fix unit tests test_img, need to fix on visualization

qim3d/io/_ome_zarr.py

@@ -33,7 +33,7 @@ from skimage.transform import (
 
 from qim3d.utils import log
 from qim3d.utils import OmeZarrExportProgressBar
-from qim3d.utils import get_n_chunks
+from qim3d.utils._ome_zarr import get_n_chunks
 
 
 ListOfArrayLike = Union[List[da.Array], List[np.ndarray]]

qim3d/tests/viz/test_img.py

@@ -36,11 +36,11 @@ def test_grid_pred():
     n = 4
     temp_data(folder, n=n)
 
-    model = qim3d.models.UNet()
-    augmentation = qim3d.models.Augmentation()
-    train_set, _, _ = qim3d.models.prepare_datasets(folder, 0.1, model, augmentation)
+    model = qim3d.ml.models.UNet()
+    augmentation = qim3d.ml.Augmentation()
+    train_set, _, _ = qim3d.ml.prepare_datasets(folder, 0.1, model, augmentation)
 
-    in_targ_pred = qim3d.models.inference(train_set, model)
+    in_targ_pred = qim3d.ml.inference(train_set, model)
 
     fig = qim3d.viz.grid_pred(in_targ_pred)
 
@@ -52,7 +52,7 @@ def test_grid_pred():
 # unit tests for slices function
 def test_slices_numpy_array_input():
     example_volume = np.ones((10, 10, 10))
-    fig = qim3d.viz.slices_grid(example_volume, n_slices=1)
+    fig = qim3d.viz.slices_grid(example_volume, num_slices=1)
     assert isinstance(fig, plt.Figure)
 
 
@@ -77,7 +77,7 @@ def test_slices_wrong_position_format1():
         ValueError,
         match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
     ):
-        qim3d.viz.slices_grid(example_volume, position="invalid_slice")
+        qim3d.viz.slices_grid(example_volume, slice_positions="invalid_slice")
 
 
 def test_slices_wrong_position_format2():
@@ -86,7 +86,7 @@ def test_slices_wrong_position_format2():
         ValueError,
         match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
     ):
-        qim3d.viz.slices_grid(example_volume, position=1.5)
+        qim3d.viz.slices_grid(example_volume, slice_positions=1.5)
 
 
 def test_slices_wrong_position_format3():
@@ -95,16 +95,16 @@ def test_slices_wrong_position_format3():
         ValueError,
         match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
     ):
-        qim3d.viz.slices_grid(example_volume, position=[1, 2, 3.5])
+        qim3d.viz.slices_grid(example_volume, slice_positions=[1, 2, 3.5])
 
 
 def test_slices_invalid_axis_value():
     example_volume = np.ones((10, 10, 10))
     with pytest.raises(
         ValueError,
-        match="Invalid value for 'axis'. It should be an integer between 0 and 2",
+        match=f"Invalid value for 'slice_axis'. It should be an integer between 0 and {example_volume.ndim - 1}.",
     ):
-        qim3d.viz.slices_grid(example_volume, axis=3)
+        qim3d.viz.slices_grid(example_volume, slice_axis=3)
 
 
 def test_slices_interpolation_option():
@@ -113,8 +113,8 @@ def test_slices_interpolation_option():
     interpolation_method = "bilinear"
     fig = qim3d.viz.slices_grid(
         example_volume,
-        n_slices=1,
-        img_width=img_width,
+        num_slices=1,
+        image_width=img_width,
         interpolation=interpolation_method,
     )
 
@@ -128,27 +128,27 @@ def test_slices_interpolation_option():
 
 def test_slices_multiple_slices():
     example_volume = np.ones((10, 10, 10))
-    img_width = 3
-    n_slices = 3
-    fig = qim3d.viz.slices_grid(example_volume, n_slices=n_slices, img_width=img_width)
+    image_width = 3
+    num_slices = 3
+    fig = qim3d.viz.slices_grid(example_volume, num_slices=num_slices, image_width=image_width)
     # Add assertions for the expected number of subplots in the figure
-    assert len(fig.get_axes()) == n_slices
+    assert len(fig.get_axes()) == num_slices
 
 
 def test_slices_axis_argument():
     # Non-symmetric input
     example_volume = np.arange(1000).reshape((10, 10, 10))
-    img_width = 3
+    image_width = 3
 
