Export annotations for a project in QuPath

QuPath_export_annotations_for_project.groovy

/*
 * QuPath v0.1.2 has some bugs that make exporting annotations a bit annoying, specifically it doesn't include the 'dot' 
 * needed in the filename if you run it in batch, and it might put the 'slashes' the wrong way on Windows.
 * Manually fixing these afterwards is not very fun.
 * 
 * Anyhow, until this is fixed you could try the following script with Run -> Run for Project.
 * It should create a new subdirectory in the project, and write text files containing results there.
 *
 * @author Pete Bankhead
 */

def name = getProjectEntry().getImageName() + '.txt'
def path = buildFilePath(PROJECT_BASE_DIR, 'annotation results')
mkdirs(path)
path = buildFilePath(path, name)
saveAnnotationMeasurements(path)
print 'Results exported to ' + path

Thank you Pete. While I am not an expert, it seems I have generated some interest in Qupath. 2 PhDs will meet me on Monday. I an sure we will send questions to the discussion forum. Thanks Rakiya

…

On 03 Oct 2020, at 14:16, Pete ***@***.***> wrote: @petebankhead commented on this gist. HI @rakiyasaid <https://github.com/rakiyasaid>, the main thing is to cite the QuPath paper: https://qupath.readthedocs.io/en/latest/docs/intro/citing.html <https://qupath.readthedocs.io/en/latest/docs/intro/citing.html> This script is really short and just calls methods that exist in QuPath - because it is so simple, I don't think it really requires separate citation but if you like you can use the webpage URL. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://gist.github.com/a473b817eac36caabdffc21daf93231d#gistcomment-3475902>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AECF66WIRJGBT76P2NO4VHTSI4I3LANCNFSM4SCSMWPQ>.