if p.startswith("sub-")), s["id"] + # Extract BIDS parts once for reuse + subject_part, session_part = _extract_bids_parts(s["orig_path"], s["id"]) + + # Create a unique identifier using subject ID and counter + # unique_id = f"{s['id']}_{node_counter}" + + # Skip if we've already processed this exact file pair + # file_pair = (s["orig_path"], s["defaced_path"]) + # if file_pair in seen_hashes: + # print( + # f"Skipping duplicate file pair: {s['orig_path']} -> {s['defaced_path']}" + # ) + # continue + # seen_hashes.add(file_pair) + + # print( + # f"Processing file pair {node_counter}: {s['orig_path']} -> {s['defaced_path']}" + # ) + + if "pet" in s["orig_path"] and s.get("target_image"): + print(f"Processing PET file: {s['orig_path']}") + print(f"Target image: {s.get('target_image')}") + + # Transform PET image to target space (regardless of target type) + # Transform PET image to T1w space + transform_orig_node = Node( + ApplyVolTransform( + source_file=s["orig_path"], + reg_file=s["registration_file"], + target_file=s["target_image"], + ), + name=f"transform_pet_orig_{subject_part}_{session_part}", + ) + + transform_defaced_node = Node( + ApplyVolTransform( + source_file=s["defaced_path"], + reg_file=s["registration_file"], + target_file=s["target_image"], + ), + name=f"transform_pet_defaced_{subject_part}_{session_part}", + ) + + # Create SimpleBeforeAfterRPT node for transformed PET + report_node = Node( + SimpleBeforeAfterRPT( + before_label="Original PET", + after_label="Defaced PET", + out_report=f"{s['id']}_pet_simple_before_after.svg", + ), + name=f"before_after_pet_{subject_part}_{session_part}", ) - session_part = next((p for p in path_parts if p.startswith("ses-")), "") - if session_part: - valid_name = f"before_after_{subject_part}_{session_part}".replace( - "-", "_" + # Connect the nodes properly (this automatically adds them to workflow) + wf.connect(transform_orig_node, "transformed_file", report_node, "before") + wf.connect(transform_defaced_node, "transformed_file", report_node, "after") + + # Add overlay report if target is T1w + if "t1w" in s.get("target_image", "").lower(): + overlay_node = Node( + SimpleBeforeAfterRPT( + before=s["target_image"], + after=s["defaced_path"], + before_label="T1w", + after_label="Defaced PET", + out_report=f"{s['id']}_PET_T1W_registration.svg", + ), + name=f"PET_Registration_to_T1w_{subject_part}_{session_part}", ) - else: - valid_name = f"before_after_{subject_part}".replace("-", "_") + # This node isn't connected, so add it manually + unconnected_nodes.append(overlay_node) + + # run t1ws too + if "t1w" in s["orig_path"].lower(): node = Node( SimpleBeforeAfterRPT( before=s["orig_path"], after=s["defaced_path"], before_label="Original", after_label="Defaced", - out_report=f"{s['id']}_simple_before_after.svg", + out_report=f"{s['id']}_T1w_simple_before_after.svg", ), - name=valid_name, + name=f"before_after_T1w_{subject_part}_{session_part}", ) - nodes.append(node) + # This node isn't connected, so add it manually + unconnected_nodes.append(node) + # node_counter += 1 - # Add all nodes to the workflow - wf.add_nodes(nodes) + # Add unconnected nodes to workflow + if unconnected_nodes: + wf.add_nodes(unconnected_nodes) # Only run if we have nodes to process - if nodes: + if unconnected_nodes or list(wf.list_node_names()): wf.run(plugin="MultiProc", plugin_args={"n_procs": mp.cpu_count()}) # Collect SVG files and move them to images folder collect_svg_reports(wf, output_dir) @@ -820,6 +903,17 @@ def get_nifti_files(directory): orig_files = get_nifti_files(orig_dir) defaced_files = get_nifti_files(defaced_dir) + # collect the registration files for the defaced dataset + def get_registration_files(directory): + filtered_files = [] + reg_files = glob(os.path.join(directory, "**", "*.lta"), recursive=True) + for reg in reg_files: + if ("petdeface_wf" or "single_subject_") not in reg: + filtered_files.append(reg) + return filtered_files + + registration_files_defaced_dir = get_registration_files(defaced_dir) + def strip_ext(path): base = os.path.basename(path) if base.endswith(".gz"): @@ -860,11 +954,24 @@ def get_unique_key(file_path): else: subject_id = sub_id + registration_paths = [ + reg_file + for reg_file in registration_files_defaced_dir + if subject_id in reg_file + ] + + # just take the first one as there "should" only be one match + if len(registration_paths) > 0: + registration_path = registration_paths[0] + else: + registration_path = "" + subjects.append( { "id": subject_id, "orig_path": orig_path, "defaced_path": defaced_path, + "registration_file": registration_path, } ) @@ -1351,6 +1458,7 @@ def run_qa( open_browser=False, flask_port=8000, launch_flask=True, + defacing_method="default", ): """ Run QA report generation programmatically. @@ -1411,6 +1519,47 @@ def run_qa( # Preprocess all images once (4D→3D conversion) preprocessed_subjects = preprocess_images(subjects, output_dir, n_jobs) + # Depending on the defacing method we have several different ways to perform the registration of + # the pet images to the defaced "space". Aka if the method is "pet" we're going to want to + # use the 3D image we created in preprocessed subjects + if defacing_method == "pet": + for i, subject in enumerate(preprocessed_subjects): + preprocessed_subjects[i]["target_image"] = subject["defaced_path"] + elif defacing_method == "t1": + # Hardcode path relative to qa.py location + qa_dir = os.path.dirname(os.path.abspath(__file__)) + target_image_path = os.path.join( + qa_dir, + "..", + "data", + "sub-01", + "ses-baseline", + "anat", + "sub-01_ses-baseline_T1w.nii", + ) + subject["target_image"] = target_image_path + elif defacing_method == "mni": + # TODO add path to MNI image + pass + elif defacing_method == "default": + # just go ahead and collect the original T1w path from the faced directory + matching_dictionary = collect_anat_and_pet(Path(faced_dir)) + # attempt to lookup the original image used for defacing + for i, preproccessed in enumerate(preprocessed_subjects): + sub_id_match = re.match(r"sub-([a-zA-Z0-9]+)", preproccessed["id"]) + if sub_id_match: + sub_id = sub_id_match.group(1) + # Look up the subject in the matching dictionary + if sub_id in matching_dictionary: + # Get the first anatomical image for this subject + subject_data = matching_dictionary.get(sub_id) + if subject_data: + # Take the first T1w image (values are T1w files) + first_t1w = next(iter(subject_data.values())) + preprocessed_subjects[i]["target_image"] = first_t1w + else: + preprocessed_subjects[i]["target_image"] = None + # create nireports svg's for comparison generate_simple_before_and_after( preprocessed_subjects=preprocessed_subjects, output_dir=output_dir @@ -1526,7 +1675,7 @@ def run_qa( ] if n_jobs: command_parts.extend(["--n-jobs", str(n_jobs)]) - if subject: + if subject and type(subject) is str: command_parts.extend(["--subject", subject]) if open_browser: command_parts.append("--open-browser") @@ -1623,6 +1772,12 @@ def main(): action="store_true", help="Do not launch Flask server (default: launches Flask server)", ) + parser.add_argument( + "--defacing-method", + choices=["mni", "t1", "pet", "default"], + default="default", + help="Method used for defacing, this is important as it provides context to the QA to check on the registration of this pipeline", + ) args = parser.parse_args() return run_qa( @@ -1635,6 +1790,7 @@ def main(): open_browser=args.open_browser, flask_port=args.flask_port, launch_flask=not args.no_flask, + defacing_method=args.defacing_method, ) diff --git a/petdeface/serve.py b/petdeface/serve.py index e85af69..823f13a 100644 --- a/petdeface/serve.py +++ b/petdeface/serve.py @@ -80,8 +80,6 @@ def scan_page(subject_id, scan_type): current_scan_type = "anat" elif "pet" in path_parts: current_scan_type = "pet" - elif "defacemask" in path_parts: - current_scan_type = "defacemask" if current_scan_type == scan_type: sessions.append(session) @@ -229,15 +227,11 @@ def strip_ext(path): "sessions": [ { "label": "Original", - "nifti_path": orig_path, # os.path.relpath( - # orig_path, os.path.dirname(__file__) - # ), + "nifti_path": orig_path, }, { "label": "Defaced", - "nifti_path": defaced_path, # os.path.relpath( - # defaced_path, os.path.dirname(__file__) - # ), + "nifti_path": defaced_path, }, ], } diff --git a/petdeface/templates/niivue.html b/petdeface/templates/niivue.html new file mode 100644 index 0000000..bafc63d --- /dev/null +++ b/petdeface/templates/niivue.html @@ -0,0 +1,99 @@ + + + + + PET Deface Comparison Viewer + + + +
+

