Bugfix for rolling frame filter with all indices out of range

mianalysis · May 27, 2024 · fbaf9f6 · fbaf9f6
1 parent 6d2a4c7
commit fbaf9f6
Show file tree

Hide file tree

Showing 15 changed files with 16 additions and 5,709 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -1,5 +1,12 @@
 {
     "configurations": [
+        {
+            "type": "java",
+            "name": "CommaSeparatedStringInterpreter",
+            "request": "launch",
+            "mainClass": "io.github.mianalysis.mia.process.string.CommaSeparatedStringInterpreter",
+            "projectName": "mia-algorithms"
+        },
         {
             "type": "java",
             "name": "MIA_",

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/images/process/FilterImage.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/images/process/FilterImage.java
@@ -21,6 +21,7 @@
 import ij.process.ImageProcessor;
 import inra.ijpb.morphology.Morphology;
 import inra.ijpb.morphology.strel.DiskStrel;
+import io.github.mianalysis.mia.MIA;
 import io.github.mianalysis.mia.module.Categories;
 import io.github.mianalysis.mia.module.Category;
 import io.github.mianalysis.mia.module.Module;
@@ -433,6 +434,10 @@ public static void runRollingFrameFilter(ImagePlus inputImagePlus, String window
                     frames.add(frame);
             }
 
+            boolean emptyFrame = frames.size() == 0;
+            if (emptyFrame)
+                frames.add(1);
+
             // Creating a local substack and switching T and Z, so time (not Z) is averaged
             ImagePlus currentSubstack = SubHyperstackMaker.makeSubhyperstack(tempImagePlus, channels, slices, frames);
             currentSubstack = Hyperstack_rearranger.reorderHyperstack(currentSubstack, "CTZ", true, false);
@@ -469,6 +474,10 @@ public static void runRollingFrameFilter(ImagePlus inputImagePlus, String window
             // Switching T and Z back
             iplOut = Hyperstack_rearranger.reorderHyperstack(iplOut, "CTZ", true, false);
 
+            // If this frame was added in just so there's some content, set all pixels to zero
+            if (emptyFrame)
+                ImageMath.process(iplOut,ImageMath.CalculationModes.MULTIPLY,0);
+
             // Adding the new image into outputImagePlus
             for (int z = 1; z <= iplOut.getNSlices(); z++) {
                 for (int c = 1; c <= iplOut.getNChannels(); c++) {

diff --git a/target/site/dependencies.html b/target/site/dependencies.html
diff --git a/target/site/images/close.gif b/target/site/images/close.gif
diff --git a/target/site/images/collapsed.gif b/target/site/images/collapsed.gif
diff --git a/target/site/images/expanded.gif b/target/site/images/expanded.gif
diff --git a/target/site/images/external.png b/target/site/images/external.png
diff --git a/target/site/images/icon_error_sml.gif b/target/site/images/icon_error_sml.gif
diff --git a/target/site/images/icon_info_sml.gif b/target/site/images/icon_info_sml.gif
diff --git a/target/site/images/icon_success_sml.gif b/target/site/images/icon_success_sml.gif
diff --git a/target/site/images/icon_warning_sml.gif b/target/site/images/icon_warning_sml.gif
diff --git a/target/site/images/logos/build-by-maven-black.png b/target/site/images/logos/build-by-maven-black.png
diff --git a/target/site/images/logos/build-by-maven-white.png b/target/site/images/logos/build-by-maven-white.png
diff --git a/target/site/images/logos/maven-feather.png b/target/site/images/logos/maven-feather.png
diff --git a/target/site/images/newwindow.png b/target/site/images/newwindow.png