Fix 3D meshes never loading for uploaded scans

PanTS-Demo/src/components/viewer/MeshViewer.tsx

@@ -19,15 +19,21 @@
   crosshairMm: Vec3 | null
   customOrgans?: CheckBoxData[];
   labelColorMap?: { [key: number]: Color };
+  // Uploaded scans have no pre-baked meshes; fetch from the session route, which
+  // builds them on demand from the session's combined_labels.
+  isSession?: boolean;
 };
 
-export async function fetchMeshManifest(caseId: string): Promise<MeshManifest> {
-  const res = await fetch(`${APP_CONSTANTS.API_ORIGIN}/api/cases/${caseId}/mesh-manifest`);
+export async function fetchMeshManifest(caseId: string, isSession = false): Promise<MeshManifest> {
+  const base = isSession
+    ? `${APP_CONSTANTS.API_ORIGIN}/api/sessions/${caseId}/mesh-manifest`
+    : `${APP_CONSTANTS.API_ORIGIN}/api/cases/${caseId}/mesh-manifest`;
+  const res = await fetch(base);
   if (!res.ok) throw new Error(`Failed to fetch mesh manifest: ${res.status}`);
   return res.json();
 }
 
-export function SegmentationMeshViewer({ caseId, checkState, loading, opacity, crosshairMm, customOrgans = [], labelColorMap = {}}: SegmentationMeshViewerProps) {
+export function SegmentationMeshViewer({ caseId, checkState, loading, opacity, crosshairMm, customOrgans = [], labelColorMap = {}, isSession = false}: SegmentationMeshViewerProps) {
   const [manifest, setManifest] = useState<MeshManifest | null>(null);
   const [loaded, setLoaded] = useState<Record<number, boolean>>({});
   // Bumped on every mask edit so editedSegments below is recomputed — the 3D pane
@@ -41,7 +47,7 @@
 
   // Segment indices touched since the case loaded — includes edits to the STATIC
   // 32-organ catalog, not just brand-new custom classes.
   const editedSegments = useMemo(() => getEditedSegments(), [editVersion]);
 
   const crosshairPosition = useMemo(() => {
     if (!manifest || !crosshairMm) return null;
@@ -50,7 +56,7 @@
 
   useEffect(() => {
     let alive = true;
-    fetchMeshManifest(caseId)
+    fetchMeshManifest(caseId, isSession)
       .then((data) => {
         if (!alive) return;
         setManifest(data);
@@ -60,7 +66,7 @@
       })
       .catch((err) => console.error(err));
     return () => { alive = false; };
-  }, [caseId]);
+  }, [caseId, isSession]);
 
   const organs = useMemo(() => manifest?.organs ?? [], [manifest]);
 

PanTS-Demo/src/routes/VisualizationPage.tsx

@@ -3445,7 +3445,7 @@ const aiAvailableOrgans = useMemo(() => {
 									<span>(switch to Volume rendering above)</span>
 								</div>
 							) : (
-								<SegmentationMeshViewer caseId={caseId} crosshairMm={crosshairMm} checkState={checkState} loading={loading} opacity={opacityValue} customOrgans={customOrgans} labelColorMap={labelColorMap} />
+								<SegmentationMeshViewer caseId={caseId} isSession={!!sessionId && !pantsCase} crosshairMm={crosshairMm} checkState={checkState} loading={loading} opacity={opacityValue} customOrgans={customOrgans} labelColorMap={labelColorMap} />
 							)}
 						</div>
 						{!loading && (

flask-server/api/api_blueprint.py

@@ -1527,6 +1527,56 @@
     return response
 
 
+def _session_seg_path(session_id):
+    """Return the combined_labels.nii.gz path for a finished session, or None."""
+    job = _get_inference_job(session_id) or {}
+    output_mask_dir = job.get("output_mask_dir")
+    if not output_mask_dir:
+        return None
+    seg_path = os.path.join(output_mask_dir, "combined_labels.nii.gz")
+    return seg_path if os.path.exists(seg_path) else None
+
+
+# 3D organ meshes for an UPLOADED scan. Unlike dataset cases (whose meshes are
+# pre-baked into MESH_PATH by preprocess_meshes.py), a session has no pre-baked
+# meshes, so we build them on demand from the session's combined_labels and cache
+# them next to it. Without these routes the 3D pane hangs on "Loading 3D
+# segmentation..." because /cases/<id>/mesh-manifest 404s for a session id.
+@api_blueprint.route('/sessions/<session_id>/mesh-manifest', methods=['GET'])
+def get_session_mesh_manifest(session_id):
+    if not _is_safe_id(session_id):
+        return jsonify({"error": "Invalid id"}), 400
+    seg_path = _session_seg_path(session_id)
+    if not seg_path:
+        return jsonify({"error": "Segmentation not ready for session"}), 404
+    manifest = generate_mesh_manifest(session_id, seg_path, route_base="sessions")
+    return jsonify(manifest)
+
+
+@api_blueprint.route('/sessions/<session_id>/render_only/<filename>', methods=['GET'])
+def get_session_mesh_file(session_id, filename):
+    if not _is_safe_id(session_id):
+        return jsonify({"error": "Invalid id"}), 400
+    filename = secure_filename(filename)
+    seg_path = _session_seg_path(session_id)
+    if not seg_path:
+        return jsonify({"error": "Segmentation not ready for session"}), 404
+    # Cache the generated GLB next to the mask so repeat views / organ toggles
+    # don't re-run marching cubes.
+    cache_dir = os.path.join(os.path.dirname(seg_path), "render_only")
+    os.makedirs(cache_dir, exist_ok=True)
+    glb_path = os.path.join(cache_dir, filename)
+    if not os.path.exists(glb_path):
+        organ_key = os.path.splitext(filename)[0]
+        try:
+            glb_bytes = generate_organ_glb_bytes(organ_key, seg_path)
+        except ValueError as e:
+            return jsonify({"error": str(e)}), 404
+        with open(glb_path, "wb") as f:
+            f.write(glb_bytes)
+    return send_file(glb_path, mimetype="model/gltf-binary", conditional=False)
+
+
 @api_blueprint.route('/session-reconstruction/<session_id>', methods=['GET'])
 def get_session_reconstruction(session_id):
     """Serves the OpenVAE reconstructed CT for a session."""

flask-server/services/mesh_generation.py

@@ -47,6 +47,9 @@
     30: {"key": "renal_vein_left", "name": "Left Renal Vein"},
     31: {"key": "renal_vein_right", "name": "Right Renal Vein"},
     32: {"key": "cbd_stent", "name": "Common Bile Duct Stent"},
+    33: {"key": "liver_lesion", "name": "Liver Lesion"},
+    34: {"key": "kidney_lesion", "name": "Kidney Lesion"},
+    35: {"key": "colon_lesion", "name": "Colon Lesion"},
 }
 
 
@@ -176,7 +179,11 @@ def generate_organ_glb_bytes(
 def generate_mesh_manifest(
     case_id: str,
     label_nifti_path: str,
+    route_base: str = "cases",
 ) -> dict:
+    # route_base selects which serving route the per-organ GLB URLs point at:
+    # "cases" for pre-baked dataset meshes, "sessions" for on-demand meshes
+    # generated from an uploaded scan's combined_labels.
     img, data = load_clean_label_data(label_nifti_path)
 
     present_labels = set(np.unique(data).astype(int).tolist())
@@ -200,7 +207,7 @@ def generate_mesh_manifest(
                 "id": key,
                 "key": meta["key"],
                 "name": meta["name"],
-                "url": f"{os.getenv('API_ORIGIN', 'http://localhost:5001')}/api/cases/{case_id}/render_only/{filename}",
+                "url": f"{os.getenv('API_ORIGIN', 'http://localhost:5001')}/api/{route_base}/{case_id}/render_only/{filename}",
             }
         )