Migrate unit tests from cdl to sigima_ (cont'd)

Author: PierreRaybaut

…es/images/offset_correction_unit_test.py …/features/images/imagebgdlg_unit_test.pycdl/tests/features/images/offset_correction_unit_test.py renamed to cdl/tests/features/images/imagebgdlg_unit_test.py cdl/tests/features/images/offset_correction_unit_test.py renamed to cdl/tests/features/images/imagebgdlg_unit_test.py

@@ -1,7 +1,7 @@
 # Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
 
 """
-Image offset correction unit test.
+Image background dialog unit test.
 """
 
 # pylint: disable=invalid-name  # Allows short reference names like x, y, ...
@@ -10,22 +10,19 @@
 
 from __future__ import annotations
 
-import numpy as np
-import pytest
 from guidata.qthelpers import exec_dialog, qt_app_context
 
 import sigima_.computation.image as sigima_image
 import sigima_.obj
 import sigima_.param
-from cdl.adapters_plotpy.factories import create_adapter_from_object
 from cdl.env import execenv
 from cdl.widgets.imagebackground import ImageBackgroundDialog
+from sigima_.tests import vistools
 from sigima_.tests.data import create_noisygauss_image
-from sigima_.tests.vistools import view_images_side_by_side
 
 
-def test_image_offset_correction_interactive() -> None:
-    """Image offset correction interactive test."""
+def test_image_background_dialog() -> None:
+    """Image background dialog test."""
     with qt_app_context():
         i1 = create_noisygauss_image()
         dlg = ImageBackgroundDialog(i1)
@@ -46,30 +43,12 @@ def test_image_offset_correction_interactive() -> None:
             param.x0, param.y0, param.dx, param.dy = ix0, iy0, ix1 - ix0, iy1 - iy0
             i2 = sigima_image.offset_correction(i1, param)
             i3 = sigima_image.clip(i2, sigima_.param.ClipParam.create(lower=0))
-            view_images_side_by_side(
-                [
-                    create_adapter_from_object(i1).make_item(),
-                    create_adapter_from_object(i3).make_item(),
-                ],
+            vistools.view_images_side_by_side(
+                [i1, i3],
                 titles=["Original image", "Corrected image"],
                 title="Image offset correction and thresholding",
             )
 
 
-@pytest.mark.validation
-def test_image_offset_correction() -> None:
-    """Image offset correction validation test."""
-    i1 = create_noisygauss_image()
-    param = sigima_.obj.ROI2DParam.create(x0=0, y0=0, dx=10, dy=10)
-    i2 = sigima_image.offset_correction(i1, param)
-
-    # Check that the offset correction has been applied
-    x0, y0 = param.x0, param.y0
-    x1, y1 = x0 + param.dx, y0 + param.dy
-    offset = np.mean(i1.data[y0:y1, x0:x1])
-    assert np.allclose(i2.data, i1.data - offset), "Offset correction failed"
-
-
 if __name__ == "__main__":
-    test_image_offset_correction_interactive()
-    test_image_offset_correction()
+    test_image_background_dialog()

…tests/features/images/fft2d_unit_test.py …s/sigima_tests/images/fft2d_unit_test.pycdl/tests/features/images/fft2d_unit_test.py renamed to cdl/tests/sigima_tests/images/fft2d_unit_test.py cdl/tests/features/images/fft2d_unit_test.py renamed to cdl/tests/sigima_tests/images/fft2d_unit_test.py

@@ -16,16 +16,18 @@
 import sigima_.obj
 import sigima_.param
 import sigima_.tests.data as ctd
-from cdl.env import execenv
+from sigima_.env import execenv
 from sigima_.tests.helpers import check_array_result, check_scalar_result
-from sigima_.tests.vistools import view_images_side_by_side
 
 
+@pytest.mark.gui
 def test_image_fft_interactive():
     """2D FFT interactive test."""
     # pylint: disable=import-outside-toplevel
     from guidata.qthelpers import qt_app_context
 