     # Call the function with different values of the axis
     fig_axis_0 = qim3d.viz.slices_grid(
-        example_volume, n_slices=1, img_width=img_width, axis=0
+        example_volume, num_slices=1, image_width=image_width, slice_axis=0
     )
     fig_axis_1 = qim3d.viz.slices_grid(
-        example_volume, n_slices=1, img_width=img_width, axis=1
+        example_volume, num_slices=1, image_width=image_width, slice_axis=1
     )
     fig_axis_2 = qim3d.viz.slices_grid(
-        example_volume, n_slices=1, img_width=img_width, axis=2
+        example_volume, num_slices=1, image_width=image_width, slice_axis=2
     )
 
     # Ensure that different axes result in different plots
@@ -216,7 +216,7 @@ def test_orthogonal_with_numpy_array():
     # Create a sample NumPy array
     vol = np.random.rand(10, 10, 10)
     # Call the orthogonal function with the NumPy array
-    orthogonal_obj = qim3d.viz.orthogonal(vol)
+    orthogonal_obj = qim3d.viz.slicer_orthogonal(vol)
     # Assert that the orthogonal object is created successfully
     assert isinstance(orthogonal_obj, widgets.HBox)
 
@@ -225,28 +225,28 @@ def test_orthogonal_with_torch_tensor():
     # Create a sample PyTorch tensor
     vol = torch.rand(10, 10, 10)
     # Call the orthogonal function with the PyTorch tensor
-    orthogonal_obj = qim3d.viz.orthogonal(vol)
+    orthogonal_obj = qim3d.viz.slicer_orthogonal(vol)
     # Assert that the orthogonal object is created successfully
     assert isinstance(orthogonal_obj, widgets.HBox)
 
 
 def test_orthogonal_with_different_parameters():
     # Test with different colormaps
-    for cmap in ["viridis", "gray", "plasma"]:
-        orthogonal_obj = qim3d.viz.orthogonal(np.random.rand(10, 10, 10), cmap=cmap)
+    for color_map in ["viridis", "gray", "plasma"]:
+        orthogonal_obj = qim3d.viz.slicer_orthogonal(np.random.rand(10, 10, 10), color_map=color_map)
         assert isinstance(orthogonal_obj, widgets.HBox)
 
     # Test with different image sizes
-    for img_height, img_width in [(2, 2), (4, 4)]:
-        orthogonal_obj = qim3d.viz.orthogonal(
-            np.random.rand(10, 10, 10), img_height=img_height, img_width=img_width
+    for image_height, image_width in [(2, 2), (4, 4)]:
+        orthogonal_obj = qim3d.viz.slicer_orthogonal(
+            np.random.rand(10, 10, 10), image_height=image_height, image_width=image_width
         )
         assert isinstance(orthogonal_obj, widgets.HBox)
 
     # Test with show_position set to True and False
-    for show_position in [True, False]:
-        orthogonal_obj = qim3d.viz.orthogonal(
-            np.random.rand(10, 10, 10), show_position=show_position
+    for display_positions in [True, False]:
+        orthogonal_obj = qim3d.viz.slicer_orthogonal(
+            np.random.rand(10, 10, 10), display_positions=display_positions
         )
         assert isinstance(orthogonal_obj, widgets.HBox)
 
@@ -255,7 +255,7 @@ def test_orthogonal_initial_slider_value():
     # Create a sample NumPy array
     vol = np.random.rand(10, 7, 19)
     # Call the orthogonal function with the NumPy array
-    orthogonal_obj = qim3d.viz.orthogonal(vol)
+    orthogonal_obj = qim3d.viz.slicer_orthogonal(vol)
     for idx, slicer in enumerate(orthogonal_obj.children):
         assert slicer.children[0].value == vol.shape[idx] // 2
 
@@ -264,7 +264,7 @@ def test_orthogonal_slider_description():
     # Create a sample NumPy array
     vol = np.random.rand(10, 10, 10)
     # Call the orthogonal function with the NumPy array
-    orthogonal_obj = qim3d.viz.orthogonal(vol)
+    orthogonal_obj = qim3d.viz.slicer_orthogonal(vol)
     for idx, slicer in enumerate(orthogonal_obj.children):
         assert slicer.children[0].description == ["Z", "Y", "X"][idx]