Is there a
Converter to do this? If not, is there a reason why?
Still, I'm surprised there's no
Converter for it...
1 reply
@ctrueden I'm working on some of those low hanger fruit image conversion functions in imagej-common. When I run mvn the ImgLabelingConversionTest test incorrectly grabs the RAIToDatasetConverter.class we wrote instead of ImgLabelingToImgConverter.
Here's the output:
[INFO] Results:
[INFO]
[ERROR] Failures:
[ERROR] ImgLabelingConversionTest.testImgLabelingToImgConversion:81 expected:<class net.imagej.convert.ImgLabelingToImgConverter> but was:<class net.imagej.convert.RAIToDatasetConverter>
[ERROR] Errors:
[ERROR] ImgLabelingConversionTest.testTwoWayConversion:92 » IllegalArgument Only RealT...
[INFO]
[ERROR] Tests run: 293, Failures: 1, Errors: 1, Skipped: 0Here is the line that fails in the test
assertEquals(ImgLabelingToImgConverter.class, convertService.getHandler(labeling, Img.class).getClass());I'm guessing convertService.getHandler() is returning the wrong class because the RAIToDatasetConverter is vague enough that ImgLabeling is caught. Its not obvious to me...how do I limit the scope to avoid this?
But really, the
RAIToDatasetConverter doesn't work unless the RAI in question has RealType samples.
So, we'll need to add some additional constraint to check for that, I think.
For this reason, IIRC, we deprecated the functions that ask "can I convert from Class X to Class Y?" because, just from the class, you might not actually be able to answer the question.
We need an actual instance of the class in order to check it.
But... some places deep in the framework might still use the deprecated "Class X to Class Y" methods.
So, potential for bugs here is higher.
The only tricky bit is that I guess we need to also override some
supports or canConvert method.
I'll use one of them as a guide and override the
supports & canConvert method.
Try adding this:
@Override
public boolean canConvert(final Object src, final Type dest) {
if (!hasCompatibleType(src)) return false;
return super.canConvert(src, dest);
}
@Override
public boolean canConvert(final Object src, final Class<?> dest) {
if (!hasCompatibleType(src)) return false;
return super.canConvert(src, dest);
}
And then you'll have to implement
hasCompatibleType(Object). net.imglib2.util.Util.getTypeFromInterval((RandomAccessibleInterval) src) is your friend here.
- Today I got
net.imagej:ij:1.53kthroughnet.imagej:ij:1.53pdeployed to OSS Sonatype. Yay! - The ImageJ project also has a README on GitHub now, a POM file for building with Maven, unit tests (though some of them do not currently pass), and Ant targets for running those tests. The ImageJ repository on GitHub also now has tags for all the old versions back to v1.20.
- The GitHub Actions CI now builds ImageJ at version
1.x-SNAPSHOTwhenever it changes, which is always accessible from maven.scijava.org and should be equivalent to the latest daily build. - Tomorrow, I will finish teaching the CI to deploy release versions of
net.imagej:ijto OSS Sonatype automatically, so it doesn't fall behind again.
@dfperrault that would be a good question to ask on forum.image.sc (if it hasn't been asked already :sweat_smile:)
A quick search for 'raspberry pi' shows many different results
Hello everyone I am sorry I am really a beginner in using Image but I would have a question about the timestamp in imageJ i would like to plot the %area vs the time in order to analyze cell migration.
I also created a macro code but I am not able to include the known time interval and starting time. Maybe you have time to help me thank you in andvanced! :)
I also created a macro code but I am not able to include the known time interval and starting time. Maybe you have time to help me thank you in andvanced! :)
Hello all. I need to count nuclei and gamma H2AX foci inside nuclei. I have about 120 images to do so. I would highly appreciate a faster method which can be applied to all the images reliably. Please help. It would save a lot of my time, and analysis can be done in unbiased and timely manner.
I used analyze particles to count nuclei and find maxima to get foci inside nuclei. But how to apply this to all the images, I need to learn?
@soniajain1:matrix.org The best place for you to get this type of image analysis help is on the image.sc forum - post your question there. And include a sample image - as well as the exact steps you've tried thus far... We can help you get started with scripting to batch process your images.
There is some dormant code on the imagej.net front page for a plugin highlight carousel, lifted from the fiji.sc Bootstrap site. I could get it working, but I'm wondering: do y'all think it would be nice to have a plugin carousel on imagej.net, with a broader community-driven set of highlighted plugins? And if so, should it live on imagej.net front page, or imagej.net/plugins, or imagej.net/list-of-extensions, or...? Or should we not bother? Opinions?
Hello everyone, I'm a member of the tomancak lab now. Since one and a halve weeks now!
@ctrueden / @hinerm Could you please create a new update site https://sites.imagej.net/TomancakLab/ and give access rights to me "Maarzt" and @xulman "xulman"
2 replies
I think this belongs here? Is the radius in pixels?
Some users and I have run into a problem calling BoneJ's ImageJ2-style 'wrapper' plugins from ImageJ macros in batch mode
setBatchMode(true): the output images are never created or made available to the user in a way they can be readily accessed in macro code. My guess is that the output parameter processing is not occurring, or is occurring but the data are not 'presented' in a macro accessible way. In a batch mode macro images can normally be accessed with selectImage(), but no images are available to be selected. Macros run fine with setBatchMode(false).
One workaround is to use Python instead: