From 3a1405e2c3aefe7401141cd4fc17c71ea8aac3b6 Mon Sep 17 00:00:00 2001
From: Jakub Both <jakub.both@uib.no>
Date: Thu, 23 Jan 2025 12:50:03 +0100
Subject: [PATCH 1/2] STY: Improve readibility of code

---
 src/darsia/utils/interpolation.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/src/darsia/utils/interpolation.py b/src/darsia/utils/interpolation.py
index 73d218bb..efb1cadf 100644
--- a/src/darsia/utils/interpolation.py
+++ b/src/darsia/utils/interpolation.py
@@ -232,15 +232,13 @@ def interpolate_to_image(
             interpolated_image.coordinatesystem,
         )
     elif method.lower() in ["linear", "quadratic", "cubic", "quartic"]:
-        degree = (
-            1
-            if method.lower() == "linear"
-            else (
-                2
-                if method.lower() == "quadratic"
-                else 3 if method.lower() == "cubic" else 4
-            )
-        )
+        degrees = {
+            "linear": 1,
+            "quadratic": 2,
+            "cubic": 3,
+            "quartic": 4,
+        }
+        degree = degrees[method.lower()]
         interpolated_image.img = polynomial_interpolation(
             data,
             interpolated_image.coordinatesystem,

From 8933955c730d1812ba6831fd94d7dc37109648e1 Mon Sep 17 00:00:00 2001
From: Jakub Both <jakub.both@uib.no>
Date: Thu, 23 Jan 2025 12:51:15 +0100
Subject: [PATCH 2/2] MAINT: Add logging possibility for setup of illumination
 correction

---
 .../color/illuminationcorrection.py           | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/src/darsia/corrections/color/illuminationcorrection.py b/src/darsia/corrections/color/illuminationcorrection.py
index 8233d18a..63caff18 100644
--- a/src/darsia/corrections/color/illuminationcorrection.py
+++ b/src/darsia/corrections/color/illuminationcorrection.py
@@ -28,6 +28,7 @@ def setup(
         interpolation: Literal["rbf", "quartic", "illumination"] = "quartic",
         show_plot: bool = False,
         rescale: bool = False,
+        log: Optional[Path] = None,
     ):
         """Initialize an illumination correction.
 
@@ -220,6 +221,74 @@ def objective_function(scaling):
             )
             plt.show()
 
+        # Logging
+        if log:
+
+            # Create a directory for the log
+            (log / "illumination_correction").mkdir(parents=True, exist_ok=True)
+
+            # Log the original image, with patches and the determined scaling
+            plt.figure("Log samples")
+            # Plot the base image
+            plt.imshow(base[0].img)
+            # Overlay with ~mask
+            if mask is not None:
+                plt.imshow(mask, alpha=0.5)
+            # Plot the patches as red boxes, and fill with the determined scaling
+            for sample in samples:
+                plt.plot(
+                    [
+                        sample[1].start,
+                        sample[1].start,
+                        sample[1].stop,
+                        sample[1].stop,
+                        sample[1].start,
+                    ],
+                    [
+                        sample[0].start,
+                        sample[0].stop,
+                        sample[0].stop,
+                        sample[0].start,
+                        sample[0].start,
+                    ],
+                    "r-",
+                )
+                plt.fill_between(
+                    [sample[1].start, sample[1].stop],
+                    sample[0].start,
+                    sample[0].stop,
+                    color="r",
+                    alpha=0.2,
+                )
+                plt.text(
+                    0.5 * (sample[1].start + sample[1].stop),
+                    0.5 * (sample[0].start + sample[0].stop),
+                    f"{scaling[samples.index(sample)]}",
+                    color="w",
+                    ha="center",
+                    va="center",
+                    fontsize=5,
+                )
+            plt.savefig(log / "illumination_correction" / "samples.png")
+            plt.close()
+
+            # Log the before and after scaling in a side-by-side plot
+            fig, ax = plt.subplots(1, 3)
+            ax[0].imshow(base[0].img)
+            ax[0].set_title("Original")
+            ax[1].imshow(self.correct_array(base[0].img))
+            ax[1].set_title("Corrected")
+            ax[2].imshow(self.local_scaling[0].img, vmin=0, vmax=2)
+            ax[2].set_title("Scaling")
+            fig.colorbar(
+                ax[2].imshow(self.local_scaling[0].img),
+                ax=ax[2],
+                orientation="vertical",
+                fraction=0.05,
+            )
+            plt.savefig(log / "illumination_correction" / "scaling.png")
+            plt.close()
+
     def correct_array(self, img: np.ndarray) -> np.ndarray:
         """Rescale an array using local WB.