http://imagej.273.s1.nabble.com/Writing-a-Custom-version-of-ImageJ-tp5000477p5000624.html
Thank you for your suggestion Curtis. I am starting to wonder if I
should postpone this project until IJ2 is closer to being released. It
want is written specifically for IJ2. Just out of curiosity, suppose there
> Hi Aaron,
>
> > I am aware that IJ2 is still under beta testing but was wondering if
> > there was any documentation on how this new functionally worked (i.e.
> > generating user interfaces).
>
> There is short explanation and example of an ImageJ2 command at:
>
http://developer.imagej.net/extensibility>
> In short, you create an ImageJ2 command by declaring its inputs and
> outputs, and ImageJ2 takes care of the rest. No need to write any
> UI-specific code at all.
>
> You can also peruse the ImageJ2 Tutorials at:
>
https://github.com/imagej/imagej-tutorials>
> HTH,
> Curtis
>
>
> On Tue, Oct 23, 2012 at 7:28 AM, Aaron Hendrickson <
[hidden email]
> >wrote:
>
> > All,
> >
> > I am very greatful for all the suggestions you have provided
> > me....many of which seem to be viable options for working towards my
> > goal of automating my procedures. One reply that caught mt interest
> > was from Birgit. Birgit mentioned that ImageJ 2.0 and Alida provide
> > "functionality for automatically generating user interfaces for
> > processing units, i.e. plugins in ImageJ 2.0 and so-called operators
> > in Alida. These GUIs allow for example to configure certain
> > parameters, i.e. to set directory paths or check options, and to
> > finally run the operator/plugin". What I am gathering from this is if
> > a series of plugins were to be created, I could use the functionallity
> > of IJ2 and/or Alida to generate a user interface that could call on
> > these plugins and run the processes I am trying to perform (and with
> > relative ease in comparison to create my own gui). I am aware that
> > IJ2 is still under beta testing but was wondering if there was any
> > documentation on how this new functionally worked (i.e. generating
> > user interfaces). With a little self teaching in Java, would this be
> > a reasonable task for me to accomplish? The only thing that is
> > holding me back is not the amount of work involved, but rather
> > figuring out the steps I would need to take to acheive the final
> > product I am seeking. Essentially what I am trying to say is I am
> > lost in how I become a good programmer with IJ, but do not care if it
> > means a lot of work.
> >
> > Thanks again everyone,
> > Aaron.
> >
> > On 10/23/12, Alexandre Dufour <
[hidden email]> wrote:
> > > Dear Aaron,
> > >
> > > I second Birgit's opinion. With little to no programming knowledge, you
> > > might want to look towards 100% graphical alternatives to start from.
> > >
> > > Our lab develops the ImageJ-friendly Icy software, which specifically
> > > targets (among others) our collaborators with no programming knowledge,
> > by
> > > providing a graphical front-end (called 'Protocols',
> > >
http://icy.bioimageanalysis.org/plugin/Protocols) to create entire
> image
> > > processing workflows (you can think of this as a graphical batch) by
> > > graphically assembling image processing blocks, one after the other
> (not
> > > unlike solutions like Blender or Labview), and this might also fit with
> > what
> > > you are searching for.
> > >
> > > The current interface lets you run all Icy plugins, and with minimal
> > > programming, you can add your own blocks to the system and go from
> there.
> > > Also, since ImageJ is provided inside Icy, I'm currently writing the
> > wrapper
> > > to let ImageJ plugins available for insertion in these workflows as
> well.
> > >
> > > Hope these opinions will enlighten your horizon !
> > >
> > > All the best,
> > > Alexandre
> > >
> > > ---
> > > Alexandre Dufour, PhD
> > > Institut Pasteur, Quantitative Image Analysis Unit,
> > bioimageanalysis.org
> > > IEEE BISP Tech. Committee,
> > > signalprocessingsociety.org/technical-committees/list/bisp-tc
> > > 25-28 rue du Dr. Roux, 75724 Paris cedex 15
> > > ---
> > >
> > > On 23 oct. 2012, at 09:52, Birgit Möller wrote:
> > >
> > >> Hi Aaron,
> > >> I agree with Herbie and the others that without any programming
> > experience
> > >> your plans sound quite ambigious. Even for using the macro language,
> as
> > >> Herbie stated, basic programming skills are unevitable, and it will
> > take a
> > >> considerable amount of time to learn how to use it effectively.
