Fix skipped tests for Python 3.14

Author: alexlib

openpiv/PIV_3D_plotting.py

@@ -71,7 +71,7 @@ def scatter_3D(a, cmap="jet", sca_args=None, control="color", size=60):
         sm = matplotlib.cm.ScalarMappable(cmap=cmap, norm=norm)
         sm.set_array([])
         # different option
-        cm = matplotlib.cm.get_cmap(cmap)
+        cm = matplotlib.colormaps.get_cmap(cmap)
         colors = cm(norm(a)).reshape(a.shape[0] * a.shape[1] * a.shape[2], 4)  #
         # plotting
         nan_filter = ~np.isnan(a.flatten())
@@ -83,7 +83,7 @@ def scatter_3D(a, cmap="jet", sca_args=None, control="color", size=60):
             s=size,
             **scatter_args
         )
-        plt.colorbar(sm)
+        fig.colorbar(sm, ax=ax)
 
     if control == "alpha":
         # untested #
@@ -92,8 +92,12 @@ def scatter_3D(a, cmap="jet", sca_args=None, control="color", size=60):
         plt.show()
 
     if control == "size":
-        sizes = (a - a.min()) * size / a.ptp()
-        ax.scatter(x, y, z, a, s=sizes, **scatter_args)
+        value_range = np.ptp(a)
+        if value_range == 0:
+            sizes = np.full(a.shape, size, dtype=float)
+        else:
+            sizes = (a - a.min()) * size / value_range
+        ax.scatter(x, y, z, c=a.flatten(), s=sizes.flatten(), **scatter_args)
         ax_scale = plt.axes([0.88, 0.1, 0.05, 0.7])
         # ax_scale.set_ylim((0.1,1.2))
         nm = 5
@@ -172,12 +176,13 @@ def plot_3D_alpha(data):
     z[:, :, 1::2] += 0.95
 
     fig = plt.figure()
-    ax = fig.gca(projection="3d")
+    ax = fig.add_subplot(projection="3d")
     ax.voxels(x, y, z, fill, facecolors=col_exp, edgecolors=col_exp)
     ax.set_xlabel("x")
     ax.set_ylabel("y")
     ax.set_zlabel("z")
     plt.show()
+    return fig
 
 
 def quiver_3D(
@@ -332,11 +337,11 @@ def quiver_3D(
 
     # plotting
     fig = plt.figure()
-    ax = fig.gca(projection="3d", rasterized=True)
+    ax = fig.add_subplot(projection="3d", rasterized=True)
     ax.quiver(
         xf, yf, zf, vf * scale, uf * scale, wf * scale, colors=colors, **quiver_args
     )
-    plt.colorbar(sm)
+    fig.colorbar(sm, ax=ax)
 
     ax.set_xlim(ax_dims[0])
     ax.set_ylim(ax_dims[1])
@@ -348,8 +353,9 @@ def quiver_3D(
     ax.set_xlabel("x")
     ax.set_ylabel("y")
     ax.set_zlabel("z")
-    ax.w_xaxis.set_pane_color((0.2, 0.2, 0.2, 1.0))
-    ax.w_yaxis.set_pane_color((0.2, 0.2, 0.2, 1.0))
-    ax.w_zaxis.set_pane_color((0.2, 0.2, 0.2, 1.0))
+    for axis in (ax.xaxis, ax.yaxis, ax.zaxis):
+        pane = getattr(axis, "pane", None)
+        if pane is not None:
+            pane.set_facecolor((0.2, 0.2, 0.2, 1.0))
 
     return fig

openpiv/filters.py

@@ -174,22 +174,21 @@ def replace_outliers(
     # regardless the grid_mask (which is a user-provided masked region)
 
