Fix main CI with Sigima 1.3.0: pixel-coordinate tests and Sigima >= 1.3.0

datalab/tests/features/common/auto_analysis_recompute_unit_test.py

@@ -54,9 +54,12 @@ def test_analysis_recompute_after_roi_change():
     with datalab_test_app_context(console=False) as win:
         panel = win.imagepanel
 
-        # Create a 2D Gaussian image in a 200x200 image
+        # Create a 2D Gaussian image in a 200x200 image (pixel coordinates, as
+        # the ROIs and expected centroids below)
         size = 200
-        param = Gauss2DParam.create(height=size, width=size, sigma=20)
+        param = Gauss2DParam.create(
+            height=size, width=size, sigma=20, physical_coords=False
+        )
         img = create_image_from_param(param)
         panel.add_object(img)
 
@@ -202,10 +205,12 @@ def test_analysis_recompute_after_recompute_1_to_1():
         size = 200
         # In Gauss2DParam, x0 and y0 are the center coordinates with Xmin=-10.0,
         # Ymin=-10.0, Xmax=10.0, Ymax=10.0 by default.
-        # The centroid position should be at (49.75, 99.5).
+        # The centroid position should be at (49.75, 99.5) in pixel coordinates.
         # After a 45° rotation, it should move closer to (64.32, 134.68).
         # Or after a 90° rotation, it should move to (99.5, 149.2).
-        param = Gauss2DParam.create(height=size, width=size, x0=-5.0)
+        param = Gauss2DParam.create(
+            height=size, width=size, x0=-5.0, physical_coords=False
+        )
         img = create_image_from_param(param)
         panel.add_object(img)
 

datalab/tests/features/common/creation_metadata_unit_test.py

@@ -14,10 +14,13 @@
     PEAK_PARAMETERIZATION,
     GaussParam,
     SineParam,
+    SinusoidalGrating2DParam,
+    create_image,
     create_signal,
 )
 from sigima.tools.signal.pulse import GaussianModel, LegacyPeakParameterizationError
 
+from datalab.gui.creation import create_image_from_param
 from datalab.gui.newobject import (
     CREATION_PARAMETERS_FORMAT_VERSION,
     CREATION_PARAMETERS_OPTION,
@@ -26,6 +29,7 @@
     extract_creation_parameters,
     insert_creation_parameters,
 )
+from datalab.history.core import decode_kwargs
 
 
 def _legacy_gaussian_json(
@@ -117,3 +121,42 @@ def test_creation_parameter_formats_never_fall_back_implicitly() -> None:
     obj.set_metadata_option(LEGACY_CREATION_PARAMETERS_OPTION, _legacy_gaussian_json())
     with pytest.raises(ValueError, match="Conflicting creation parameter formats"):
         extract_creation_parameters(obj)
+
+
+def test_domain_image_creation_parameters_keep_their_coordinates() -> None:
+    """Images created before the "Physical coordinates" option stay in pixels.
+
+    Recreating an image from creation parameters stored by DataLab 1.3 (without
+    the option) must give back the original pixel coordinates, while parameters
+    stored by this version are restored as they were.
+    """
+    param = SinusoidalGrating2DParam.create(height=16, width=32)
+    image = create_image_from_param(param)
+    assert (image.x0, image.dx) == (param.xmin, (param.xmax - param.xmin) / 31)
+    restored = extract_creation_parameters(image)
+    assert isinstance(restored, SinusoidalGrating2DParam)
+    assert restored.physical_coords is True
+
+    payload = json.loads(dataset_to_json(param))
+    del payload["physical_coords"]
+    legacy = create_image("Legacy grating", np.zeros((16, 32)))
+    legacy.set_metadata_option(
+        CREATION_PARAMETERS_OPTION,
+        {
+            "format_version": CREATION_PARAMETERS_FORMAT_VERSION,
+            "dataset_json": json.dumps(payload),
+        },
+    )
+    legacy_param = extract_creation_parameters(legacy)
+    assert isinstance(legacy_param, SinusoidalGrating2DParam)
+    assert legacy_param.physical_coords is False
+    recreated = create_image_from_param(legacy_param)
+    assert (recreated.x0, recreated.y0, recreated.dx, recreated.dy) == (
+        0.0,
+        0.0,
+        1.0,
+        1.0,
+    )
+
+    history_kwargs = decode_kwargs({"param": {"__dataset_json__": json.dumps(payload)}})
+    assert history_kwargs["param"].physical_coords is False

