fix a few isigs in code that were logging warnings;

loosen RecStack navigation limit since it was causing error in hs.plot.plot_images update example notebook
usnistgov · Nov 4, 2024 · f095397 · f095397
1 parent 30f4743
commit f095397
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diff --git a/docs/examples/etspy_demo.ipynb b/docs/examples/etspy_demo.ipynb
diff --git a/etspy/align.py b/etspy/align.py
@@ -1012,7 +1012,7 @@ def tilt_maximage(
         shifted = ali.isig[0:nshifts, :].deepcopy()
         for i in range(nshifts):
             shifted.data[:, :, i] = np.roll(
-                ali.isig[idx, :].data.squeeze(),
+                ali.isig[idx:idx+1, :].data.squeeze(),
                 int(shifts[i]),
             )
         shifted_rec = shifted.reconstruct("SIRT", 100, constrain=True)

diff --git a/etspy/base.py b/etspy/base.py
@@ -2053,7 +2053,7 @@ def recon_error(
             else:
                 cuda = False
                 logger.info("CUDA not detected with Astra")
-        sinogram = self.isig[nslice, :].data.squeeze()
+        sinogram = self.isig[nslice:nslice+1, :].data.squeeze()
         rec_stack, error = recon.astra_error(
             sinogram,
             angles=self.tilts.data,
@@ -2104,7 +2104,7 @@ def extract_sinogram(
 
         Returns
         -------
-        sino : Signal2D
+        sino : :py:class:`~hyperspy.api.signals.Signal2D`
             A single image representing the single column data over the range of
             projections in the original TomoStack.
 
@@ -2177,9 +2177,9 @@ def __init__(self, *args, **kwargs):
         """
         super().__init__(*args, **kwargs)
 
-        if self.axes_manager.navigation_dimension != 1:
-            msg = ("A RecStack must have a singular navigation axis. Navigation "
-                   f"shape was: {self.axes_manager.navigation_shape}")
+        if self.axes_manager.navigation_dimension not in (0, 1):
+            msg = ("A RecStack must have a singular (or no) navigation axis. "
+                   f"Navigation shape was: {self.axes_manager.navigation_shape}")
             raise ValueError(msg)
 
         self.inav = _RecStackSlicer(self, isNavigation=True)

diff --git a/etspy/tests/test_base.py b/etspy/tests/test_base.py
@@ -1416,7 +1416,7 @@ def test_rec_stack_init_bad_dims(self):
         with pytest.raises(
             ValueError,
             match=re.escape(
-                "A RecStack must have a singular navigation axis. "
+                "A RecStack must have a singular (or no) navigation axis. "
                 "Navigation shape was: (8, 10)",
             ),
         ):

diff --git a/etspy/tests/test_cuda.py b/etspy/tests/test_cuda.py
@@ -93,7 +93,7 @@ def test_astra_sirt_error_gpu(self):
         stack = ds.get_needle_data(aligned=True)
         _, ny, _ = stack.data.shape
         angles = stack.tilts.data.squeeze()
-        stack = stack.isig[120, :].squeeze()
+        stack = stack.isig[120:121, :].squeeze()
         rec_stack, error = recon.astra_error(
             stack.data,
             angles,
@@ -109,7 +109,7 @@ def test_astra_sirt_error_gpu_bad_dims(self):
         stack = ds.get_needle_data(aligned=True)
         _, ny, _ = stack.data.shape
         angles = stack.tilts.data.squeeze()
-        stack = stack.isig[120, :]
+        stack = stack.isig[120:121, :]
         with pytest.raises(ValueError, match=re.escape(
             "Sinogram must be two-dimensional (ntilts, y). "
             "Provided shape was (77, 256, 1).",

diff --git a/etspy/tests/test_recon.py b/etspy/tests/test_recon.py
@@ -28,7 +28,7 @@ def test_recon_no_tilts(self):
 
     def test_recon_single_slice(self):
         stack = ds.get_needle_data(aligned=True)
-        slices = stack.isig[120, :]
+        slices = stack.isig[120:121, :]
         tilts = stack.tilts.data.squeeze()
         rec = recon.run(slices.data, tilts, "FBP", cuda=False)
         assert isinstance(stack, TomoStack)
@@ -246,7 +246,7 @@ def test_astra_sirt_error_cpu(self):
         stack = ds.get_needle_data(aligned=True)
         _, ny, _ = stack.data.shape
         angles = stack.tilts.data.squeeze()
-        sino = stack.isig[120, :].data.squeeze()
+        sino = stack.isig[120:121, :].data.squeeze()
         rec_stack, error = recon.astra_error(
             sino,
             angles,
@@ -262,7 +262,7 @@ def test_astra_sart_error_cpu(self):
         stack = ds.get_needle_data(aligned=True)
         _, ny, _ = stack.data.shape
         angles = stack.tilts.data.squeeze()
-        sino = stack.isig[120, :].data.squeeze()
+        sino = stack.isig[120:121, :].data.squeeze()
         rec_stack, error = recon.astra_error(
             sino,
             angles,