Fixing improper pixel size changes.

uw-loci · Jan 16, 2024 · c5ca5ee · c5ca5ee
1 parent 7cb98a7
commit c5ca5ee
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Showing 2 changed files with 3 additions and 7 deletions.
diff --git a/src/main/groovy/qupath/ext/qp_scope/functions/QP_scope_GUI.groovy b/src/main/groovy/qupath/ext/qp_scope/functions/QP_scope_GUI.groovy
@@ -373,12 +373,6 @@ class QP_scope_GUI {
             }
             String imageName = QP.getCurrentImageName()
 
-            // Determine the pixel size based on imageName
-            if (imageName.contains("3600")) {
-                pixelSize = "2.0"
-            } else if (imageName.contains("7200")) {
-                pixelSize = "1.0"
-            }
 
             // Expect the classifier file path to be in a specific location
             // get the classifier from the groovyScripts folder, which should be "next to" the pythonScripts folder
@@ -450,6 +444,7 @@ class QP_scope_GUI {
             // the transformation consists of an X-shift in stage microns, a Y-shift in stage microns, and a magnification
             def viewer = QuPathGUI.getInstance().getViewer()
             viewer.centerImage()
+            viewer.getOverlayOptions().setShowNames(true)
             def x= viewer.getCenterPixelX()
             def y= viewer.getCenterPixelY()
             def frameWidth = (preferences.frameWidth as Double)
@@ -459,6 +454,7 @@ class QP_scope_GUI {
             def FOVAnnotation = PathObjects.createAnnotationObject(tileROI)
             FOVAnnotation = PathObjectTools.transformObject(FOVAnnotation,transformation, true)
             QP.addObject(FOVAnnotation)
+            FOVAnnotation.setName("MOVE ME AND THE LIVE VIEW UNTIL THE VIEWS MATCH!\n     Tissue edge might be easiest.")
             boolean gui4Success = stageToQuPathAlignmentGUI1()
             if (!gui4Success) {
                 // User cancelled GUI4, so end GUI3 and do not proceed

diff --git a/src/main/groovyScripts/DetectTissue.groovy b/src/main/groovyScripts/DetectTissue.groovy
@@ -3,4 +3,4 @@ setColorDeconvolutionStains('{"Name" : "H&E default", "Stain 1" : "Hematoxylin",
 //Set pixel size
 setPixelSizeMicrons(2.0, 2.0)
 //createFullImageAnnotation(true)
-createAnnotationsFromPixelClassifier("C:/ImageAnalysis/python/Tissue-lowres.json", 500000.0, 50000.0, "SPLIT", "SELECT_NEW")
+createAnnotationsFromPixelClassifier("C:/ImageAnalysis/python/Tissue-lowres.json", 5000000.0, 50000.0, "SPLIT", "SELECT_NEW")