: RE File type on Mac

[Goldsmith, Noel]

Hi,
I hope this is not off topic.
For some time I have been having problems with the file type and automatic
assignment of such on OSX.
We take images using the Spot software (Diagnostic Instruments) and tick the
box for producing files of .tif and of type IMAG (but on OSX this last is a
fiction I guess).
When I select a file and double click it it will open in Preview.
When I option click or right click it will then allow me to select ImageJ in
"other" as the desired application.
How do I get ImageJ to appear in the list of default applications?
There must be a way, as many other applications appear in the list, whereas
ImageJ must be found by ticking other.
Then, once the file is "typed" by this action, the icon changes to a bare
document icon and the image will open in ImageJ iff  double clicked.
Any information will be useful.
Noel

--
Noel Goldsmith
DSTO
506 Lorimer Street
Port Melbourne
Victoria
Australia
3207

Phone [phone]
Mobile [phone]
Fax   [phone]
Email [hidden email]



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[Shane Harding-2]

I have been having trouble with OSX Leopard. On occasion when I use  
the file>import>image sequence command the program crashes. I have the  
RAM limit set to 1000MB (on a 2GB intel machine) with 2 threads.  
Usually I am opening ~75 image planes. Has anyone else had a similar  
problem? Any fixes?

Thank you,
Shane


On 18-Jan-08, at 12:17 AM, Goldsmith, Noel wrote:

> Hi,
> I hope this is not off topic.
> For some time I have been having problems with the file type and  
> automatic
> assignment of such on OSX.
> We take images using the Spot software (Diagnostic Instruments) and  
> tick the
> box for producing files of .tif and of type IMAG (but on OSX this  
> last is a
> fiction I guess).
> When I select a file and double click it it will open in Preview.
> When I option click or right click it will then allow me to select  
> ImageJ in
> "other" as the desired application.
> How do I get ImageJ to appear in the list of default applications?
> There must be a way, as many other applications appear in the list,  
> whereas
> ImageJ must be found by ticking other.
> Then, once the file is "typed" by this action, the icon changes to a  
> bare
> document icon and the image will open in ImageJ iff  double clicked.
> Any information will be useful.
> Noel
>
> --
> Noel Goldsmith
> DSTO
> 506 Lorimer Street
> Port Melbourne
> Victoria
> Australia
> 3207
>
> Phone [phone]
> Mobile [phone]
> Fax   [phone]
> Email [hidden email]
>
>
>
> IMPORTANT: This email remains the property of the Australian Defence  
> Organisation and is subject to the jurisdiction of section 70 of the  
> CRIMES ACT 1914.  If you have received this email in error, you are  
> requested to contact the sender and delete the email.

[Ben Tupper]

On Jan 18, 2008, at 12:17 AM, Goldsmith, Noel wrote:

> Hi,
> I hope this is not off topic.
> For some time I have been having problems with the file type and  
> automatic
> assignment of such on OSX.
> We take images using the Spot software (Diagnostic Instruments) and  
> tick the
> box for producing files of .tif and of type IMAG (but on OSX this  
> last is a
> fiction I guess).
> When I select a file and double click it it will open in Preview.
> When I option click or right click it will then allow me to select  
> ImageJ in
> "other" as the desired application.
> How do I get ImageJ to appear in the list of default applications?
> There must be a way, as many other applications appear in the list,  
> whereas
> ImageJ must be found by ticking other.
> Then, once the file is "typed" by this action, the icon changes to  
> a bare
> document icon and the image will open in ImageJ iff  double clicked.
> Any information will be useful.
> Noel
>

Hello,

My experience is almost exclusively with MacOS 10.4(ish).

Diagnostic Instruments makes a TWAIN interface for ImageJ called  
"Third Party" that will deliver acquired images immediately to  
ImageJ.  We have never been that wowed by "Third Party", but it does  
what it advertises.

If you want to TIFFs to be opened by ImageJ in general then you  
should be able to select any TIFF file in the Finder, then mouse your  
way to File>GetInfo and then change the association in the window  
that appears.  You have the option to associate all TIFFs with  
whatever application you select.  In general this works, but I still  
find that some software packages (especially text file handlers) tend  
to ignore that.

Hope this info is helpful,
Ben

P.S. Hi to Andrew Cool if you know him!

Ben Tupper
[hidden email]

I GoodSearch for Ashwood Waldorf School.