 
-    # Only create masked array if needed
-    if isinstance(u, np.ma.MaskedArray):
-        grid_mask = u.mask.copy()
-    else:
-        u = np.ma.masked_array(u, mask=np.ma.nomask)
-        grid_mask = np.ma.nomask
-
-    u[flags] = np.nan
-    v[flags] = np.nan
+    has_mask = isinstance(u, np.ma.MaskedArray)
+    grid_mask = np.ma.getmaskarray(u).copy() if has_mask else np.ma.nomask
+
+    u_data = np.array(np.ma.getdata(u), copy=True)
+    v_data = np.array(np.ma.getdata(v), copy=True)
+
+    u_data[flags] = np.nan
+    v_data[flags] = np.nan
 
     uf = replace_nans(
-        u, method=method, max_iter=max_iter, tol=tol,
+        u_data, method=method, max_iter=max_iter, tol=tol,
         kernel_size=kernel_size
     )
     vf = replace_nans(
-        v, method=method, max_iter=max_iter, tol=tol,
+        v_data, method=method, max_iter=max_iter, tol=tol,
         kernel_size=kernel_size
     )
 
@@ -198,9 +197,10 @@ def replace_outliers(
     vf = np.ma.masked_array(vf, mask=grid_mask)
 
     if isinstance(w, np.ndarray):
-        w[flags] = np.nan
+        w_data = np.array(np.ma.getdata(w), copy=True)
+        w_data[flags] = np.nan
         wf = replace_nans(
-            w, method=method, max_iter=max_iter, tol=tol,
+            w_data, method=method, max_iter=max_iter, tol=tol,
             kernel_size=kernel_size
         )
         wf = np.ma.masked_array(wf, mask=grid_mask)

openpiv/test/test_PIV_3D_plotting.py

@@ -3,6 +3,10 @@
 import os
 import numpy as np
 import pytest
+import matplotlib
+
+matplotlib.use("Agg")
+
 import matplotlib.pyplot as plt
 from mpl_toolkits.mplot3d import Axes3D
 from matplotlib.testing.compare import compare_images
@@ -15,9 +19,7 @@
     quiver_3D
 )
 
-# Skip all tests that require displaying plots if running in a headless environment
-# or if there are compatibility issues with the current matplotlib version
-SKIP_PLOT_TESTS = True
+SKIP_PLOT_TESTS = False
 
 # Create a temporary directory for test images
 @pytest.fixture
@@ -91,7 +93,6 @@ def test_explode():
     assert np.all(result_4d[::2, ::2, ::2, :] == 1)
     assert np.all(result_4d[1::2, ::2, ::2, :] == 0)
 
-@pytest.mark.skipif(SKIP_PLOT_TESTS, reason="Skipping plot tests due to compatibility issues")
 def test_scatter_3D():
     """Test scatter_3D function with color control"""
     # Create a simple 3D array
@@ -119,7 +120,6 @@ def test_scatter_3D():
     # Clean up
     plt.close(fig)
 
-@pytest.mark.skipif(SKIP_PLOT_TESTS, reason="Skipping plot tests due to compatibility issues")
 def test_scatter_3D_size_control():
     """Test scatter_3D function with size control"""
     # Create a simple 3D array
@@ -144,7 +144,6 @@ def test_scatter_3D_size_control():
     # Clean up
     plt.close(fig)
 
-@pytest.mark.skipif(SKIP_PLOT_TESTS, reason="Skipping plot tests due to compatibility issues")
 def test_quiver_3D():
     """Test quiver_3D function"""
     # Create simple vector field
@@ -174,7 +173,6 @@ def test_quiver_3D():
     # Clean up
     plt.close(fig)
 
-@pytest.mark.skipif(SKIP_PLOT_TESTS, reason="Skipping plot tests due to compatibility issues")
 def test_quiver_3D_with_coordinates():
     """Test quiver_3D function with custom coordinates"""
     # Create simple vector field
@@ -207,7 +205,6 @@ def test_quiver_3D_with_coordinates():
     # Clean up
     plt.close(fig)
 
-@pytest.mark.skipif(SKIP_PLOT_TESTS, reason="Skipping plot tests due to compatibility issues")
 def test_quiver_3D_with_filter():
     """Test quiver_3D function with filtering"""
     # Create vector field with multiple vectors
@@ -222,9 +219,18 @@ def test_quiver_3D_with_filter():
     # Clean up
     plt.close(fig)
 
