Merge pull request #414 from ComputationalCryoEM/fix_413

Simulation n=1

Author: garrettwrong

src/aspire/apple/picking.py

@@ -23,7 +23,7 @@
 
 
 class Picker:
-    """ This class does the actual picking with help from PickerHelper class. """
+    """This class does the actual picking with help from PickerHelper class."""
 
     def __init__(
         self,

src/aspire/reconstruction/estimator.py

@@ -63,7 +63,7 @@ def compute_kernel(self):
         raise NotImplementedError("Subclasses must implement the compute_kernel method")
 
     def estimate(self, b_coeff=None, tol=None):
-        """ Return an estimate as a Volume instance. """
+        """Return an estimate as a Volume instance."""
         if b_coeff is None:
             b_coeff = self.src_backward()
         est_coeff = self.conj_grad(b_coeff, tol=tol)

src/aspire/source/image.py

@@ -119,7 +119,7 @@ def __init__(self, L, n, dtype="double", metadata=None, memory=None):
 
     @property
     def states(self):
-        return self.get_metadata("_rlnClassNumber")
+        return np.atleast_1d(self.get_metadata("_rlnClassNumber"))
 
     @states.setter
     def states(self, values):
@@ -164,15 +164,17 @@ def filter_indices(self, indices):
 
     @property
     def offsets(self):
-        return self.get_metadata(["_rlnOriginX", "_rlnOriginY"], default_value=0.0)
+        return np.atleast_2d(
+            self.get_metadata(["_rlnOriginX", "_rlnOriginY"], default_value=0.0)
+        )
 
     @offsets.setter
     def offsets(self, values):
         return self.set_metadata(["_rlnOriginX", "_rlnOriginY"], values)
 
     @property
     def amplitudes(self):
-        return self.get_metadata("_rlnAmplitude", default_value=1.0)
+        return np.atleast_1d(self.get_metadata("_rlnAmplitude", default_value=1.0))
 
     @amplitudes.setter
     def amplitudes(self, values):

src/aspire/volume/__init__.py

@@ -176,7 +176,7 @@ def project(self, vol_idx, rot_matrices):
         return aspire.image.Image(np.real(im_f))
 
     def to_vec(self):
-        """ Returns an N x resolution ** 3 array."""
+        """Returns an N x resolution ** 3 array."""
         return self._data.reshape((self.n_vols, self.resolution ** 3))
 
     @staticmethod

tests/test_BlkDiagMatrix.py

@@ -56,16 +56,16 @@ def tearDown(self):
         pass
 
     def allallfunc(self, A, B, func=np.allclose):
-        """ Checks assertTrue(func()) as it iterates through A, B. """
+        """Checks assertTrue(func()) as it iterates through A, B."""
         for (a, b) in zip(A, B):
             self.assertTrue(func(a, b))
 
     def allallid(self, A, B_ids, func=np.allclose):
-        """ Checks id(a) matches b_id for (a, b_id) in zip(A, B_ids). """
+        """Checks id(a) matches b_id for (a, b_id) in zip(A, B_ids)."""
         return self.allallfunc(A, B_ids, func=lambda x, y: id(x) == y)
 
     def testBlkDiagMatrixCompat(self):
-        """ Check incompatible matrix raises exception. """
+        """Check incompatible matrix raises exception."""
         # Create a differently shaped matrix
         x = BlkDiagMatrix.from_list(self.blk_a[1:-1])
         # code should raise
@@ -208,7 +208,7 @@ def testBlkDiagMatrixDeepCopy(self):
         self.allallfunc(blk_a_copy_2, self.blk_a)
 
     def testBlkDiagMatrixInPlace(self):
-        """ Tests sequence of in place optimized arithmetic (add, sub, mul) """
+        """Tests sequence of in place optimized arithmetic (add, sub, mul)"""
         _ = [x + x + 10.0 for x in self.blk_a]
         _ = [np.ones(x.shape) * 5.0 for x in self.blk_a]
 
@@ -316,7 +316,7 @@ def testBlkDiagMatrixIsFinite(self):
         self.assertFalse(blk_nan.isfinite)
 
     def testBlkDiagMatrixDense(self):
-        """ Test we correctly compute the right shape and array. """
+        """Test we correctly compute the right shape and array."""
         self.assertTrue(np.allclose(self.dense, self.blk_a.dense()))
 
     def testBlkDiagMatrixArith(self):

tests/test_simulation.py

@@ -13,6 +13,20 @@
 DATA_DIR = os.path.join(os.path.dirname(__file__), "saved_test_data")
 
 
+class SingleSimTestCase(TestCase):
+    """Test we can construct a length 1 Sim."""
+
+    def setUp(self):
+        self.sim = Simulation(
+            n=1,
+            L=8,
+        )
+
+    def testImage(self):
+        """Test we can get an Image from a length 1 Sim."""
+        _ = self.sim.images(0, 1)
+
+
 class SimTestCase(TestCase):
     def setUp(self):
         self.sim = Simulation(

tests/test_volume.py

@@ -121,27 +121,27 @@ def testProject(self):
             self.assertTrue(np.allclose(vol_along_axis, prj_along_axis))
 
     def to_vec(self):
-        """ Compute the to_vec method and compare. """
+        """Compute the to_vec method and compare."""
         result = self.vols_1.to_vec()
         self.assertTrue(result == self.vec)
         self.assertTrue(isinstance(result, np.ndarray))
 
     def testFromVec(self):
-        """ Compute Volume from_vec method and compare. """
+        """Compute Volume from_vec method and compare."""
         vol = Volume.from_vec(self.vec)
         self.assertTrue(np.allclose(vol, self.vols_1))
         self.assertTrue(isinstance(vol, Volume))
 
     def testVecId1(self):
-        """ Test composition of from_vec(to_vec). """
+        """Test composition of from_vec(to_vec)."""
         # Construct vec
         vec = self.vols_1.to_vec()
 
         # Convert back to Volume and compare
         self.assertTrue(np.allclose(Volume.from_vec(vec), self.vols_1))
 
     def testVecId2(self):
-        """ Test composition of to_vec(from_vec). """
+        """Test composition of to_vec(from_vec)."""
         # Construct Volume
         vol = Volume.from_vec(self.vec)