Do not apply scaling to neurites when correcting for slice shrinkage

Add an optional keyword argument scale_radius=True to the transform Apply scale correction witht scale_radius=False
AllenInstitute · May 21, 2020 · 2f941d7 · 2f941d7
1 parent 9577f70
commit 2f941d7
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Showing 3 changed files with 18 additions and 7 deletions.
diff --git a/neuron_morphology/transforms/affine_transform.py b/neuron_morphology/transforms/affine_transform.py
@@ -160,14 +160,19 @@ def _get_scaling_factor(self) -> float:
         determinant = np.linalg.det(self.affine)
         return np.power(abs(determinant), 1.0 / 3.0)
 
-    def transform_morphology(self, morphology: Morphology,
-                             clone: bool = False) -> Morphology:
+    def transform_morphology(self,
+                             morphology: Morphology,
+                             clone: bool = False,
+                             scale_radius: bool = True,
+                             ) -> Morphology:
         """
             Apply this transform to all nodes in a morphology.
 
             Parameters
             ----------
             morphology: a Morphology loaded from an swc file
+            clone: make a new object if True
+            scale_radius: apply radius scaling if True
 
             Returns
             -------
@@ -176,7 +181,10 @@ def transform_morphology(self, morphology: Morphology,
         if clone:
             morphology = morphology.clone()
 
-        scaling_factor = self._get_scaling_factor()
+        if scale_radius:
+            scaling_factor = self._get_scaling_factor()
+        else:
+            scaling_factor = 1
 
         for node in morphology.nodes():
             coordinates = np.array((node['x'], node['y'], node['z']),

diff --git a/neuron_morphology/transforms/scale_correction/compute_scale_correction.py b/neuron_morphology/transforms/scale_correction/compute_scale_correction.py
@@ -94,7 +94,8 @@ def run_scale_correction(
          [0, 0, scale_correction]]
     )
     at = aff.AffineTransform(scale_transform)
-    morphology_scaled = at.transform_morphology(morphology)
+    morphology_scaled = at.transform_morphology(morphology,
+                                                scale_radius=False)
 
     return {
         "morphology_scaled": morphology_scaled,

diff --git a/tests/transforms/test_scale_correction.py b/tests/transforms/test_scale_correction.py
@@ -18,8 +18,8 @@ def setUp(self):
 
         self.morphology = (
             MorphologyBuilder()
-                .root(1, 2, 3)
-                    .axon(0, 2, 100)
+                .root(1, 2, 3, radius=1.3)
+                    .axon(0, 2, 100, radius=0.4)
                         .build()
         )
         self.max_morphology = (
@@ -79,12 +79,14 @@ def test_scale_correction_end_to_end(self):
         self.assertAlmostEqual(outputs['scale_correction'], 2.0)
 
         aff_t = AffineTransform.from_dict(outputs['scale_transform'])
-        morph_t = aff_t.transform_morphology(self.morphology)
+        morph_t = aff_t.transform_morphology(self.morphology,
+                                             scale_radius=False)
 
         axon = morph_t.node_by_id(1)
         self.assertAlmostEqual(axon['x'], 0)
         self.assertAlmostEqual(axon['y'], 2)
         self.assertAlmostEqual(axon['z'], 200)
+        self.assertAlmostEqual(axon['radius'], 0.4)
 
     def test_run_scale_correction(self):