Import Atlas regions in QuPath from an ABBA registered project #BIOP #ABBA #QuPath

ImportABBARegions.groovy

/**
* Import regions from an ABBA registered project into QuPath
* See https://biop.github.io/ijp-imagetoatlas/
* Author: Olivier Burri, Nicolas Chiaruttini, BIOP, EPFL
* Date: 2022-01-26 
*/

// Erase and re import regions, the string should specify an existing key in the atlas ontology
// Available properties for Allen Brain Atlas are "acronym", "atlas_id", "color_hex_triplet", "graph_order", "hemisphere_id", "id", "name", "ontology_id", "parent_structure_id", "st_level"
importAbbaRegions( "acronym" )

// ------------- FUNCTIONS ------------------------
// 0 - Re-import regions

// Necessary import, requires qupath-extension-abba, see: https://github.com/BIOP/qupath-biop-extensions
def importAbbaRegions( String namingProperty ) {
    clearAllObjects()
    
    ImageData imageData = getCurrentImageData()
    
    List<String> atlasNames = AtlasTools.getAvailableAtlasRegistration( imageData )
    if ( atlasNames.size() == 0 ) {
        logger.error( "No atlas registration found for image {}.", getProjectEntry().getImageName() )
        return;
    }
    
    // Pick a default one in case there are multiple.
    String atlasName = atlasNames.get( 0 )
    if ( atlasNames.size() > 1 ) {
        logger.warn( "{} Atlases Registrations have been found. Importing atlas: {}", atlasNames.size(), atlasName )
    }

    // Figure out the Ontology for finally loading the annotations
    Path ontologyPath = Paths.get( Projects.getBaseDirectory( getProject() ).getAbsolutePath(), atlasName + "-Ontology.json" )
    
    AtlasOntology ontology = AtlasHelper.openOntologyFromJsonFile( ontologyPath.getAbsolutePath() )

    // Get naming possibilities
    ontology.setNamingProperty( namingProperty )
    AtlasTools.loadWarpedAtlasAnnotations( ontology, imageData, atlasName, true )
    
    logger.info( "Finished loading regions named after '{}' for image '{}' from Atlas {}", namingProperty, getProjectEntry().getImageName(), atlasName )
}

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

I think here should be ontologyPath.toString()

Path has no signature of method: getAbsolutePath()

toString() of ontologyPath can give you the absolutepath