http://imagej.273.s1.nabble.com/Writing-ImageJ-Macros-a-better-way-tp5020818p5020835.html
> Hi Alex,
>
> > Any thoughts on why Script Parameters might not be working?
>
> The script parameters are SciJava's extension to the script languages. In
> order for them to work, the code must be executed through the SciJava
> framework, not via the respective script language's usual launch mechanism.
>
> You can work around this by specifying the desired input values in a
> temporary block at the top, while developing in your IDE.
>
> Suppose you have the following SciJava Jython script:
>
> #@ UIService ui
> #@ String name
> #@ int(style="scroll bar", min=1, max=20) count
>
> greeting = "H" + ("i" * count) + ", " + name + "!"
> ui.showDialog(greeting)
>
> You can develop in an IDE by adding a short section, as follows:
>
> #@ UIService ui
> #@ String name
> #@ int(style="scroll bar", min=1, max=20) count
>
> # TEMP - Populate parameter values for testing.
> from net.imagej import ImageJ
> ij = ImageJ()
> ui = ij.ui()
> name = "Chuckles"
> count = 20
>
> greeting = "H" + ("i" * count) + ", " + name + "!"
> ui.showDialog(greeting)
>
> And then hack to your heart's content, including use of the IDE's
> debugger. When finished, delete those extra lines.
>
> 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 Thu, Jun 21, 2018 at 10:50 AM, Alex <00000313423ff55b-dmarc-reques
>
[hidden email]> wrote:
>
>>
>> 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>> >
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
>