Raise money for your favorite charity or school just by searching the  
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[lechristophe]

If you need a very granular control over file type associations in OSX, I
suggest you use the RCDefaultApp preference panel :
http://rubicode.com/Software/RCDefaultApp/
It is an add-on to the System Properties pref panel, allowing you to specify
application for files, MIME types, and even URLs, and is more strict than
OSX which often "forgets" the application you chose, reverting to some of
it's core app like preview, safari, etc.

Christophe

On Jan 21, 2008 1:35 AM, Ben Tupper <[hidden email]> wrote:

> On Jan 18, 2008, at 12:17 AM, Goldsmith, Noel wrote:
>
> > Hi,
> > I hope this is not off topic.
> > For some time I have been having problems with the file type and
> > automatic
> > assignment of such on OSX.
> > We take images using the Spot software (Diagnostic Instruments) and
> > tick the
> > box for producing files of .tif and of type IMAG (but on OSX this
> > last is a
> > fiction I guess).
> > When I select a file and double click it it will open in Preview.
> > When I option click or right click it will then allow me to select
> > ImageJ in
> > "other" as the desired application.
> > How do I get ImageJ to appear in the list of default applications?
> > There must be a way, as many other applications appear in the list,
> > whereas
> > ImageJ must be found by ticking other.
> > Then, once the file is "typed" by this action, the icon changes to
> > a bare
> > document icon and the image will open in ImageJ iff  double clicked.
> > Any information will be useful.
> > Noel
> >
>
> Hello,
>
> My experience is almost exclusively with MacOS 10.4(ish).
>
> Diagnostic Instruments makes a TWAIN interface for ImageJ called
> "Third Party" that will deliver acquired images immediately to
> ImageJ.  We have never been that wowed by "Third Party", but it does
> what it advertises.
>
> If you want to TIFFs to be opened by ImageJ in general then you
> should be able to select any TIFF file in the Finder, then mouse your
> way to File>GetInfo and then change the association in the window
> that appears.  You have the option to associate all TIFFs with
> whatever application you select.  In general this works, but I still
> find that some software packages (especially text file handlers) tend
> to ignore that.
>
> Hope this info is helpful,
> Ben
>
> P.S. Hi to Andrew Cool if you know him!
>
> Ben Tupper
> [hidden email]
>
> I GoodSearch for Ashwood Waldorf School.
>
> Raise money for your favorite charity or school just by searching the
> Internet with GoodSearch - www.goodsearch.com - powered by Yahoo!
>

[Joachim Wesner]

Hi group,

I just discovered that somebody is starting a new ImageJ branch called
"ImageJ2x", which seems to be somewhat incompatible (Plugins must
use/extend Swing).

http://www.rawak.de/ij2x/doc/index.html

Is this really necessary? What are the real benefits? Can somebody comment
on this? I do not want to follow the development on 2 incompatible
branches!


Mit freundlichen Grüßen / Best regards

Joachim Wesner
Projektleiter Optik Technologiesysteme

____________________________________________

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Träger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis


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[Gabriel Landini]

On Monday 21 January 2008 08:57:25 Joachim Wesner wrote:

> I just discovered that somebody is starting a new ImageJ branch called
> "ImageJ2x", which seems to be somewhat incompatible (Plugins must
> use/extend Swing).
> http://www.rawak.de/ij2x/doc/index.html
>
> Is this really necessary?

Hmm... not, if you asked me...

> What are the real benefits?  

Mostly aesthetic, I guess? (not a priority for me).
Do you know who is maintaining it?

Regards,

Gabriel

[Michael Schmid]

Hi Joachim, Gabriel,

this seems to be based on a pretty old version of ImageJ, 1.36
or so, with a quite a few bugs added.

Possibly it was an attempt to convert ImageJ to swing for
handling images - there have wishes for a swing version a few
times in the mailinglist.

Michael
________________________________________________________________

On 21 Jan 2008, at 10:40, Gabriel Landini wrote:

> On Monday 21 January 2008 08:57:25 Joachim Wesner wrote:
>
>> I just discovered that somebody is starting a new ImageJ branch  
>> called
>> "ImageJ2x", which seems to be somewhat incompatible (Plugins must
>> use/extend Swing).
>> http://www.rawak.de/ij2x/doc/index.html
>>
>> Is this really necessary?
>
> Hmm... not, if you asked me...
>
>> What are the real benefits?
>
> Mostly aesthetic, I guess? (not a priority for me).
> Do you know who is maintaining it?
>
> Regards,
>
> Gabriel

[dscho]

Hi,

On Mon, 21 Jan 2008, Joachim Wesner wrote:

> I just discovered that somebody is starting a new ImageJ branch called
> "ImageJ2x", which seems to be somewhat incompatible (Plugins must
> use/extend Swing).
>
> http://www.rawak.de/ij2x/doc/index.html
>
> Is this really necessary? What are the real benefits? Can somebody
> comment on this? I do not want to follow the development on 2
> incompatible branches!

