These are chat archives for fiji/fiji

24th
May 2018
Hadrien Mary
@hadim
May 24 2018 13:40
@tinevez Have you been able to get FilamentDetector to work on MacOSX? I have a question from a user where the plugin freeze his Fiji instance on MacOSX.
Jean-Yves Tinevez
@tinevez
May 24 2018 14:53
I had the same problem.
Curtis Rueden
@ctrueden
May 24 2018 14:55
Guys, it is very likely due to the file chooser on macOS.
IIRC, in some scenarios it deadlocks if you show the file chooser on the EDT, and in others it deadlocks if you don't. :-(
There are bugfixes in imagej-legacy flipflopping back and forth. But still no real solution.
What code are you using to show the file chooser? uiService.chooseFile?
Or if the code isn't using a file chooser then I am probably wrong. :-)
Varun Kapoor
@kapoorlab
May 24 2018 15:16
@ctrueden Thanks for the ITK tip, another question, I have X Y co-ordinates and I want to draw on the image giving each X-Y co-ordinate a different color code, any examples for this kind of drawing?
Curtis Rueden
@ctrueden
May 24 2018 15:24
@kapoorlab You want draw on the image in... ImageJ classic interface? In Jupyter? Sorry I lost the context here.
If you want to annotate images in Jupyter, apparently there is a combination bokeh + holoviews? See https://github.com/scisprints/2018_05_sklearn_skimage_dask/issues/12#issuecomment-391685328. Maybe @VolkerH can elaborate more...
Varun Kapoor
@kapoorlab
May 24 2018 15:26
No this is to visualize the results of the program which spits out XY and K value associated with each XY, I can use randomaccessibleintervals or classic imageJ, just want some cool visualization at the end of the program
Curtis Rueden
@ctrueden
May 24 2018 15:27
If you meant ImageJ classic UI, the built-in multipoint tool has limitations regarding colors. But you could add individual point ROIs to the overlay, each one a different color. See e.g. http://imagej.net/macros/examples/Overlay_Polygons.txt
Varun Kapoor
@kapoorlab
May 24 2018 15:28
Like creating an empty image and giving different intensity value K for the associated XY else 0 and somehow adding it on top of the active image for which it is displaying the result.
Curtis Rueden
@ctrueden
May 24 2018 15:28
Yeah, use an IJ1 Overlay.
Varun Kapoor
@kapoorlab
May 24 2018 15:29
ok kul, thanks
Curtis Rueden
@ctrueden
May 24 2018 15:30
The linked example is a macro, but the Java API for overlays is pretty straightforward. http://javadoc.scijava.org/ImageJ1/ij/gui/Overlay.html
And then imp.setOverlay(myOverlay) IIRC. Have fun.
Here is an example where I fake a color bar using an overlay.
Varun Kapoor
@kapoorlab
May 24 2018 15:32
ah thats kul
Hadrien Mary
@hadim
May 24 2018 16:24
@ctrueden The plugin doesn't use any file chooser but a @Dataset parameter instead. The interface uses JavaFX. Is there any known issue between MacOSX and JavaFX in ImageJ?
I can't debug it without a Mac unfortunately...
Curtis Rueden
@ctrueden
May 24 2018 16:46
@hadim No known issue with JavaFX that deadlocks. Do you have a GitHub issue tracking this issue? If you make one with instructions to reproduce, I can do so locally and paste a thread dump with the deadlock.
Hadrien Mary
@hadim
May 24 2018 19:01
@ctrueden ty for looking into it. See here hadim/FilamentDetector#12. From my understanding, to reproduce it, you only have to open the plugin with an image opened in Fiji.
Curtis Rueden
@ctrueden
May 24 2018 19:37
@hadim hadim/FilamentDetector#13.
It is a pretty nasty issue relating to JavaFX on macOS. :-(
Hadrien Mary
@hadim
May 24 2018 19:41
Wow. Thank you @ctrueden. I'll test that soon to see if it also works ok on Linux/Windows. And indeed it looks pretty nasty...
Curtis Rueden
@ctrueden
May 24 2018 19:42
🤞