+    from sigima_.tests import vistools
+
     with qt_app_context():
         # Create a 2D ring image
         execenv.print("Generating 2D ring image...", end=" ")
@@ -45,7 +47,7 @@ def test_image_fft_interactive():
 
         images = [data, f.real, f.imag, np.abs(f), data2.real, data2.imag]
         titles = ["Original", "Re(FFT)", "Im(FFT)", "Abs(FFT)", "Re(iFFT)", "Im(iFFT)"]
-        view_images_side_by_side(images, titles, rows=2, title="2D FFT/iFFT")
+        vistools.view_images_side_by_side(images, titles, rows=2, title="2D FFT/iFFT")
 
 
 @pytest.mark.validation

…eatures/images/hough_circle_unit_test.py …a_tests/images/hough_circle_unit_test.pycdl/tests/features/images/hough_circle_unit_test.py renamed to cdl/tests/sigima_tests/images/hough_circle_unit_test.py cdl/tests/features/images/hough_circle_unit_test.py renamed to cdl/tests/sigima_tests/images/hough_circle_unit_test.py

@@ -9,18 +9,21 @@
 # guitest: show
 
 import numpy as np
-from guidata.qthelpers import qt_app_context
-from plotpy.builder import make
+import pytest
 from skimage.feature import canny
 
-from cdl.env import execenv
 from sigima_.algorithms.image import get_hough_circle_peaks
+from sigima_.env import execenv
 from sigima_.tests.data import get_peak2d_data
-from sigima_.tests.vistools import view_image_items
 
 
 def __exec_hough_circle_test(data):
     """Peak detection using circle Hough transform"""
+    # pylint: disable=import-outside-toplevel
+    from plotpy.builder import make
+
+    from sigima_.tests import vistools
+
     edges = canny(
         data,
         sigma=30,
@@ -47,11 +50,15 @@ def __exec_hough_circle_test(data):
         xc, yc, r = shapeargs
         item = make.circle(xc - r, yc, xc + r, yc)
         items.append(item)
-    view_image_items(items)
+    vistools.view_image_items(items)
 
 
+@pytest.mark.gui
 def test_hough_circle():
     """2D peak detection test"""
+    # pylint: disable=import-outside-toplevel
+    from guidata.qthelpers import qt_app_context
+
     with qt_app_context():
         __exec_hough_circle_test(get_peak2d_data(multi=False))
 

cdl/tests/sigima_tests/images/offset_correction_unit_test.py

@@ -0,0 +1,73 @@
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+Image offset correction unit test.
+"""
+
+# pylint: disable=invalid-name  # Allows short reference names like x, y, ...
+# pylint: disable=duplicate-code
+# guitest: show
+
+from __future__ import annotations
+
+import numpy as np
+import pytest
+
+import sigima_.computation.image as sigima_image
+import sigima_.obj
+import sigima_.param
+from sigima_.tests.data import create_noisygauss_image
+
+
+@pytest.mark.gui
+def test_image_offset_correction_interactive() -> None:
+    """Image offset correction interactive test."""
+    # pylint: disable=import-outside-toplevel
+    from guidata.qthelpers import qt_app_context
+    from plotpy.builder import make
+    from plotpy.items import RectangleShape
+    from plotpy.tools import RectangleTool
+    from plotpy.widgets.selectdialog import SelectDialog, select_with_shape_tool
+
+    from sigima_.tests import vistools
+
+    with qt_app_context():
+        i1 = create_noisygauss_image()
+        shape: RectangleShape = select_with_shape_tool(
+            None,
+            RectangleTool,
+            make.image(i1.data, interpolation="nearest", eliminate_outliers=1.0),
+            "Select background area",
+            tooldialogclass=SelectDialog,
+        )
+        if shape is not None:
+            param = sigima_.obj.ROI2DParam()
+            # pylint: disable=unbalanced-tuple-unpacking
+            ix0, iy0, ix1, iy1 = i1.physical_to_indices(shape.get_rect())
+            param.x0, param.y0, param.dx, param.dy = ix0, iy0, ix1 - ix0, iy1 - iy0
+            i2 = sigima_image.offset_correction(i1, param)
+            i3 = sigima_image.clip(i2, sigima_.param.ClipParam.create(lower=0))
+            vistools.view_images_side_by_side(
+                [i1, i3],
+                titles=["Original image", "Corrected image"],
+                title="Image offset correction and thresholding",
+            )
+
+
+@pytest.mark.validation
+def test_image_offset_correction() -> None:
+    """Image offset correction validation test."""
+    i1 = create_noisygauss_image()
+    param = sigima_.obj.ROI2DParam.create(x0=0, y0=0, dx=10, dy=10)
+    i2 = sigima_image.offset_correction(i1, param)
+
+    # Check that the offset correction has been applied
+    x0, y0 = param.x0, param.y0
+    x1, y1 = x0 + param.dx, y0 + param.dy
+    offset = np.mean(i1.data[y0:y1, x0:x1])
+    assert np.allclose(i2.data, i1.data - offset), "Offset correction failed"
+
+
+if __name__ == "__main__":
+    test_image_offset_correction_interactive()
+    test_image_offset_correction()