PET Deface Comparison Viewer

+

Compare original and defaced neuroimaging data

+
+ +
+ {% for subject in subjects %} + {% for session in subject.sessions %} + {% if session.label == "Original" %} + {% set original_session = session %} + {% set defaced_session = subject.sessions | selectattr("label", "equalto", "Defaced") | first %} + {% if defaced_session %} +
+
+ {{ subject.id }} - {{ session.label }} vs Defaced +
+
+
+
Original
+ +
+
+
Defaced
+ +
+
+
+ {% endif %} + {% endif %} + {% endfor %} + {% endfor %} +
+ + \ No newline at end of file diff --git a/petdeface/templates/viewer.html b/petdeface/templates/viewer.html new file mode 100644 index 0000000..6f053ae --- /dev/null +++ b/petdeface/templates/viewer.html @@ -0,0 +1,20 @@ + + + + + NiiVue Viewer + + + + + + + \ No newline at end of file From f9e8ca75f88aad5ea78abfb1d75b533164743f7d Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Tue, 22 Jul 2025 14:49:24 -0400 Subject: [PATCH 08/19] update avg and warp to occur during main pipeline --- petdeface/pet.py | 20 +++++++-- petdeface/petdeface.py | 100 +++++++++++++++++++++++++++++++++++++++-- 2 files changed, 113 insertions(+), 7 deletions(-) diff --git a/petdeface/pet.py b/petdeface/pet.py index e2631fe..2c4e6a8 100644 --- a/petdeface/pet.py +++ b/petdeface/pet.py @@ -12,6 +12,11 @@ class WeightedAverageInputSpec(BaseInterfaceInputSpec): pet_file = File(exists=True, desc="Dynamic PET", mandatory=True) + sidecar_file = File( + exists=True, + desc="Optional sidecar JSON file for timing info. If not provided, uses sidecar from pet_file.", + mandatory=False, + ) class WeightedAverageOutputSpec(TraitedSpec): @@ -47,9 +52,18 @@ def _run_interface(self, runtime): img = nib.load(pet_file) data = img.get_fdata() - meta = ReadSidecarJSON( - in_file=pet_file, bids_dir=bids_dir, bids_validate=False - ).run() + # Use optional sidecar file if provided, otherwise use pet_file's sidecar + if hasattr(self.inputs, "sidecar_file") and self.inputs.sidecar_file: + sidecar_file = self.inputs.sidecar_file + sidecar_bids_dir = os.path.dirname(sidecar_file) + meta = ReadSidecarJSON( + in_file=sidecar_file, bids_dir=sidecar_bids_dir, bids_validate=False + ).run() + else: + # Default behavior: use pet_file's sidecar + meta = ReadSidecarJSON( + in_file=pet_file, bids_dir=bids_dir, bids_validate=False + ).run() frames_start = np.array(meta.outputs.out_dict["FrameTimesStart"]) frames_duration = np.array(meta.outputs.out_dict["FrameDuration"]) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index a91f8ac..6582aae 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -14,7 +14,7 @@ import subprocess from typing import Union -from nipype.interfaces.freesurfer import MRICoreg +from nipype.interfaces.freesurfer import MRICoreg, ApplyVolTransform from nipype.interfaces.io import DataSink from nipype.interfaces.base.traits_extension import File as traits_extensionFile from nipype.pipeline import Node @@ -482,12 +482,37 @@ def init_single_subject_wf( coreg_pet_to_t1w = Node(mricoreg, "coreg_pet_to_t1w") + # warp pet image to T1w space for later QA + warp_pet_to_t1w_space = Node(ApplyVolTransform(), "warp_pet_to_t1w_space") + warp_pet_to_t1w_space.inputs.target_file = t1w_file + + # warp defaced pet image to T1w space for QA comparison + warp_defaced_pet_to_t1w_space = Node( + ApplyVolTransform(), "warp_defaced_pet_to_t1w_space" + ) + warp_defaced_pet_to_t1w_space.inputs.target_file = t1w_file + + # weighted average of the defaced PET image (4D -> 3D) using timing from original PET + # Use the modified WeightedAverage interface with the original PET's sidecar + weighted_average_defaced = Node( + WeightedAverage(pet_file=pet_file), name="weighted_average_defaced" + ) + # Set the original PET file as the sidecar source for timing info + weighted_average_defaced.inputs.sidecar_file = pet_file + deface_pet = Node(ApplyMideface(in_file=pet_file), name="deface_pet") + # Connect all the nodes in the PET workflow pet_wf.connect( [ + # Connection 1: weighted_average -> coreg_pet_to_t1w + # Takes the averaged PET image and feeds it as the source for registration (weighted_average, coreg_pet_to_t1w, [("out_file", "source_file")]), + # Connection 2: coreg_pet_to_t1w -> deface_pet + # Takes the registration matrix (LTA file) and feeds it to the defacing node (coreg_pet_to_t1w, deface_pet, [("out_lta_file", "lta_file")]), + # Connection 3: coreg_pet_to_t1w -> datasink + # Saves the registration matrix (LTA file) to the output directory ( coreg_pet_to_t1w, datasink, @@ -498,6 +523,34 @@ def init_single_subject_wf( ) ], ), + # Connection 4: weighted_average -> warp_pet_to_t1w_space + # Takes the averaged PET image and feeds it as the source for warping to T1w space + ( + weighted_average, + warp_pet_to_t1w_space, + [("out_file", "source_file")], + ), + # Connection 5: coreg_pet_to_t1w -> warp_pet_to_t1w_space + # Takes the registration matrix and feeds it as the transformation for warping + ( + coreg_pet_to_t1w, + warp_pet_to_t1w_space, + [("out_lta_file", "reg_file")], + ), + # Connection 6: warp_pet_to_t1w_space -> datasink + # Saves the PET image warped to T1w space for QA purposes + ( + warp_pet_to_t1w_space, + datasink, + [ + ( + "transformed_file", + f"{pet_string.replace('_', '.')}.pet.@warped{run_id}", + ) + ], + ), + # Connection 7: deface_pet -> datasink + # Saves the final defaced PET image to the output directory ( deface_pet, datasink, @@ -508,17 +561,56 @@ def init_single_subject_wf( ) ], ), + # Connection 8: deface_pet -> weighted_average_defaced + # Takes the defaced PET image (4D) and feeds it to weighted averaging + ( + deface_pet, + weighted_average_defaced, + [("out_file", "pet_file")], + ), + # Connection 9: weighted_average_defaced -> warp_defaced_pet_to_t1w_space + # Takes the weighted averaged defaced PET image (3D) and feeds it as the source for warping + ( + weighted_average_defaced, + warp_defaced_pet_to_t1w_space, + [("out_file", "source_file")], + ), + # Connection 10: coreg_pet_to_t1w -> warp_defaced_pet_to_t1w_space + # Takes the registration matrix and feeds it as the transformation for warping defaced PET + ( + coreg_pet_to_t1w, + warp_defaced_pet_to_t1w_space, + [("out_lta_file", "reg_file")], + ), + # Connection 11: warp_defaced_pet_to_t1w_space -> datasink + # Saves the defaced PET image warped to T1w space for QA comparison + ( + warp_defaced_pet_to_t1w_space, + datasink, + [ + ( + "transformed_file", + f"{pet_string.replace('_', '.')}.pet.@defaced_warped{run_id}", + ) + ], + ), ] ) + # Connect the T1w workflow to the PET workflow + # This connects the facemask from the T1w defacing to the PET defacing workflow.connect( [ ( - t1w_workflows[t1w_file]["workflow"], - pet_wf, + t1w_workflows[t1w_file][ + "workflow" + ], # Source: T1w defacing workflow + pet_wf, # Target: PET workflow [ ( + # Output from T1w defacing: the facemask file f"deface_t1w_{t1w_workflows[t1w_file]['anat_string']}.out_facemask", + # Input to PET defacing: the facemask file (same mask used for both T1w and PET) "deface_pet.facemask", ) ], @@ -1293,7 +1385,7 @@ def main(): # noqa: max-complexity: 12 " ".join(args.participant_label) if args.participant_label else None ), open_browser=args.open_browser, - defacing_method="default" + defacing_method="default", ) print("\n" + "=" * 60) From 5cef427521a3cfcb81215a4be924e4f222ef9334 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Wed, 23 Jul 2025 15:09:30 -0400 Subject: [PATCH 09/19] generating svg's for comparison w/ good ole nipype --- petdeface/petdeface.py | 56 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index 6582aae..7852839 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -22,6 +22,7 @@ from niworkflows.utils.bids import collect_data from niworkflows.utils.bids import collect_participants from niworkflows.utils.misc import check_valid_fs_license +from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT from petutils.petutils import collect_anat_and_pet from importlib.metadata import version @@ -502,6 +503,33 @@ def init_single_subject_wf( deface_pet = Node(ApplyMideface(in_file=pet_file), name="deface_pet") + # create simple before and after reports + t1w_before_after_report = Node( + SimpleBeforeAfterRPT( + before_label="Faced T1w", + after_label="Defaced T1w", + out_report=f"{anat_string}_before_after.svg" + ), + name=f"{anat_string}_before_and_after_report" + ) + + t1w_before_after_report.inputs.before = t1w_file + + pet_before_and_after_report = Node( + SimpleBeforeAfterRPT( + before_label=f"Faced {pet_string}", + after_label=f"Defaced {pet_string}", + out_report=f"{pet_string}_before_after.svg" + ), + name=f"{pet_string}_before_and_after_report") + pet_to_t1w_coregistration = Node( + SimpleBeforeAfterRPT( + before_label=f"{pet_string}", + after_label=f"{anat_string}", + out_report=f"{pet_string}_registration_to_t1w.svg" + ), + name=f"{pet_string}_to_{anat_string}_registration") + # Connect all the nodes in the PET workflow pet_wf.connect( [ @@ -594,6 +622,34 @@ def init_single_subject_wf( ) ], ), + # create simple before and after report for pet image + ( + warp_pet_to_t1w_space, + pet_before_and_after_report, + [("transformed_file", "before")] + ), + ( + warp_defaced_pet_to_t1w_space, + pet_before_and_after_report, + [("transformed_file", "after")] + ), + # create a simple report showing the registration for pet + ( + warp_defaced_pet_to_t1w_space, + pet_to_t1w_coregistration, + [("transformed_file", "before")] + ), + ( + t1w_workflows[t1w_file]["workflow"].get_node(f"deface_t1w_{t1w_workflows[t1w_file]['anat_string']}"), + pet_to_t1w_coregistration, + [("out_file", "after")] + ), + # create a before and after image for the t1w defacing + ( + t1w_workflows[t1w_file]["workflow"].get_node(f"deface_t1w_{t1w_workflows[t1w_file]['anat_string']}"), + t1w_before_after_report, + [("out_file", "after")] + ) ] ) From b40d3601dc5d7b84990002cbab0bd4ce4523d82d Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:01:42 -0400 Subject: [PATCH 10/19] made bare minimum report --- petdeface/petdeface.py | 74 +- petdeface/qa.py | 1907 +++++----------------------------------- 2 files changed, 259 insertions(+), 1722 deletions(-) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index 7852839..73e6419 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -381,6 +381,9 @@ def init_single_subject_wf( datasink.inputs.substitutions = [ (".face-after", "_desc-faceafter_T1w"), (".face-before", "_desc-facebefore_T1w"), + (".anat.@beforeafter", "_desc-beforeafter_T1w.svg"), + (".pet.@beforeafter", "_desc-beforeafter_pet.svg"), + (".pet.@registration", "_desc-petregistration_pet.svg"), ] # deface t1w(s) @@ -508,27 +511,29 @@ def init_single_subject_wf( SimpleBeforeAfterRPT( before_label="Faced T1w", after_label="Defaced T1w", - out_report=f"{anat_string}_before_after.svg" + out_report=f"{anat_string}_before_after.svg", ), - name=f"{anat_string}_before_and_after_report" + name=f"{anat_string}_before_and_after_report", ) - + t1w_before_after_report.inputs.before = t1w_file pet_before_and_after_report = Node( SimpleBeforeAfterRPT( before_label=f"Faced {pet_string}", after_label=f"Defaced {pet_string}", - out_report=f"{pet_string}_before_after.svg" + out_report=f"{pet_string}_before_after.svg", ), - name=f"{pet_string}_before_and_after_report") + name=f"{pet_string}_before_and_after_report", + ) pet_to_t1w_coregistration = Node( SimpleBeforeAfterRPT( before_label=f"{pet_string}", after_label=f"{anat_string}", - out_report=f"{pet_string}_registration_to_t1w.svg" + out_report=f"{pet_string}_registration_to_t1w.svg", ), - name=f"{pet_string}_to_{anat_string}_registration") + name=f"{pet_string}_to_{anat_string}_registration", + ) # Connect all the nodes in the PET workflow pet_wf.connect( @@ -626,30 +631,65 @@ def init_single_subject_wf( ( warp_pet_to_t1w_space, pet_before_and_after_report, - [("transformed_file", "before")] + [("transformed_file", "before")], ), ( warp_defaced_pet_to_t1w_space, pet_before_and_after_report, - [("transformed_file", "after")] + [("transformed_file", "after")], ), # create a simple report showing the registration for pet ( warp_defaced_pet_to_t1w_space, pet_to_t1w_coregistration, - [("transformed_file", "before")] + [("transformed_file", "before")], ), ( - t1w_workflows[t1w_file]["workflow"].get_node(f"deface_t1w_{t1w_workflows[t1w_file]['anat_string']}"), + t1w_workflows[t1w_file]["workflow"].get_node( + f"deface_t1w_{t1w_workflows[t1w_file]['anat_string']}" + ), pet_to_t1w_coregistration, - [("out_file", "after")] + [("out_file", "after")], ), # create a before and after image for the t1w defacing ( - t1w_workflows[t1w_file]["workflow"].get_node(f"deface_t1w_{t1w_workflows[t1w_file]['anat_string']}"), + t1w_workflows[t1w_file]["workflow"].get_node( + f"deface_t1w_{t1w_workflows[t1w_file]['anat_string']}" + ), t1w_before_after_report, - [("out_file", "after")] - ) + [("out_file", "after")], + ), + # Move svg reports to datasink + ( + pet_before_and_after_report, + datasink, + [ + ( + "out_report", + f"{pet_string.replace('_','.')}.pet.@beforeafter{run_id}", + ) + ], + ), + ( + pet_to_t1w_coregistration, + datasink, + [ + ( + "out_report", + f"{pet_string.replace('_', '.')}.pet.@registration{run_id}", + ) + ], + ), + ( + t1w_before_after_report, + datasink, + [ + ( + "out_report", + f"{anat_string.replace('_', '.')}.anat.@beforeafter{run_id}", + ) + ], + ), ] ) @@ -802,6 +842,10 @@ def wrap_up_defacing( shutil.rmtree(output_dir) pathlib.Path(output_dir).mkdir(parents=True, exist_ok=True, mode=0o775) + # collect all svg images and place them into a qa folder + svg_report_files = glob.glob(f"{path_to_dataset}/**/*.svg", recursive=True) + warped_files = glob.glob(f"{path_to_dataset}/**/*warped*", recursive=True) + # create dictionary of original images and defaced images mapping_dict = {} for defaced in defacing_files: diff --git a/petdeface/qa.py b/petdeface/qa.py index a9e8448..3ddd21d 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -1,1699 +1,249 @@ -import argparse +#!/usr/bin/env python3 +""" +Simple QA system for PET deface SVG reports. +""" + import os -import re -import tempfile -import shutil -from glob import glob -import nilearn -from nilearn import plotting +import glob +import argparse import webbrowser -import nibabel as nib -import numpy as np -from nilearn import image -import matplotlib.pyplot as plt -from matplotlib.animation import FuncAnimation -import imageio -import multiprocessing as mp -from functools import partial -import seaborn as sns -from PIL import Image, ImageDraw -from petutils.petutils import collect_anat_and_pet -from nipype import Workflow, Node -from nipype.interfaces.freesurfer import ApplyVolTransform -from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT -from tempfile import TemporaryDirectory +import shutil from pathlib import Path -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") - - # 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"]) - - # Extract the meaningful part (e.g., "sub-01_ses-baseline_T1w" or "sub-01_ses-baseline_pet") - def extract_bids_name(basename): - # Remove .nii.gz extension - name = basename.replace(".nii.gz", "").replace(".nii", "") - return name - - orig_bids_name = extract_bids_name(orig_basename) - defaced_bids_name = extract_bids_name(defaced_basename) - - # Preprocess original image - orig_result = load_and_preprocess_image(s["orig_path"]) - if isinstance(orig_result, nib.Nifti1Image): - # Need to save the averaged image with meaningful name - orig_3d_path = os.path.join(temp_dir, f"orig_{orig_bids_name}.nii.gz") - nib.save(orig_result, orig_3d_path) - orig_img = orig_result - else: - # Already 3D, use original path and load image - orig_3d_path = orig_result - orig_img = nib.load(orig_result) - - # Preprocess defaced image - defaced_result = load_and_preprocess_image(s["defaced_path"]) - if isinstance(defaced_result, nib.Nifti1Image): - # Need to save the averaged image with meaningful name - defaced_3d_path = os.path.join(temp_dir, f"defaced_{defaced_bids_name}.nii.gz") - nib.save(defaced_result, defaced_3d_path) - defaced_img = defaced_result - else: - # Already 3D, use original path and load image - defaced_3d_path = defaced_result - defaced_img = nib.load(defaced_result) - - # Create new subject dict with preprocessed paths (update paths to 3D versions) - preprocessed_subject = { - "id": s["id"], - "orig_path": orig_3d_path, # Update to 3D path - "defaced_path": defaced_3d_path, # Update to 3D path - "orig_img": orig_img, # Keep loaded image for direct use - "defaced_img": defaced_img, # Keep loaded image for direct use - "registration_file": s.get("registration_file"), - } - - print(f" Preprocessed {s['id']}") - return preprocessed_subject - - -def preprocess_images(subjects: dict, output_dir, n_jobs=None): - """Preprocess all images once: load and convert 4D to 3D if needed.""" - print("Preprocessing images (4D→3D conversion)...") - - # Create temp directory - temp_dir = os.path.join(output_dir, "temp_3d_images") - os.makedirs(temp_dir, exist_ok=True) - - # Set number of jobs for parallel processing - if n_jobs is None: - n_jobs = mp.cpu_count() - print(f"Using {n_jobs} parallel processes for preprocessing") - - # Process subjects in parallel - with mp.Pool(processes=n_jobs) as pool: - # Create a partial function with the output_dir fixed - preprocess_func = partial(preprocess_single_subject, output_dir=output_dir) - - # Process all subjects in parallel - preprocessed_subjects = pool.map(preprocess_func, subjects) - - print(f"Preprocessed {len(preprocessed_subjects)} subjects") - return preprocessed_subjects - - -def _extract_bids_parts(orig_path, subject_id): - """Extract subject and session parts from BIDS path.""" - path_parts = orig_path.split(os.sep) - subject_part = next((p for p in path_parts if p.startswith("sub-")), subject_id) - session_part = next((p for p in path_parts if p.startswith("ses-")), "") - return subject_part, session_part - - -def _create_valid_node_name(prefix, subject_part, session_part): - """Create a valid node name from BIDS parts.""" - if session_part: - return f"{prefix}_{subject_part}_{session_part}".replace("-", "_") - else: - return f"{prefix}_{subject_part}".replace("-", "_") - - -def generate_simple_before_and_after(preprocessed_subjects: dict, output_dir): - if not output_dir: - output_dir = TemporaryDirectory() - # Create a unique workflow name to avoid conflicts - workflow_name = f"simple_before_after_report" - - wf = Workflow(name=workflow_name, base_dir=Path(output_dir) / "images/") - - # Create a list to store nodes that need to be added manually (not connected) - unconnected_nodes = [] - # node_counter = 0 # Add counter to ensure unique names - # seen_hashes = set() # Track which hashes we've already processed - - for s in preprocessed_subjects: - # Extract BIDS parts once for reuse - subject_part, session_part = _extract_bids_parts(s["orig_path"], s["id"]) - - # Create a unique identifier using subject ID and counter - # unique_id = f"{s['id']}_{node_counter}" - - # Skip if we've already processed this exact file pair - # file_pair = (s["orig_path"], s["defaced_path"]) - # if file_pair in seen_hashes: - # print( - # f"Skipping duplicate file pair: {s['orig_path']} -> {s['defaced_path']}" - # ) - # continue - # seen_hashes.add(file_pair) - - # print( - # f"Processing file pair {node_counter}: {s['orig_path']} -> {s['defaced_path']}" - # ) - - if "pet" in s["orig_path"] and s.get("target_image"): - print(f"Processing PET file: {s['orig_path']}") - print(f"Target image: {s.get('target_image')}") - - # Transform PET image to target space (regardless of target type) - # Transform PET image to T1w space - transform_orig_node = Node( - ApplyVolTransform( - source_file=s["orig_path"], - reg_file=s["registration_file"], - target_file=s["target_image"], - ), - name=f"transform_pet_orig_{subject_part}_{session_part}", - ) - - transform_defaced_node = Node( - ApplyVolTransform( - source_file=s["defaced_path"], - reg_file=s["registration_file"], - target_file=s["target_image"], - ), - name=f"transform_pet_defaced_{subject_part}_{session_part}", - ) - - # Create SimpleBeforeAfterRPT node for transformed PET - report_node = Node( - SimpleBeforeAfterRPT( - before_label="Original PET", - after_label="Defaced PET", - out_report=f"{s['id']}_pet_simple_before_after.svg", - ), - name=f"before_after_pet_{subject_part}_{session_part}", - ) - - # Connect the nodes properly (this automatically adds them to workflow) - wf.connect(transform_orig_node, "transformed_file", report_node, "before") - wf.connect(transform_defaced_node, "transformed_file", report_node, "after") - - # Add overlay report if target is T1w - if "t1w" in s.get("target_image", "").lower(): - overlay_node = Node( - SimpleBeforeAfterRPT( - before=s["target_image"], - after=s["defaced_path"], - before_label="T1w", - after_label="Defaced PET", - out_report=f"{s['id']}_PET_T1W_registration.svg", - ), - name=f"PET_Registration_to_T1w_{subject_part}_{session_part}", - ) - # This node isn't connected, so add it manually - unconnected_nodes.append(overlay_node) - - # run t1ws too - if "t1w" in s["orig_path"].lower(): - node = Node( - SimpleBeforeAfterRPT( - before=s["orig_path"], - after=s["defaced_path"], - before_label="Original", - after_label="Defaced", - out_report=f"{s['id']}_T1w_simple_before_after.svg", - ), - name=f"before_after_T1w_{subject_part}_{session_part}", - ) - # This node isn't connected, so add it manually - unconnected_nodes.append(node) - # node_counter += 1 - - # Add unconnected nodes to workflow - if unconnected_nodes: - wf.add_nodes(unconnected_nodes) - - # Only run if we have nodes to process - if unconnected_nodes or list(wf.list_node_names()): - wf.run(plugin="MultiProc", plugin_args={"n_procs": mp.cpu_count()}) - # Collect SVG files and move them to images folder - collect_svg_reports(wf, output_dir) - else: - print("No T1w images found for SVG report generation") - - -def collect_svg_reports(wf, output_dir): - """Collect SVG reports from workflow and move them to images folder.""" - import glob - - # Find all SVG files in the workflow directory - workflow_dir = wf.base_dir - svg_files = glob.glob(os.path.join(workflow_dir, "**", "*.svg"), recursive=True) - - print(f"Found {len(svg_files)} SVG reports") +def collect_svg_reports(defaced_dir, output_dir): + """Collect SVG files from derivatives/petdeface directory.""" + derivatives_dir = os.path.join(defaced_dir, "derivatives", "petdeface") + if not os.path.exists(derivatives_dir): + print( + f"Warning: derivatives/petdeface directory not found at {derivatives_dir}" + ) + print("Looking for SVG files in the main defaced directory...") + derivatives_dir = defaced_dir - # Move each SVG to the images folder - for svg_file in svg_files: - filename = os.path.basename(svg_file) - dest_path = os.path.join(output_dir, "images", filename) - shutil.move(svg_file, dest_path) - print(f" Moved: {filename}") + # Find all SVG files recursively + svg_files = glob.glob(os.path.join(derivatives_dir, "**", "*.svg"), recursive=True) - # Create HTML page for SVG reports - create_svg_index_html(svg_files, output_dir) + if not svg_files: + print("No SVG files found!") + return [] + print(f"Found {len(svg_files)} SVG files") -def create_svg_index_html(svg_files, output_dir): - """Create HTML index page for SVG reports.""" + # Copy SVG files to output directory + images_dir = os.path.join(output_dir, "images") + os.makedirs(images_dir, exist_ok=True) - svg_entries = "" + copied_files = [] for svg_file in svg_files: filename = os.path.basename(svg_file) - subject_id = filename.replace("_simple_before_after.svg", "") - - svg_entries += f""" -
-

{subject_id}

- -

Your browser does not support SVG. Download SVG

- -
- """ - - html_content = f""" - - - - - PET Deface SVG Reports - - - - -
- - -
- Use arrow keys or spacebar -
-
+ dest_path = os.path.join(images_dir, filename) + shutil.copy2(svg_file, dest_path) + copied_files.append(dest_path) + print(f"Copied: {filename}") + + return copied_files + + +def create_simple_viewer_html(svg_files, output_dir): + """Create simple HTML viewer with all SVG images on one page.""" + + # Create HTML content + html_content = """ + + + + + PET Deface SVG Reports + - - - -
- - -
- Use arrow keys or spacebar -
-
+ .svg-item { + background: white; + padding: 10px; + border-radius: 5px; + box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1); + text-align: center; + min-height: 90vh; + display: flex; + flex-direction: column; + } -
-

PET Deface Comparison - {subject_id}

-

Side-by-side comparison of original vs defaced neuroimaging data

-
+ .svg-item h3 { + margin: 0 0 10px 0; + color: #2c3e50; + font-size: 16px; + word-break: break-all; + } -
- """ + .svg-item svg { + flex: 1; + max-width: 100%; + max-height: calc(90vh - 50px); + width: auto; + height: auto; + border: 1px solid #ddd; + border-radius: 4px; + } + + + +
+

PET Deface SVG Reports

+

All generated SVG reports

+
+ +
+""" + + # Add all SVG files + for svg_file in svg_files: + filename = os.path.basename(svg_file) + with open(svg_file, "r") as f: + svg_content = f.read() - # Add content based on display mode - if display_mode == "side-by-side": - # Add images side by side only html_content += f""" -
-

{image_files[0][0].title()}: {image_files[0][1]}

- {image_files[0][0].title()}: {image_files[0][1]} -
-
-

{image_files[1][0].title()}: {image_files[1][1]}

- {image_files[1][0].title()}: {image_files[1][1]} -
+
+

{filename}

+ {svg_content}
- """ - elif display_mode == "gif": - # Show only the GIF - if len(image_files) > 2: - html_content += f""" -
-

