Install Issues - ImageJ and FIJI

[Robert Baer]

I have a clean Windows 8 machine and want to report some minor FIJI and  
ImageJ Installation issues.  I installed to E:\ rather than C:\.  I
think they are generic, but one never knows ...
*
**FIJI**- Download using Windows 64-bit link*

  * I have both 32-bit and 64-bit Java Java 7, Update 11 installed on my
    machine.  My native screen resolution is 1920 x 1080 and have the
    magnifier at 150%.  When I start FIJI the main window looks great.
    If I rename the Java directory of FIJI, so that it uses the new
    Java, the FIJI main window is very much smaller -- too small for
    these old eyes.  Not sure what compatibility issues are across Java
    versions.  Note that FIJI DOES find the 64-bit version of Java 7,
    Update 11 according to Help About.
  * For some time now, the icon for FIJI is replaced with the generic
    ICON.  Further, there is no Fiji.ico file in the Images file that
    the user can use manually, The user must create their own .ico with
    GIMP or some other program from the supplied .png file.  I think the
    .ico used to be a resource in the .exe which let it appear
    automatically.. (I believe this problem also exists on Windows 7 and
    has to do with the resource no longer being available).  Having this
    icon was nice  Even retaining the vanilla ImageJ icon would be
    superior to having no icon resource.

*Vanilla ImageJ -- downloaded for 64-bit Windows with Java Included*

  * After ImageJ installs it goes through a startup than involves
    creating the .cfg file.  When it is done it pops up a diagol from
    opener which says "File is not in a supported format, a reader
    plugin is not available, or it was not found. E:\Program
    Files\Files\ImageJ"  ImageJ 1.46r.   This message repeats even if I
    choose JFileChooser in input/output. The problem seems related to my
    installation on E: drive, because if I install instead on c:\, the
    problem does not occur.  Because of limited space on c: i would
    rather not do this.  The issue does not keep ImageJ from opening
    sample images and functionality seems otherwise normal.
  * In the process of trouble-shooting bullet I I tried to do an ImageJ
    unitstalle.  I got the following message "Internal Error: Cannot
    find utCompileCode for this version of uninsaller"  I have not
    tracked this down yet, but I got the same message even after
    reinstalling on C:\ drive.  Again, this might relate to having moved
    some user folders from C: to E:, but that remains to be determined.
  * It would be nice to have a version without the JRE for those with
    Java already installed, but when I rename the JRE subdirectory,
    ImageJ only find the 32-bit version of Java and not the 64-bit
    version of Java that is installed on  my machine.  I don't know if
    this an issue with the .cfg file that I can change.  Still working
    on that part, but it would be nice if this happened automatically.
    FIJI did find the 64-bit version so there is a difference in
    approach here.
  * When I start ImageJ the main panel is very small at my current
    screen resolution even when using the 1.6 version of Java contained
    in the JRE folder that comes with ImaageJ.  Again, this differs from
    FIJI with the same Java version, but it is similar to FIJI behavior
    if I let FIJI use my installed Java 7.

I should emphasize that none of these issues are show-stoppers for using
ImageJ, and I'm grateful to all the hard work done by the developers!  
Hope the feedback is useful.

Rob

--
Robert W. Baer, Ph.D.
Department of Physiology
Kirksville College of Osteopathic Medicine
A. T. Still University of Health Sciences
Kirksvi a generlle, MO 63501


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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Robert,

On Tue, 22 Jan 2013, Robert Baer wrote:

> I have a clean Windows 8 machine and want to report some minor FIJI and
> ImageJ Installation issues.  I installed to E:\ rather than C:\.  I
> think they are generic, but one never knows ...  *
> **FIJI**- Download using Windows 64-bit link*
>
>  * I have both 32-bit and 64-bit Java Java 7, Update 11 installed on my
>    machine.  My native screen resolution is 1920 x 1080 and have the
>    magnifier at 150%.  When I start FIJI the main window looks great. If I
>    rename the Java directory of FIJI, so that it uses the new
>    Java, the FIJI main window is very much smaller -- too small for
>    these old eyes.  Not sure what compatibility issues are across Java
>    versions.  Note that FIJI DOES find the 64-bit version of Java 7,
>    Update 11 according to Help About.

This might be an issue with Java 7, or with Windows 8. Can you please file
a bug report at http://fiji.sc/bugzilla/ so that the issue is not
forgotten?

>  * For some time now, the icon for FIJI is replaced with the generic
>    ICON.

Which icon do you mean? The one attached to ImageJ-win64.exe? Or the icon
in the task bar? Or when switching windows with Alt+Tab? Or the one in the
upper left corner of the main window? And again, could you file a bug
report? You could even attach a screenshot displaying the issue...

Thanks,
Johannes

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Yisong Zhen]

Hi, Robert,

you can use this online tool to generate icon.
http://www.icoconverter.com/

In win8, Fiji does miss the icon for desktop.


And when I update  Fiji in win8, there is an error which said that
" java.io.IOException: The system can not find the path specified."

Yisong

On Sat, Feb 2, 2013 at 6:58 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Robert,
>
> On Tue, 22 Jan 2013, Robert Baer wrote:
>
> > I have a clean Windows 8 machine and want to report some minor FIJI and
> > ImageJ Installation issues.  I installed to E:\ rather than C:\.  I
> > think they are generic, but one never knows ...  *
> > **FIJI**- Download using Windows 64-bit link*
> >
> >  * I have both 32-bit and 64-bit Java Java 7, Update 11 installed on my
> >    machine.  My native screen resolution is 1920 x 1080 and have the
> >    magnifier at 150%.  When I start FIJI the main window looks great. If
> I
> >    rename the Java directory of FIJI, so that it uses the new
> >    Java, the FIJI main window is very much smaller -- too small for
> >    these old eyes.  Not sure what compatibility issues are across Java
> >    versions.  Note that FIJI DOES find the 64-bit version of Java 7,
> >    Update 11 according to Help About.
>
> This might be an issue with Java 7, or with Windows 8. Can you please file
> a bug report at http://fiji.sc/bugzilla/ so that the issue is not
> forgotten?
>
> >  * For some time now, the icon for FIJI is replaced with the generic
> >    ICON.
>
> Which icon do you mean? The one attached to ImageJ-win64.exe? Or the icon
> in the task bar? Or when switching windows with Alt+Tab? Or the one in the
> upper left corner of the main window? And again, could you file a bug
> report? You could even attach a screenshot displaying the issue...
>
> Thanks,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Yisong,

On Sat, 2 Feb 2013, Yisong Zhen wrote:

> you can use this online tool to generate icon.
> http://www.icoconverter.com/

Fiji can save .ico files with File>Save As>Ico...

> In win8, Fiji does miss the icon for desktop.

See my reply to Robert.

> And when I update  Fiji in win8, there is an error which said that
> " java.io.IOException: The system can not find the path specified."

Please file a bug report via http://fiji.sc/bugzilla/ or with Fiji's
built-in Help>Report a Bug. In particular, please describe which files
Fiji tried to update and a full stacktrace (that's the block of lines
under the IOException which might look like gibberish to you but which is
really helpful for me to identify the exact issue) would be nice.

Also, make sure that the bug report includes the path where you unpacked
Fiji.

Thanks,
Johannes

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Robert,

On Fri, 1 Feb 2013, Robert Baer wrote:

> I'll work on bug report for the Win8/Java7 issue

Thank you very much!

> The icon bug is probably replicates bug report 526 by another user, so I
> won't file an additional report, but I will answer your direct question
> here.

A comment on the bug would be more visible (read: open) to others, but
okay.

> Just to quickly follow up on the icon thing (which is a tiny issue), I
> mean the icon associated with ImageJ-win64.exe .  The program has a
> generic desktop look in the folder.

