Fixed some datasets and simluation tests

tomotools/datasets.py

@@ -42,7 +42,7 @@ def get_catalyst_tilt_series(
     maxshift=5,
     tiltshift=0,
     tiltrotate=0,
-    xonly=False,
+    yonly=False,
     noise=False,
     noise_factor=0.2,
 ):
@@ -87,7 +87,7 @@ def get_catalyst_tilt_series(
             max_shift=maxshift,
             tilt_shift=tiltshift,
             tilt_rotate=tiltrotate,
-            x_only=xonly,
+            y_only=yonly,
         )
     if noise:
         catalyst = add_noise(catalyst, "gaussian", noise_factor)

tomotools/simulation.py

@@ -220,7 +220,7 @@ def misalign_stack(stack, min_shift=-5, max_shift=5, tilt_shift=0, tilt_rotate=0
         Number of pixels by which to offset the tilt axis from the center
     tilt_rotate : int
         Amount of rotation to apply to the stack
-    x_only : bool
+    y_only : bool
         If True, limit the application of jitter to the x-direction only.
         Default is False
 

tomotools/tests/test_datasets.py

@@ -26,7 +26,6 @@ def test_get_noisy_simulated_series(self):
         stack = ds.get_catalyst_tilt_series(noise=True)
         assert type(stack) is tomotools.TomoStack
 
-    def test_get_noisy_misaligned_simulated_series(self, noise=True,
-                                                   misalign=True):
+    def test_get_noisy_misaligned_simulated_series(self, noise=True, misalign=True):
         stack = ds.get_catalyst_tilt_series()
         assert type(stack) is tomotools.TomoStack

tomotools/tests/test_simulation.py

@@ -54,7 +54,7 @@ def test_misalign_stack_with_shift(self):
     def test_misalign_stack_with_xonly(self):
         model = sim.create_catalyst_model(0, volsize=[10, 10, 10])
         stack = sim.create_model_tilt_series(model)
-        shifted = sim.misalign_stack(stack, x_only=True)
+        shifted = sim.misalign_stack(stack, y_only=True)
         assert shifted.data.shape == (90, 10, 10)
 
     def test_misalign_stack_with_rotation(self):