Animated Comparison

-

Switching between Original and Defaced images

- Animated comparison -
-
- """ - else: - html_content += """ -
- """ - - # Determine scan type from file paths - scan_type = "pet" - if orig_path and "anat" in orig_path: - scan_type = "anat" - elif orig_path and "defacemask" in orig_path: - scan_type = "defacemask" +""" - # Create NiiVue URL - niivue_url = f"http://localhost:{flask_port}/scan/{subject_id}/{scan_type}" + html_content += """ + + + +""" - html_content += f""" -
- - 🔄 View in NiiVue (Interactive 3D) - -
- ← Back to Index -
- - - """ - - # Save the comparison HTML - comparison_file = os.path.join(output_dir, f"comparison_{subject_id}.html") - with open(comparison_file, "w") as f: + # Write the HTML file + html_file = os.path.join(output_dir, "svg_reports.html") + with open(html_file, "w") as f: f.write(html_content) - return comparison_file - - -def process_subject(subject, output_dir, size="compact", flask_port=8000): - """Process a single subject (for parallel processing).""" - print(f"Processing {subject['id']}...") - try: - comparison_file = create_comparison_html( - subject["orig_img"], - subject["defaced_img"], - subject["id"], - output_dir, - "side-by-side", # Always generate side-by-side for individual pages - size, - subject["orig_path"], - subject["defaced_path"], - flask_port, - ) - print(f" Completed: {subject['id']}") - return comparison_file - except Exception as e: - print(f" Error processing {subject['id']}: {e}") - return None - - -def build_subjects_from_datasets(orig_dir, defaced_dir): - """Build subject list with file paths.""" - - # Get all NIfTI files but exclude derivatives and workflow folders - def get_nifti_files(directory): - all_files = glob(os.path.join(directory, "**", "*.nii*"), recursive=True) - # Filter out files in derivatives, workflow, or other processing folders - filtered_files = [] - for file_path in all_files: - # Skip files in derivatives, workflow, or processing-related directories - path_parts = file_path.split(os.sep) - skip_dirs = ["derivatives", "work", "wf", "tmp", "temp", "scratch", "cache"] - if not any(skip_dir in path_parts for skip_dir in skip_dirs): - filtered_files.append(file_path) - return filtered_files - - orig_files = get_nifti_files(orig_dir) - defaced_files = get_nifti_files(defaced_dir) - - # collect the registration files for the defaced dataset - def get_registration_files(directory): - filtered_files = [] - reg_files = glob(os.path.join(directory, "**", "*.lta"), recursive=True) - for reg in reg_files: - if ("petdeface_wf" or "single_subject_") not in reg: - filtered_files.append(reg) - return filtered_files - - registration_files_defaced_dir = get_registration_files(defaced_dir) - - def strip_ext(path): - base = os.path.basename(path) - if base.endswith(".gz"): - base = os.path.splitext(os.path.splitext(base)[0])[0] - else: - base = os.path.splitext(base)[0] - return base - - def get_unique_key(file_path): - """Create a unique key that includes session information.""" - parts = file_path.split(os.sep) - sub_id = next((p for p in parts if p.startswith("sub-")), "") - session = next((p for p in parts if p.startswith("ses-")), "") - basename = strip_ext(file_path) - - # Create unique key that includes session if present - if session: - return f"{sub_id}_{session}_{basename}" - else: - return f"{sub_id}_{basename}" - - # Create maps with unique keys - orig_map = {get_unique_key(f): f for f in orig_files} - defaced_map = {get_unique_key(f): f for f in defaced_files} - common_keys = sorted(set(orig_map.keys()) & set(defaced_map.keys())) - - subjects = [] - for key in common_keys: - orig_path = orig_map[key] - defaced_path = defaced_map[key] - parts = orig_path.split(os.sep) - sub_id = next((p for p in parts if p.startswith("sub-")), key) - session = next((p for p in parts if p.startswith("ses-")), "") - - # Create a unique subject ID that includes session if present - if session: - subject_id = f"{sub_id}_{session}" - else: - subject_id = sub_id - - registration_paths = [ - reg_file - for reg_file in registration_files_defaced_dir - if subject_id in reg_file - ] - - # just take the first one as there "should" only be one match - if len(registration_paths) > 0: - registration_path = registration_paths[0] - else: - registration_path = "" - - subjects.append( - { - "id": subject_id, - "orig_path": orig_path, - "defaced_path": defaced_path, - "registration_file": registration_path, - } - ) - - if not subjects: - print("No matching NIfTI files found in both datasets.") - exit(1) - - return subjects - - -def create_side_by_side_index_html( - subjects, output_dir, size="compact", flask_port=8000 -): - """Create index page for side-by-side comparisons.""" - - comparisons_html = "" - for subject in subjects: - subject_id = subject["id"] - - # Use actual filenames with BIDS suffixes instead of generic names - orig_basename = os.path.basename(subject["orig_path"]) - defaced_basename = os.path.basename(subject["defaced_path"]) - - # Check if the PNG files exist - orig_png = f"images/original_{subject_id}.png" - defaced_png = f"images/defaced_{subject_id}.png" - - # Determine scan type from file paths - scan_type = "pet" - if "anat" in orig_basename: - scan_type = "anat" - elif "defacemask" in orig_basename: - scan_type = "defacemask" + return html_file - # Create NiiVue URL - niivue_url = f"http://localhost:{flask_port}/scan/{subject_id}/{scan_type}" - comparisons_html += f""" -
-

{subject_id}

-
-
-

Original: {orig_basename}

- Original: {orig_basename} -
-
-

Defaced: {defaced_basename}

- Defaced: {defaced_basename} -
-
-
- - 🔄 View in NiiVue (Interactive 3D) - -
-
- """ - - html_content = f""" - - - - - PET Deface Comparisons - Side by Side - - - - -
- - -
- Use arrow keys or spacebar -
-
- -
-

PET Deface Comparisons - Side by Side

-

Static side-by-side comparison of original vs defaced neuroimaging data

-
- -
- {comparisons_html} -
- - - """ - - index_file = os.path.join(output_dir, "side_by_side.html") - with open(index_file, "w") as f: - f.write(html_content) - - return index_file - - -def create_gif_index_html(subjects, output_dir, size="compact"): - """Create index page for GIF comparisons.""" - - comparisons_html = "" - for subject in subjects: - subject_id = subject["id"] - overlay_gif = f"images/overlay_{subject_id}.gif" - - comparisons_html += f""" -
-

{subject_id}

-
-

Animated Comparison

-

Switching between Original and Defaced images

- Animated comparison -
-
- """ - - html_content = f""" - - - - - PET Deface Comparisons - Animated - - - - -
- - -
- Use arrow keys or spacebar -
-
- -
-

PET Deface Comparisons - Animated

-

Animated GIF comparison of original vs defaced neuroimaging data

-
- -
- {comparisons_html} -
- - - """ - - index_file = os.path.join(output_dir, "animated.html") - with open(index_file, "w") as f: - f.write(html_content) - - return index_file - - -def launch_flask_server(subjects, port, output_dir): +def run_qa(defaced_dir, output_dir=None, open_browser=False): """ - Launch Flask server with the averaged PET files from QA preprocessing. + Run QA report generation for SVG reports in derivatives/petdeface. Args: - subjects: List of preprocessed subjects with averaged file paths - port: Port to run Flask server on - output_dir: Output directory containing temp_3d_images - - Returns: - subprocess.Popen: Flask server process - """ - import subprocess - import sys - import json - import tempfile - - # Convert subjects to the format expected by serve.py - flask_subjects = [] - for subject in subjects: - # Determine scan type from the original file path or basename - orig_basename = os.path.basename(subject["orig_path"]) - scan_type = "pet" # default - - # Check if it's anatomical or defacemask - if "T1w" in orig_basename or "anat" in orig_basename: - scan_type = "anat" - elif "defacemask" in orig_basename: - scan_type = "defacemask" - - flask_subjects.append( - { - "id": subject["id"], - "scan_type": scan_type, # Add scan type to the subject object - "sessions": [ - { - "label": "Original", - "nifti_path": subject["orig_path"], # Use actual file path - }, - { - "label": "Defaced", - "nifti_path": subject["defaced_path"], # Use actual file path - }, - ], - } - ) - - # Create a temporary JSON file with the subjects data - subjects_file = os.path.join(output_dir, "flask_subjects.json") - with open(subjects_file, "w") as f: - json.dump(flask_subjects, f, indent=2) - - # Launch Flask server using serve.py - serve_script = os.path.join(os.path.dirname(__file__), "serve.py") - - # Check if serve.py exists - if not os.path.exists(serve_script): - print(f"Warning: serve.py not found at {serve_script}") - print("Flask server will not be launched.") - return None - - try: - # Launch Flask server in background - cmd = [ - sys.executable, - serve_script, - "--subject-list", - subjects_file, - "--port", - str(port), - ] - - # Start the Flask server process - process = subprocess.Popen( - cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True - ) - - # Give it a moment to start - import time - - time.sleep(2) - - # Check if process is still running - if process.poll() is None: - print(f"Flask server started successfully on port {port}") - return process - else: - stdout, stderr = process.communicate() - print(f"Failed to start Flask server:") - print(f"STDOUT: {stdout}") - print(f"STDERR: {stderr}") - return None - - except Exception as e: - print(f"Error launching Flask server: {e}") - return None - - -def run_qa( - faced_dir, - defaced_dir, - output_dir=None, - subject=None, - n_jobs=None, - size="compact", - open_browser=False, - flask_port=8000, - launch_flask=True, - defacing_method="default", -): - """ - Run QA report generation programmatically. - - Args: - faced_dir (str): Path to original (faced) dataset directory - defaced_dir (str): Path to defaced dataset directory + defaced_dir (str): Path to defaced dataset directory (containing derivatives/petdeface) output_dir (str, optional): Output directory for HTML files - subject (str, optional): Filter to specific subject - n_jobs (int, optional): Number of parallel jobs - size (str): Image size - 'compact' or 'full' open_browser (bool): Whether to open browser automatically Returns: dict: Information about generated files """ - faced_dir = os.path.abspath(faced_dir) defaced_dir = os.path.abspath(defaced_dir) - # Create output directory name based on input directories + # Create output directory name if output_dir: output_dir = os.path.abspath(output_dir) else: - orig_folder = os.path.basename(faced_dir) - defaced_folder = os.path.basename(defaced_dir) - output_dir = os.path.abspath(f"{orig_folder}_{defaced_folder}_qa") + dataset_name = os.path.basename(defaced_dir) + output_dir = os.path.abspath(f"{dataset_name}_svg_qa") - # Create output directory and images subdirectory + # Create output directory os.makedirs(output_dir, exist_ok=True) - os.makedirs(os.path.join(output_dir, "images"), exist_ok=True) print(f"Output directory: {output_dir}") - # Build subjects list - subjects = build_subjects_from_datasets(faced_dir, defaced_dir) - print(f"Found {len(subjects)} subjects with matching files") - - # Filter to specific subject if requested - if subject: - original_count = len(subjects) - subjects = [s for s in subjects if subject in s["id"]] - print( - f"Filtered to {len(subjects)} subjects matching '{subject}' (from {original_count} total)" - ) - - if not subjects: - print(f"No subjects found matching '{subject}'") - print("Available subjects:") - all_subjects = build_subjects_from_datasets(faced_dir, defaced_dir) - for s in all_subjects: - print(f" - {s['id']}") - raise ValueError(f"No subjects found matching '{subject}'") - - # Set number of jobs for parallel processing - if n_jobs is None: - n_jobs = mp.cpu_count() - print(f"Using {n_jobs} parallel processes") - - # Preprocess all images once (4D→3D conversion) - preprocessed_subjects = preprocess_images(subjects, output_dir, n_jobs) - - # Depending on the defacing method we have several different ways to perform the registration of - # the pet images to the defaced "space". Aka if the method is "pet" we're going to want to - # use the 3D image we created in preprocessed subjects - if defacing_method == "pet": - for i, subject in enumerate(preprocessed_subjects): - preprocessed_subjects[i]["target_image"] = subject["defaced_path"] - elif defacing_method == "t1": - # Hardcode path relative to qa.py location - qa_dir = os.path.dirname(os.path.abspath(__file__)) - target_image_path = os.path.join( - qa_dir, - "..", - "data", - "sub-01", - "ses-baseline", - "anat", - "sub-01_ses-baseline_T1w.nii", - ) - subject["target_image"] = target_image_path - elif defacing_method == "mni": - # TODO add path to MNI image - pass - elif defacing_method == "default": - # just go ahead and collect the original T1w path from the faced directory - matching_dictionary = collect_anat_and_pet(Path(faced_dir)) - # attempt to lookup the original image used for defacing - for i, preproccessed in enumerate(preprocessed_subjects): - sub_id_match = re.match(r"sub-([a-zA-Z0-9]+)", preproccessed["id"]) - if sub_id_match: - sub_id = sub_id_match.group(1) - # Look up the subject in the matching dictionary - if sub_id in matching_dictionary: - # Get the first anatomical image for this subject - subject_data = matching_dictionary.get(sub_id) - if subject_data: - # Take the first T1w image (values are T1w files) - first_t1w = next(iter(subject_data.values())) - preprocessed_subjects[i]["target_image"] = first_t1w - else: - preprocessed_subjects[i]["target_image"] = None - - # create nireports svg's for comparison - generate_simple_before_and_after( - preprocessed_subjects=preprocessed_subjects, output_dir=output_dir - ) - - # Process subjects in parallel - print("Generating comparisons...") - with mp.Pool(processes=n_jobs) as pool: - # Create a partial function with the output_dir and size fixed - process_func = partial( - process_subject, - output_dir=output_dir, - size=size, - flask_port=flask_port, - ) - - # Process all subjects in parallel - results = pool.map(process_func, preprocessed_subjects) + # Collect SVG reports + print(f"Collecting SVG reports from {defaced_dir}...") + svg_files = collect_svg_reports(defaced_dir, output_dir) - # Count successful results - successful = [r for r in results if r is not None] - print( - f"Successfully processed {len(successful)} out of {len(preprocessed_subjects)} subjects" - ) + if not svg_files: + print("No SVG files found to process!") + return {"output_dir": output_dir, "error": "No SVG files found"} - # Create both HTML files - side_by_side_file = create_side_by_side_index_html( - preprocessed_subjects, output_dir, size, flask_port - ) - animated_file = create_gif_index_html(preprocessed_subjects, output_dir, size) + # Create HTML viewer + print("Creating HTML viewer...") + html_file = create_simple_viewer_html(svg_files, output_dir) - # Create a simple index that links to both + # Create simple index index_html = f""" - - - - - PET Deface Comparisons - - - -
-

