Bugfix for modules that expand objects from a tight image

Prior to fix, output objects near image edge would become shifted.
mianalysis · Sep 2, 2024 · e7e70f9 · e7e70f9
1 parent ef6b6dc
commit e7e70f9
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Showing 49 changed files with 80 additions and 79 deletions.
diff --git a/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/FitEllipsoid.java b/mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/FitEllipsoid.java
@@ -354,7 +354,7 @@ public Status process(Workspace workspace) {
         if (showOutput) {
             inputObjects.showMeasurements(this, modules);
             if (!objectOutputMode.equals(OutputModes.DO_NOT_STORE)) {
-                outputObjects.convertToImageIDColours().show();
+                outputObjects.convertToImageIDColours().show(false);
             }
         }
 

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/Objs.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/Objs.java
@@ -314,6 +314,7 @@ public Image convertToImageIDColours() {
 
         ImagePlus dispIpl = dispImage.getImagePlus();
         dispIpl.setLut(LUTs.Random(true, false));
+        dispIpl.setDisplayRange(0, 255);
         dispIpl.setPosition(1, 1, 1);
         dispIpl.updateChannelAndDraw();
 

diff --git a/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java b/mia-core/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java
@@ -765,19 +765,16 @@ public Image getAsTightImage(String imageName, @Nullable int[][] borderWidths) {
             return getAsImage(imageName, 0, 1);
 
         double[][] extents = getExtents(true, false);
-        int xOffs = Math.max(0, (int) Math.round(extents[0][0]) - borderWidths[0][0]);
-        int yOffs = Math.max(0, (int) Math.round(extents[1][0]) - borderWidths[1][0]);
-        int zOffs = Math.max(0, (int) Math.round(extents[2][0]) - borderWidths[2][0]);
-
-        int width = Math.min(spatCal.getWidth(),
-                (int) Math.round(extents[0][1]) - (int) Math.round(extents[0][0]) + borderWidths[0][0]
-                        + borderWidths[0][1] + 1);
-        int height = Math.min(spatCal.getHeight(),
-                (int) Math.round(extents[1][1]) - (int) Math.round(extents[1][0]) + borderWidths[1][0]
-                        + borderWidths[1][1] + 1);
-        int nSlices = Math.min(spatCal.getNSlices(),
-                (int) Math.round(extents[2][1]) - (int) Math.round(extents[2][0]) + borderWidths[2][0]
-                        + borderWidths[2][1] + 1);
+        int xOffs = (int) Math.round(extents[0][0]) - borderWidths[0][0];
+        int yOffs = (int) Math.round(extents[1][0]) - borderWidths[1][0];
+        int zOffs = (int) Math.round(extents[2][0]) - borderWidths[2][0];
+
+        int width = (int) Math.round(extents[0][1]) - (int) Math.round(extents[0][0]) + borderWidths[0][0]
+                        + borderWidths[0][1] + 1;
+        int height = (int) Math.round(extents[1][1]) - (int) Math.round(extents[1][0]) + borderWidths[1][0]
+                        + borderWidths[1][1] + 1;
+        int nSlices = (int) Math.round(extents[2][1]) - (int) Math.round(extents[2][0]) + borderWidths[2][0]
+                        + borderWidths[2][1] + 1;
 
         ImagePlus ipl = IJ.createImage(imageName, width, height, nSlices, 8);
         spatCal.setImageCalibration(ipl);
@@ -787,7 +784,7 @@ public Image getAsTightImage(String imageName, @Nullable int[][] borderWidths) {
             ipl.setPosition(point.z - zOffs + 1);
             ipl.getProcessor().putPixel(point.x - xOffs, point.y - yOffs, 255);
         }
-
+        
         return ImageFactory.createImage("Tight", ipl);
 
     }

diff --git a/...odules/src/main/java/io/github/mianalysis/mia/module/inputoutput/LoadObjectsFromROIs.java b/...odules/src/main/java/io/github/mianalysis/mia/module/inputoutput/LoadObjectsFromROIs.java
@@ -340,7 +340,7 @@ public Status process(Workspace workspace) {
             if (assignTracks)
                 TrackObjects.showObjects(outputObjects, trackObjectsName);
             else
-                outputObjects.convertToImageIDColours().show();
+                outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/inputoutput/ObjectLoader.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/inputoutput/ObjectLoader.java
@@ -611,7 +611,7 @@ public Status process(Workspace workspace) {
         loadObjects(outputObjects, inputFile, workspace, parentObjects);
 
