From 6c353cf4a1526c3dab2f510721d9f81ed309a6e4 Mon Sep 17 00:00:00 2001
From: Michael Innerberger <innerbergerm@hhmi.org>
Date: Wed, 27 Nov 2024 16:19:09 -0500
Subject: [PATCH] Add filter for affine intensity transformation

---
 .../filter/AffineIntensityFilter.java         | 50 +++++++++++++++++++
 .../filter/ExponentialIntensityFilter.java    |  1 -
 2 files changed, 50 insertions(+), 1 deletion(-)
 create mode 100644 render-app/src/main/java/org/janelia/alignment/filter/AffineIntensityFilter.java

diff --git a/render-app/src/main/java/org/janelia/alignment/filter/AffineIntensityFilter.java b/render-app/src/main/java/org/janelia/alignment/filter/AffineIntensityFilter.java
new file mode 100644
index 000000000..f5f93ac44
--- /dev/null
+++ b/render-app/src/main/java/org/janelia/alignment/filter/AffineIntensityFilter.java
@@ -0,0 +1,50 @@
+package org.janelia.alignment.filter;
+
+import ij.process.ImageProcessor;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+/**
+ * A simple filter that applies an affine transformation y = a*x + b to the intensity values of an image.
+ */
+public class AffineIntensityFilter implements Filter {
+
+    private double a;
+    private double b;
+
+    // empty constructor required to create instances from specifications
+    @SuppressWarnings("unused")
+    public AffineIntensityFilter() {
+        this(0.0, 0.0);
+    }
+
+    public AffineIntensityFilter(final double a, final double b) {
+        this.a = a;
+        this.b = b;
+    }
+
+    @Override
+    public void init(final Map<String, String> params) {
+        this.a = Filter.getDoubleParameter("a", params);
+        this.b = Filter.getDoubleParameter("b", params);
+    }
+
+    @Override
+    public Map<String, String> toParametersMap() {
+        final Map<String, String> map = new LinkedHashMap<>();
+        map.put("a", String.valueOf(a));
+        map.put("b", String.valueOf(b));
+        return map;
+    }
+
+    @Override
+    public void process(final ImageProcessor ip, final double scale) {
+        for (int y = 0; y < ip.getHeight(); y++) {
+            for (int x = 0; x < ip.getWidth(); x++) {
+                final float intensity = ip.getf(x, y);
+                ip.setf(x, y, (float) (a * intensity + b));
+            }
+        }
+    }
+}
diff --git a/render-app/src/main/java/org/janelia/alignment/filter/ExponentialIntensityFilter.java b/render-app/src/main/java/org/janelia/alignment/filter/ExponentialIntensityFilter.java
index 6b4201f46..817526257 100644
--- a/render-app/src/main/java/org/janelia/alignment/filter/ExponentialIntensityFilter.java
+++ b/render-app/src/main/java/org/janelia/alignment/filter/ExponentialIntensityFilter.java
@@ -60,5 +60,4 @@ public void process(final ImageProcessor ip, final double scale) {
             }
         }
     }
-
 }