PET Deface Comparisons

-

Choose your preferred viewing mode:

- - Side by Side View - Animated GIF View - SVG Reports View - -

- Generated with {len(preprocessed_subjects)} subjects -

-
- - - """ + + + + + PET Deface QA Reports + + + +
+

PET Deface QA Reports

+

Quality assessment reports for defacing workflow

+
+ +
+

Available Reports

+

Click the link below to view all SVG reports:

+ + View All SVG Reports + +

+ Found {len(svg_files)} SVG report(s) +

+
+ + +""" index_file = os.path.join(output_dir, "index.html") with open(index_file, "w") as f: f.write(index_html) - # Save the command with full expanded paths - import sys - - command_parts = [ - sys.executable, - os.path.abspath(__file__), - "--faced-dir", - faced_dir, - "--defaced-dir", - defaced_dir, - "--output-dir", - output_dir, - "--size", - size, - ] - if n_jobs: - command_parts.extend(["--n-jobs", str(n_jobs)]) - if subject and type(subject) is str: - command_parts.extend(["--subject", subject]) - if open_browser: - command_parts.append("--open-browser") - - command_str = " ".join(command_parts) - - command_file = os.path.join(output_dir, "command.txt") - with open(command_file, "w") as f: - f.write(f"# Command used to generate this comparison\n") - f.write( - f"# Generated on: {__import__('datetime').datetime.now().isoformat()}\n\n" - ) - f.write(command_str + "\n") - - print(f"Created side-by-side view: {side_by_side_file}") - print(f"Created animated view: {animated_file}") print(f"Created main index: {index_file}") - print(f"Saved command to: {command_file}") + print(f"Created SVG viewer: {html_file}") # Open browser if requested if open_browser: @@ -1701,96 +251,39 @@ def run_qa( print(f"Opened browser to: {index_file}") print(f"\nAll files generated in: {output_dir}") - print(f"Open index.html in your browser to view comparisons") - - # Launch Flask server with averaged files if requested - flask_process = None - if launch_flask: - print(f"\nLaunching Flask NiiVue server on port {flask_port}...") - flask_process = launch_flask_server( - preprocessed_subjects, flask_port, output_dir - ) - print(f"Flask server started at: http://localhost:{flask_port}") - print(f"NiiVue links in the QA report will now work!") + print(f"Open index.html in your browser to view reports") return { "output_dir": output_dir, - "side_by_side_file": side_by_side_file, - "animated_file": animated_file, "index_file": index_file, - "command_file": command_file, - "subjects_processed": len(successful), - "total_subjects": len(preprocessed_subjects), - "flask_process": flask_process, + "svg_viewer": html_file, + "svg_files_count": len(svg_files), } def main(): parser = argparse.ArgumentParser( - description="Generate static HTML comparisons of PET deface results using nilearn." - ) - parser.add_argument( - "--faced-dir", required=True, help="Directory for original (faced) dataset" + description="Generate SVG QA reports for PET deface workflow." ) parser.add_argument( - "--defaced-dir", required=True, help="Directory for defaced dataset" + "--defaced-dir", + required=True, + help="Directory for defaced dataset (containing derivatives/petdeface)", ) parser.add_argument( "--output-dir", - help="Output directory for HTML files (default: {orig_folder}_{defaced_folder}_qa)", + help="Output directory for HTML files (default: {dataset_name}_svg_qa)", ) parser.add_argument( "--open-browser", action="store_true", help="Open browser automatically" ) - parser.add_argument( - "--n-jobs", - type=int, - default=None, - help="Number of parallel jobs (default: all cores)", - ) - parser.add_argument( - "--subject", - type=str, - help="Filter to specific subject (e.g., 'sub-01' or 'sub-01_ses-baseline')", - ) - parser.add_argument( - "--size", - type=str, - choices=["compact", "full"], - default="compact", - help="Image size: 'compact' for closer together or 'full' for entire page width", - ) - parser.add_argument( - "--flask-port", - type=int, - default=8000, - help="Port for Flask NiiVue server (default: 8000)", - ) - parser.add_argument( - "--no-flask", - action="store_true", - help="Do not launch Flask server (default: launches Flask server)", - ) - parser.add_argument( - "--defacing-method", - choices=["mni", "t1", "pet", "default"], - default="default", - help="Method used for defacing, this is important as it provides context to the QA to check on the registration of this pipeline", - ) args = parser.parse_args() return run_qa( - faced_dir=args.faced_dir, defaced_dir=args.defaced_dir, output_dir=args.output_dir, - subject=args.subject, - n_jobs=args.n_jobs, - size=args.size, open_browser=args.open_browser, - flask_port=args.flask_port, - launch_flask=not args.no_flask, - defacing_method=args.defacing_method, ) From d86ead9b18174898044c45fd3e2457053aa6f312 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:55:38 -0400 Subject: [PATCH 11/19] renamed svg outputs --- petdeface/petdeface.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index 73e6419..a40dffd 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -381,9 +381,10 @@ def init_single_subject_wf( datasink.inputs.substitutions = [ (".face-after", "_desc-faceafter_T1w"), (".face-before", "_desc-facebefore_T1w"), - (".anat.@beforeafter", "_desc-beforeafter_T1w.svg"), - (".pet.@beforeafter", "_desc-beforeafter_pet.svg"), - (".pet.@registration", "_desc-petregistration_pet.svg"), + # Fix SVG naming to match actual file names + ("_t1w_before_after.svg", "_desc-beforeafter_T1w.svg"), + ("_pet_before_after.svg", "_desc-beforeafter_pet.svg"), + ("_registration_to_t1w.svg", "_desc-petregistration_pet.svg"), ] # deface t1w(s) @@ -511,7 +512,7 @@ def init_single_subject_wf( SimpleBeforeAfterRPT( before_label="Faced T1w", after_label="Defaced T1w", - out_report=f"{anat_string}_before_after.svg", + out_report=f"{anat_string}_t1w_before_after.svg", ), name=f"{anat_string}_before_and_after_report", ) @@ -522,7 +523,7 @@ def init_single_subject_wf( SimpleBeforeAfterRPT( before_label=f"Faced {pet_string}", after_label=f"Defaced {pet_string}", - out_report=f"{pet_string}_before_after.svg", + out_report=f"{pet_string}_pet_before_after.svg", ), name=f"{pet_string}_before_and_after_report", ) From 36d4947e1b0461b3e298240fe35b5926af72197e Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 25 Jul 2025 14:18:31 -0400 Subject: [PATCH 12/19] happy with this, now with niivue shanigans --- petdeface/petdeface.py | 11 +-------- petdeface/qa.py | 52 +++++++++++++++++++++++++++--------------- 2 files changed, 35 insertions(+), 28 deletions(-) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index a40dffd..12949fd 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -843,10 +843,6 @@ def wrap_up_defacing( shutil.rmtree(output_dir) pathlib.Path(output_dir).mkdir(parents=True, exist_ok=True, mode=0o775) - # collect all svg images and place them into a qa folder - svg_report_files = glob.glob(f"{path_to_dataset}/**/*.svg", recursive=True) - warped_files = glob.glob(f"{path_to_dataset}/**/*warped*", recursive=True) - # create dictionary of original images and defaced images mapping_dict = {} for defaced in defacing_files: @@ -1480,13 +1476,8 @@ def main(): # noqa: max-complexity: 12 # Run QA qa_result = run_qa( - faced_dir=str(args.bids_dir), - defaced_dir=str(defaced_dir), - subject=( - " ".join(args.participant_label) if args.participant_label else None - ), + defaced_dir=str(args.bids_dir), open_browser=args.open_browser, - defacing_method="default", ) print("\n" + "=" * 60) diff --git a/petdeface/qa.py b/petdeface/qa.py index 3ddd21d..1713dcd 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -7,7 +7,6 @@ import glob import argparse import webbrowser -import shutil from pathlib import Path @@ -21,8 +20,14 @@ def collect_svg_reports(defaced_dir, output_dir): print("Looking for SVG files in the main defaced directory...") derivatives_dir = defaced_dir - # Find all SVG files recursively - svg_files = glob.glob(os.path.join(derivatives_dir, "**", "*.svg"), recursive=True) + # Find all SVG files recursively, excluding the qa directory + svg_files = [] + for svg_file in glob.glob( + os.path.join(derivatives_dir, "**", "*.svg"), recursive=True + ): + # Skip files in the qa directory + if "qa" not in svg_file: + svg_files.append(svg_file) if not svg_files: print("No SVG files found!") @@ -30,19 +35,11 @@ def collect_svg_reports(defaced_dir, output_dir): print(f"Found {len(svg_files)} SVG files") - # Copy SVG files to output directory - images_dir = os.path.join(output_dir, "images") - os.makedirs(images_dir, exist_ok=True) - - copied_files = [] + # Just return the original file paths - no copying needed for svg_file in svg_files: - filename = os.path.basename(svg_file) - dest_path = os.path.join(images_dir, filename) - shutil.copy2(svg_file, dest_path) - copied_files.append(dest_path) - print(f"Copied: {filename}") + print(f"Found: {Path(svg_file).name}") - return copied_files + return svg_files def create_simple_viewer_html(svg_files, output_dir): @@ -146,7 +143,7 @@ def run_qa(defaced_dir, output_dir=None, open_browser=False): Args: defaced_dir (str): Path to defaced dataset directory (containing derivatives/petdeface) - output_dir (str, optional): Output directory for HTML files + output_dir (str, optional): Output directory for HTML files (defaults to derivatives/petdeface/qa/) open_browser (bool): Whether to open browser automatically Returns: @@ -154,12 +151,31 @@ def run_qa(defaced_dir, output_dir=None, open_browser=False): """ defaced_dir = os.path.abspath(defaced_dir) - # Create output directory name + # Create output directory in derivatives/petdeface/qa/ if output_dir: output_dir = os.path.abspath(output_dir) else: - dataset_name = os.path.basename(defaced_dir) - output_dir = os.path.abspath(f"{dataset_name}_svg_qa") + # Look for derivatives/petdeface directory + derivatives_dir = os.path.join(defaced_dir, "derivatives", "petdeface") + if not os.path.exists(derivatives_dir): + print( + f"Warning: derivatives/petdeface directory not found at {derivatives_dir}" + ) + print("Looking for derivatives directory in parent...") + # Try parent directory (in case defaced_dir is the derivatives folder) + derivatives_dir = os.path.join( + os.path.dirname(defaced_dir), "derivatives", "petdeface" + ) + if not os.path.exists(derivatives_dir): + print( + f"Warning: derivatives/petdeface directory not found at {derivatives_dir}" + ) + print("Creating QA output in current directory...") + output_dir = os.path.abspath("qa_reports") + else: + output_dir = os.path.join(derivatives_dir, "qa") + else: + output_dir = os.path.join(derivatives_dir, "qa") # Create output directory os.makedirs(output_dir, exist_ok=True) From 4580b404281a3e383596d761a33ed356ba03c86f Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 25 Jul 2025 14:55:31 -0400 Subject: [PATCH 13/19] rotating heads are back --- petdeface/petdeface.py | 10 +- petdeface/qa.py | 551 ++++++++++++++++++++++++++++++++++++++++- 2 files changed, 549 insertions(+), 12 deletions(-) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index 12949fd..cf19562 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -1254,6 +1254,12 @@ def cli(): default=False, help="Open browser automatically after QA report generation", ) + parser.add_argument( + "--qa-port", + type=int, + default=8000, + help="User can manually choose a default port to serve the nifti images at for 3D previewing of defacing should the default value of 8000 not work.", + ) arguments = parser.parse_args() return arguments @@ -1474,10 +1480,12 @@ def main(): # noqa: max-complexity: 12 else args.bids_dir / "derivatives" / "petdeface" ) - # Run QA + # Run QA with server if open_browser is requested qa_result = run_qa( defaced_dir=str(args.bids_dir), open_browser=args.open_browser, + start_server=args.open_browser, # Start server when opening browser + server_port=args.qa_port, ) print("\n" + "=" * 60) diff --git a/petdeface/qa.py b/petdeface/qa.py index 1713dcd..e9edd4b 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -7,6 +7,13 @@ import glob import argparse import webbrowser +import json +import http.server +import socketserver +import threading +import time +import subprocess +import signal from pathlib import Path @@ -42,6 +49,392 @@ def collect_svg_reports(defaced_dir, output_dir): return svg_files +def kill_process_on_port(port): + """Kill any process using the specified port.""" + try: + # Find process using the port + result = subprocess.run( + ["lsof", "-ti", str(port)], capture_output=True, text=True, check=False + ) + + if result.returncode == 0 and result.stdout.strip(): + pids = result.stdout.strip().split("\n") + for pid in pids: + if pid: + print(f"Killing process {pid} using port {port}") + try: + os.kill(int(pid), signal.SIGKILL) + except ProcessLookupError: + print(f"Process {pid} already terminated") + except ValueError: + print(f"Invalid PID: {pid}") + + # Give it a moment to fully terminate + time.sleep(0.5) + print(f"Port {port} is now free") + else: + print(f"Port {port} is already free") + + except FileNotFoundError: + print("Warning: 'lsof' command not found, cannot check for existing processes") + except Exception as e: + print(f"Error killing process on port {port}: {e}") + + +def start_local_server(port=8000, directory=None): + """Start a simple HTTP server to serve files locally.""" + if directory is None: + directory = os.getcwd() + + os.chdir(directory) + + class CustomHTTPRequestHandler(http.server.SimpleHTTPRequestHandler): + def end_headers(self): + # Add CORS headers to allow cross-origin requests + self.send_header("Access-Control-Allow-Origin", "*") + self.send_header("Access-Control-Allow-Methods", "GET, POST, OPTIONS") + self.send_header("Access-Control-Allow-Headers", "*") + super().end_headers() + + handler = CustomHTTPRequestHandler + + with socketserver.TCPServer(("", port), handler) as httpd: + print(f"Server started at http://localhost:{port}") + print(f"Serving files from: {directory}") + print("Press Ctrl+C to stop the server") + + try: + httpd.serve_forever() + except KeyboardInterrupt: + print("\nServer stopped.") + + +def collect_nifti_files(defaced_dir): + """Collect NIfTI files containing 'defaced' from derivatives/petdeface directory.""" + derivatives_dir = os.path.join(defaced_dir, "derivatives", "petdeface") + if not os.path.exists(derivatives_dir): + print( + f"Warning: derivatives/petdeface directory not found at {derivatives_dir}" + ) + return {} + + # Find all NIfTI files containing 'defaced' + nifti_files = {} + for nifti_file in glob.glob( + os.path.join(derivatives_dir, "**", "*.nii*"), recursive=True + ): + filename = Path(nifti_file).name + + # Check if file contains 'defaced' + if ("defaced" in filename and "T1w" in filename) or ( + "defaced" in filename and "wavg" in filename and "pet" in filename + ): + # Extract subject ID from path + path_parts = Path(nifti_file).parts + subject_id = None + for part in path_parts: + if part.startswith("sub-"): + subject_id = part + break + + if subject_id: + if subject_id not in nifti_files: + nifti_files[subject_id] = [] + nifti_files[subject_id].append(nifti_file) + + print(f"Found NIfTI files for {len(nifti_files)} subjects") + for subject_id, files in nifti_files.items(): + print(f" {subject_id}: {len(files)} files") + for file in files: + print(f" {Path(file).name}") + + return nifti_files + + +def create_nifti_viewer_html(subject_id, nifti_files, output_dir, server_port=8000): + """Create HTML viewer with rotating NIfTI images for a subject.""" + + # Filter files to include only specific types + filtered_files = [] + for nifti_file in nifti_files: + filename = Path(nifti_file).name.lower() + + # Include files that are: + # 1. T1w defaced images + # 2. PET defaced images that are averaged (wavg) + # 3. PET defaced images that are warped + # 4. PET defaced images that are in T1w space + if "defaced" in filename: + if "t1w" in filename: + # Include T1w defaced images + filtered_files.append(nifti_file) + elif "pet" in filename: + # For PET images, only include if they are averaged (wavg) or have special processing + if ( + "wavg" in filename + or "warped" in filename + or "space-t1w" in filename + ): + filtered_files.append(nifti_file) + + if not filtered_files: + print(f"No qualifying NIfTI files found for {subject_id}") + return None + + # Create HTML content + html_content = f""" + + + + + NiiVue - {subject_id} Defaced Images + + + +
+
{subject_id}
+
Defaced NIfTI Images
+
+ +
+""" + + # Add a viewer for each NIfTI file + for i, nifti_file in enumerate(filtered_files): + filename = Path(nifti_file).name + # Create a label based on the filename + label = filename.replace(".nii.gz", "").replace(".nii", "") + label = label.replace("_", " ").replace("-", " ") + + # Convert file path to HTTP URL + # Get the relative path from the derivatives directory + derivatives_dir = os.path.join(os.path.dirname(output_dir), "..") + relative_path = os.path.relpath(nifti_file, derivatives_dir) + http_url = f"http://localhost:{server_port}/{relative_path}" + + html_content += f""" +
+
{label}
+
{http_url}
+ +
+""" + + html_content += ( + """ +
+ +
+
+ + + 0 +
+ +
+ + + + +""" + ) + + # Save the HTML file + html_path = os.path.join(output_dir, f"{subject_id}_nifti_viewer.html") + with open(html_path, "w") as f: + f.write(html_content) + + print(f"Created NIfTI viewer: {html_path}") + return html_path + + def create_simple_viewer_html(svg_files, output_dir): """Create simple HTML viewer with all SVG images on one page.""" @@ -137,7 +530,13 @@ def create_simple_viewer_html(svg_files, output_dir): return html_file -def run_qa(defaced_dir, output_dir=None, open_browser=False): +def run_qa( + defaced_dir, + output_dir=None, + open_browser=False, + start_server=False, + server_port=8000, +): """ Run QA report generation for SVG reports in derivatives/petdeface. @@ -145,6 +544,8 @@ def run_qa(defaced_dir, output_dir=None, open_browser=False): defaced_dir (str): Path to defaced dataset directory (containing derivatives/petdeface) output_dir (str, optional): Output directory for HTML files (defaults to derivatives/petdeface/qa/) open_browser (bool): Whether to open browser automatically + start_server (bool): Whether to start a local HTTP server for NIfTI files + server_port (int): Port for the HTTP server Returns: dict: Information about generated files @@ -189,9 +590,32 @@ def run_qa(defaced_dir, output_dir=None, open_browser=False): print("No SVG files found to process!") return {"output_dir": output_dir, "error": "No SVG files found"} - # Create HTML viewer - print("Creating HTML viewer...") - html_file = create_simple_viewer_html(svg_files, output_dir) + # Create HTML viewer for SVG reports + print("Creating SVG HTML viewer...") + svg_html_file = create_simple_viewer_html(svg_files, output_dir) + + # Collect and create NIfTI viewers + print("Collecting NIfTI files...") + nifti_files_by_subject = collect_nifti_files(defaced_dir) + + nifti_viewer_files = [] + if nifti_files_by_subject: + print("Creating NIfTI viewers...") + for subject_id, nifti_files in nifti_files_by_subject.items(): + viewer_file = create_nifti_viewer_html( + subject_id, nifti_files, output_dir, server_port + ) + if viewer_file: + nifti_viewer_files.append(viewer_file) + else: + print("No NIfTI files found for viewing") + + # Generate NIfTI viewer links with server detection + nifti_links = "" + for viewer_file in nifti_viewer_files: + viewer_name = Path(viewer_file).name + subject_id = viewer_name.replace("_nifti_viewer.html", "") + nifti_links += f'{subject_id} NIfTI Viewer\n ' # Create simple index index_html = f""" @@ -242,14 +666,81 @@ def run_qa(defaced_dir, output_dir=None, open_browser=False):

