Re-import ABBA regions then filter out regions based on name #BIOP #ABBA #QuPath

RemoveABBARegions.groovy

 
// Modify the sequence of functions according to your need:
// - reImportAbbaRegions()
// - clearAllExcept(['Left: TH', 'Left: MB']) 
// - clearRight()
// - clearLeft()
//

reImportAbbaRegions() // Erase and re import regions

// First way of selecting regions : make a text file with each region that you want to keep, one region per line, take care with spaces!
// def listOfRegions = new File("C:/Users/chiarutt/Downloads/ListRegions.txt") as String[]

// Second way : modify the list below
def listOfRegions=[
'Left: PL5',
'Left: PL6a',
'Right: PL5',
'Right: PL6a',
'Left: ILA1',
'Left: ILA2/3',
'Left: ILA5',
'Left: ILA6a',
'Right: ACAd1',
'Right: ACAd2/3',
'Right: ACAd5',
'Right: ACAd6a',
'Right: ACAv1'
]

// print them out
listOfRegions.each {
    println it
}

clearAllExcept(listOfRegions)
 

// ------------- FUNCTIONS ------------------------
// 0 - Re-import regions
// Necessary import, requires qupath-extension-abba, see: https://github.com/BIOP/qupath-biop-extensions
def reImportAbbaRegions() {
    clearAllObjects();
    
    ImageData imageData = getCurrentImageData()
    
    List<String> atlasNames = AtlasTools.getAvailableAtlasRegistration(imageData);
    if (atlasNames.size()==0) {
        logger.error("No atlas registration found."); // TODO : show an error message for the user
        return;
    }

    String atlasName = atlasNames.get(0);
    if (atlasNames.size()>1) {
        logger.warn("Several atlases registration have been found. Importing atlas: "+atlasName);
    }


    Path ontologyPath = Paths.get(Projects.getBaseDirectory(getProject()).getAbsolutePath(), atlasName+"-Ontology.json");
    AtlasOntology ontology = AtlasHelper.openOntologyFromJsonFile(ontologyPath.toString());

    // Get naming possibilities
    String namingProperty = "acronym"
    /*            Dialogs.showChoiceDialog("Regions names",
                    "Please select the property for naming the imported regions.",
                    AtlasTools.getNamingProperties(ontology).toArray(new String[0]),
                    "ID");*/

    ontology.setNamingProperty(namingProperty);

    AtlasTools.loadWarpedAtlasAnnotations(ontology, imageData, atlasName, true);

}

// 1 - Remove right region
def clearRight() {
    removeObjects(getAnnotationObjects().findAll{it.getName().equals('Root')}, true) 
    removeObjects(getAnnotationObjects().findAll{it.getPathClass().toString().contains('Right:')}, false) 
}

// 2 - Remove left region
def clearLeft() {
    removeObjects(getAnnotationObjects().findAll{it.getName().equals('Root')}, true) 
    removeObjects(getAnnotationObjects().findAll{it.getPathClass().toString().contains('Left:')}, false) 
}

// 3 - Delete All Regions except the ones on the list
def clearAllExcept(regionsToKeep) {
    removeObjects(
        getAnnotationObjects()
        .findAll{!(regionsToKeep.contains(it.getPathClass().toString()))}, true) 
}
  
// 4 - Print all regions
//getAnnotationObjects().each{println(it.getPathClass().toString())}   


import qupath.ext.biop.abba.struct.AtlasHelper
import qupath.ext.biop.abba.struct.AtlasOntology
import qupath.ext.biop.abba.AtlasTools
import qupath.lib.images.ImageData
import java.nio.file.Path
import java.nio.file.Paths
import java.util.List