Feat integrate node features (#142)

* bug: dataset construction * bug: dataset generation --------- Co-authored-by: anna-grim <[email protected]>
AllenInstitute · May 11, 2024 · fbec0ae · fbec0ae
1 parent 6c735b3
commit fbec0ae
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Showing 2 changed files with 12 additions and 11 deletions.
diff --git a/src/deep_neurographs/geometry.py b/src/deep_neurographs/geometry.py
@@ -188,7 +188,7 @@ def smooth_branch(xyz, s=None):
 
     Returns
     -------
-    xyz : numpy.ndarray
+    numpy.ndarray
         Smoothed points.
 
     """
@@ -199,7 +199,7 @@ def smooth_branch(xyz, s=None):
     return xyz.astype(np.float32)
 
 
-def fit_spline(xyz, s=None):
+def fit_spline(xyz, k=3, s=None):
     """
     Fits a cubic spline to an array containing xyz coordinates.
 
@@ -222,9 +222,9 @@ def fit_spline(xyz, s=None):
     """
     s = xyz.shape[0] / 10 if not s else xyz.shape[0] / s
     t = np.linspace(0, 1, xyz.shape[0])
-    spline_x = UnivariateSpline(t, xyz[:, 0], s=s, k=3)
-    spline_y = UnivariateSpline(t, xyz[:, 1], s=s, k=3)
-    spline_z = UnivariateSpline(t, xyz[:, 2], s=s, k=3)
+    spline_x = UnivariateSpline(t, xyz[:, 0], k=k, s=s)
+    spline_y = UnivariateSpline(t, xyz[:, 1], k=k, s=s)
+    spline_z = UnivariateSpline(t, xyz[:, 2], k=k, s=s)
     return spline_x, spline_y, spline_z
 
 
@@ -245,8 +245,9 @@ def sample_curve(xyz_arr, n_pts):
         Resampled points along curve.
 
     """
+    k = 1 if xyz_arr.shape[0] <= 3 else 3
     t = np.linspace(0, 1, n_pts)
-    spline_x, spline_y, spline_z = fit_spline(xyz_arr, s=0)
+    spline_x, spline_y, spline_z = fit_spline(xyz_arr, k=k, s=0)
     xyz = np.column_stack((spline_x(t), spline_y(t), spline_z(t)))
     return xyz.astype(int)
 

diff --git a/src/deep_neurographs/machine_learning/heterogeneous_graph_datasets.py b/src/deep_neurographs/machine_learning/heterogeneous_graph_datasets.py
@@ -164,11 +164,11 @@ def init_edge_attrs(self, x_nodes):
         """
         # Proposal edges
         edge_type = ("proposal", "to", "proposal")
-        attrs = self.set_edge_attrs(x_nodes, edge_type, self.idxs_proposals)
-        # --> set attr
+        self.set_edge_attrs(x_nodes, edge_type, self.idxs_proposals)
 
         # Branch edges
         edge_type = ("branch", "to", "branch")
+        self.set_edge_attrs(x_nodes, edge_type, self.idxs_branches)
 
         # Branch-Proposal edges
         edge_type = ("branch", "to", "proposal")
@@ -270,9 +270,9 @@ def set_edge_attrs(self, x_nodes, edge_type, idx_mapping):
             e1, e2 = self.data[edge_type][:, i]
             v = node_intersection(idx_mapping, e1, e2)
             attrs.append(x_nodes[v])
-            print(v)
-            print(attrs)
-            stop
+        arrs = torch.tensor(np.array(attrs), dtype=DTYPE)
+        self.data[edge_type].edge_attr = arrs
+
 
 # -- utils --
 def init_idxs(idxs):