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  • 03:35
    ctrueden commented #240
  • Nov 25 15:26
    imagejan commented #240
  • Nov 23 12:37
    biosciflo opened #240
  • Nov 22 22:45
    ctrueden commented #55
  • Nov 22 22:39
    ctrueden synchronize #55
  • Nov 22 22:39

    ctrueden on python-script-runner

    Add an object for SciJava scrip… (compare)

  • Nov 22 22:38
    ctrueden synchronize #55
  • Nov 22 22:38

    ctrueden on python-script-runner

    Add an object for SciJava scrip… (compare)

  • Nov 22 19:36
    codecov-commenter commented #239
  • Nov 22 19:35
    gselzer edited #239
  • Nov 22 19:29
    gselzer review_requested #239
  • Nov 22 19:29
    gselzer labeled #239
  • Nov 22 19:29
    gselzer review_requested #239
  • Nov 22 19:29
    gselzer assigned #239
  • Nov 22 19:29
    gselzer opened #239
  • Nov 22 19:28

    gselzer on prioritize-user-specified-ij-legacy

    Check for ij legacy in original… (compare)

  • Nov 22 18:47
    elevans converted_to_draft #238
  • Nov 22 18:45
    elevans opened #238
  • Nov 21 20:47

    elevans on dim-order-kwargs-tests

    Refactor direct to xarray tests… Add additional case for RAI's w… (compare)

  • Nov 18 21:12

    ctrueden on master

    Add jpype as direct project dep… Fix name of jpype conda package Add shortcuts for common dev ta… (compare)

Gabriel Selzer
@gselzer
@ctrueden see imagej/napari-imagej#54
5 replies
Gabriel Selzer
@gselzer

@gselzer Heh, thanks for verifying that. In a way it's good that it's not a bug in v3.

Looks like someone else has made actions/setup-java#333

Gabriel Selzer
@gselzer
@ctrueden it appears that imagej/napari-imagej#41 builds with just the environment variable
Curtis Rueden
@ctrueden
Cool. So let's go with that.
Gabriel Selzer
@gselzer
Alright, I'm going to squash all 9(!) of the commits, as the diff is like 5 lines :laughing:
If that builds I'll merge it
Curtis Rueden
@ctrueden
:+1:
Gabriel Selzer
@gselzer
Do you think we should be setting that environment variable in the startup of our code?
Curtis Rueden
@ctrueden
I don't know, sorry.
You could do some testing on the office Mac.
If it improves matters, then yeah, I think we should.
Gabriel Selzer
@gselzer
It does not seem to make any difference on the office mac, so I'm left it in the Github Actions script
@ctrueden any opinions on imagej/napari-imagej#57 ?
Curtis Rueden
@ctrueden
Looks good to me. I confess I don't really understand the layers thing that well. I still need to dig into how napari-imagej is passing all these layers around. I get confused about "inputs being layers" because in my view, the inputs are things like Dataset and other Java types. You can have a Dataset which was converted from a numpy array which was inside of a napari layer, but the input itself is not a layer. But the language you're using in napari-imagej differs from my thinking.
23 replies
Edward Evans
@elevans
@ctrueden I'm back from vacation and all charged up. I just got through the reviewer comments and I'm oganzing what needs to be done. I'll make a project board on the repo for it as well.
5 replies
Curtis Rueden
@ctrueden
@gselzer I'm not sure switching to Groovy is going to help. I can replicate the problem using Groovy as well.
47 replies
Curtis Rueden
@ctrueden
Hey @gselzer, did you know about the numpy ArrayType type hint?
Gabriel Selzer
@gselzer
Huh, I did not! We should remember that when we get around to type-hinting imglyb and pyimagej!
Nicolas Chiaruttini
@NicoKiaru

I'll post an issue with a minimal reproducible on the forum soon, but here's a quick question : have you ever found a situation where you define a function with JPype like this:

@JImplements(Function)
class DeepSliceProcessor:
    @JOverride
    def apply(self,folder):
        print('0')
        Model.predict(str(folder.getParent()))
        print('1')
        out = File(folder,JString('results'))
        Model.Save_Results(out.getAbsolutePath())
        return File(folder,JString('results.xml'))

and this function runs when started from the jupyter notebook, but it hangs when the same function is called from the Java side ?

