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bendhouseartbendhouseart
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added SimpleBeforeAfterRPT image view for T1w
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3 files changed

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3 files changed

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‎petdeface/qa.py‎

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Original file line numberDiff line numberDiff line change
@@ -16,6 +16,218 @@
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from functools import partial
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import seaborn as sns
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from PIL import Image, ImageDraw
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from nipype import Workflow, Node
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from nireports.interfaces.reporting.base import SimpleBeforeAfterRPT
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from tempfile import TemporaryDirectory
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from pathlib import Path
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def generate_simple_before_and_after(subjects: dict, output_dir):
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if not output_dir:
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output_dir = TemporaryDirectory()
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wf = Workflow(
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name="simple_before_after_report", base_dir=Path(output_dir) / "images/"
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)
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# Create a list to store all nodes
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nodes = []
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for s in subjects:
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# only run this on the T1w images for now
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if "T1w" in s["orig_path"]:
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o_path = Path(s["orig_path"])
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# Create a valid node name by replacing invalid characters
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valid_name = f"before_after_{s['id'].replace('-', '_').replace('_', '')}"
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node = Node(
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SimpleBeforeAfterRPT(
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before=s["orig_path"],
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after=s["defaced_path"],
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before_label="Original",
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after_label="Defaced",
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out_report=f"{s['id']}_simple_before_after.svg",
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),
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name=valid_name,
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)
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nodes.append(node)
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# Add all nodes to the workflow
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wf.add_nodes(nodes)
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wf.run(plugin="MultiProc", plugin_args={"n_procs": mp.cpu_count()})
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# Collect SVG files and move them to images folder
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collect_svg_reports(wf, output_dir)
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def collect_svg_reports(wf, output_dir):
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"""Collect SVG reports from workflow and move them to images folder."""
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import glob
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# Find all SVG files in the workflow directory
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workflow_dir = wf.base_dir
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svg_files = glob.glob(os.path.join(workflow_dir, "**", "*.svg"), recursive=True)
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print(f"Found {len(svg_files)} SVG reports")
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# Move each SVG to the images folder
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for svg_file in svg_files:
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filename = os.path.basename(svg_file)
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dest_path = os.path.join(output_dir, "images", filename)
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shutil.move(svg_file, dest_path)
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print(f" Moved: {filename}")
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# Create HTML page for SVG reports
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create_svg_index_html(svg_files, output_dir)
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def create_svg_index_html(svg_files, output_dir):
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"""Create HTML index page for SVG reports."""
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svg_entries = ""
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for svg_file in svg_files:
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filename = os.path.basename(svg_file)
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subject_id = filename.replace("_simple_before_after.svg", "")
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svg_entries += f"""
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<div class="svg-report">
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<h3>{subject_id}</h3>
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<object data="images/{filename}" type="image/svg+xml" style="width: 100%; height: 600px;">
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<p>Your browser does not support SVG. <a href="images/{filename}">Download SVG</a></p>
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</object>
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</div>
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"""
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html_content = f"""
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<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8">
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<title>PET Deface SVG Reports</title>
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<style>
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body {{
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font-family: Arial, sans-serif;
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margin: 20px;
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background: #f5f5f5;
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}}
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.header {{
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text-align: center;
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margin-bottom: 30px;
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color: #333;
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}}
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.svg-report {{
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background: white;
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margin-bottom: 40px;
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padding: 20px;
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border-radius: 10px;
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box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1);
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}}
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.svg-report h3 {{
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color: #2c3e50;
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margin-top: 0;
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margin-bottom: 15px;
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text-align: center;
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}}
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.navigation {{
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position: fixed;
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top: 20px;
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right: 20px;
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background: white;
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padding: 15px;
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border-radius: 10px;
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box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
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z-index: 1000;
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}}
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.nav-button {{
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display: block;
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margin: 5px 0;
