Merge pull request #690 from ComputationalCryoEM/ctf_regression

Ctf regression

Author: garrettwrong

src/aspire/ctf/ctf_estimator.py

@@ -340,7 +340,8 @@ def background_subtract_1d(
             convex_condition = np.concatenate(
                 (np.zeros((N, N)), convex_condition), axis=1
             )
-            convex_condition = convex_condition[1 : N - 1]
+            convex_condition = np.roll(convex_condition, -1, axis=0)
+            convex_condition[N - 2 :] = 0
 
             positivity_condition = np.concatenate(
                 (np.zeros((N, N)), -1 * np.eye(N)), axis=1

tests/test_CtfEstimate.py

@@ -19,9 +19,9 @@ class CtfEstimatorTestCase(TestCase):
     def setUp(self):
         self.test_input_fn = "sample.mrc"
         self.test_output = {
-            "defocus_u": 1.1142363760e03,
-            "defocus_v": 1.0920983202e03,
-            "defocus_ang": -8.3521800000e-03,
+            "defocus_u": 1.137359876e03,
+            "defocus_v": 9.617226108e02,
+            "defocus_ang": 1.5706205116381249,
             "cs": 2.0,
             "voltage": 300.0,
             "pixel_size": 1,
@@ -63,18 +63,28 @@ def testEstimateCTF(self):
                     # the following parameters have higher tolerances
 
                     # defocusU
-                    np.allclose(
-                        result["defocus_u"], self.test_output["defocus_u"], atol=5e-2
+                    self.assertTrue(
+                        np.allclose(
+                            result["defocus_u"],
+                            self.test_output["defocus_u"],
+                            atol=5e-2,
+                        )
                     )
                     # defocusV
-                    np.allclose(
-                        result["defocus_v"], self.test_output["defocus_v"], atol=5e-2
+                    self.assertTrue(
+                        np.allclose(
+                            result["defocus_u"],
+                            self.test_output["defocus_u"],
+                            atol=5e-2,
+                        )
                     )
                     # defocusAngle
-                    np.allclose(
-                        result["defocus_ang"],
-                        self.test_output["defocus_ang"],
-                        atol=5e-5,
+                    self.assertTrue(
+                        np.allclose(
+                            result["defocus_ang"],
+                            self.test_output["defocus_ang"],
+                            atol=5e-2,
+                        )
                     )
 
                     for param in ["cs", "amplitude_contrast", "voltage", "pixel_size"]: