Add a REPL widget that supports the SciJava ScriptREPL #265
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BTW, one thing I noticed with this is that the |
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I'm not sure that I'll have the chance to look at the code until Tuesday or so @kephale, but this looks really awesome - thanks for implementing it! One quick comment - have you considered adding the REPL to the bottom by default? I really like how the napari console sits at the bottom - naively this seems like it should go in the same place. |
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I'm very open to where it goes. I have some concerns about all the consoles/repls getting confused. I was actually a little worried about making this icon so similar to the napari-console icon. |
Yeah, I thought about that too. As far as the button goes, maybe we could color it differently, or add the ImageJ Logo somewhere? Another option would be to just make the SciJava Script REPL a separate napari plugin - making it show up in the napari menus - then we don't have to worry about a button. Then there's the question of differentiating the two consoles - does the SciJava Script REPL have a Java UI that we could launch (i.e. launch a separate window), and if so, would that detract from your probing properties if it was in a different window? That could be one way to do it, and would require less Qt code to maintain. |
Yes, but I was particularly keen on this for the headless situation, so I do hope that the UI is on the Python side. |
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@gselzer I emailed you 1 more figure for this addition to the docs: https://github.com/kephale/napari-imagej/blob/4ccab72c0d8e2890e9ed27d8e4b5e1bff3da547e/doc/Configuration.rst?plain=1#L106 I've added tooltips + a section in the docs about the REPL. |
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After looking at this again, I'm actually pretty happy with the visual appearance of the REPL - I don't think it's too easy to confuse with the napari console.
One thing that I did think would be cool would be to put a shadow of the napari-imagej logo behind the text edit for a visual reminder of which textedit is which, but I have no idea how you'd do that, so I'm just going to leave it here as an idea.
| Using the SciJava REPL | ||
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| You can use the SciJava REPL to interactively run SciJava code. This makes it possible to do things like paste existing SciJava scripts into the REPL. More information on scripting in SciJava can be found `here <https://imagej.net/scripting/>`_. |
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So I played a little with the Script REPL, and I couldn't get anything beyond 2+4 to work. I was trying to print Hello World, but I couldn't even figure out how to do that.
So, as a result, I looked here, and I checked out imagej.net/scripting. As someone who is not intimately familiar with that page, I wasn't super sure where to go. I did find the ScriptInterpreter page from that page, which appears to me to be what this is, but I tried typing :help and I didn't get anything.
Then, I typed help, and my napari froze. I went back to my terminal, and I saw this:
(napari-imagej-dev) ➜ napari-imagej git:(scijava-repl) napari
hello
[java.lang.Enum.toString] hello[java.lang.Enum.toString]
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString]
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString]
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString]
Hello World
[java.lang.Enum.toString] Hello World[java.lang.Enum.toString]
Welcome to Python 2.7! This is the online help utility.
If this is your first time using Python, you should definitely check out
the tutorial on the Internet at http://docs.python.org/2.7/tutorial/.
Enter the name of any module, keyword, or topic to get help on writing
Python programs and using Python modules. To quit this help utility and
return to the interpreter, just type "quit".
To get a list of available modules, keywords, or topics, type "modules",
"keywords", or "topics". Each module also comes with a one-line summary
of what it does; to list the modules whose summaries contain a given word
such as "spam", type "modules spam".
help> [java.lang.Enum.toString]
Welcome to Python 2.7! This is the online help utility.
If this is your first time using Python, you should definitely check out
the tutorial on the Internet at http://docs.python.org/2.7/tutorial/.
Enter the name of any module, keyword, or topic to get help on writing
Python programs and using Python modules. To quit this help utility and
return to the interpreter, just type "quit".
To get a list of available modules, keywords, or topics, type "modules",
"keywords", or "topics". Each module also comes with a one-line summary
of what it does; to list the modules whose summaries contain a given word
such as "spam", type "modules spam".
help> So, long story short, it looks like the output is not being captured by the TextEdit, and also I'm wondering if we can link to documentation that is more specific to the SciJava REPL.
To solve the output not being captured by the TextEdit, is there an option in SciJava for this @ctrueden?
| Using the SciJava REPL | ||
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I'm wondering if this would be better suited to the new Usage page of the ReadTheDocs...
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Or the Troubleshooting page...
| icon = QColoredSVGIcon(resource_path("repl")) | ||
| self.setIcon(icon.colored(theme=viewer.theme)) |
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If you could replace this with the way that we set the icon here, then the icon will be recolored when the user changes the theme.
src/napari_imagej/widgets/menu.py
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| from scyjava import jimport | ||
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| ByteArrayOutputStream = jimport("java.io.ByteArrayOutputStream") | ||
| ScriptREPL = jimport("org.scijava.script.ScriptREPL") |
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Can we put these imports in java.py, along with all of the other imports? It's kinda nice to use jimport in one place
src/napari_imagej/widgets/repl.py
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| from scyjava import jimport | ||
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| ScriptException = jimport("javax.script.ScriptException") |
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It would also be cool if this jimport was moved to java.py.
| self.repl_button.setToolTip("Show/hide the SciJava REPL") | ||
| self.layout().addWidget(self.repl_button) | ||
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| self.settings_button: SettingsButton = SettingsButton(viewer) | ||
| self.settings_button.setToolTip("Show napari-imagej settings") |
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Generally I've been putting the tool tips in the constructors of each button - could we move these there for consistency?
Thanks so much for adding the tooltip to the settings button - can't believe I forgot that!
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@gselzer It seems you started reviewing this as I was actively trying to fix the same problems you discovered. This PR needs some additional work to squash bugs before it can be merged. If you want to get looped into fixing it (which would be really helpful!), I can give you a primer on how the SciJava |
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I'm still working on this. Need to change |
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Progress: scijava/scijava-common@0f3bf44. Was going to release it, but updating scijava-common to pom-scijava 36.0.0 breaks some tests, so gotta sort that out first. Then we can start using the improved |
And use jc mechanism instead of jimport for REPL-related classes.
This provides a place to keep track of not only the ImageJ2 gateway, but also any affiliated data structures, such as our singleton ScriptREPL.
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Progress today: scijava-common 2.95.0 was released. And I worked further on this branch, rebasing it on top of the latest mainline. Some tests pass now, but others fail. I need to scrutinize the design changes a bit more, and probably reshuffle the commit order to minimize the footprint of the commit implementing the changeover to the nij object. |
This PR adds a widget for the SciJava ScriptREPL, allowing users to interactively write SciJava friendly code directly within napari.
When I was exploring the compatibility of various ImageJ/Fiji plugins with napari-imagej, I frequently found myself wanting to poke at variables/state. That led me to writing this REPL widget so we can quickly poke around on the JVM instead of always needing to deal with jpipe/jimport stuff.
Caption: This is a screenshot of napari-imagej with the REPL widget active and some example output from Jython.
Now updated to have the corrected icon:
