Pixel Size Pass-through

src/aspire/denoising/class_avg.py

@@ -83,6 +83,7 @@ def __init__(
             n=self.averager.src.n,
             dtype=self.averager.src.dtype,
             symmetry_group=self.src.symmetry_group,
+            pixel_size=self.src.pixel_size,
         )
 
         # Any further operations should not mutate this instance.

src/aspire/denoising/denoised_src.py

@@ -19,7 +19,13 @@ def __init__(self, src, denoiser):
         :param denoiser: A `Denoiser` object for specifying a method for denoising
         """
 
-        super().__init__(src.L, src.n, dtype=src.dtype, metadata=src._metadata.copy())
+        super().__init__(
+            src.L,
+            src.n,
+            dtype=src.dtype,
+            pixel_size=src.pixel_size,
+            metadata=src._metadata.copy(),
+        )
         # TODO, we can probably setup a reasonable default here.
         self.denoiser = denoiser
         if not isinstance(denoiser, Denoiser):

src/aspire/reconstruction/estimator.py

@@ -144,6 +144,7 @@ def estimate(self, b_coef=None, x0=None, tol=1e-5, regularizer=0):
             b_coef = self.src_backward()
         est_coef = self.conj_grad(b_coef, x0=x0, tol=tol, regularizer=regularizer)
         est = Coef(self.basis, est_coef).evaluate()
+        est.pixel_size = self.src.pixel_size
 
         return est
 

src/aspire/source/simulation.py

@@ -117,14 +117,21 @@ def __init__(
             )
         symmetry_group = symmetry_group or self.vols.symmetry_group
 
+        if pixel_size and (pixel_size != self.vols.pixel_size):
+            logger.warning(
+                f"Overriding volume pixel size, {self.vols.pixel_size}, with "
+                f"user provided pixel size of {pixel_size} angstrom."
+            )
+        pixel_size = pixel_size or self.vols.pixel_size
+
         # Infer the details from volume when possible.
         super().__init__(
             L=self.vols.resolution,
             n=n,
             dtype=self.vols.dtype,
             memory=memory,
             symmetry_group=symmetry_group,
-            pixel_size=self.vols.pixel_size,
+            pixel_size=pixel_size,
         )
 
         # If a user provides both `L` and `vols`, resolution should match.

tests/test_class_src.py

@@ -144,6 +144,7 @@ def class_sim_fixture(dtype, img_size):
         C=1,
         angles=true_rots.angles,
         symmetry_group="C4",  # For testing symmetry_group pass-through.
+        pixel_size=1,  # For testing pixel_size pass-through
     )
     # Prefetch all the images
     src = src.cache()
@@ -209,6 +210,9 @@ class averages.
     # Check symmetry_group pass-through.
     assert test_src.symmetry_group == class_sim_fixture.symmetry_group
 
+    # Check pixel_size pass-through.
+    assert test_src.pixel_size == class_sim_fixture.pixel_size
+
 
 # Test the _HeapItem helper class
 def test_heap_helper():

tests/test_covar2d_denoiser.py

@@ -14,8 +14,9 @@
 num_imgs = 1024
 noise_var = 0.1848
 noise_adder = WhiteNoiseAdder(var=noise_var)
+pixel_size = 5
 filters = [
-    RadialCTFFilter(5, 200, defocus=d, Cs=2.0, alpha=0.1)
+    RadialCTFFilter(pixel_size, 200, defocus=d, Cs=2.0, alpha=0.1)
     for d in np.linspace(1.5e4, 2.5e4, 7)
 ]
 
@@ -63,6 +64,7 @@ def sim():
         amplitudes=1.0,
         dtype=dtype,
         noise_adder=noise_adder,
+        pixel_size=pixel_size,
     )
     sim = sim.cache()
     return sim
@@ -110,6 +112,9 @@ def test_batched_rotcov2d_MSE(sim, basis):
         imgs_denoised, src.images[:], rtol=1e-05, atol=utest_tolerance(src.dtype)
     )
 
+    # Test pixel_size pass-through.
+    assert sim.pixel_size == src.pixel_size
+
 
 def test_source_mismatch(sim, basis):
     """

tests/test_mean_estimator.py

@@ -56,6 +56,7 @@ def sim(L, dtype):
         ],
         dtype=dtype,
         seed=SEED,
+        pixel_size=1,
     )
 
     sim = sim.cache()  # precompute images
@@ -104,6 +105,9 @@ def test_estimate(sim, estimator, mask):
         est / np.linalg.norm(est), vol / np.linalg.norm(vol), atol=0.1
     )
 
+    # Check pixel_size pass-through
+    np.testing.assert_array_equal(sim.pixel_size, estimate.pixel_size)
+
 
 def test_adjoint(sim, basis, estimator):
     """

tests/test_simulation.py

@@ -763,6 +763,42 @@ def check_metadata(sim_src, relion_src):
             )
 
 
+def test_pixel_size(caplog):
+    """
+    Check pixel size is instantiated properly and warnings occur if pixel
+    size is overridden.
+    """
+    vol_px_sz = 10.0
+    L = 8
+    data = np.ones(L**3).reshape(L, L, L)
+    vol = Volume(data, pixel_size=vol_px_sz)
+
+    # Ensure vol pixel size
+    assert vol.pixel_size == vol_px_sz
+
+    # Generate Simulation and check pixel_size is inhereted from vol
+    sim = Simulation(vols=vol)
+    assert sim.pixel_size == vol_px_sz
+
+    # Generate Simulation with provided pixel_size and check
+    # that vol.pixel_size is overridden.
+    caplog.clear()
+    caplog.set_level(logging.WARN)
+
+    sim_px_sz = 5.0
+    msg = (
+        f"Overriding volume pixel size, {vol_px_sz}, with "
+        f"user provided pixel size of {sim_px_sz} angstrom."
+    )
+
+    assert msg not in caplog.text
+
+    sim = Simulation(vols=vol, pixel_size=sim_px_sz)
+
+    assert msg in caplog.text
+    assert sim.pixel_size == sim_px_sz
+
+
 def test_mismatched_pixel_size():
     """
     Confirm raises error when explicit Simulation and CTFFilter pixel sizes mismatch.