Merge pull request #3 from ibs-lab/test-image-recon

TwoSurfaceHeadModel: make landmarks optional

src/cedalion/dataclasses/geometry.py

@@ -129,7 +129,12 @@ def decimate(self, face_count: int) -> "TrimeshSurface":
             The surface with a decimated mesh
         """
 
-        decimated = self.mesh.simplify_quadric_decimation(face_count)
+        try:
+            decimated = self.mesh.simplify_quadric_decimation(face_count)
+        except:
+            # deprecated trimesh function, please update trimesh!
+            decimated = self.mesh.simplify_quadratic_decimation(face_count)
+
         return TrimeshSurface(decimated, self.crs, self.units)
 
     def smooth(self, lamb: float) -> "TrimeshSurface":

src/cedalion/imagereco/forward_model.py

@@ -27,7 +27,7 @@ class TwoSurfaceHeadModel:
     segmentation_masks: xr.DataArray
     brain: cdc.Surface
     scalp: cdc.Surface
-    landmarks: cdt.LabeledPointCloud
+    landmarks: Optional[cdt.LabledPointCloud]
     t_ijk2ras: cdt.AffineTransform
     t_ras2ijk: cdt.AffineTransform
     voxel_to_vertex_brain: scipy.sparse.spmatrix
@@ -46,7 +46,7 @@ def from_segmentation(
             "skull": "skull.nii",
             "wm": "wm.nii",
         },
-        landmarks_ras_file: str = "landmarks.mrk.json",
+        landmarks_ras_file: Optional[str] = None,
         brain_seg_types: list[str] = ["gm", "wm"],
         scalp_seg_types: list[str] = ["scalp"],
         smoothing: float = 0.5,
@@ -71,11 +71,14 @@ def from_segmentation(
 
         # load landmarks. Other than the segmentation masks which are in voxel (ijk)
         # space, these are already in RAS space.
-        if not os.path.isabs(landmarks_ras_file):
-            landmarks_ras_file = os.path.join(segmentation_dir, landmarks_ras_file)
+        if landmarks_ras_file is not None:
+            if not os.path.isabs(landmarks_ras_file):
+                landmarks_ras_file = os.path.join(segmentation_dir, landmarks_ras_file)
 
-        landmarks_ras = cedalion.io.read_mrk_json(landmarks_ras_file, crs=crs_ras)
-        landmarks_ijk = landmarks_ras.points.apply_transform(t_ras2ijk)
+            landmarks_ras = cedalion.io.read_mrk_json(landmarks_ras_file, crs=crs_ras)
+            landmarks_ijk = landmarks_ras.points.apply_transform(t_ras2ijk)
+        else:
+            landmarks_ijk = None
 
         # derive surfaces from segmentation masks
         brain_ijk = surface_from_segmentation(segmentation_masks, brain_seg_types)
@@ -127,13 +130,15 @@ def from_segmentation(
     @property
     def crs(self):
         assert self.brain.crs == self.scalp.crs
-        assert self.scalp.crs == self.landmarks.points.crs
+        if self.landmarks is not None:
+            assert self.scalp.crs == self.landmarks.points.crs
         return self.brain.crs
 
     def apply_transform(self, transform: cdt.AffineTransform) -> "TwoSurfaceHeadModel":
         brain = self.brain.apply_transform(transform)
         scalp = self.scalp.apply_transform(transform)
-        landmarks = self.landmarks.points.apply_transform(transform)
+        landmarks = self.landmarks.points.apply_transform(transform) \
+                    if self.landmarks is not None else None
 
         return TwoSurfaceHeadModel(
             segmentation_masks=self.segmentation_masks,
@@ -152,6 +157,8 @@ def apply_transform(self, transform: cdt.AffineTransform) -> "TwoSurfaceHeadMode
     def align_and_snap_to_scalp(
         self, points: cdt.LabeledPointCloud
     ) -> cdt.LabeledPointCloud:
+        assert self.landmarks is not None, "Please add landmarks in RAS to head \
+                                            instance."
         t = register_trans_rot_isoscale(self.landmarks, points)
         transformed = points.points.apply_transform(t)
         snapped = self.scalp.snap(transformed)