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app.py

@@ -7,8 +7,33 @@ from datasets import load_dataset
 
 # Load the dataset
 print("Loading dataset...")
-dataset = load_dataset("rntc/biomed-fr-pancreas-annotations", split="train")
-print(f"Loaded {len(dataset)} samples")
+full_dataset = load_dataset("rntc/biomed-fr-pancreas-annotations", split="train")
+print(f"Loaded {len(full_dataset)} samples")
+
+# Filter: keep only samples with >= 10 real annotations
+MIN_ANNOTATIONS = 10
+
+def count_real_annotations(annotation):
+    """Count real annotations (excluding 'not found' placeholders)."""
+    count = 0
+    for var_data in annotation.values():
+        if var_data and isinstance(var_data, dict):
+            value = var_data.get("value")
+            span = var_data.get("span", "")
+            if value:
+                if span and "pas de mention" in span.lower():
+                    continue
+                if "not performed" in str(value).lower():
+                    continue
+                count += 1
+    return count
+
+# Filter dataset
+filtered_indices = [
+    i for i, sample in enumerate(full_dataset)
+    if count_real_annotations(sample.get("annotation", {})) >= MIN_ANNOTATIONS
+]
+print(f"Filtered to {len(filtered_indices)} samples with >= {MIN_ANNOTATIONS} annotations")
 
 # Colors for highlighting
 COLORS = [
@@ -60,16 +85,13 @@ def highlight_text(cr_text, annotation):
     color_idx = 0
 
     for s in filtered:
-        # Text before span
         if s["start"] > pos:
             html.append(escape_html(cr_text[pos:s["start"]]))
 
-        # Assign color
         if s["var"] not in color_map:
             color_map[s["var"]] = COLORS[color_idx % len(COLORS)]
             color_idx += 1
 
-        # Highlighted span
         color = color_map[s["var"]]
         html.append(
             f'<mark style="background:{color};padding:1px 3px;border-radius:3px;" '
@@ -78,11 +100,10 @@ def highlight_text(cr_text, annotation):
         )
         pos = s["end"]
 
-    # Remaining text
     if pos < len(cr_text):
         html.append(escape_html(cr_text[pos:]))
 
-    return f"<pre style='white-space:pre-wrap;line-height:1.6;'>{' '.join(html)}</pre>"
+    return f"<pre style='white-space:pre-wrap;line-height:1.6;'>{''.join(html)}</pre>"
 
 
 def format_table(annotation):
@@ -99,8 +120,10 @@ def format_table(annotation):
             var_label = var_name.replace("_", " ").title()
 
             if value:
-                # Check if span is a "not found" explanation
-                if span and ("pas de mention" in span.lower() or "not performed" in str(value).lower()):
+                if span and "pas de mention" in span.lower():
+                    display_value = "/"
+                    display_span = ""
+                elif "not performed" in str(value).lower():
                     display_value = "/"
                     display_span = ""
                 else:
@@ -126,26 +149,30 @@ def format_table(annotation):
     </table>"""
 
 
-def display_sample(idx):
+def display_sample(slider_idx):
     """Display a sample."""
-    idx = int(idx)
-    if idx < 0 or idx >= len(dataset):
+    slider_idx = int(slider_idx)
+    if slider_idx < 0 or slider_idx >= len(filtered_indices):
         return "Invalid index", "Invalid index"
 
-    sample = dataset[idx]
+    real_idx = filtered_indices[slider_idx]
+    sample = full_dataset[real_idx]
     cr = sample.get("CR", "")
     annotation = sample.get("annotation", {})
 
-    return highlight_text(cr, annotation), format_table(annotation)
+    n_annotations = count_real_annotations(annotation)
+    header = f"<p><b>Sample #{real_idx}</b> — {n_annotations} annotations</p>"
+
+    return header + highlight_text(cr, annotation), format_table(annotation)
 
 
 # Build UI
 with gr.Blocks(title="Pancreas Annotations", theme=gr.themes.Base()) as demo:
     gr.Markdown("# 🔬 Pancreas Cancer Annotations Explorer")
-    gr.Markdown("Hover over highlighted text to see extracted values. `/` means not found.")
+    gr.Markdown(f"Showing {len(filtered_indices)} samples with >= {MIN_ANNOTATIONS} annotations. Hover over highlights to see values.")
 
     with gr.Row():
-        slider = gr.Slider(0, len(dataset) - 1, value=0, step=1, label="Sample")
+        slider = gr.Slider(0, len(filtered_indices) - 1, value=0, step=1, label="Sample")
 
     with gr.Row():
         with gr.Column():