-# Skip test_plot_3D_alpha for now as it's more complex and requires more setup
-@pytest.mark.skip(reason="Complex test requiring more setup")
 def test_plot_3D_alpha():
     """Test plot_3D_alpha function"""
-    # This would require more complex setup and validation
-    pass
+    data = np.zeros((3, 3, 3), dtype=float)
+    data[1, 1, 1] = 1.0
+
+    fig = plot_3D_alpha(data)
+
+    assert isinstance(fig, plt.Figure)
+    ax = fig.axes[0]
+    assert isinstance(ax, Axes3D)
+    assert ax.get_xlabel() == "x"
+    assert ax.get_ylabel() == "y"
+    assert ax.get_zlabel() == "z"
+
+    plt.close(fig)

openpiv/test/test_performance.py

@@ -90,11 +90,14 @@ def test_replace_outliers_performance():
     u = np.random.randn(50, 50) * 10
     v = np.random.randn(50, 50) * 10
     flags = np.random.rand(50, 50) > 0.95  # 5% outliers
+
+    # Warm up the compiled/scipy-backed path before timing.
+    filters.replace_outliers(u, v, flags, method='localmean', max_iter=3)
 
     # Test with regular arrays
-    start = time.time()
+    start = time.perf_counter()
     uf, vf = filters.replace_outliers(u, v, flags, method='localmean', max_iter=3)
-    elapsed = time.time() - start
+    elapsed = time.perf_counter() - start
 
     assert uf.shape == u.shape
     assert vf.shape == v.shape

openpiv/test/test_tools_background.py

@@ -38,7 +38,6 @@ def create_test_images(num_images=3, size=(20, 20)):
     return image_files
 
 
-@pytest.mark.skip(reason="Requires fixing mark_background function")
 def test_mark_background():
     """Test mark_background function"""
     try:
@@ -112,7 +111,6 @@ def test_mark_background2():
             os.unlink(output_file)
 
 
-@pytest.mark.skip(reason="Requires fixing find_reflexions function")
 def test_find_reflexions():
     """Test find_reflexions function"""
     try:
@@ -149,7 +147,6 @@ def test_find_reflexions():
             os.unlink(output_file)
 
 
-@pytest.mark.skip(reason="Requires fixing find_boundaries function")
 def test_find_boundaries():
     """Test find_boundaries function"""
     try:

openpiv/test/test_tools_image_processing.py

@@ -205,9 +205,25 @@ def test_imsave_tiff_format():
         os.unlink(tmp.name)
 
 
-@pytest.mark.skip(reason="Requires creating a 16-bit TIFF file")
 def test_convert_16bits_tif():
     """Test convert_16bits_tif function"""
-    # This test would require creating a 16-bit TIFF file
-    # For now, we'll skip it and implement it later
-    pass
+    img = np.zeros((10, 10), dtype=np.uint16)
+    img[2:8, 2:8] = np.iinfo(np.uint16).max
+
+    with tempfile.NamedTemporaryFile(suffix='.tif', delete=False) as source:
+        Image.fromarray(img).save(source.name, format='TIFF')
+
+    with tempfile.NamedTemporaryFile(suffix='.png', delete=False) as destination:
+        output_name = destination.name
+
+    try:
+        convert_16bits_tif(source.name, output_name)
+
+        read_img = imread(output_name)
+
+        assert read_img.shape == (10, 10)
+        assert np.all(read_img[2:8, 2:8] == 255)
+        assert np.all(read_img[0:2, 0:2] == 0)
+    finally:
+        os.unlink(source.name)
+        os.unlink(output_name)

openpiv/test/test_tools_vector_field.py

@@ -205,7 +205,6 @@ def test_display_vector_field_from_arrays(show_invalid):
 
 
 @pytest.mark.parametrize("method", ["standard", "random"])
-@pytest.mark.skip(reason="Requires interactive matplotlib backend")
 def test_display_windows_sampling(method):
     """Test display_windows_sampling function"""
     # Create test data