> However,
> > >> as you stated that a graphical user interface is very important for
> > you, I
> > >> would like to point you to another option. The new ImageJ 2.0 and
> > likewise
> > >> our own library called 'Alida' (
> >
http://www.informatik.uni-halle.de/alida)
> > >> both provide functionality for automatically generating user
> interfaces
> > >> for processing units, i.e. plugins in ImageJ 2.0 and so-called
> operators
> > >> in Alida. These GUIs allow for example to configure certain
> parameters,
> > >> i.e. to set directory paths or check options, and to finally run the
> > >> operator/plugin. Alida is compatible with ImageJ, i.e. Alida operators
> > can
> > >> be run within ImageJ/ImageJ 2.0. Of course, for using both systems
> again
> > >> programming knowledge in terms of plain Java is strongly required!
> But,
> > at
> > >> least in case of Alida the overall goal of that library is exactly to
> > >> overcome the need of GUI programming in algorithm development. GUIs
> (and
> > >> also corresponding commandline tools) are directly available for each
> > >> operator implemented based on Alida, and this operator can also be
> used
> > >> within ImageJ. This post is of course not the ultimate answer to your
> > >> question, but just gives you another idea of available options - if
> you
> > >> are really willing to start programming in ImageJ.
> > >> Best,
> > >>
> > >> Birgit
> > >>
> > >>
> > >> On Tue, 23 Oct 2012 08:52:15 +0200, Herbie <
[hidden email]> wrote:
> > >>
> > >>> Aaron,
> > >>>
> > >>> without considerable experience with Java, I see no chance that you
> > come
> > >>> up with what you are aiming for. Of course, you may get some plug-ins
> > >>> working but they will only be parts of your big project and it will
> > take
> > >>> quite a while until they are of professional quality, i.e. efficient
> > and
> > >>> mostly flawless.
> > >>>
> > >>> That said, I should like to recommend learning the IJ-macro language
> > >>> which provides some GUI-support that may suffice for your goals.
> > >>>
> > >>> For instance, I've created a rather extended system with GUI (a
> > >>> commercial product) for the simulation of digital camera front-ends
> > that
> > >>> includes the properties of the optics, the optical low-pass and the
> > >>> sensor, all written as IJ-macros. Because the time-critical parts are
> > >>> IJ-routines, operational speed is sufficient and won't be much higher
> > if
> > >>> programmed in Java.
> > >>>
> > >>> For a beginner, a comparable system will take many month to program
> and
> > >>> especially to test and to refine, when using the IJ-macro language.
> > >>>
> > >>> I hope that the above will help with estimating the required effort
> in
> > >>> your case.
> > >>>
> > >>> Best
> > >>>
> > >>> Herbie
> > >>> _________________________
> > >>> On 23.10.12 00:53, Aaron Hendrickson wrote:
> > >>>> Thank you all for your responses so far. To answer your question
> > Adam,
> > >>>> I
> > >>>> am an engineer for a goverment facility that uses a large volume of
> > >>>> imaging
> > >>>> devices (high-speed, infrared, etc) a big issue within our
> community
> > to
> > >>>> to
> > >>>> standardize a series of proceures for evaluating/verifying the
> > >>>> performance
> > >>>> of the electro-optical devices. As a result of extensive research,
> I
> > >>>> have
> > >>>> created a series of testing procedures for performing these
> > >>>> experiments.
> > >>>> The reason why I am trying to work towards a user friendly gui that
> > >>>> the
> > >>>> user can interact with is because the goal I am aiming towards is to
> > >>>> provide to several other similar facilities a program to use in
> > >>>> evaluating
> > >>>> their own imaging devices. I figured this would make it a lot
> easier
> > >>>> to
> > >>>> use (and a lot more work for me!). One reason why I have stuck with
> > >>>> imageJ
> > >>>> is because the document I wrote is specifically geared towards using
> > >>>> image
> > >>>> to processing and measuring all my test images. Another major
> reason
> > >>>> is
> > >>>> that ImageJ is open source and could be distributed to any facility
> > >>>> that
> > >>>> wanted it for free. The general consensus is that this would be a
> > huge
> > >>>> undertaking for someone like myself with virtually no background in
> > >>>> programming.....and the consensus is right. I figured it would be a
> > lot
> > >>>> of
> > >>>> work but I would figure it out on my own (unlikely). Anyways, I
> would
> > >>>> be
> > >>>> more than glad to provide some of the procedures to the list to view
> > if
> > >>>> anyone is curious in attempting to help me with this. I opted not
> to
> > >>>> ask
> > >>>> list members to help me tackle this because I felt like it was too
> big
> > >>>> of
> > >>>> a project to simply ask people to help me do. Plus I find ImageJ to
> > be
> > >>>> a
> > >>>> very useful resource for image processing and I would love to learn
> > how
> > >>>> to
> > >>>> write quality plugins for extending its capabilities. But I realize
> > >>>> this
> > >>>> dream is a long way down the road if I go that route. Anyways that
> my
> > >>>> long
> > >>>> drawn out story. Any thoughts?
> > >>>>
> > >>>
> > >>>> On Mon, Oct 22, 2012 at 5:56 PM, Adam Hughes<
[hidden email]
> >
> > >>>> wrote:
> > >>>>
> > >>>>> IMHO, this would be a larger undertaking than you're probably
> > >>>>> anticipating
> > >>>>> at this point, especially with no GUI programming background.
> > >>>>>
> > >>>>> Why is it that you think the GUI would be helpful? If you
> elaborate
> > >>>>> some
> > >>>>> more on the project you are trying to achieve, it may be possible
> for
> > >>>>> some
> > >>>>> of the list to give you ideas on how to do this within the confines
> > of
> > >>>>> ImageJ, and its default GUI.
> > >>>>>
> > >>>>> On Mon, Oct 22, 2012 at 3:01 PM, Aaron Hendrickson<
>
[hidden email]
> > >>>>>> wrote:
> > >>>>>
> > >>>>>> Hi everyone,
> > >>>>>>
> > >>>>>> I am doing a lot of work with radiometric performance testing of
> > >>>>>> electro-optical systems. In short I capture large sets of test
> > >>>>>> images
> > >>>>> from
> > >>>>>> the imaging devices I want to characterize and then perform all
> the
> > >>>>>> data
> > >>>>>> reduction processing, and measurements using ImageJ. While ImageJ
> > >>>>>> has
> > >>>>> been
> > >>>>>> an amazing software for doing all my data reduction, the one
> problem
> > >>>>>> I
> > >>>>> have
> > >>>>>> ran into the large amount of time it takes me to do all the data
> > >>>>> reduction
> > >>>>>> by hand. Most of the data reduction I am referring to is creating
> > >>>>>> master
> > >>>>>> images from large image stacks (for example creating a median or
> > mean
> > >>>>>> master image from a stack of 200 test images). Anyways, after
> > >>>>>> looking
> > >>>>>> around online I stumbled into the custom version of ImageJ known
> as
> > >>>>>> AstroImageJ and quickly realized this is exactly what I need. The
> > >>>>>> goal I
> > >>>>>> need to work towards is creating a set of custom plugins for doing
> > all
> > >>>>>> my
> > >>>>>> image processing and making a user friendly gui which can be used
> by
> > >>>>> many.
> > >>>>>> So to my question......I have no programming background and am
> > trying
> > >>>>>> to
> > >>>>>> learn how to write ImageJ plugins and create a gui from which I
> can
> > >>>>> select
> > >>>>>> directories where my test images are located and allow the user to
> > >>>>>> check
> > >>>>>> off checkboxes for each type of test they want to perform (by the
> > >>>>>> way....many of the processing procedures I am doing originated
> from
> > >>>>>> astronomy and are seen in astroImageJ). I know this is a rather
> > >>>>>> enormous undertaking for someone with little programming language
> > and
> > >>>>>> am
> > >>>>>> not sure where to start. I purchased the "Digital Image
> Processing"
> > >>>>>> book
> > >>>>>> by Burger and Burge which helps teach the reader writing plugins
> in
> > >>>>> ImageJ,
> > >>>>>> however I don't have a good enough background to actually use this
> > >>>>>> book.
> > >>>>>> Does anyone have any suggestions for me to get started? This is
> a
> > >>>>>> challenging situation for me because I know all the processing
> > >>>>>> pipelines
> > >>>>> I
> > >>>>>> need to perform but no way to implement it in a time friendly
> > manner.
> > >>>>> Any
> > >>>>>> suggestions would be greatly appreciated.
> > >>>>>>
> > >>>>>> Thanks,
> > >>>>>>
> > >>>>>> Aaron.
> > >>>>>>
> > >>>>>> --
> > >>>>>> 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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