Merge pull request #5 from Naveiras-Lab/update-qp0.5.1

Update qp0.5.1

Code/AdipoQuant.groovy

@@ -78,7 +78,7 @@ mq_classes.each { the_class ->
     }
 }    
 
-getQuPath().getAvailablePathClasses().setAll(all_classes)
+Platform.runLater{ getQuPath().getAvailablePathClasses().setAll(all_classes) }
 fireHierarchyUpdate()
 
 def ij = IJExtension.getImageJInstance()
@@ -105,7 +105,7 @@ tissues.eachWithIndex{ tissue, i ->
 }
 
 fireHierarchyUpdate()	
-def imageName = getCurrentImageData().getServer().getShortServerName()
+def imageName = getCurrentImageNameWithoutExtension()
 println("Processing complete for " +  imageName );
 //ij.quit()
 
@@ -121,8 +121,11 @@ class AdipocyteDetector {
         IJ.run("Close All")
 
         // Returns the image as an ImageJ ImagePlus object with ROIs and the overlay
-        def image = GUIUtils.getImagePlus(tissue, this.downsample, true, true)
-
+        def request = RegionRequest.createInstance( getCurrentServerPath(), this.downsample, tissue.getROI() )
+        def pathImage = IJExtension.extractROIWithOverlay(getCurrentServer(), tissue, getCurrentHierarchy(), request, true, getCurrentViewer().getOverlayOptions());		
+
+        def image = pathImage.getImage()
+
         // Pick up pixel size
         def px_size = image.getCalibration().pixelWidth
 
@@ -146,24 +149,17 @@ class AdipocyteDetector {
         IJ.run(hsb_image, "HSB Stack", "")
         hsb_image.show()
 
-        // Call Color Deconvolution and recover the images (must be done through GUI for now)
-        IJ.run(image, "Colour Deconvolution", "vectors=H&E hide")
-
-        //Pickup the images for later processing
-        def col1 = WindowManager.getImage( image.getTitle()+"-(Colour_1)" )
-        def col2 = WindowManager.getImage( image.getTitle()+"-(Colour_2)" )
-        def col3 = WindowManager.getImage( image.getTitle()+"-(Colour_3)" )
-
+        // Call Color Deconvolution and recover the images )
+        def cols = colorDeconvolution( image, "H&E" )
+
         // Creates the final image we are going to process from the hue and brightness image obtained
         def ic = new ImageCalculator()
-        def adip_raw_image = ic.run("Subtract create", col3, col1)
+        def adip_raw_image = ic.run("Subtract create", cols[2], cols[0])
 
         adip_raw_image.show()
 
         image.close()
-        col1.close()
-        col2.close()
-        col3.close()
+        cols.each{ it.close() }
 
         def saturation = hsb_image.getStack().getProcessor(2) // Saturation is the second image
         saturation.multiply(8)
@@ -181,8 +177,11 @@ class AdipocyteDetector {
         IJ.run( adip_mask, "Invert", "") // IB?
         IJ.run( adip_mask, "Watershed", "" )
         adip_mask.show()
+
+
         IJ.run( adip_mask, "Options...", "iterations=50 count=5 pad do=Erode" )
 
+
         adip_mask.setRoi( all_edges )
         //IJ.run(adip_mask, "Make Inverse", "")
         IJ.setRawThreshold(adip_mask, 0, 127, null)
@@ -192,25 +191,29 @@ class AdipocyteDetector {
         def rm = RoiManager.getInstance() ?: new RoiManager()
         // Save as Detections in QuPath
         def adips = rm.getRoisAsArray() as List
-        rm.runCommand("Reset")    
+        rm.reset()
         rm.close()
+
+        def um = GeneralTools.micrometerSymbol()
+
         def total_area = 0
 
 	// Measurement of adipocytes areas and displaying of the data in QuPath
         adips.eachWithIndex{ adip, idx ->
-            def qu_adip = ROIConverterIJ.convertToPathROI( adip, image.getCalibration(), this.downsample, 0,0,0)
-            def det = new PathDetectionObject(qu_adip, getPathClass("Adipocyte"))            
+            def det = IJTools.convertToDetection( adip, this.downsample, image )
+            det.setPathClass( getPathClass("Adipocyte") )
             def area = adip.getStatistics().area
             det.getMeasurementList().putMeasurement( "Adipocyte Index", idx+1 )
-            det.getMeasurementList().putMeasurement( "Area "+Utils.um+"^2", area *  px_size *  px_size )
+            det.getMeasurementList().putMeasurement( "Area "+um+"^2", area *  px_size *  px_size )
 
-            tissue.addPathObject(det)
+            tissue.addChildObject(det)
             total_area += area
         }
 