…s/features/images/operation_unit_test.py …gima_tests/images/operation_unit_test.pycdl/tests/features/images/operation_unit_test.py renamed to cdl/tests/sigima_tests/images/operation_unit_test.py cdl/tests/features/images/operation_unit_test.py renamed to cdl/tests/sigima_tests/images/operation_unit_test.py

@@ -19,15 +19,13 @@
 import numpy as np
 import pytest
 import scipy.ndimage as spi
-from guidata.qthelpers import qt_app_context
 
 import sigima_.computation.image as sigima_image
 import sigima_.obj
 import sigima_.param
-from cdl.env import execenv
+from sigima_.env import execenv
 from sigima_.tests.data import create_noisygauss_image
 from sigima_.tests.helpers import check_array_result
-from sigima_.tests.vistools import view_images_side_by_side
 
 
 def __iterate_images() -> Generator[sigima_.obj.ImageObj, None, None]:
@@ -154,7 +152,7 @@ def test_image_product() -> None:
 
 
 @pytest.mark.validation
-def test_image_division() -> None:
+def test_image_division(request: pytest.FixtureRequest) -> None:
     """Image division test."""
     execenv.print("*** Testing image division:")
     for ima1, ima2 in __iterate_image_couples():
@@ -164,10 +162,16 @@ def test_image_division() -> None:
         exp = ima1.data.astype(float) / ima2.data.astype(float)
         ima3 = sigima_image.division(ima1, ima2)
         if not np.allclose(ima3.data, exp):
-            with qt_app_context():
-                view_images_side_by_side(
-                    [ima1.data, ima2.data, ima3.data], ["ima1", "ima2", "ima3"]
-                )
+            if request.config.getoption("--gui"):
+                # pylint: disable=import-outside-toplevel
+                from guidata.qthelpers import qt_app_context
+
+                from sigima_.tests.vistools import view_images_side_by_side
+
+                with qt_app_context():
+                    view_images_side_by_side(
+                        [ima1.data, ima2.data, ima3.data], ["ima1", "ima2", "ima3"]
+                    )
         check_array_result("Image division", ima3.data, exp)
 
 

sigima_/tests/vistools.py

@@ -299,7 +299,7 @@ def __compute_grid(
 
 
 def view_images_side_by_side(
-    images: list[ImageItem | np.ndarray],
+    images: list[ImageItem | np.ndarray | ImageObj],
     titles: list[str],
     share_axes: bool = True,
     rows: int | None = None,
@@ -309,7 +309,7 @@ def view_images_side_by_side(
     """Show sequence of images
 
     Args:
-        images: List of `ImageItem` or `np.ndarray` objects to display
+        images: List of `ImageItem`, `np.ndarray`, or `ImageObj` objects to display
         titles: List of titles for each image
         share_axes: Whether to share axes across plots, default is True
         rows: Fixed number of rows in the grid, or None to compute automatically
@@ -326,7 +326,13 @@ def view_images_side_by_side(
             if isinstance(img, ImageItem):
                 item = img
             else:
-                item = make.image(img, interpolation="nearest", eliminate_outliers=0.1)
+                if isinstance(img, ImageObj):
+                    data = img.data
+                elif isinstance(img, np.ndarray):
+                    data = img
+                else:
+                    raise TypeError(f"Unsupported image type: {type(img)}")
+                item = make.image(data, interpolation="nearest", eliminate_outliers=0.1)
             plot.add_item(item)
             win.add_plot(row, col, plot, sync=share_axes)
         win.finalize_configuration()