Rename pixel_distance to radius

Author: Bobafotz

src/main/java/net/haesleinhuepf/clijx/plugins/GenerateGreyValueCooccurrenceMatrixBox.java

@@ -26,7 +26,7 @@ public boolean executeCL() {
         return result;
     }
 
-    public static boolean generateGreyValueCooccurrenceMatrixBox(CLIJ2 clij2, ClearCLBuffer src, ClearCLBuffer dst_cooccurrence_matrix, Float minimum_intensity, Float maximum_intensity, int pixel_distance) {
+    public static boolean generateGreyValueCooccurrenceMatrixBox(CLIJ2 clij2, ClearCLBuffer src, ClearCLBuffer dst_cooccurrence_matrix, Float minimum_intensity, Float maximum_intensity, int radius) {
         ClearCLBuffer flip = clij2.create(src.getDimensions(), NativeTypeEnum.Float);
         ClearCLBuffer flop = clij2.create(src.getDimensions(), NativeTypeEnum.Float);
 
@@ -37,7 +37,7 @@ public static boolean generateGreyValueCooccurrenceMatrixBox(CLIJ2 clij2, ClearC
 
         ClearCLBuffer temp_matrix = clij2.create(dst_cooccurrence_matrix.getDimensions(), NativeTypeEnum.Float);
 
-        GenerateIntegerGreyValueCooccurrenceCountMatrixHalfBox.generateIntegerGreyValueCooccurrenceCountMatrixHalfBox(clij2, flip, temp_matrix, pixel_distance);
+        GenerateIntegerGreyValueCooccurrenceCountMatrixHalfBox.generateIntegerGreyValueCooccurrenceCountMatrixHalfBox(clij2, flip, temp_matrix, radius);
         double sum = clij2.sumOfAllPixels(temp_matrix);
 
         clij2.multiplyImageAndScalar(temp_matrix, dst_cooccurrence_matrix, 1.0 / sum);
@@ -50,7 +50,7 @@ public static boolean generateGreyValueCooccurrenceMatrixBox(CLIJ2 clij2, ClearC
 
     @Override
     public String getParameterHelpText() {
-        return "Image integer_image, ByRef Image grey_value_cooccurrence_matrix_destination, Number min_grey_value, Number max_grey_value, Number pixel_distance";
+        return "Image integer_image, ByRef Image grey_value_cooccurrence_matrix_destination, Number min_grey_value, Number max_grey_value, Number radius";
     }
 
 

src/main/java/net/haesleinhuepf/clijx/plugins/GenerateIntegerGreyValueCooccurrenceCountMatrixHalfBox.java

@@ -26,7 +26,7 @@ public boolean executeCL() {
         return result;
     }
 
-    public static boolean generateIntegerGreyValueCooccurrenceCountMatrixHalfBox(CLIJ2 clij2, ClearCLBuffer src_label_map1, ClearCLBuffer dst_cooccurrence_matrix, int pixel_distance) {
+    public static boolean generateIntegerGreyValueCooccurrenceCountMatrixHalfBox(CLIJ2 clij2, ClearCLBuffer src_label_map1, ClearCLBuffer dst_cooccurrence_matrix, int radius) {
         int num_threads = (int) src_label_map1.getDepth();
 
         long[][][] counts = new long[num_threads][(int)dst_cooccurrence_matrix.getWidth()][(int)dst_cooccurrence_matrix.getHeight()];
@@ -62,7 +62,7 @@ public static boolean generateIntegerGreyValueCooccurrenceCountMatrixHalfBox(CLI
             }
 
 
-            statisticians[i] = new Statistician(counts[i], image_slice, image_next_slice, (int)src_label_map1.getWidth(), (int)src_label_map1.getHeight(), (int)pixel_distance);
+            statisticians[i] = new Statistician(counts[i], image_slice, image_next_slice, (int)src_label_map1.getWidth(), (int)src_label_map1.getHeight(), (int)radius);
             threads[i] = new Thread(statisticians[i]);
             threads[i].start();
         }
@@ -107,53 +107,53 @@ public String getCategories() {
     private static class Statistician implements Runnable{
         private final int width;
         private final int height;
-        private final int pixel_distance;
+        private final int radius;
 
         long[][] counts;
 
         private float[] image;
         private float[] image_next_slice;
 
-        Statistician(long[][] counts, float[] image, float[] image_next_slice, int width, int height, int pixel_distance) {
+        Statistician(long[][] counts, float[] image, float[] image_next_slice, int width, int height, int radius) {
             this.counts = counts;
             this.image = image;
             this.image_next_slice = image_next_slice;
             this.width = width;
             this.height = height;
-            this.pixel_distance = pixel_distance;
+            this.radius = radius;
         }
 
         @Override
         public void run() {
 
             int x = 0;
             int y = 0;
-            for (int i = 0; i < image.length - pixel_distance; i++) {
+            for (int i = 0; i < image.length - radius; i++) {
                 int value_1 = (int) image[i];
                 int value_2;
 
                 // right
-                if (x < width - pixel_distance) {
-                    value_2 = (int) image[i + pixel_distance];
+                if (x < width - radius) {
+                    value_2 = (int) image[i + radius];
                     counts[value_1][value_2]++;
                     counts[value_2][value_1]++;
                }
                 // bottom
-                if (y < height - pixel_distance) {
-                    value_2 = (int) image[i + (width * pixel_distance)];
+                if (y < height - radius) {
+                    value_2 = (int) image[i + (width * radius)];
                     counts[value_1][value_2]++;
                     counts[value_2][value_1]++;
                 }
                 // bottom, right
-                if (x < width - pixel_distance && y < height - pixel_distance) {
-                    value_2 = (int) image[i + (width * pixel_distance) + pixel_distance];
+                if (x < width - radius && y < height - radius) {
+                    value_2 = (int) image[i + (width * radius) + radius];
                     counts[value_1][value_2]++;
                     counts[value_2][value_1]++;
                 }
 
                 // top, right
-                if (y > pixel_distance && x < (width * pixel_distance) - pixel_distance) {
-                    value_2 = (int) image[i - (width * pixel_distance) + pixel_distance];
+                if (y > radius && x < (width * radius) - radius) {
+                    value_2 = (int) image[i - (width * radius) + radius];
                     counts[value_1][value_2]++;
                     counts[value_2][value_1]++;
                 }
@@ -162,12 +162,12 @@ public void run() {
                 if (image_next_slice != null) {
                     for (int delta_x = -1; delta_x <= 1; delta_x ++) {
                         for (int delta_y = -1; delta_y <= 1; delta_y ++) {
-                            int index = i + delta_x + width * pixel_distance * delta_y;
-                            if (x + delta_x < width * pixel_distance &&
+                            int index = i + delta_x + width * radius * delta_y;
+                            if (x + delta_x < width * radius &&
                                 x - delta_x >= 0 &&
-                                y + delta_y < height * pixel_distance &&
+                                y + delta_y < height * radius &&
                                 y - delta_y >= 0 &&
-                                index >= 0 && index < image_next_slice.length - pixel_distance) {
+                                index >= 0 && index < image_next_slice.length - radius) {
                                 value_2 = (int) image_next_slice[index];
                                 counts[value_1][value_2]++;
                                 counts[value_2][value_1]++;
@@ -177,7 +177,7 @@ public void run() {
                 }
 
                 x++;
-                if (x >= width - pixel_distance) {
+                if (x >= width - radius) {
                     x = 0;
                     y++;
                 }