Fix/21 contour detection produces incorrect results

doc/release_notes/release_1.01.md

@@ -1,5 +1,20 @@
 # Version 1.1 #
 
+## Sigima Version 1.1.3 (unreleased) ##
+
+### 🛠️ Bug Fixes since version 1.1.2 ###
+
+* **Ellipse/circle contour detection**: Fixed swapped X/Y coordinates when using scikit-image ≥ 0.26.0
+  * The new `EllipseModel`/`CircleModel` API returns center coordinates as `(row, col)` but the code was treating them as `(x, y)`, causing detected ellipses and circles to appear at wrong positions on the image
+  * Semi-axis lengths were also swapped for ellipses, resulting in incorrect aspect ratios
+  * This bug only affected scikit-image ≥ 0.26.0; older versions were handled correctly
+* **Ellipse visualization**: Fixed incorrect minor axis direction in `ellipse_to_diameters` coordinate conversion
+  * The minor axis endpoints were computed with a wrong sign, making the minor axis non-perpendicular to the major axis for rotated ellipses (e.g., at θ=45° both axes pointed in the same direction). This caused distorted ellipse overlays in DataLab when displaying detected or annotated ellipses at non-trivial rotation angles
+* **Circle/ellipse detection with calibrated images**: Fixed radius and semi-axes not being converted from pixel units to physical units
+  * When an image had non-default pixel calibration (e.g., dx=2 mm/pixel), center coordinates were correctly converted to physical units but the radius and semi-axes remained in pixels, causing values to be wrong by a factor equal to the pixel size
+
+
+
 ## Sigima Version 1.1.2 (2026-04-20) ##
 
 ### 💥 Breaking changes since version 1.1.1 ###

sigima/proc/image/base.py

@@ -308,6 +308,17 @@ def compute_geometry_from_obj(
                 colx, coly = 0, 1
             coords[:, colx] = obj.dx * coords[:, colx] + obj.x0
             coords[:, coly] = obj.dy * coords[:, coly] + obj.y0
+            if coords.shape[1] % 2 != 0:
+                # Scale distance-like values (radius, semi-axes) from pixel to
+                # physical units. Use average pixel size for isotropic scaling.
+                pixel_scale = (obj.dx + obj.dy) / 2
+                if coords.shape[1] >= 3:
+                    # Column 2: radius (circle) or semi-axis a (ellipse)
+                    coords[:, 2] *= pixel_scale
+                if coords.shape[1] >= 4:
+                    # Column 3: semi-axis b (ellipse)
+                    coords[:, 3] *= pixel_scale
+                # Column 4 (theta) is an angle: no scaling needed
             if obj.roi is not None:
                 x0, y0, _x1, _y1 = obj.roi.get_single_roi(i_roi).get_bounding_box(obj)
                 coords[:, colx] += x0 - obj.x0

sigima/tools/coordinates.py

@@ -98,7 +98,7 @@ def ellipse_to_diameters(
         Ellipse X/Y diameters (major/minor axes) coordinates
     """
     dxa, dya = a * np.cos(theta), a * np.sin(theta)
-    dxb, dyb = b * np.sin(theta), b * np.cos(theta)
+    dxb, dyb = -b * np.sin(theta), b * np.cos(theta)
     x0, y0, x1, y1 = xc - dxa, yc - dya, xc + dxa, yc + dya
     x2, y2, x3, y3 = xc - dxb, yc - dyb, xc + dxb, yc + dyb
     return x0, y0, x1, y1, x2, y2, x3, y3
@@ -117,7 +117,7 @@ def array_ellipse_to_diameters(data: np.ndarray) -> np.ndarray:
     """
     xc, yc, a, b, theta = data[:, 0], data[:, 1], data[:, 2], data[:, 3], data[:, 4]
     dxa, dya = a * np.cos(theta), a * np.sin(theta)
-    dxb, dyb = b * np.sin(theta), b * np.cos(theta)
+    dxb, dyb = -b * np.sin(theta), b * np.cos(theta)
     x0, y0, x1, y1 = xc - dxa, yc - dya, xc + dxa, yc + dya
     x2, y2, x3, y3 = xc - dxb, yc - dyb, xc + dxb, yc + dyb
     result = np.column_stack((x0, y0, x1, y1, x2, y2, x3, y3)).astype(float)

sigima/tools/image/preprocessing.py

@@ -48,7 +48,8 @@ def fit_circle_model(contour: np.ndarray) -> tuple[float, float, float] | None:
     if _USE_NEW_SHAPE_API:
         model = measure.CircleModel.from_estimate(contour)
         if model:
-            return model.center[0], model.center[1], model.radius
+            # model.center is (row, col) = (y, x), swap to (x, y)
+            return model.center[1], model.center[0], model.radius
     else:
         model = measure.CircleModel()
         if model.estimate(contour):
@@ -73,8 +74,10 @@ def fit_ellipse_model(
     if _USE_NEW_SHAPE_API:
         model = measure.EllipseModel.from_estimate(contour)
         if model:
-            xc, yc = model.center[0], model.center[1]
-            a, b = model.axis_lengths[0], model.axis_lengths[1]
+            # model.center is (row, col) = (y, x), swap to (x, y)
+            # model.axis_lengths is (semi_row, semi_col), swap to (semi_x, semi_y)
+            xc, yc = model.center[1], model.center[0]
+            a, b = model.axis_lengths[1], model.axis_lengths[0]
             return xc, yc, a, b, model.theta
     else:
         model = measure.EllipseModel()