Created
February 20, 2018 20:16
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Save petebankhead/a473b817eac36caabdffc21daf93231d to your computer and use it in GitHub Desktop.
Export annotations for a project in QuPath
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/* | |
* 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 |
Hi Pete,
How do I cite this script?
RAkiya
HI @rakiyasaid, the main thing is to cite the QuPath paper: 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.
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.
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Hi Pete,
I used this script fr my thesis and I want to cite it. Whats the best way to write the citation?