make detection of a define size

Seurat.groovy

/* = CODE DESCRIPTION =
 * This QuPath script fills thae image Annotations objects with circular detections objects of a user defined diameter.
 * In combination with "Measure > Show measurements maps" it can be helpfull to quickly create meaningful heatmaps.
 *
 * == INPUTS ==
 * Annotation(s) and RegionOfInterest diamater (in microns)
 *
 * == OUTPUTS ==
 * circular detections objects of a user defined diameter
 *
 * = DEPENDENCIES =
 * QuPath
 *
 * = INSTALLATION =
 * Darg and drop the script on QuPath, open an image with annotation(s), press RUN
 *
 * = AUTHOR INFORMATION =
 * Code written by romain guiet, EPFL - SV - PTECH - BIOP
 * for XXX XXX, Lab XXX
 * 2023.01.18
 *
 * = COPYRIGHT =
 * (c) All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2023
 *
 * Licensed under the BSD-3-Clause License:
 * Redistribution and use in source and binary forms, with or without modification, are permitted provided
 * that the following conditions are met:
 * 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer
 *    in the documentation and/or other materials provided with the distribution.
 * 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products
 *     derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,
 * BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
 * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
 * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */


roi_microns = 20

px_width = getCurrentServer().getPixelCalibration().getAveragedPixelSizeMicrons()
roi_width = Math.round (roi_microns/px_width ) // in microns
roi_height = roi_width
roi_spacing = roi_width + Math.round (roi_width/10 ) as int

clearDetections()

annots = getAnnotationObjects()

annots.each{ annot ->
    println (annot)
    roi = annot.getROI()
    xO = roi.getBoundsX()
    yO = roi.getBoundsY()
    w = roi.getBoundsWidth()
    h = roi.getBoundsHeight()
    
    circles = []
    (0..h).step(roi_spacing).each{ y ->
        (0..w).step(roi_spacing).each{  x -> 
            if ( roi.contains( xO+x, yO+y) ){
                def circle = ROIs.createEllipseROI(xO+x, yO+y, roi_width, roi_height, roi.getImagePlane() )
                def detection = PathObjects.createDetectionObject( circle)
                circles.add(detection)
            }
        }
    }
    addObjects(circles)
}

fireHierarchyUpdate()
 
selectDetections();
runPlugin('qupath.lib.algorithms.IntensityFeaturesPlugin', '{"pixelSizeMicrons": '+roi_microns+',  "region": "ROI",  "tileSizeMicrons": 25.0,  "channel1": true,  "channel2": true,  "channel3": true,  "channel4": true,  "channel5": true,  "channel6": false,  "doMean": true,  "doStdDev": true,  "doMinMax": true,  "doMedian": true,  "doHaralick": false,  "haralickMin": NaN,  "haralickMax": NaN,  "haralickDistance": 1,  "haralickBins": 32}');

println "done!"




import qupath.lib.roi.*
import qupath.lib.roi.EllipseROI