-        tissue.getMeasurementList().clear();
-        tissue.getMeasurementList().putMeasurement( "Total Adipocyte Area "+Utils.um+"^2", total_area *  px_size *  px_size )       
+        tissue.getMeasurementList().clear()
+        tissue.getMeasurementList().putMeasurement( "Total Adipocyte Area "+um+"^2", total_area *  px_size *  px_size )       
         Interpreter.batchMode = false
+        fireHierarchyUpdate()
     }
 
 	// Excludes the artifacts from the ROI we want to process
@@ -219,20 +222,20 @@ class AdipocyteDetector {
             return tissue_roi 
         }
 
-        if (artifacts.size > 0) {
+        if (artifacts.size() > 0) {
 
             def rm = RoiManager.getInstance() ?: new RoiManager()
-            rm.runCommand("Reset")    
+            rm.reset()    
             artifacts.each{ rm.addRoi(it) }
             def all_artifacts
-            if ( artifacts.size == 1 ) {
+            if ( artifacts.size() == 1 ) {
                 all_artifacts = artifacts[0]
             } else {
                 rm.setSelectedIndexes((0..rm.getCount()-1) as int[])
                 rm.runCommand(image, "OR")
                 all_artifacts = image.getRoi()
             }
-            rm.runCommand("Reset")
+            rm.reset()
             // AND then XOR with tissue
             IJ.log(""+all_artifacts)
             rm.addRoi(all_artifacts)
@@ -243,13 +246,32 @@ class AdipocyteDetector {
             rm.addRoi( overlap_artifacts )
             rm.setSelectedIndexes([1,2] as int[])
             rm.runCommand(image, "XOR")
+            rm.reset()
             rm.close()
             return image.getRoi()
         }
     }
+
+    // Use Color Deconvolution Plugin in MarrowQuant
+    public ImagePlus[] colorDeconvolution ( ImagePlus image, String stain ) {
+            def cd = new Colour_Deconvolution()
+            def matList = cd.getStainList()
+            def mt = matList.get( stain )
+            def stackList = mt.compute( false, true, image )
+            // This returns an array of ImageStacks
+
+            // Make into an ImagePlus            
+            def imageStack = new ImageStack( stackList[0].getWidth(), stackList[0].getHeight() )
+
+            stackList.each { imageStack.addSlice( it.getProcessor( 1 ) ) }
+
+            def deconvolved = stackList.collect{ new ImagePlus( image.getTitle()+"-"+stain, it ) }
+
+            return deconvolved      
+    }
 }
-// Import BIOP library to do fun things
-import ch.epfl.biop.qupath.utils.*
+
+
 import ij.IJ
 import sc.fiji.colourDeconvolution.*
 import ij.WindowManager
@@ -258,18 +280,15 @@ import ij.ImagePlus
 import ij.process.ImageProcessor
 import ij.plugin.frame.RoiManager
 import qupath.lib.objects.PathDetectionObject
-import qupath.imagej.objects.ROIConverterIJ
 import ij.macro.Interpreter
-import ch.epfl.biop.qupath.utils.Utils
+import ij.ImageStack
 import ij.gui.Roi
 import qupath.imagej.gui.IJExtension
-import qupath.lib.gui.helpers.DisplayHelpers
+
 import qupath.imagej.helpers.*
-import qupath.lib.roi.PathObjectToolsAwt
 import qupath.lib.objects.PathAnnotationObject
 
 
 
 
-
 

Code/AdipoQuant_Export_Results.groovy → Code/Export_AdipoQuant_results.groovy

@@ -9,13 +9,14 @@
 
 
 
-import ch.epfl.biop.qupath.utils.*
+import qupath.ext.biop.utils.Results
 
 
 selectDetections();
 runPlugin('qupath.lib.plugins.objects.ShapeFeaturesPlugin', '{"area": false,  "perimeter": true,  "circularity": true,  "useMicrons": true}');
 
-def um = Utils.um
+def um = GeneralTools.micrometerSymbol()
+
 def columns = ["Adipocyte Index", "Parent", "Area "+um+"^2"]
 
 def resultsfolder = buildFilePath(PROJECT_BASE_DIR, "results")
@@ -25,6 +26,6 @@ def resultsfile = new File(resultsfolder, "adipocyte-measurements.txt")
 println(resultsfile.getAbsolutePath())
 
 def detections = getDetectionObjects()
-Utils.sendResultsToFile(columns, detections,  resultsfile)
+Results.sendResultsToFile(columns, detections,  resultsfile)
 
 println("Completed")

Code/Export_MarrowQuant_Results_QuPath_0.4.3.groovy → Code/Export_MarrowQuant_results.groovy

@@ -37,7 +37,7 @@ def outputPath = buildFilePath( PROJECT_BASE_DIR, 'results' )
 mkdirs( outputPath )
 
