save segs to sep meshes

SEGMENTATION/SEGMENTATION.py

@@ -167,7 +167,8 @@ def run(self, meshes_dir, mrk_dir, out_dir,
       labV = self._project_labels(V, P, labels)
       labV = self._smooth_labels(V, F, labV, smooth_iters)
       if write_vtp:
-        self._write_vtp_with_labels_world(meshPath, out_dir, labV, labV); wrote += 1
+        #self._write_vtp_with_labels_world(meshPath, out_dir, labV, labV); wrote += 1 # TO DO
+        self._write_ply_segments(meshPath, out_dir, labV); wrote += 1
       if i < previewN:
         self._preview_in_scene(meshPath, labV)
 
@@ -219,7 +220,7 @@ def _load_model_node(self, path):
     before = self._ids_of_class("vtkMRMLModelNode")
     node = None
     try:
-      node = slicer.util.loadModel(path, properties={"coordinateSystem":"LPS"})
+      node = slicer.util.loadModel(path, properties={"coordinateSystem":"RAS"})
     except TypeError:  # very old Slicer: no properties kw
       ok = slicer.util.loadModel(path)
       if not ok: raise RuntimeError(f"Failed to load model: {path}")
@@ -232,7 +233,7 @@ def _load_markups_node(self, path):
     before = self._ids_of_class("vtkMRMLMarkupsNode")
     node = None
     try:
-      node = slicer.util.loadMarkups(path, properties={"coordinateSystem":"LPS"})
+      node = slicer.util.loadMarkups(path, properties={"coordinateSystem":"RAS"})
     except TypeError:
       ok = slicer.util.loadMarkups(path)
       if not ok: raise RuntimeError(f"Failed to load markups: {path}")
@@ -422,13 +423,49 @@ def _smooth_labels(self,V,F,lab,iters):
       maj=np.argmax(votes,1); lab=np.where(deg>0,maj,lab)
     return lab
 
+# TO DO: substitute _write_ply_segments() to save ply's of each segment instead of a colored vtp
   def _write_vtp_with_labels_world(self,meshPath,out_dir,labV_raw,labV_smooth):
     n=self._load_model_node(meshPath); pdW=self._polydata_world(n)
     a1=vtk_np.numpy_to_vtk(labV_raw, deep=True, array_type=vtk.VTK_INT); a1.SetName("SegID"); pdW.GetPointData().AddArray(a1)
     a2=vtk_np.numpy_to_vtk(labV_smooth, deep=True, array_type=vtk.VTK_INT); a2.SetName("SegID_smooth"); pdW.GetPointData().AddArray(a2); pdW.GetPointData().SetActiveScalars("SegID_smooth")
     w=vtk.vtkXMLPolyDataWriter(); base=os.path.splitext(os.path.basename(meshPath))[0]; out=os.path.join(out_dir,base+"_seg.vtp"); w.SetFileName(out); w.SetInputData(pdW); w.Write()
     slicer.mrmlScene.RemoveNode(n)
 
+# TO DO: added func to output ply segments
+  def _write_ply_segments(self, meshPath, out_dir, labels):
+    n = self._load_model_node(meshPath)
+    pd = self._polydata_world(n)
+    # attach labels as active point scalars
+    arr = vtk_np.numpy_to_vtk(labels.astype(np.int32), deep=True, array_type=vtk.VTK_INT)
+    arr.SetName("SegID")
+    pd.GetPointData().SetScalars(arr)
+    base = os.path.splitext(os.path.basename(meshPath))[0]
+    for seg in np.unique(labels):
+        if seg < 0:
+            continue  # optional: skip background
+        t = vtk.vtkThreshold()
+        t.SetInputData(pd)
+        # make sure we threshold on point scalars "SegID"
+        t.SetInputArrayToProcess(
+            0, 0, 0,
+            vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
+            "SegID"
+        )
+        # tighter bounds are safer than exact equality in floating pipelines
+        t.SetLowerThreshold(float(seg) - 0.5) 
+        t.SetUpperThreshold(float(seg) + 0.5)
+        t.Update()
+        g = vtk.vtkGeometryFilter()
+        g.SetInputConnection(t.GetOutputPort())
+        g.Update()
+        out_path = os.path.join(out_dir, f"{base}_seg_{int(seg):02d}.ply")
+        w = vtk.vtkPLYWriter()
+        w.SetFileName(out_path)
+        w.SetInputData(g.GetOutput())
+        w.SetFileTypeToBinary()
+        w.Write()
+    slicer.mrmlScene.RemoveNode(n)
+
   def _preview_in_scene(self, meshPath, labV):
     n = self._load_model_node(meshPath)
     if n is None: return
@@ -837,9 +874,4 @@ def _assert_finite(self, what, arr, path):
       raise RuntimeError(
         f"Non-finite values in {what} of '{os.path.basename(path)}' "
         f"(first bad indices: {bad})."
-      )
-
-
-
-
-
+      )