http://imagej.273.s1.nabble.com/Writing-ImageJ-Macros-a-better-way-tp5020818p5020832.html
I think I've basically got it working in IntelliJ. I followed the instructions here :
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.
you can use ImageJ e.g. from a Jupyter notebook with Python kernel. More
> 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> >
>
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