AFAICT you need not bother with ij2x:

- there was no announcement on this list,

- the source is apparently not available,

- as you say, it is incompatible.

Note: I have the source for converting ImageJ to use Swing instead of AWT
somewhere, and when I find the time, I will upload it as a branch to
ImageJA.

But my hunch is that using Swing will only lead to problems (remember all
those questions why Swing and AWT do not play nicely together?)

Ciao,
Dscho

[Joachim Wesner]

Hi there,

I know this has been already been discussed in this list, but I do notseem
to find the info I´m interested in, resp. maybe what I want to acchieve is
simply not possible....

Up to now, I have exclusively used the built in Editor and compiler
mechanism of ImageJ to develop small to medium size plugins, which works
quite well. However, for more complex plugins,
having at hand a more complex IDE and debugger would be great. There are
quite a lot of HOWTOs to use Eclipse for this, I also managed to compile
and run ImageJ with JCreator, for example. So far so good.

However, if I understand correctly, using an external IDE like Eclipse for
plugin development effectively mean restarting ImageJ everytime I change my
code, RIGHT? So I am forced to reload any data, stacks, ROis etc,
I need to test my plugin!?

I consider this a BIG minus, one of the advantages of the built-in solution
actually IMHO is that I can leave the windows with my test cases open all
the time.

Is there a way to do this with an external IDE/debugger? Somehow to
"attach" to the already running Imagej process?


Mit freundlichen Grüßen / Best regards

Joachim Wesner
____________________________________________

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Träger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis


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[dscho]

Hi,

On Mon, 21 Jan 2008, Joachim Wesner wrote:

> Is there a way to do this with an external IDE/debugger? Somehow to
> "attach" to the already running Imagej process?

From a quick search, it seems that you can attach to an existing JVM
process only if you started it in a special way.  See e.g.

        http://jswat.sourceforge.net/howto-applet.shtml

To your other question: the only way I see to debug another version of a
plugin without restarting ImageJ is to load the new version of the
class(es) like the internal "Compile & Run..." does.

Though I have no idea if JSwat (or other debuggers) would get confused,
now having _two_ implementations of the same class.

However, I think you'd need support code in ImageJ proper if you want to
have a breakpoint when the run() method (or setup()) is entered...

A trick that _might_ work is to call "Compile & Run" on the .class that
you generated in Eclipse (_with_ debugging information, please), but
having set a breakpoint before, at IJ.runUserPlugIn() just after the line

        thePlugIn = (loader.loadClass(className)).newInstance();

Hth,
Dscho

[Albert Cardona]

Hi Joachim,

> However, if I understand correctly, using an external IDE like Eclipse for
> plugin development effectively mean restarting ImageJ everytime I change my
> code, RIGHT? So I am forced to reload any data, stacks, ROis etc,
> I need to test my plugin!?
>
> I consider this a BIG minus, one of the advantages of the built-in solution
> actually IMHO is that I can leave the windows with my test cases open all
> the time.
>
> Is there a way to do this with an external IDE/debugger? Somehow to
> "attach" to the already running Imagej process?
>  

The best way I've found is to use Jython instead of Java: dynamically
interpreted language,
as powerful (or more) than java itself.

After setting Jython up, just include it's jar in ImageJ's classpath,
and install the Jython Utilities from my webpage.

Then:

- edit a .py text file from any editor you want
- run it as many times as you want, within the same running ImageJ instance
  just by selecting it from the plugin menus. The menu item is just a
place holder for the file path of the script, which is executed  
directly as is and never cached or compiled.

The "Refresh Jython List" will make it appear the first time in the menus.
The only gotcha is to save the file in the plugins/Jython/ directory.

Any changes to the text are immediately available (i.e. no need to
compile and then run,
just run).


