These are chat archives for fiji/fiji

4th
Dec 2018
Stefan Helfrich
@stelfrich
Dec 04 2018 06:43
@gogenes_twitter This is a general issue and I assume that this has nothing to do with the opening of your files. Where exactly have you extracted the ImageJ archive to? If you are on Windows and it’s in C:\Program Files\, copy it to your user folder and try again..
filippogambarota
@filippogambarota
Dec 04 2018 08:38
Hi, I'm working on a scientific paper with some images processed by fiji. Unfortunately i'm not skilled in image editing. I'm trying to create some images that i can see trough red-green glasses (similar to anaglyph but im not interested in 3d vision). Anyway i've found that the "merge color channels" function is perfect for me. I open 2 images, i select the red channel for one and the green for the other and the merging is perfect. However i need to know exactly what the program do with this command. Does change any luminosity, contrast or transparency parameters?
Curtis Rueden
@ctrueden
Dec 04 2018 08:42
@filippogambarota Type "merge color channels" into the search bar, select the correct command in the results, and click the Source button to view the code online.
filippogambarota
@filippogambarota
Dec 04 2018 08:44
@ctrueden Thank you!
Curtis Rueden
@ctrueden
Dec 04 2018 10:30
[INFO] Building Melting Pot 0.0.0-SNAPSHOT                            [164/164]
...
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 06:06 min
[INFO] Finished at: 2018-12-04T04:28:27-06:00
tpietzsch
@tpietzsch
Dec 04 2018 10:31
:clap:
Curtis Rueden
@ctrueden
Dec 04 2018 13:33
Fiji 2.0.0-pre-8 uploaded built on ImageJ 2.0.0-rc-69/1.52i.
Please report here if you have any problems updating.
Jan Eglinger
@imagejan
Dec 04 2018 14:27

Thanks, @ctrueden!
On Windows, the updater seems to pull in a dependency that - upon the required restart before continuing - leads to a bunch of error messages in the console, such as:

[ERROR] Malfunctioning plugin: net.imagej.legacy.convert.TableToResultsTableConverters$ShortTableToResultsTable
java.lang.NoClassDefFoundError: net/imagej/table/ShortTable
    at net.imagej.legacy.convert.TableToResultsTableConverters$ShortTableToResultsTable.getInputType(TableToResultsTableConverters.java:221)
    at org.scijava.convert.AbstractConverter.canConvert(AbstractConverter.java:113)
    at org.scijava.convert.AbstractConverter.canConvert(AbstractConverter.java:158)
    at org.scijava.convert.AbstractConverter.canConvert(AbstractConverter.java:97)
    at org.scijava.convert.AbstractConverter.canConvert(AbstractConverter.java:89)
    at org.scijava.convert.AbstractConverter.supports(AbstractConverter.java:144)
    at org.scijava.convert.AbstractConverter.supports(AbstractConverter.java:69)
    at org.scijava.plugin.HandlerService.getHandler(HandlerService.java:61)
    at org.scijava.plugin.HandlerService.supports(HandlerService.java:84)
    at org.scijava.convert.AbstractConvertService.supports(AbstractConvertService.java:87)
    at org.scijava.module.DefaultModuleService.save(DefaultModuleService.java:304)
    at org.scijava.module.process.SaveInputsPreprocessor.saveValue(SaveInputsPreprocessor.java:77)
    at org.scijava.module.process.SaveInputsPreprocessor.process(SaveInputsPreprocessor.java:68)
    at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:105)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:157)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
    at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

It's all fine after running Help > Update... and restarting again, but it might scare some Windows users.

Hm, I guess I've caused some trouble with the hard switch of the table API :-/
I guess this issue could be worked around by adding yet more dependencies to the updater, so they get pulled in before the first restart on Windows system... but that's probably not the nicest thing to do.
(It's just imagej-legacy, I guess ?!)
Curtis Rueden
@ctrueden
Dec 04 2018 14:49
@imagejan I'm glad it ultimately works. I think the next-generation version of the updater needs to have fewer dependencies, rather than more. At one point (maybe even still), to work around problems like this, even imagej-ops became one of those "early update" artifacts.
@imagejan Anyway: that was an absurd amount of work! But the org.scijava.table switch is fully done, including all downstream users I know about. New imagej-omero (also with improved ROI equality semantics), new imagej-server. The batch-processor et al. should also be fully included and released. Let me know if I missed anything.
Jan Eglinger
@imagejan
Dec 04 2018 15:26
Just tested and confirmed working (i.e. batch processor including imagej-plugins-batch)!
Curtis Rueden
@ctrueden
Dec 04 2018 15:32
Yaay
Now to complete 100000 slides before PAvel murders me.