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/.../src/main/java/io/github/mianalysis/mia/module/objects/convert/ConvertImageToObjects.java b/.../src/main/java/io/github/mianalysis/mia/module/objects/convert/ConvertImageToObjects.java
@@ -150,7 +150,7 @@ public Status process(Workspace workspace) {
             if (createParents)
                 TrackObjects.showObjects(objects, parentObjectsName);
             else
-                objects.convertToImageIDColours().show();
+                objects.convertToImageIDColours().show(false);
 
         workspace.addObjects(objects);
 

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/detect/ClusterPoints.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/detect/ClusterPoints.java
@@ -305,7 +305,7 @@ public Status process(Workspace workspace) {
         workspace.addObjects(outputObjects);
 
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...src/main/java/io/github/mianalysis/mia/module/objects/detect/CreateWholeSliceObjects.java b/...src/main/java/io/github/mianalysis/mia/module/objects/detect/CreateWholeSliceObjects.java
@@ -160,7 +160,7 @@ public Status process(Workspace workspace) {
         }
         // Showing objects
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...modules/src/main/java/io/github/mianalysis/mia/module/objects/detect/IdentifyObjects.java b/...modules/src/main/java/io/github/mianalysis/mia/module/objects/detect/IdentifyObjects.java
@@ -502,7 +502,7 @@ public Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...odules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByChildren.java b/...odules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByChildren.java
@@ -120,7 +120,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...les/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMeasurement.java b/...les/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMeasurement.java
@@ -127,7 +127,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMeasurementExtremes.java b/...main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMeasurementExtremes.java
@@ -264,7 +264,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...odules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMetadata.java b/...odules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByMetadata.java
@@ -120,9 +120,9 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput) {
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
             if (moveObjects && outputObjects != null)
-                outputObjects.convertToImageIDColours().show();
+                outputObjects.convertToImageIDColours().show(false);
 
         }
 

diff --git a/...odules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByPartners.java b/...odules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByPartners.java
@@ -121,7 +121,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...dules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByProximity.java b/...dules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterByProximity.java
@@ -246,7 +246,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterObjects.java
@@ -629,7 +629,7 @@ public Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...dules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java b/...dules/src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterOnImageEdge.java
@@ -233,7 +233,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterSpecificObjectIDs.java b/...src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterSpecificObjectIDs.java
@@ -228,7 +228,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...ain/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutMeasurement.java b/...ain/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutMeasurement.java
@@ -162,7 +162,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...c/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutMetadata.java b/...c/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutMetadata.java
@@ -160,7 +160,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutParent.java b/...src/main/java/io/github/mianalysis/mia/module/objects/filter/FilterWithWithoutParent.java
@@ -161,7 +161,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            inputObjects.convertToImageIDColours().show();
+            inputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/.../java/io/github/mianalysis/mia/module/objects/measure/spatial/MeasureObjectCurvature.java b/.../java/io/github/mianalysis/mia/module/objects/measure/spatial/MeasureObjectCurvature.java
@@ -657,7 +657,7 @@ public Status process(Workspace workspace) {
         if (showOutput)
             inputObjects.showMeasurements(this, modules);
         if (showOutput & !objectOutputMode.equals(ObjectOutputModes.DO_NOT_STORE)) {
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
         }
 
         return Status.PASS;

diff --git a/...es/src/main/java/io/github/mianalysis/mia/module/objects/process/CreateBoundingBoxes.java b/...es/src/main/java/io/github/mianalysis/mia/module/objects/process/CreateBoundingBoxes.java
@@ -114,7 +114,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...es/src/main/java/io/github/mianalysis/mia/module/objects/process/CreateDistanceBands.java b/...es/src/main/java/io/github/mianalysis/mia/module/objects/process/CreateDistanceBands.java
@@ -1,12 +1,11 @@
-// TODO: Distance limits
-
 package io.github.mianalysis.mia.module.objects.process;
 
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;
 
 import com.drew.lang.annotations.Nullable;
 
+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;
@@ -368,16 +367,20 @@ public Status process(Workspace workspace) {
             maxDist = Double.MAX_VALUE;
 
         // Calculating border widths for image cropping
-        int[][] borderWidths = null;
+        int[][] borderWidths = new int[][] { { 0, 0 }, { 0, 0 }, { 0, 0 } };
         if (applyMaxDist) {
             int maxDistXY = (int) Math.ceil(maxDist);
             int maxDistZ = (int) Math.ceil(maxDist * inputObjects.getDppXY() / inputObjects.getDppZ());
-            borderWidths = new int[][] { { maxDistXY, maxDistXY }, { maxDistXY, maxDistXY },
-                    { maxDistZ, maxDistZ } };
-            if (inputObjects.getNSlices() == 1) {
+
+            // Only add borders if using bands outside the object
+            if (!bandMode.equals(BandModes.INSIDE_OBJECTS))
+                borderWidths = new int[][] { { maxDistXY, maxDistXY }, { maxDistXY, maxDistXY },
+                        { maxDistZ, maxDistZ } };
+
+            if (inputObjects.getNSlices() == 1)
                 borderWidths[2][0] = 0;
-                borderWidths[2][1] = 0;
-            }
+            borderWidths[2][1] = 0;
+
         }
 