Later, either convert the plugin to java source code (using jython's
jythonc compiler),
or just use it like that. If the plugin is mostly high-level, there are
no speed differences.
For speed, just make a pure java class that implements the few methods
that need to do
pixel bit shifting, etc., and call them from your jython script. I
prefer static methods to keep a clean functional programming style, but
that's totally up to you.

Speeds up things enormously.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Jon Harman]

Hi,

I very recently discovered Pendrivelinux.  Although I have a windows
machine, it is easy to run Linux using the Pendrivelinux routines.
I don't have to reboot my machine from a CD or pendrive.  This is a
great way for me to check that my plugin will run on different flavors
of Linux.  Pendrivelinux has Knoppix, Ubuntu, plus others.  So far I
have checked out Knoppix and Ubuntu.  Knoppix can run imagej and my
plugin, no problem, although the look of ImageJ and my plugin leaves
much to be desired.  The Knoppix KDE desktop seems very old fashioned.  
I next tried Ubuntu:
http://www.pendrivelinux.com/2008/01/11/run-ubuntu-710-from-windows/
Seems like a great flavor of Lunix.  For someone used to windows it has
a very modern, intuitive desktop.  But it won't run ImageJ.  Apparently
it does not have Java, but something called gij and this (or the doesn't
support AWT.  I tried loading the ImageJ+jre distribution for Linux but
libjava.so is missing.

Running Linux this way is just great.  The QEMU emulator  is very well
done and is fast!.  Too bad about gij and Ubuntu.

I am a little worried that Java implementations may jettison AWT to save
space.

Jon

[dscho]

Hi,

On Mon, 21 Jan 2008, Jon Harman wrote:

> Apparently it [Pendrivelinux' Ubuntu] does not have Java, but something
> called gij and this (or the doesn't support AWT.

This is GNU's java clone.  It is known that it is slow (does not have a
just-in-time compiler) and that it is not complete.

So there is no surprise here...

Ciao,
Dscho

[Gabriel Landini]

On Monday 21 January 2008, Jon Harman wrote:

> have checked out Knoppix and Ubuntu.  Knoppix can run imagej and my
> plugin, no problem, although the look of ImageJ and my plugin leaves
> much to be desired.

The fonts? or the widget set? icons? or...?
It is possible that knoppix may not have set the best possible graphics mode.

> The Knoppix KDE desktop seems very old fashioned.
Think again :-) :
http://kde.org/announcements/4.0/guide.php
I do not know if knoppix will feature KDE4, though (KDE4 has been just
released and it is still in development stage).

> I next tried Ubuntu:
> http://www.pendrivelinux.com/2008/01/11/run-ubuntu-710-from-windows/

You are comparing the window managers (KDE, Gnome, xfce, etc), One can change
from one to another.

> But it won't run ImageJ.  Apparently  it does not have Java, but something
> called gij and this (or the doesn't  support AWT.  I tried loading the
> ImageJ+jre distribution for Linux but  libjava.so is missing.

It is very likely that you would be able to install Java (and uninstall
whatever it comes with).

For some time I have been thinking that it would be ideal to have a ImageJ
live CD. But for this one needs to carefully choose what to put in and then
maintain it! It is certainly not a job to do alone.

Regards

G.

[Burger Wilhelm]

Joachim,

this is not the case. You can use Eclipse to develop plugins for ImageJ without having to stop ImageJ and leaving test images open all the time. Only in very rare cases I launch ImageJ from within the Eclipse IDE to use its debugging facilities.

Regards,
Wilhelm

http://www.imagingbook.com
 

 

> However, if I understand correctly, using an external IDE
> like Eclipse for
> plugin development effectively mean restarting ImageJ
> everytime I change my
> code, RIGHT? So I am forced to reload any data, stacks, ROis etc,
> I need to test my plugin!?
>
> I consider this a BIG minus, one of the advantages of the
> built-in solution
> actually IMHO is that I can leave the windows with my test
> cases open all
> the time.
>
> Is there a way to do this with an external IDE/debugger? Somehow to
> "attach" to the already running Imagej process?
>
>
> Mit freundlichen Grüßen / Best regards
>
> Joachim Wesner
> ____________________________________________
>
> Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
> Wetzlar  HRB 2432
> Geschäftsführer:  Dr. Stefan Träger | Dr. Wolf-Otto Reuter |
> Dr. David Roy
> Martyr | Colin Davis
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email 
> ______________________________________________________________________
>

[ctrueden]

Hi Jon,

I agree about gij; I have had nothing but bad luck with it. However, Sun's
Java is now open source, and I have not kept up on any recent ramifications
of that (Will gij continue to be developed? Can gij legally use any of Sun's
code? Etc.).

