Changing v1 scripts to work on v2

[nicholas...@gmail.com]

Hi All, I am trying to use a script that worked great on the older version of Qupath but I am running into trouble using it on version two. It is apparently failing to resolve some classes and I don't know enough to figure out how to fix it!

Here is the code itself, or at least the part containing the lines where the error messages are popping up:

selectAnnotations ();

//get superpixels. AdjustspacingMicrons as necessary

runPlugin('qupath.imagej.superpixels.SLICSuperpixelsPlugin', '{"sigmaMicrons": 5.0,  "spacingMicrons": 50.0,  "maxIterations": 10,  "regularization": 0.25,  "adaptRegularization": false,  "useDeconvolved": false}');

runPlugin('qupath.lib.analysis.objects.TileClassificationsToAnnotationsPlugin', '{"pathClass": "All classes",  "deleteTiles": false,  "clearAnnotations": true,  "splitAnnotations": false}');

selectDetections();

runPlugin('qupath.lib.algorithms.IntensityFeaturesPlugin', '{"pixelSizeMicrons": 2.0,  "region": "ROI",  "tileSizeMicrons": 200,  "colorOD": false,  "colorStain1": false,  "colorStain2": true,  "colorStain3": false,  "colorRed": false,  "colorGreen": false,  "colorBlue": false,  "colorHue": false,  "colorSaturation": false,  "colorBrightness": false,  "doMean": true,  "doStdDev": false,  "doMinMax": false,  "doMedian": false,  "doHaralick": true,  "haralickDistance": 1,  "haralickBins": 32}');

def roi = 'ROI: 2.00 ' + qupath.lib.common.GeneralTools.micrometerSymbol() + ' per pixel: DAB:  Mean'

// seperate superpixels into 1+, 2+ etc

setIntensityClassifications(qupath.lib.objects.PathTileObject, roi , 0.22, 0.25, 0.33);

def name1 = getProjectEntry().getImageName() + '.txt'

def path1 = buildFilePath(PROJECT_BASE_DIR, 'annotation results')

mkdirs(path1)

path1 = buildFilePath(path1, name1)

saveAnnotationMeasurements(path1)

print 'Results exported to ' + path1

selectAnnotations();

import qupath.lib.gui.helpers.MeasurementMapper

import static qupath.lib.scripting.QPEx.*

// Define measurement & display range

def measure = 'ROI: 2.00 ' + qupath.lib.common.GeneralTools.micrometerSymbol() + ' per pixel: DAB:  Mean'

double minValue = -0.04

double maxValue = 0.6

// Request current viewer & objects

def viewer = getCurrentViewer()

def options = viewer.getOverlayOptions()

def detections = getDetectionObjects()

// Update the display

if (measure) {

    print String.format('Setting measurement map: %s (%.2f - %.2f)', measure, minValue, maxValue)

    def mapper = new MeasurementMapper(measure, detections)

    mapper.setDisplayMinValue(minValue)

    mapper.setDisplayMaxValue(maxValue)

    options.setMeasurementMapper(mapper)

} else {

    print 'Resetting measurement map'

    options.setMeasurementMapper(null)

}

import ij.IJ

import ij.ImagePlus

import qupath.lib.gui.ImageWriterTools

import qupath.imagej.images.servers.ImagePlusServer

import qupath.imagej.images.servers.ImagePlusServerBuilder

import qupath.lib.images.servers.ImageServer

import qupath.lib.regions.RegionRequest

import qupath.lib.scripting.QP

import java.awt.image.BufferedImage

And here is the error: 

ERROR: Error: startup failed:

Script36.groovy: 48: unable to resolve class qupath.imagej.images.servers.ImagePlusServer

 @ line 48, column 1.

   import qupath.imagej.images.servers.ImagePlusServer

   ^

Script36.groovy: 49: unable to resolve class qupath.imagej.images.servers.ImagePlusServerBuilder

 @ line 49, column 1.

   import qupath.imagej.images.servers.ImagePlusServerBuilder

   ^

Script36.groovy: 22: unable to resolve class qupath.lib.scripting.QPEx

 @ line 22, column 1.

   import static qupath.lib.scripting.QPEx.*

   ^

Script36.groovy: 22: unable to resolve class qupath.lib.scripting.QPEx

 @ line 22, column 1.

   import static qupath.lib.scripting.QPEx.*

   ^

4 errors

ERROR: Script error

    at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:311)

    at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:980)

    at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:647)

    at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:596)

    at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:390)

    at groovy.lang.GroovyClassLoader.access$300(GroovyClassLoader.java:89)

    at groovy.lang.GroovyClassLoader$5.provide(GroovyClassLoader.java:330)

    at groovy.lang.GroovyClassLoader$5.provide(GroovyClassLoader.java:327)

    at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:147)

    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:325)

    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:309)

    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:251)

    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.getScriptClass(GroovyScriptEngineImpl.java:331)

    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:153)

    at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:767)

    at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:697)

    at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:677)

    at qupath.lib.gui.scripting.DefaultScriptEditor$2.run(DefaultScriptEditor.java:1034)

    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)

    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)

    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

    at java.base/java.lang.Thread.run(Thread.java:834)

Sorry for the long post but I don't know enough to fix it myself. Any help would be amazing. 

Thank you!

[micros...@gmail.com]

As described in the header, the forums have moved!

Part of your question is covered here on the new forum: https://forum.image.sc/t/quex-on-qupath2-0/23697

and part here: https://github.com/qupath/qupath/issues/280

[nicholas...@gmail.com]

Thank you!