These are chat archives for fiji/fiji

18th
Mar 2019
Curtis Rueden
@ctrueden
Mar 18 14:10
@joaopapereira Does your plugin rely on the specific APIs of the formats-gpl component (e.g. calling ZVIReader directly)? If not, simply do not depend on formats-gpl in your plugin. If it is present on the classpath, those formats will work, and if not, they won’t. But you aren’t directly linking to formats-gpl so you aren’t bound by the terms of the GPL.
@joaopapereira Regarding “is there a way of programmatically removing an entry in the summary”: sorry, I don’t understand the question. Could you please rephrase? Or you might be better served asking on forum.image.sc instead of here.
João Pereira
@joaopapereira
Mar 18 17:13
@ctrueden thanks for the reply. I only use BF.openImagePlus to open images, some are zvi some are tiff eventually other microscop formats, not sure yet. But after the image is open i do not use anything else. I need to ad them as a dependency just for compilation purposes.
About the summary I realized that underneath it uses ResultsTable and I just do a deleteRow on it when I want to discard something. Nevertheless I just realized that I am using a lot of imagej1 dependencies.... I will have to work on it to decouple to use only imagej2 stuff
Curtis Rueden
@ctrueden
Mar 18 17:15
@joaopapereira Ah, right, because you use BF.openImagePlus, which is part of bio-formats_plugins, which is GPL. So yeah, you are stuck.
Instead of using BF.openImagePlus, you can use SCIFIO, yeah, which is BSD-licensed.
But you will get back an ImgLib2 image, not an ImageJ1 ImagePlus.
You can wrap it to an ImagePlus afterward if you want, though.
João Pereira
@joaopapereira
Mar 18 17:17
interesting
are there any examples of SCFIO for opening multi layer images and splitting them? Because that was in fact what I needed :D
Curtis Rueden
@ctrueden
Mar 18 17:18
What is a “multi layer image”? One with multiple resolutions? Or just multidimensional?
João Pereira
@joaopapereira
Mar 18 17:18
ZVI
as an example
Curtis Rueden
@ctrueden
Mar 18 17:19
Sorry, I cannot remember, can ZVI store multiple image resolutions? Or are you just talking about e.g. multiple Z planes?
Anyway, you can try feeding your ZVI to the standard ImageJ2 image opener. Here is example code.
João Pereira
@joaopapereira
Mar 18 17:20
I am not 100% sure about my answer but the ZVI that I am using are microscope images with 3 different layers
basically they are 3 different color images
RGB
Curtis Rueden
@ctrueden
Mar 18 17:57
OK, I have seen these ZVI files; I had one example that was four layers, with each layer being stored as RGB. So 3x4=12 “channels” total.
Try the example code I linked. Keep in mind that in practice, SCIFIO will call Bio-Formats under the hood, which will call the formats-gpl readers, which means users will need to have that library installed. But with Fiji, it will be installed already. For your own licensing, you do not depend on any GPLed things.