Yes, ImageJ-win64.exe always was without icon. Only the Fiji launcher has
an icon. The reason is that ImageJ-win64.exe is supposed to be more
general purpose: it is intended to be *the* ImageJ launcher. It can launch
ImageJ 1.x, it can launch Fiji and it can launch ImageJ2. It can do so on
Linux (i386/x86_64), Windows (i386/x86_64) and MacOSX (PPC32/i386/x86_64).
In my tests, it was even easy to build and launch it on FreeBSD. It is
written in portable C and offers the exact same user experience on all
those platforms.

> It's been since the dark ages since I've done serious programming, but I
> think that icons could be associated with .exe files from resource files
> at either compile or link time (I forget).

It is both compile and link time; you have to compile an .rc file which
looks pretty much like this:

        101 ICON images/fiji.ico

This files needs to be compiled with the 'windres' program, not with the C
compiler. Then the resulting .o file needs to be linked into the
executable.

There are some programs to change the icon in existing .exe files, some of
them even claiming to run on the command-line (which would be needed for
us since we do not want to build everything by hand; our launchers are
built for all the supported platforms automatically as soon as the source
code has changed in the public source code repository; that way, I cannot
forget to compile it for one platform). The only one which worked for me
is RCEDIT.exe from the WinRun4J project:
https://github.com/poidasmith/winrun4j/

It is this program we use in our Jenkins job called
'Windows-Fiji-launcher-with-icons' whose sole purpose is to take the
ImageJ launchers for 32-bit and 64-bit Windows and equip them with icons.
The resulting Fiji launchers are really just the ImageJ launchers with a
Fiji icon, and they can be downloaded from here:

        http://jenkins.imagej.net/job/Windows-Fiji-launcher-with-icons/label=Windows/lastSuccessfulBuild/artifact/

Of course, you could use RCEDIT.exe or any other resource hacker to insert
your own icon into the launcher, but there is a subtle issue with that:
the ImageJ-win64.exe file is managed by the updater, and if you modify
that, you will not get updates (even critical ones) automatically.

It is better to download the respective Fiji launcher, however, you could
just do the same using the advanced mode of the updater, since the Fiji
launcher *is* still in the updater (but updated less regularly than the
ImageJ updater).

Now, why does the Fiji distribution bundle the ImageJ launcher, rather
than the Fiji one (i.e. the ImageJ launcher with icon attached)?

The problem is confusion. You would not believe how often I hear: "but I
want to use ImageJ, not Fiji!". Seriously, the intention of the bunch of
people starting the Fiji project was never to make a separate software,
even if the name may suggest so. The strong desire was to contribute
something useful back to the community that is so helpful, and personally,
I never even wanted to use a different name than ImageJ. So it does affect
me a lot when users confuse Fiji for something separate from ImageJ.

To help the situation, we figured that making clear that Fiji is just a
distribution of ImageJ by using the ImageJ launcher directly would make
sense.

If you have an idea how to address the problem more properly, please let
me know!

>  When I first used Fiji, it had a FIJI icon that looked like the images
>  in my C:\Fiji.app\images directory.  As Fiji now distributes, I get a
>  generic icon that results from the OS not finding one within the .exe
>  file.  There are two image in that folder, C:\Fiji.app\images that seem
>  similar to the Fiji icon I used to get.  If I load the icon.png into
>  GIMP and save it as Fiji.ico, I get an icon that serves my icon
>  purposes nicely for desktop shorcut purposes.  If its too hard to bind
>  the resource to the .exe, it would be nice to not at least not have to
>  regenerate a .ico file for each computer I install Fiji on.

The .ico file is available pre-generated here:

        https://github.com/fiji/fiji/raw/master/images/fiji.ico

It was made using the original script to make the Fiji launcher which used
Fiji's File>Save As>Ico... to write an .ico file.

Ciao,
Johannes

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