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padding: 8px 12px;
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background: #3498db;
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color: white;
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border: none;
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border-radius: 5px;
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cursor: pointer;
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font-size: 12px;
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text-decoration: none;
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}}
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.nav-button:hover {{
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background: #2980b9;
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}}
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</style>
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<script>
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function scrollToReport(direction) {{
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const reports = document.querySelectorAll('.svg-report');
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const currentScroll = window.pageYOffset;
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const windowHeight = window.innerHeight;
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let targetReport = null;
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if (direction === 'next') {{
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for (let report of reports) {{
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if (report.offsetTop > currentScroll + windowHeight * 0.3) {{
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targetReport = report;
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break;
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}}
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}}
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if (!targetReport && reports.length > 0) {{
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targetReport = reports[0];
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}}
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}} else if (direction === 'prev') {{
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for (let i = reports.length - 1; i >= 0; i--) {{
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if (reports[i].offsetTop < currentScroll - windowHeight * 0.3) {{
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targetReport = reports[i];
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break;
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}}
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}}
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if (!targetReport && reports.length > 0) {{
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targetReport = reports[reports.length - 1];
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}}
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}}
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if (targetReport) {{
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targetReport.scrollIntoView({{ behavior: 'smooth', block: 'center' }});
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}}
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}}
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// Keyboard navigation
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document.addEventListener('keydown', function(e) {{
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if (e.key === 'ArrowDown' || e.key === ' ') {{
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e.preventDefault();
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scrollToReport('next');
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}} else if (e.key === 'ArrowUp') {{
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e.preventDefault();
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scrollToReport('prev');
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}}
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}});
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</script>
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</head>
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<body>
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<div class="navigation">
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<button class="nav-button" onclick="scrollToReport('prev')">↑ Previous</button>
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<button class="nav-button" onclick="scrollToReport('next')">↓ Next</button>
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<div style="margin-top: 10px; font-size: 10px; color: #666;">
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Use arrow keys or spacebar
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</div>
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</div>
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<div class="header">
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<h1>PET Deface SVG Reports</h1>
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<p>Before/After comparison reports using nireports</p>
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</div>
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<div class="reports-container">
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{svg_entries}
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</div>
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<div style="text-align: center; margin-top: 30px;">
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<a href="index.html">← Back to Index</a>
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</div>
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</body>
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</html>
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"""
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svg_index_file = os.path.join(output_dir, "SimpleBeforeAfterRPT.html")
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with open(svg_index_file, "w") as f:
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f.write(html_content)
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print(f"Created SVG reports index: {svg_index_file}")
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def create_overlay_comparison(orig_path, defaced_path, subject_id, output_dir):
@@ -932,6 +1144,9 @@ def main():
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print(f" - {s['id']}")
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exit(1)
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# create nireports svg's for comparison
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generate_simple_before_and_after(subjects=subjects, output_dir=output_dir)
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# Set number of jobs for parallel processing
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n_jobs = args.n_jobs if args.n_jobs else mp.cpu_count()
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print(f"Using {n_jobs} parallel processes")
@@ -1010,6 +1225,7 @@ def main():
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<a href="side_by_side.html" class="link-button">Side by Side View</a>
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<a href="animated.html" class="link-button">Animated GIF View</a>
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<a href="SimpleBeforeAfterRPT.html" class="link-button">SVG Reports View</a>
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<p style="margin-top: 30px; color: #999; font-size: 14px;">
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Generated with {len(subjects)} subjects

‎poetry.lock‎

Lines changed: 51 additions & 9 deletions
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‎pyproject.toml‎

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@@ -21,6 +21,16 @@ petutils = "^0.0.1"
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niworkflows = "^1.11.0"
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niftifixer = {git = "https://github.com/openneuropet/nifti_fixer.git"}
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bids-validator-deno = "^2.0.5"
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nipreps = "^1.0"
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nireports = "^25.2.0"
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nibabel = "^5.3.2"
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nilearn = "^0.10.4"
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matplotlib = "^3.9.2"
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numpy = "^2.1.3"
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scipy = "^1.14.1"
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seaborn = "^0.13.2"
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pillow = "^11.0.0"
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imageio = "^2.36.0"
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[tool.poetry.group.dev.dependencies]

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