datalab/tests/features/image/geometry_transform_unit_test.py

@@ -20,13 +20,15 @@
 
 def __create_test_image() -> sio.ImageObj:
     """Create a test image with geometry results for testing."""
+    # Geometry results and ROI below are defined in pixel coordinates
     param = sio.Gauss2DParam.create(
         height=600,
         width=600,
         x0=2.5,
         y0=7.5,
         title="Test image (with geometry results)",
         dtype=sio.ImageDatatypes.UINT16,
+        physical_coords=False,
     )
     obj = sio.create_image_from_param(param)
     for geometry in test_data.generate_geometry_results():

doc/locale/fr/LC_MESSAGES/release_notes/release_1.03.po

@@ -12,6 +12,18 @@ msgstr ""
 msgid "Version 1.3"
 msgstr "Version 1.3"
 
+msgid "DataLab Version 1.3.1"
+msgstr "DataLab Version 1.3.1"
+
+msgid "🔧 Improvements since version 1.3.0"
+msgstr "🔧 Améliorations depuis la version 1.3.0"
+
+msgid "**Compatibility:**"
+msgstr "**Compatibilité :**"
+
+msgid "Updated minimum Sigima requirement from 1.2.0 to 1.3.0: Gaussian, 2D ramp, sinusoidal grating, ring pattern, Siemens star and 2D sinc images are now created in physical coordinates (over their [x<sub>min</sub>, x<sub>max</sub>] × [y<sub>min</sub>, y<sub>max</sub>] domain) instead of pixel coordinates, unless the new \"Physical coordinates\" option is disabled. Images created with earlier versions keep their pixel coordinates when they are recreated"
+msgstr "Mise à jour de la version minimale requise de Sigima de 1.2.0 à 1.3.0 : les images gaussienne, rampe 2D, réseau sinusoïdal, anneaux, étoile de Siemens et sinus cardinal 2D sont désormais créées en coordonnées physiques (sur leur domaine [x<sub>min</sub>, x<sub>max</sub>] × [y<sub>min</sub>, y<sub>max</sub>]) au lieu de coordonnées en pixels, sauf si la nouvelle option « Coordonnées physiques » est désactivée. Les images créées avec des versions antérieures conservent leurs coordonnées en pixels lorsqu'elles sont recréées"
+
 msgid "DataLab Version 1.3.0"
 msgstr "DataLab Version 1.3.0"
 

doc/release_notes/release_1.03.md

@@ -1,5 +1,13 @@
 # Version 1.3 #
 
+## DataLab Version 1.3.1 ##
+
+### 🔧 Improvements since version 1.3.0 ###
+
+**Compatibility:**
+
+* Updated minimum Sigima requirement from 1.2.0 to 1.3.0: Gaussian, 2D ramp, sinusoidal grating, ring pattern, Siemens star and 2D sinc images are now created in physical coordinates (over their [x<sub>min</sub>, x<sub>max</sub>] × [y<sub>min</sub>, y<sub>max</sub>] domain) instead of pixel coordinates, unless the new "Physical coordinates" option is disabled. Images created with earlier versions keep their pixel coordinates when they are recreated
+
 ## DataLab Version 1.3.0 ##
 
 ### ✨ New Features ###

doc/requirements.rst

@@ -17,7 +17,7 @@ The `datalab-platform` package requires the following Python modules:
       - >= 2.11.0
       - Curve and image plotting tools for Python/Qt applications
     * - Sigima
-      - >= 1.2.0
+      - >= 1.3.0
       - Scientific computing engine for 1D signals and 2D images, part of the DataLab open-source platform.
     * - SigimaX
       - >= 1.0.2

pyproject.toml

@@ -43,7 +43,7 @@ requires-python = ">=3.9, <4"
 dependencies = [
     "guidata >= 3.15.1",
     "PlotPy >= 2.11.0",
-    "Sigima >= 1.2.0",
+    "Sigima >= 1.3.0",
     "SigimaX >= 1.0.2",
     "NumPy >= 1.22, < 2.5",
     "SciPy >= 1.10.1, < 1.17",

requirements.txt

@@ -4,7 +4,7 @@ PlotPy >= 2.11.0
 PyQt5 >= 5.15.6
 PyWavelets >= 1.2, < 2.0
 SciPy >= 1.10.1, < 1.17
-Sigima >= 1.2.0
+Sigima >= 1.3.0
 SigimaX >= 1.0.2
 babel
 build