// WORKS!
run_deep_slice = DeepSliceProcessor()
run_deep_slice.apply(File('deepslice/images'))
// HANGS
ij.command().run(RegistrationDeepSliceCommand, True,\
                 "slices_string_channels", JString('0'),\
                 "image_name_prefix", JString('Section'),\
                 "mp", mp,\
                 "allow_slicing_angle_change", True,\
                 "allow_change_slicing_position", True,\
                 "maintain_slices_order", True,\
                 "affine_transform", True,\
                 "deepSliceProcessor", run_deep_slice \\ passing the function as an argument
                )

I have some weak indication that tensorflow (1.15 CPU) is not starting

10 replies
Nicolas Chiaruttini
@NicoKiaru
I'm writing from my phone, so the answer won't go into the thread, sorry. Imo the best place is still the image.sc forum. I could write a small post about this. Sounds good?
Curtis Rueden
@ctrueden
Sounds good!
Gabriel Selzer
@gselzer
@ctrueden @hinerm any opinions on this?
11 replies
Gabriel Selzer
@gselzer
Curtis Rueden
@ctrueden
The beartype thing? Oh yeah, I looked at that a few days ago when I saw it in there... pretty hilarious documentation. And amazing—incredibly thorough.
Edward Evans
@elevans
thoughts on this new figure 1?
image.png
this is to address reviewer comment "On the same note, I suggest the authors modify their figure. The current figure implies two-way communication between imageJ and Python. However, this is currently true only within a Python environment."
Curtis Rueden
@ctrueden
Shouldn't the gradient be centered on JPype?
Edward Evans
@elevans
hmm yeah lol
Curtis Rueden
@ctrueden
Otherwise, I like it. But... I don't remember the old figure, and what was different.
Edward Evans
@elevans
image.png
this is the old one
Curtis Rueden
@ctrueden
Ah I see, you extended the blue surrounding the JVM. Cool.
Edward Evans
@elevans
image.png
how about that?
Curtis Rueden
@ctrueden
Perfect.
Edward Evans
@elevans
excellent. I'll do some clean up :sunglasses:
Simon Wetzel
@SimonWetzel
Hi guys, first I am very impressed by the effort you put in the pyimageJ package to use ImageJ/Fiji via Python. Right now, I am working on a small project for automated gel quantification as part of a university course and would like to use pyimagej as part of my script.
I would like to implement a IJ1 Macro in Python. However, I am having issues to make the macro run with pyimageJ and spent some time solving the issue (tried on Linux and Windows system) but get the same error (not self.legacy.isActive) every time, even with very simple macros. Change in initialization could not solve this (https://github.com/imagej/pyimagej/blob/master/doc/Initialization.md)
What is causing this, and how can I fix it?
Thank you in advance,
Simon
Simon Wetzel
@SimonWetzel
ImportError: The original ImageJ is not available in this environment. Use of original ImageJ macros is not possible. See: https://github.com/imagej/pyimagej/blob/master/doc/Initialization.md
Gabriel Selzer
@gselzer
@SimonWetzel this would be a fantastic question to ask on the image.sc forum
Gabriel Selzer
@gselzer
I'd write a post there, including the code you've written so far.
Jackie Carson
@quothbonney
Is it possible to actually write plugins with PyImageJ, or just to use them in python?
1 reply
Simon Wetzel
@SimonWetzel
@gselzer Thank you very much for your reply! I posted the question on the forum (https://forum.image.sc/t/pyimagej-macro-run-error/68515), would by fantastic if any of you could have a look on it.
giovanniani
@giovanniani
Hi everyone, I'm having issues with a local and server installation of pyimage, I'm using pyimage==0.4.0 and scyjava==1.5.1, but I keep getting the error that there is no module named scyjava_config. Any ideas?
Gabriel Selzer
@gselzer
@giovanniani can you please repost this question on either the Imagesc zulip chat or on the imagesc forum? You'll get more eyes there
Curtis Rueden
@ctrueden
@giovanniani pyimagej is up to 1.2.1 now, with 1.3.0 out very soon... 0.4.0 is super old, so definitely update it. If you need more help, like Gabe said, please post on Zulip or Image.sc! Thanks.
giovanniani
@giovanniani
@ctrueden @gselzer I understand thanks for your help, I'll post it there, the issue I have with newer versions is that I managed to put the GUI to work on 0.4.0 but couldn't do it on newer version, the headless=False flag was deprecated and I couldn't find its counterpart, right now I have a server dedicated to run pyimages macros in parallel using Ray Clusters. and out of nowhere the pyiamgej library decided to stop working and I've been scratching my head around it.
Curtis Rueden
@ctrueden
mode='interactive' or mode=imagej.Mode.INTERACTIVE
But headless=False should still work... if not, that's a bug...
For anyone stumbling across this exchange, the conversation has now moved to Zulip.