 // Give the results file a name
-def fileName = 'MarrowQuant_Results.txt'
+def fileName = 'MarrowQuant_Results_20230721_final.txt'
 
 // Write results in the desired directory to the desired filename
 def file = new File( outputPath, fileName )
@@ -54,12 +54,12 @@ def columns = [ "Image Name",
                 "Tt.Ad.Ar_"+U+"^2",
                 "It.Ar_"+U+"^2",
                 "Ma.Ar_"+U+"^2",
-                "Other.Ar_"+U+"^2",
+                "Un.Ar_"+U+"^2",
                 "Hm.Ar/(Hm.Ar+Tt.Ad.Ar)_%_Equation_1",
                 "Hm.Ar/Ma.Ar_%_Equation_2",
                 "Tt.Ad.Ar/Ma.Ar_%",
                 "It.Ar/Ma.Ar_%",
-                "Other.Ar/Ma.Ar_%",
+                "Un.Ar/Ma.Ar_%",
                 "Aj.Ad.N",
                 "Ad_Min_Size",
                 "Ad_Max_Size", 

Code/MarrowQuant_Mouse_QuPath_0.4.3.groovy → Code/MarrowQuant.groovy

@@ -83,9 +83,9 @@ ij.quit()
 
 // end of script// 
 
-// MarrowQnat class starts below
+// MarrowQuat class starts below
 @ToString(includeNames=true)
-class MarrowQuant {
+class MarrowQuant1 {
 
     def downsample       = 4
     def adipMin 	 = 5
@@ -120,7 +120,7 @@ class MarrowQuant {
     def boneMaskImage
     def hematoMaskImage
 
-    final private static Logger logger = LoggerFactory.getLogger( MarrowQuant.class ) 
+    final private static Logger logger = LoggerFactory.getLogger( MarrowQuant1.class ) 
 
     public void run() {
         def all_annotations = getAnnotationObjects()
@@ -144,7 +144,14 @@ class MarrowQuant {
         //tissueAnnotation.getChildObjects().find{ it.getPathClass() == getPathClass("BG") }
         def tissue_artifacts = tissueAnnotation.getChildObjects().findAll{ it.getPathClass() == getPathClass("Artifact") }
 
-        def mergedArtifactsAnnotation = PathUtils.merge( tissue_artifacts )
+        // Merge artifacts for later use
+        def hasMerged = mergeAnnotations( tissue_artifacts )
+        def mergedArtifactsAnnotation
+        if( hasMerged ) {
+            mergedArtifactsAnnotation = getSelectedObject()
+        } else {
+           mergedArtifactsAnnotation = tissue_artifacts[0] 
+        }
 
         this.image = getImagePlus( tissueAnnotation, downsample)
 
@@ -515,6 +522,7 @@ class MarrowQuant {
             }
                             measurements.putMeasurement( "Aj.Ad.N", rois.size() )
                             measurements.putMeasurement("Ad.MA.Ar_Nby_"+U+"^2", rois.size()/ round( ( area_hemato + area_adips + area_imv ) * px_size * px_size ,0 ) )
+            rm.reset()
             rm.close()
         }
 
@@ -670,7 +678,7 @@ class MarrowQuant {
 }
 
 // The lines below allow us to user the Builder Pattern withourh having to declare it in the MarrowQuant class
-@Builder(builderStrategy = ExternalStrategy, forClass = MarrowQuant, prefix = 'assign', buildMethodName = 'create')
+@Builder(builderStrategy = ExternalStrategy, forClass = MarrowQuant1, prefix = 'assign', buildMethodName = 'create')
 class MQBuilder {
     MQBuilder() {
         downsample       = 4

Code/Remove_Overview_And_Label_Images.groovy

@@ -7,21 +7,10 @@
  * but otherwise everything kept the same.
  */
 
-import qupath.lib.gui.QuPathGUI
-import qupath.lib.gui.panels.ProjectBrowser
-import qupath.lib.images.ImageData
-import qupath.lib.images.servers.ImageServerProvider
-import qupath.lib.io.PathIO
-import qupath.lib.projects.Project
-import qupath.lib.projects.ProjectIO
-
-import java.awt.image.BufferedImage
-
 // Get the running QuPath instance
-def qupath = QuPathGUI.getInstance()
-
+def qupath = getQuPath()
 // Get the current project
-def project = qupath.getProject()
+def project = getProject()
 if (project == null) {
     println("No project open!")
     return
@@ -36,11 +25,6 @@ for (def entry in project.getImageList()) {
 }
 
 sleep(1000)
-getQuPath().refreshProject()
-ProjectIO.writeProject(project)
-fireHierarchyUpdate()
-
-// Write the new project itself
-//ProjectIO.writeProject(projectNew)
+qupath.refreshProject()
 
-print("Done! Project written to ")
+fireHierarchyUpdate()