         // Creating output bands objects
@@ -445,7 +448,7 @@ public Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            bandObjects.convertToImageIDColours().show();
+            bandObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...modules/src/main/java/io/github/mianalysis/mia/module/objects/process/CreateSkeleton.java b/...modules/src/main/java/io/github/mianalysis/mia/module/objects/process/CreateSkeleton.java
@@ -685,14 +685,14 @@ protected Status process(Workspace workspace) {
             switch (inputMode) {
                 case InputModes.IMAGE:
                     edgeObjects.showMeasurements(this, modules);
-                    skeletonObjects.convertToImageIDColours().show();
+                    skeletonObjects.convertToImageIDColours().show(false);
                     break;
 
                 case InputModes.OBJECTS:
                     inputObjects.showMeasurements(this, modules);
                     if (addToWorkspace) {
                         edgeObjects.showMeasurements(this, modules);
-                        skeletonObjects.convertToImageIDColours().show();
+                        skeletonObjects.convertToImageIDColours().show(false);
                     }
                     break;
             }

diff --git a/.../main/java/io/github/mianalysis/mia/module/objects/process/ExtractObjectCrossSection.java b/.../main/java/io/github/mianalysis/mia/module/objects/process/ExtractObjectCrossSection.java
@@ -205,7 +205,7 @@ public Status process(Workspace workspace) {
         }
 
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...ules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitActiveContours.java b/...ules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitActiveContours.java
@@ -299,9 +299,9 @@ public Status process(Workspace workspace) {
 
         if (showOutput) {
             if (updateInputObjects)
-                inputObjects.convertToImageIDColours().show();
+                inputObjects.convertToImageIDColours().show(false);
             else
-                outputObjects.convertToImageIDColours().show();
+                outputObjects.convertToImageIDColours().show(false);
         }
 
         // If selected, adding new Objs to the Workspace

diff --git a/...dules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitConcaveHull2D.java b/...dules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitConcaveHull2D.java
@@ -168,7 +168,7 @@ protected Status process(Workspace workspace) {
         }
 
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...odules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitConvexHull2D.java b/...odules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitConvexHull2D.java
@@ -113,7 +113,7 @@ protected Status process(Workspace workspace) {
         }
 
         if (showOutput)
-        outputObjects.convertToImageIDColours().show();
+        outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitEllipse.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/FitEllipse.java
@@ -310,7 +310,7 @@ public Status process(Workspace workspace) {
         if (showOutput) {
             inputObjects.showMeasurements(this, modules);
             if (!objectOutputMode.equals(OutputModes.DO_NOT_STORE))
-                outputObjects.convertToImageIDColours().show();            
+                outputObjects.convertToImageIDColours().show(false);            
         }
 
         return Status.PASS;

diff --git a/...s/src/main/java/io/github/mianalysis/mia/module/objects/process/GetLocalObjectRegion.java b/...s/src/main/java/io/github/mianalysis/mia/module/objects/process/GetLocalObjectRegion.java
@@ -443,7 +443,7 @@ public Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/...dules/src/main/java/io/github/mianalysis/mia/module/objects/process/GetObjectSurface.java b/...dules/src/main/java/io/github/mianalysis/mia/module/objects/process/GetObjectSurface.java
@@ -96,7 +96,7 @@ protected Status process(Workspace workspace) {
 
         // Showing objects
         if (showOutput)
-            outputObjects.convertToImageIDColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;
 

diff --git a/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/GrowObjects.java b/mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/process/GrowObjects.java
@@ -295,11 +295,11 @@ public Status process(Workspace workspace) {
 
         if (outputObjects == null) {
             if (showOutput)
-                inputObjects.convertToImageIDColours().show();
+                inputObjects.convertToImageIDColours().show(false);
         } else {
             workspace.addObjects(outputObjects);
             if (showOutput)
-                outputObjects.convertToImageIDColours().show();
+                outputObjects.convertToImageIDColours().show(false);
         }
 
         return Status.PASS;

diff --git a/...odules/src/main/java/io/github/mianalysis/mia/module/objects/relate/ObjectSlicesTo3D.java b/...odules/src/main/java/io/github/mianalysis/mia/module/objects/relate/ObjectSlicesTo3D.java
@@ -215,7 +215,7 @@ protected Status process(Workspace workspace) {
         workspace.addObjects(outputObjects);
 
         if (showOutput)
-            outputObjects.convertToImageRandomColours().show();
+            outputObjects.convertToImageIDColours().show(false);
 
         return Status.PASS;