Available Reports

-

Click the link below to view all SVG reports:

- View All SVG Reports +
+

SVG Reports

+

Click the link below to view all SVG reports:

+ View All SVG Reports +

+ Found {len(svg_files)} SVG report(s) +

+
-

- Found {len(svg_files)} SVG report(s) -

+
+

NIfTI Viewers

+

Click the links below to view rotating 3D NIfTI images:

+ +

+ Found {len(nifti_viewer_files)} NIfTI viewer(s) +

+ +
+ + """ @@ -259,7 +750,9 @@ def run_qa(defaced_dir, output_dir=None, open_browser=False): f.write(index_html) print(f"Created main index: {index_file}") - print(f"Created SVG viewer: {html_file}") + print(f"Created SVG viewer: {svg_html_file}") + if nifti_viewer_files: + print(f"Created {len(nifti_viewer_files)} NIfTI viewer(s)") # Open browser if requested if open_browser: @@ -269,11 +762,34 @@ def run_qa(defaced_dir, output_dir=None, open_browser=False): print(f"\nAll files generated in: {output_dir}") print(f"Open index.html in your browser to view reports") + # Start server if requested + if start_server and nifti_viewer_files: + print(f"\nStarting HTTP server on port {server_port}...") + print("This server is needed for NIfTI file access due to CORS restrictions.") + print("Keep this terminal open while viewing NIfTI files.") + + # Kill any existing process on the port + kill_process_on_port(server_port) + + # Get the derivatives directory to serve from + derivatives_dir = os.path.join(os.path.dirname(output_dir), "..") + + print(f"Server is running at http://localhost:{server_port}") + print("NIfTI viewers will now work properly.") + print("Press Ctrl+C to stop the server") + + # Start server in foreground (this will block) + start_local_server(server_port, derivatives_dir) + return { "output_dir": output_dir, "index_file": index_file, - "svg_viewer": html_file, + "svg_viewer": svg_html_file, "svg_files_count": len(svg_files), + "nifti_viewers": nifti_viewer_files, + "nifti_viewers_count": len(nifti_viewer_files), + "server_started": start_server and nifti_viewer_files, + "server_port": server_port if start_server and nifti_viewer_files else None, } @@ -293,6 +809,17 @@ def main(): parser.add_argument( "--open-browser", action="store_true", help="Open browser automatically" ) + parser.add_argument( + "--start-server", + action="store_true", + help="Start local HTTP server for NIfTI file access (required for NIfTI viewers)", + ) + parser.add_argument( + "--qa-port", + type=int, + default=8000, + help="User can manually choose a default port to serve the nifti images at for 3D previewing of defacing should the default value of 8000 not work.", + ) args = parser.parse_args() @@ -300,6 +827,8 @@ def main(): defaced_dir=args.defaced_dir, output_dir=args.output_dir, open_browser=args.open_browser, + start_server=args.start_server, + server_port=args.qa_port, ) From 70c7e0c7fbb36f03ef180d8ed18ec4b6b2e28b3f Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 25 Jul 2025 15:02:15 -0400 Subject: [PATCH 14/19] add entrypoint for qa reports --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index c37aa7a..f760fd5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,3 +53,4 @@ build-backend = "poetry.core.masonry.api" [tool.poetry.scripts] petdeface = 'petdeface.petdeface:main' +petdeface-qa = 'petdeface.qa:main' From 1e5a00be447fa85b6e41fc1547dc287e99c1f5b7 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 28 Jul 2025 09:15:41 -0400 Subject: [PATCH 15/19] standardize commands --- petdeface/petdeface.py | 19 ++++++++++++++++++- petdeface/qa.py | 9 ++++++++- 2 files changed, 26 insertions(+), 2 deletions(-) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index cf19562..cc6860c 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -1166,6 +1166,7 @@ def cli(): help="Only deface anatomical images", ) parser.add_argument( + "--participant-label", "--participant_label", "-pl", help="The label(s) of the participant/subject to be processed. When specifying multiple subjects separate them with spaces.", @@ -1189,11 +1190,17 @@ def cli(): help="Run in singularity container", ), parser.add_argument( + "--n-procs", "--n_procs", help="Number of processors to use when running the workflow", default=2, ) - parser.add_argument("--skip_bids_validator", action="store_true", default=False) + parser.add_argument( + "--skip-bids-validator", + "--skip_bids_validator", + action="store_true", + default=False, + ) parser.add_argument( "--version", "-v", @@ -1212,6 +1219,7 @@ def cli(): default="adjacent", ) parser.add_argument( + "--remove-existing", "--remove_existing", "-r", help="Remove existing output files in output_dir.", @@ -1219,12 +1227,14 @@ def cli(): default=False, ) parser.add_argument( + "--preview-pics", "--preview_pics", help="Create preview pictures of defacing, defaults to false for docker", action="store_true", default=False, ) parser.add_argument( + "--participant-label-exclude", "--participant_label_exclude", help="Exclude a subject(s) from the defacing workflow. e.g. --participant_label_exclude sub-01 sub-02", type=str, @@ -1233,6 +1243,7 @@ def cli(): default=[], ) parser.add_argument( + "--session-label", "--session_label", help="Select only a specific session(s) to include in the defacing workflow", type=str, @@ -1241,6 +1252,7 @@ def cli(): default=[], ) parser.add_argument( + "--session-label-exclude", "--session_label_exclude", help="Select a specific session(s) to exclude from the defacing workflow", type=str, @@ -1250,12 +1262,14 @@ def cli(): ) parser.add_argument( "--open-browser", + "--open_browser", action="store_true", default=False, help="Open browser automatically after QA report generation", ) parser.add_argument( "--qa-port", + "--qa_port", type=int, default=8000, help="User can manually choose a default port to serve the nifti images at for 3D previewing of defacing should the default value of 8000 not work.", @@ -1493,10 +1507,13 @@ def main(): # noqa: max-complexity: 12 print(f"Reports available at: {qa_result['output_dir']}") print("=" * 60) + except Exception as e: print(f"\nError generating QA reports: {e}") print("QA report generation failed, but defacing completed successfully.") + print("launch QA reports with:") + print(f"petdeface-qa --defaced_dir {args.bids_dir} --open_browser --start_server") if __name__ == "__main__": main() diff --git a/petdeface/qa.py b/petdeface/qa.py index e9edd4b..56391d4 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -799,23 +799,30 @@ def main(): ) parser.add_argument( "--defaced-dir", + "--defaced_dir", required=True, help="Directory for defaced dataset (containing derivatives/petdeface)", ) parser.add_argument( "--output-dir", + "--output_dir", help="Output directory for HTML files (default: {dataset_name}_svg_qa)", ) parser.add_argument( - "--open-browser", action="store_true", help="Open browser automatically" + "--open-browser", + "--open_browser", + action="store_true", + help="Open browser automatically", ) parser.add_argument( "--start-server", + "--start_server", action="store_true", help="Start local HTTP server for NIfTI file access (required for NIfTI viewers)", ) parser.add_argument( "--qa-port", + "--qa_port", type=int, default=8000, help="User can manually choose a default port to serve the nifti images at for 3D previewing of defacing should the default value of 8000 not work.", From 289fe3661f85bfdffaa42508aaff63429db26d30 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 28 Jul 2025 12:07:56 -0400 Subject: [PATCH 16/19] cleaned up merge and moved html into template folder --- petdeface/niivue.html | 95 - petdeface/qa.py | 209 +- petdeface/serve.py | 2 +- petdeface/templates/niivue.html | 180 +- petdeface/{ => templates}/scan.html | 0 petdeface/{ => templates}/subject.html | 0 poetry.lock | 3306 ------------------------ pyproject.toml | 103 +- 8 files changed, 271 insertions(+), 3624 deletions(-) delete mode 100644 petdeface/niivue.html rename petdeface/{ => templates}/scan.html (100%) rename petdeface/{ => templates}/subject.html (100%) delete mode 100644 poetry.lock diff --git a/petdeface/niivue.html b/petdeface/niivue.html deleted file mode 100644 index dc1fb6b..0000000 --- a/petdeface/niivue.html +++ /dev/null @@ -1,95 +0,0 @@ - - - - - NiiVue - Scan Comparisons - - - -
-
NiiVue Viewer
-
Select a scan comparison to view
-
- -
- {% for comparison in scan_comparisons %} -
-
{{ comparison.subject_id }}
-
{{ comparison.scan_type.upper() }}
-
Original vs Defaced
- View Comparison -
- {% endfor %} -
- - \ No newline at end of file diff --git a/petdeface/qa.py b/petdeface/qa.py index 56391d4..47beea8 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -10,7 +10,6 @@ import json import http.server import socketserver -import threading import time import subprocess import signal @@ -183,28 +182,28 @@ def create_nifti_viewer_html(subject_id, nifti_files, output_dir, server_port=80 # Create HTML content html_content = f""" - + - - + + NiiVue - {subject_id} Defaced Images - - - -
+ }} + + + +
{subject_id}
Defaced NIfTI Images
-
- +
+
""" @@ -290,16 +289,16 @@ def create_nifti_viewer_html(subject_id, nifti_files, output_dir, server_port=80 http_url = f"http://localhost:{server_port}/{relative_path}" html_content += f""" -
+
{label}
{http_url}
-""" + """ html_content += ( """ -
+
@@ -440,22 +439,22 @@ def create_simple_viewer_html(svg_files, output_dir): # Create HTML content html_content = """ - - - - + + + + PET Deface SVG Reports - - - -
+ + +

