saving stacks with ImageJ1 Macro node

Hi (again),

I'm using the ImageJ Macro node to save image stacks during workflow execution. For that I used a line like: "saveAs("Tiff", "C:\\test_stack.tif");" together with the X,Y and Z dimension selected. That worked very well with KNIME2.8/KNIP1.0.x. It is much faster then the ImageWriter node and it can also write UnsignedShortType Images which didn't work with the ImageWriter Node (at least for me).

Now I realized after using KNIME2.9/KNIP 1.1.0 (stable built) that saving stacks using this approach doesn't work anymore. I just get an error message upon node execution. I can still save if I only select X and Y dimensions but then I only get the first slice of the stack saved of course.

I just wanted to ask whether you might have an idea of what went wrong.

Best

Christian

Hi Christian,

I was able to reproduce the bug and I already fixed it. Short explanation what happened:

Before our 1.1.0 release, we didn't match the labels of the imgs correctly, i.e. a Img X,Y,Z was represented as X,Y,Channel in IJ1. In rare cases this could have gone terrible wrong, that's why we introduced a mapping function to map from our dimensions to IJ1 dimensions. We overlooked something and therefore your bug came up. sorry for that.

Anyway, it should be fixed. The fix will be available in our nightly build in approx. 1 hour! We plan our official bug-fix release 1.1.1 for mid january.

 

Cheers,

Christian

 

 

Hi Christian,

just got an idea how you could also "solve" this problem with a workaround (if you don't want to use the nightly build). Rename your "Z" axis using the Set Image Metadata node to "Channel". This might work.


Cheers,

Christian

 

 

Hi Christian.

I tried the workaround and it works fine. I will also try the nightly build later.

Thanks a lot!

Christian