http://imagej.273.s1.nabble.com/Writing-ImageJ-Macros-a-better-way-tp5020818p5020834.html
The script parameters are SciJava's extension to the script languages. In
>
> Curtis,
> This some really seems to be the winner :
http://forum.imagej.net/t/impo> rt-python-packages-in-pycharm/3540/4
> I think I've basically got it working in IntelliJ. I followed the
> instructions here :
https://github.com/qupath/qupa> th/wiki/Advanced-scripting-with-IntelliJ#setting-up-
> intellij-idea-with-qupath but exchanged the path to QuPath.jar for the
> path to IJ.jar.
> The one thing that it doesn't seem to recognize is the Script Parameters.
> I can always use the GenericDialog class, but it would be nice to have
> Script Parameter capability. Using the GenericDialog class I'm able to
> launch GUI elements from within IntelliJ, so I know GUI capabilities are
> there.
>
> Any thoughts on why Script Parameters might not be working? I'll be sure
> to wiki this up once I have a more solid understanding of what's going on.
>
> Alex
> On Wednesday, June 20, 2018, 5:53:38 PM PDT, Curtis Rueden <
>
[hidden email]> wrote:
>
> Hi Alex,
>
> Maybe these threads are helpful?
>
> -
>
http://forum.imagej.net/t/writing-and-running-ij-scripts-in-> jython-externally/8843/3
> -
http://forum.imagej.net/t/import-python-packages-in-pycharm/3540/4>
> A guide to developing ImageJ code with PyCharm would be a welcome
> contribution to the ImageJ wiki.
>
> We also have experimental support for calling ImageJ from Python, so that
> you can use ImageJ e.g. from a Jupyter notebook with Python kernel. More
> documentation and example notebooks coming soon, but for now, you can take
> a look at
https://github.com/imagej/imagej.py#usage>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect -
https://loci.wisc.edu/software> ImageJ2 lead, Fiji maintainer -
https://imagej.net/User:Rueden> Did you know ImageJ has a forum?
http://forum.imagej.net/>
>
> On Wed, Jun 20, 2018 at 7:14 PM, Alex <
>
[hidden email]> wrote:
>
> > Curtis
> > Thanks so much for your support and for your development efforts. I know
> > what it’s like to develop be the sole maintainer for open source
> projects.
> >
> > >In general, if you want better development >tools, then I strongly
> > encourage
> > >you to use a script language other than >ImageJ macro.
> > I’m happy to move to Python me to develop Python based imagej scripts
> with
> > a real IDE (preferably pycharm) with debugger full support?
> > Thanks so much
> > Alex
> >
> > Sent from Yahoo Mail for iPhone
> >
> >
> > On Wednesday, June 20, 2018, 4:38 PM, Curtis Rueden <
> >
[hidden email]> wrote:
> >
> > Hi Alex,
> >
> > > Does anyone know why the screenshots on this page show a "Breakpoints"
> > > menu in the Fiji Script Editor that doesn't appear to be in the
> > > software?
> >
> > The debugger/breakpoint support was never completed, and removed in 2012.
> >
https://github.com/scijava/script-editor/commit/> > 87e05e3108d42c6276e786ba5d850c3d831de85c
> >
> > > Would be nice if we didn't have to resort to such trickery.
> >
> > See this issue:
> >
https://github.com/scijava/script-editor/issues/5> >
> > As I wrote there:
> >
> > > Unfortunately, I have too many other urgent priorities to work on the
> > > Script Editor right now, and there is unfortunately no one else taking
> > > care of this component besides me. However, if you or your group have
> > > any programming resources/capabilities which can be directed toward
> > > this mini-project, I would be delighted to provide guidance and
> > > support toward getting the feature implemented. Otherwise, I will get
> > > to it eventually, since this is a feature which I agree would be
> > > really useful—it's just going to be a few months at least if it falls
> > > on me personally to do it.
> >
> > In general, if you want better development tools, then I strongly
> encourage
> > you to use a script language other than ImageJ macro. The macro language
> is
> > a custom language that does not have any tooling support outside of
> ImageJ,
> > whereas the other script languages have a much broader base of community
> > support beyond ImageJ only. My personal favorite is Groovy. For a list of
> > available languages and brief summary of strengths and weaknesses, see
> >
http://imagej.net/Scripting#Supported_languages> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect -
https://loci.wisc.edu/software> > ImageJ2 lead, Fiji maintainer -
https://imagej.net/User:Rueden> > Did you know ImageJ has a forum?
http://forum.imagej.net/> >
> >
> > On Wed, Jun 20, 2018 at 6:06 PM, Alex <00000313423ff55b-dmarc-
> >
[hidden email]> wrote:
> >
> > >
> > > Thanks Bram ... slick workaround. Would be nice if we didn't have to
> > > resort to such trickery.
> > > Does anyone know why the screenshots on this page show a "Breakpoints"
> > > menu in the Fiji Script Editor that doesn't appear to be in the
> software?
> > >
https://imagej.net/Using_the_Script_Editor> > >
> > > Alex
> > >
> > >
> > >
> > > On Wednesday, June 20, 2018, 3:15:39 PM PDT, Bram van den Broek <
> > >
[hidden email]> wrote:
> > >
> > > Hi Alex,
> > >
> > > Not sure if this is any help, but I tend to put 'waitForUser'
> statements
> > > at certain points in the code to check what's going on (or wrong).
> After
> > > many years of manual typing and deleting, I've only just made this
> into a
> > > function. Something like the code below. You can quickly disable the
> > > checkpoints by setting debug_mode to false.
> > >
> > > --------------------------------------------
> > > debug_mode = true;
> > > n=1;
> > >
> > > // code
> > > checkpoint("before filter");
> > > // more code
> > > checkpoint("after filter");
> > > // more code
> > > checkpoint("");
> > > // more code
> > >
> > > function checkpoint(message) {
> > > if(debug_mode==true) {
> > > setBatchMode("show"); //If you run your macro in Batch mode.
> > > print("Checkpoint "+n+" reached");
> > > waitForUser("Checkpoint "+n+": "+message);
> > > setBatchMode("hide"); //If you run your macro in Batch mode.
> > > n++;
> > > }
> > > }
> > > ------------------------------------------
> > >
> > > Best regards,
> > > Bram
> > >
> > > ------
> > > Bram van den Broek
> > > Advanced Microscopy and Image Analysis
> > > BioImaging Facility / Cell Biology
> > > The Netherlands Cancer Institute
> > >
> > >
> > >
> > >
> > >
> > > ________________________________________
> > > From: Alex <
[hidden email]>
> > > Sent: Wednesday, June 20, 2018 7:32 PM
> > > To:
[hidden email]
> > > Subject: Re: Writing ImageJ Macros a better way
> > >
> > > Brandon,
> > >
> > > Thanks ... I found a bbedit language module a while back so I've been
> > able
> > > to look at the code with syntax highlighting. The biggest issue I can
> > see
> > > with the Fiji Editor is that there's no debugger. The only way I could
> > > figure out how to debug was to copy the code back into the main ImageJ
> > > macro editor.
> > >
> > > I guess the one thing I'm looking for is some way to debug macros with
> an
> > > editor that provides real stop, step, step into, etc functionality.
> The
> > > macro editor's "run to insertion point" is a really clumsy way to do
> > > stops. When you've got lots of loops and sub-functions it really
> doesn't
> > > work well at all.
> > >
> > > Is there something I'm missing about the Fiji Editor?
> > > ThanksAlex
> > >
> > > On Wednesday, June 20, 2018, 8:55:59 AM PDT, Brandon Hurr <
> > >
[hidden email]> wrote:
> > >
> > > Alex,
> > >
> > > I'm very much in a similar boat to you. I'm skilled in R and can manage
> > in
> > > python and C when I have to, but Java is hard for me for some reason. I
> > > typically write macros in the GUI editor in FIJI and I'm on a mac. My
> > > macros have increased in complexity and have become much more difficult
> > to
> > > manage in recent years.
> > >
> > > The syntax highlighting in FIJI's editor is the best I've used so far.
> > Most
> > > front end's don't seem to know what to do with ImageJ script, but they
> > have
> > > better tools for refactoring. Secondarily, I've used
> textWrangler/BBedit
> > > with the module mentioned here:
> > >
http://imagej.1557.x6.nabble.com/BBEdit-language-module-for-> > > ImageJ-macros-td3686081.html
> > > It works pretty well and is easier on the eyes than FIJIs editor.
> > >
> > > Advice will vary a lot as each person works best in their own way, but
> > one
> > > way that has helped me loads is to functionalize things as much as
> > > possible. If you have a piece of code that runs in many places, make a
> > > function out of it and use it instead. This abstracts pieces away from
> > the
> > > core code and allows you to focus more on the flow of things. Then when
> > you
> > > get a problem you can more easily focus on that piece. I used to have
> > > scripts that were 1500 lines long. Now the core loops and functions are
> > > more like 200 lines and the functions that run within that core are the
> > > other 1300 lines. You could even tear those pieces out into other
> scripts
> > > (functions script) or rewrite in Java for speed if you need it and can
> do
> > > that.
> > >
> > > I also know that FIJI can use python, javascript and other languages to
> > run
> > > the core functions, but the documentation around this is not nearly as
> > good
> > > as the imagej scripting language docs and examples that are on the
> > > internet. At least the last time I looked, which admittedly was a while
> > > ago.
> > >
> > > HTH,
> > > Brandon
> > >
> > >
> > >
> > > On Tue, Jun 19, 2018 at 3:33 PM Alex <
> > >
[hidden email]> wrote:
> > >
> > > > All,
> > > >
> > > > I know there's lots of information on the web but it seems very
> > scattered
> > > > and unclear what's considered "best practice."
> > > > I've been writing ImageJ macros for some time using the ImageJ Macro
> > > > language and the built in script editor. Obviously this has it's
> > > > limitations. The scope of the Macro Language itself isn't really a
> > > problem
> > > > but some of my macros have become so complex that debugging and
> > changing
> > > > them is very difficult.
> > > >
> > > > I'm pretty handy at Python, R, and C but don't have any experience
> with
> > > > Java. Also, I'm working on MacOS.
> > > > I've tired the Eclipse ImageJ plugin (
> > > >
https://github.com/Bio7/EclipseImageJ1Plugin) but it leaves a lot to
> > be
> > > > desired as it's very clunky and still only seems to show variables
> and
> > > > their values in ImageJ itself.
> > > >
> > > > What would you consider the best way to write ImageJ macros in an IDE
> > > that
> > > > offers real debugging functionality? What's the best step-by-step
> > > resource
> > > > for learning out more advanced ImageJ macro programming techniques?
> > > > ThanksAlex
> > > >
> > > > --
> > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > > >
> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
> >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
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> ImageJ mailing list:
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> ImageJ mailing list:
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