PET Deface SVG Reports

All generated SVG reports

-
- +
+
""" @@ -514,13 +513,13 @@ def create_simple_viewer_html(svg_files, output_dir):

{filename}

{svg_content}
-""" + """ html_content += """ -
- - -""" +
+ + + """ # Write the HTML file html_file = os.path.join(output_dir, "svg_reports.html") @@ -619,46 +618,46 @@ def run_qa( # Create simple index index_html = f""" - - - - + + + + PET Deface QA Reports - - - + font-size: 16px; + }} + .link-button:hover {{ + background: #2980b9; + }} + + +

PET Deface QA Reports

Quality assessment reports for defacing workflow

@@ -687,6 +686,11 @@ def run_qa(

@@ -696,8 +700,11 @@ def run_qa( async function checkServerAvailability() {{ const serverStatus = document.getElementById('server-status'); const serverMessage = document.getElementById('server-message'); + const commandHelp = document.getElementById('command-help'); + const commandText = document.getElementById('command-text'); const niftiLinks = document.querySelectorAll('.nifti-link'); const serverPort = {server_port}; + const defacedDir = "{defaced_dir}"; try {{ // Try to fetch a simple request to the server @@ -727,6 +734,11 @@ def run_qa( serverMessage.style.color = '#721c24'; serverMessage.textContent = `✗ NIfTI preview server is not running on port ${{serverPort}}. NIfTI viewers will not work.`; + // Show command help + commandHelp.style.display = 'block'; + const command = `petdeface-qa --defaced-dir "${{defacedDir}}" --start-server --open-browser`; + commandText.textContent = command; + // Disable all NIfTI links niftiLinks.forEach(link => {{ link.style.opacity = '0.5'; @@ -736,14 +748,29 @@ def run_qa( }} }} + // Copy command to clipboard + function copyCommand() {{ + const commandText = document.getElementById('command-text'); + navigator.clipboard.writeText(commandText.textContent).then(() => {{ + const button = event.target; + const originalText = button.textContent; + button.textContent = 'Copied!'; + button.style.background = '#6c757d'; + setTimeout(() => {{ + button.textContent = originalText; + button.style.background = '#28a745'; + }}, 2000); + }}); + }} + // Check server availability when page loads document.addEventListener('DOMContentLoaded', function() {{ checkServerAvailability(); }}); - - -""" + + + """ index_file = os.path.join(output_dir, "index.html") with open(index_file, "w") as f: diff --git a/petdeface/serve.py b/petdeface/serve.py index 823f13a..151feb0 100644 --- a/petdeface/serve.py +++ b/petdeface/serve.py @@ -8,7 +8,7 @@ def create_app(subjects): - app = Flask(__name__, static_folder="../", template_folder=".") + app = Flask(__name__, static_folder="../", template_folder="templates") @app.route("/") def index(): diff --git a/petdeface/templates/niivue.html b/petdeface/templates/niivue.html index bafc63d..dc1fb6b 100644 --- a/petdeface/templates/niivue.html +++ b/petdeface/templates/niivue.html @@ -1,99 +1,95 @@ - - - - PET Deface Comparison Viewer + + + + NiiVue - Scan Comparisons - - + +
-

PET Deface Comparison Viewer

-

Compare original and defaced neuroimaging data

+
NiiVue Viewer
+
Select a scan comparison to view
- -
- {% for subject in subjects %} - {% for session in subject.sessions %} - {% if session.label == "Original" %} - {% set original_session = session %} - {% set defaced_session = subject.sessions | selectattr("label", "equalto", "Defaced") | first %} - {% if defaced_session %} -
-
- {{ subject.id }} - {{ session.label }} vs Defaced -
-
-
-
Original
- -
-
-
Defaced
- -
-
-
- {% endif %} - {% endif %} - {% endfor %} - {% endfor %} + +
+ {% for comparison in scan_comparisons %} +
+
{{ comparison.subject_id }}
+
{{ comparison.scan_type.upper() }}
+
Original vs Defaced
+ View Comparison +
+ {% endfor %}
- + \ No newline at end of file diff --git a/petdeface/scan.html b/petdeface/templates/scan.html similarity index 100% rename from petdeface/scan.html rename to petdeface/templates/scan.html diff --git a/petdeface/subject.html b/petdeface/templates/subject.html similarity index 100% rename from petdeface/subject.html rename to petdeface/templates/subject.html diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index b397c86..0000000 --- a/poetry.lock +++ /dev/null @@ -1,3306 +0,0 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. - -[[package]] -name = "acres" -version = "0.5.0" -description = "Access resources on your terms" -optional = false -python-versions = ">=3.9" -files = [ - {file = "acres-0.5.0-py3-none-any.whl", hash = "sha256:fcc32b974b510897de0f041609b4234f9ff03e2e960aea088f63973fb106c772"}, - {file = "acres-0.5.0.tar.gz", hash = "sha256:128b6447bf5df3b6210264feccbfa018b4ac5bd337358319aec6563f99db8f3a"}, -] - -[[package]] -name = "alabaster" -version = "0.7.16" -description = "A light, configurable Sphinx theme" -optional = false -python-versions = ">=3.9" -files = [ - 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"petdeface/*", - "pyproject.toml", +requires-python = ">=3.10" +dependencies = [ + "setuptools>=68.1.2", + "petutils>=0.0.1", + "niworkflows>=1.11.0", + "matplotlib>=3.10.1", + "niftifixer>=0.0.2", + "bids-validator-deno>=2.0.5", + "nipreps>=1.0", + "nireports>=25.2.0", + "nibabel>=5.3.2", + "nilearn>=0.10.4", + "numpy>=2.1.3", + "scipy>=1.14.1", + "seaborn>=0.13.2", + "pillow>=11.0.0", + "imageio>=2.36.0", +] + +[project.optional-dependencies] +dev = [ + "black>=23.7.0", + "flake8>=6.1.0", + "isort>=5.12.0", + "pre-commit>=3.3.3", + "pytest>=7.4.2", + "sphinx>=7.2.6", + "sphinx-rtd-theme>=3.0.1", + "jupyterlab>=4.4.1", + "notebook>=7.4.1", + "nbconvert>=7.16.6", + "ipywidgets>=8.1.6", + "matplotlib>=3.10.1", + "pandas>=2.2.3", + "pyqt6>=6.9.0", ] +[project.scripts] +petdeface = "petdeface.petdeface:main" +petdeface-qa = "petdeface.qa:main" +petdeface_qa = "petdeface.qa:main" + # please update the bids version to the latest compliant version when making modifications to this code here [tool.bids] bids_version = "1.8.0" -[tool.poetry.dependencies] -python = ">=3.10, <4.0" -setuptools = "^68.1.2" -petutils = "^0.0.1" -niworkflows = "^1.11.0" -niftifixer = {git = "https://github.com/openneuropet/nifti_fixer.git"} -bids-validator-deno = "^2.0.5" -nipreps = "^1.0" -nireports = "^25.2.0" -nibabel = "^5.3.2" -nilearn = "^0.10.4" -matplotlib = "^3.9.2" -numpy = "^2.1.3" -scipy = "^1.14.1" -seaborn = "^0.13.2" -pillow = "^11.0.0" -imageio = "^2.36.0" - - -[tool.poetry.group.dev.dependencies] -black = "^23.7.0" -flake8 = "^6.1.0" -isort = "^5.12.0" -pre-commit = "^3.3.3" -pytest = "^7.4.2" -sphinx = "^7.2.6" -sphinx-rtd-theme = "^3.0.1" - [tool.isort] profile = "black" force_single_line = true lines_after_imports = 2 [build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +requires = ["setuptools>=68.1.2", "wheel"] +build-backend = "setuptools.build_meta" -[tool.poetry.scripts] -petdeface = 'petdeface.petdeface:main' -petdeface-qa = 'petdeface.qa:main' +[tool.setuptools] +packages = ["petdeface"] +include-package-data = false +package-data = { + "petdeface" = [ + "data/sub-01/**/*T1w.nii", + "data/sub-01/**/*T1w.nii.gz", + "data/sub-01/**/*T1w.json", + "data/sub-mni305/**/*T1w.nii", + "data/sub-mni305/**/*T1w.nii.gz", + "data/sub-mni305/**/*T1w.json", + "templates/*.html" + ] +} +exclude-package-data = { "petdeface" = ["data/sub-02/**/*"] } From 4b68be21f114b0ecb68ff25cfc12c7f4c5fdad5b Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 28 Jul 2025 19:19:44 -0400 Subject: [PATCH 17/19] refactored from defaced dir to bids dir to make qa usage more clear --- README.md | 63 +++++++++++++++++++++++++++++++++++ docs/modules.rst | 8 +++++ docs/usage.rst | 75 +++++++++++++++++++++++++++++++++++++++++- petdeface/petdeface.py | 4 +-- petdeface/qa.py | 13 +++----- 5 files changed, 152 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index ffb6f30..4e96e3e 100644 --- a/README.md +++ b/README.md @@ -78,6 +78,7 @@ options: Options: 't1' (included T1w template), 'mni' (MNI template), or 'pet' (averaged PET image). --open_browser Open browser to show QA reports after completion + --qa-port QA_PORT Port for NIfTI preview server (default: 8000) ``` Working example usage: @@ -106,6 +107,68 @@ Example usage with template anatomical: petdeface /inputfolder /outputfolder --use_template_anat t1 --n_procs 16 ``` +### Quality Assessment (QA) Reports + +PETdeface includes a comprehensive quality assessment system that generates reports to help validate defacing results. The QA system creates both SVG reports and interactive NIfTI viewers. + +#### QA Report Location + +QA reports are automatically generated in the input BIDS directory under `derivatives/petdeface/qa/`. This includes: +- SVG reports showing before/after defacing comparisons +- Interactive HTML viewers for 3D NIfTI visualization +- An index page linking to all available reports + +#### Running QA Reports + +**Automatic QA generation:** +```bash +petdeface /inputfolder /outputfolder --open_browser +``` + +**Manual QA generation using the separate QA tool:** +```bash +petdeface-qa /inputfolder --open-browser --start-server +``` + +#### NIfTI Preview Server + +For 3D NIfTI visualization, PETdeface can start a local HTTP server to serve NIfTI files. This is required due to browser security restrictions. + +**Start with server:** +```bash +petdeface-qa /inputfolder --start-server --open-browser +``` + +**Custom port:** +```bash +petdeface-qa /inputfolder --start-server --qa-port 8080 +``` + +#### QA Tool Options + +The `petdeface-qa` command provides the following options: + +```bash +usage: petdeface-qa [-h] bids_dir [--output-dir OUTPUT_DIR] + [--open-browser] [--start-server] [--qa-port QA_PORT] + +Generate SVG QA reports for PET deface workflow. + +positional arguments: + bids_dir BIDS directory containing the defaced dataset (with derivatives/petdeface) + +options: + -h, --help show this help message and exit + --output-dir OUTPUT_DIR, --output_dir OUTPUT_DIR + Output directory for HTML files (default: derivatives/petdeface/qa/) + --open-browser Open browser automatically + --start-server Start local HTTP server for NIfTI file access (required for NIfTI viewers) + --qa-port QA_PORT, --qa_port QA_PORT + Port for NIfTI preview server (default: 8000) +``` + +**Note**: The NIfTI preview server is required for 3D visualization due to browser CORS restrictions. Keep the terminal running while viewing NIfTI files. + ### Docker Usage Requirements: diff --git a/docs/modules.rst b/docs/modules.rst index e5e5987..9895ef3 100644 --- a/docs/modules.rst +++ b/docs/modules.rst @@ -26,6 +26,14 @@ petdeface.petdeface module -------------------------- .. automodule:: petdeface.petdeface + :members: + :undoc-members: + :show-inheritance: + +petdeface.qa module +------------------ + +.. automodule:: petdeface.qa :members: :undoc-members: :show-inheritance: \ No newline at end of file diff --git a/docs/usage.rst b/docs/usage.rst index 3d1fede..23867d9 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -127,6 +127,7 @@ options: Options: 't1' (included T1w template), 'mni' (MNI template), or 'pet' (averaged PET image). --open_browser Following defacing this flag will open the browser to view the defacing results + --qa-port QA_PORT Port for NIfTI preview server (default: 8000) Docker Based ------------ @@ -205,4 +206,76 @@ Example usage with template anatomical: .. code-block:: bash - petdeface /inputfolder /outputfolder --use_template_anat t1 --n_procs 16 \ No newline at end of file + petdeface /inputfolder /outputfolder --use_template_anat t1 --n_procs 16 + +Quality Assessment (QA) Reports +------------------------------ + +PETdeface includes a comprehensive quality assessment system that generates reports to help validate defacing results. The QA system creates both SVG reports and interactive NIfTI viewers. + +QA Report Location +~~~~~~~~~~~~~~~~~ + +QA reports are automatically generated in the input BIDS directory under ``derivatives/petdeface/qa/``. This includes: + +- SVG reports showing before/after defacing comparisons +- Interactive HTML viewers for 3D NIfTI visualization +- An index page linking to all available reports + +Running QA Reports +~~~~~~~~~~~~~~~~~ + +**Automatic QA generation:** + +.. code-block:: bash + + petdeface /inputfolder /outputfolder --open_browser + +**Manual QA generation using the separate QA tool:** + +.. code-block:: bash + + petdeface-qa /inputfolder --open-browser --start-server + +NIfTI Preview Server +~~~~~~~~~~~~~~~~~~~ + +For 3D NIfTI visualization, PETdeface can start a local HTTP server to serve NIfTI files. This is required due to browser security restrictions. + +**Start with server:** + +.. code-block:: bash + + petdeface-qa /inputfolder --start-server --open-browser + +**Custom port:** + +.. code-block:: bash + + petdeface-qa /inputfolder --start-server --qa-port 8080 + +QA Tool Options +~~~~~~~~~~~~~~ + +The ``petdeface-qa`` command provides the following options: + +.. code-block:: bash + + usage: petdeface-qa [-h] bids_dir [--output-dir OUTPUT_DIR] + [--open-browser] [--start-server] [--qa-port QA_PORT] + + Generate SVG QA reports for PET deface workflow. + + positional arguments: + bids_dir BIDS directory containing the defaced dataset (with derivatives/petdeface) + + options: + -h, --help show this help message and exit + --output-dir OUTPUT_DIR, --output_dir OUTPUT_DIR + Output directory for HTML files (default: derivatives/petdeface/qa/) + --open-browser Open browser automatically + --start-server Start local HTTP server for NIfTI file access (required for NIfTI viewers) + --qa-port QA_PORT, --qa_port QA_PORT + Port for NIfTI preview server (default: 8000) + +**Note**: The NIfTI preview server is required for 3D visualization due to browser CORS restrictions. Keep the terminal running while viewing NIfTI files. \ No newline at end of file diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index 1137e51..4ce5993 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -1606,13 +1606,13 @@ def main(): # noqa: max-complexity: 12 print(f"Reports available at: {qa_result['output_dir']}") print("=" * 60) - except Exception as e: print(f"\nError generating QA reports: {e}") print("QA report generation failed, but defacing completed successfully.") print("launch QA reports with:") - print(f"petdeface-qa --defaced_dir {args.bids_dir} --open_browser --start_server") + print(f"petdeface-qa {args.bids_dir} --open_browser --start_server") + if __name__ == "__main__": main() diff --git a/petdeface/qa.py b/petdeface/qa.py index 3ec5f20..b526b1c 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -43,7 +43,6 @@ def collect_svg_reports(defaced_dir, output_dir): print("Looking for SVG files in the main defaced directory...") derivatives_dir = defaced_dir - # Find all SVG files recursively, excluding the qa directory svg_files = [] for svg_file in glob.glob( @@ -754,7 +753,7 @@ def run_qa( // Show command help commandHelp.style.display = 'block'; - const command = `petdeface-qa --defaced-dir "${{defacedDir}}" --start-server --open-browser`; + const command = `petdeface-qa "${{defacedDir}}" --start-server --open-browser`; commandText.textContent = command; // Disable all NIfTI links @@ -843,15 +842,13 @@ def main(): description="Generate SVG QA reports for PET deface workflow." ) parser.add_argument( - "--defaced-dir", - "--defaced_dir", - required=True, - help="Directory for defaced dataset (containing derivatives/petdeface)", + "bids_dir", + help="BIDS directory containing the defaced dataset (with derivatives/petdeface)", ) parser.add_argument( "--output-dir", "--output_dir", - help="Output directory for HTML files (default: {dataset_name}_svg_qa)", + help="Output directory for HTML files (default: derivatives/petdeface/qa/)", ) parser.add_argument( "--open-browser", @@ -876,7 +873,7 @@ def main(): args = parser.parse_args() return run_qa( - defaced_dir=args.defaced_dir, + defaced_dir=args.bids_dir, output_dir=args.output_dir, open_browser=args.open_browser, start_server=args.start_server, From d6ba06e4d7ab8596c7cacc15ecbfe954d1f271b1 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Tue, 29 Jul 2025 09:19:21 -0400 Subject: [PATCH 18/19] clean up toml and fix import --- petdeface/qa.py | 1 + pyproject.toml | 63 +++++++------------------------------------------ 2 files changed, 10 insertions(+), 54 deletions(-) diff --git a/petdeface/qa.py b/petdeface/qa.py index b526b1c..3b15bc8 100644 --- a/petdeface/qa.py +++ b/petdeface/qa.py @@ -13,6 +13,7 @@ import time import subprocess import signal +import sys from pathlib import Path # Handle imports for both script and module execution (including debugger) diff --git a/pyproject.toml b/pyproject.toml index 2e6cc89..3254f4f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,26 +7,6 @@ authors = [ {name = "Anthony Galassi", email = "28850131+bendhouseart@users.noreply.github.com"}, {name = "Murat Bilgel", email = "bilgelm@gmail.com"} ] -license = "MIT" -readme = "README.md" -requires-python = ">=3.10" -dependencies = [ - "setuptools>=68.1.2", - "petutils>=0.0.1", - "niworkflows>=1.11.0", - "matplotlib>=3.10.1", - "niftifixer>=0.0.2", - "bids-validator-deno>=2.0.5", - "nipreps>=1.0", - "nireports>=25.2.0", - "nibabel>=5.3.2", - "nilearn>=0.10.4", - "numpy>=2.1.3", - "scipy>=1.14.1", - "seaborn>=0.13.2", - "pillow>=11.0.0", - "imageio>=2.36.0", -] license = {text = "MIT"} readme = "README.md" requires-python = ">=3.10" @@ -70,29 +50,6 @@ dev = [ petdeface = "petdeface.petdeface:main" petdeface-qa = "petdeface.qa:main" -[project.optional-dependencies] -dev = [ - "black>=23.7.0", - "flake8>=6.1.0", - "isort>=5.12.0", - "pre-commit>=3.3.3", - "pytest>=7.4.2", - "sphinx>=7.2.6", - "sphinx-rtd-theme>=3.0.1", - "jupyterlab>=4.4.1", - "notebook>=7.4.1", - "nbconvert>=7.16.6", - "ipywidgets>=8.1.6", - "matplotlib>=3.10.1", - "pandas>=2.2.3", - "pyqt6>=6.9.0", -] - -[project.scripts] -petdeface = "petdeface.petdeface:main" -petdeface-qa = "petdeface.qa:main" -petdeface_qa = "petdeface.qa:main" - # please update the bids version to the latest compliant version when making modifications to this code here [tool.bids] bids_version = "1.8.0" @@ -109,15 +66,13 @@ build-backend = "setuptools.build_meta" [tool.setuptools] packages = ["petdeface"] include-package-data = false -package-data = { - "petdeface" = [ - "data/sub-01/**/*T1w.nii", - "data/sub-01/**/*T1w.nii.gz", - "data/sub-01/**/*T1w.json", - "data/sub-mni305/**/*T1w.nii", - "data/sub-mni305/**/*T1w.nii.gz", - "data/sub-mni305/**/*T1w.json", - "templates/*.html" - ] -} +package-data = { "petdeface" = [ + "data/sub-01/**/*T1w.nii", + "data/sub-01/**/*T1w.nii.gz", + "data/sub-01/**/*T1w.json", + "data/sub-mni305/**/*T1w.nii", + "data/sub-mni305/**/*T1w.nii.gz", + "data/sub-mni305/**/*T1w.json", + "templates/*.html" +] } exclude-package-data = { "petdeface" = ["data/sub-02/**/*"] } From 9a37927c95bdb3e390502f66f6f9fd539c74e312 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Tue, 29 Jul 2025 09:25:08 -0400 Subject: [PATCH 19/19] Add missing --use_template_anat argument to fix AttributeError --- petdeface/petdeface.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index 4ce5993..89b2051 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -1371,6 +1371,14 @@ def cli(): required=False, default=[], ) + parser.add_argument( + "--use_template_anat", + help="Use template anatomical image when no T1w is available for PET scans. Options: 't1' (included T1w template), 'mni' (MNI template), or 'pet' (averaged PET image).", + type=str, + choices=["t1", "mni", "pet"], + required=False, + default=None, + ) parser.add_argument( "--open-browser", "--open_browser",