Anyway, the easiest thing to do is to install Sun Java on your Ubuntu box,
with the command:

sudo aptitude install sun-java6-jre

You will need to enable the "multiverse" additional source in your
/etc/apt/sources.list file though. For more information, see <
http://ubuntuguide.org/wiki/Ubuntu:Gutsy#How_to_add_extra_repositories>.

After that you can change which Java (Sun or gij) is the default with the
command:

sudo update-alternatives --config java

HTH,
Curtis

On Jan 21, 2008 1:21 PM, Gabriel Landini <[hidden email]> wrote:

> On Monday 21 January 2008, Jon Harman wrote:
>
> > have checked out Knoppix and Ubuntu.  Knoppix can run imagej and my
> > plugin, no problem, although the look of ImageJ and my plugin leaves
> > much to be desired.
>
> The fonts? or the widget set? icons? or...?
> It is possible that knoppix may not have set the best possible graphics
> mode.
>
> > The Knoppix KDE desktop seems very old fashioned.
> Think again :-) :
> http://kde.org/announcements/4.0/guide.php
> I do not know if knoppix will feature KDE4, though (KDE4 has been just
> released and it is still in development stage).
>
> > I next tried Ubuntu:
> > http://www.pendrivelinux.com/2008/01/11/run-ubuntu-710-from-windows/
>
> You are comparing the window managers (KDE, Gnome, xfce, etc), One can
> change
> from one to another.
>
> > But it won't run ImageJ.  Apparently  it does not have Java, but
> something
> > called gij and this (or the doesn't  support AWT.  I tried loading the
> > ImageJ+jre distribution for Linux but  libjava.so is missing.
>
> It is very likely that you would be able to install Java (and uninstall
> whatever it comes with).
>
> For some time I have been thinking that it would be ideal to have a ImageJ
> live CD. But for this one needs to carefully choose what to put in and
> then
> maintain it! It is certainly not a job to do alone.
>
> Regards
>
> G.
>

[Jon Harman]

Hi,

I am not very familiar with Linux and the various distributions.  So I
apologize for any comments that simply revealed my ignorance.  My
objections to the "look" of ImageJ was due to the fonts and in
retrospect I think they are really OK, just something I was not used
to.  My objections to the KDE environment on Knoppix has to do with the
long list of applications that I found overwhelming, plus the file
chooser that I found to be confusing.   I am sure that as I get more
experience with it I will like it better.  I already like that I can
easily find the Java plugin control panel, something I could not find in
Ubuntu

Jon


Gabriel Landini wrote:
 > On Monday 21 January 2008, Jon Harman wrote:
 >
 >> have checked out Knoppix and Ubuntu.  Knoppix can run imagej and my
 >> plugin, no problem, although the look of ImageJ and my plugin leaves
 >> much to be desired.
 >
 > The fonts? or the widget set? icons? or...?
 > It is possible that knoppix may not have set the best possible
graphics mode.
 >
 >> The Knoppix KDE desktop seems very old fashioned.
 > Think again :-) :
 > http://kde.org/announcements/4.0/guide.php
 > I do not know if knoppix will feature KDE4, though (KDE4 has been just
 > released and it is still in development stage).
 >
 >> I next tried Ubuntu:
 >> http://www.pendrivelinux.com/2008/01/11/run-ubuntu-710-from-windows/
 >
 > You are comparing the window managers (KDE, Gnome, xfce, etc), One
can change
 > from one to another.
 >
 >> But it won't run ImageJ.  Apparently  it does not have Java, but
something
 >> called gij and this (or the doesn't  support AWT.  I tried loading the
 >> ImageJ+jre distribution for Linux but  libjava.so is missing.
 >
 > It is very likely that you would be able to install Java (and uninstall
 > whatever it comes with).
 >
 > For some time I have been thinking that it would be ideal to have a
ImageJ
 > live CD. But for this one needs to carefully choose what to put in
and then
 > maintain it! It is certainly not a job to do alone.
 >
 > Regards
 >
 > G.
 >

[Gabriel Landini]

On Monday 21 January 2008, Jon Harman wrote:
> objections to the "look" of ImageJ was due to the fonts and in
> retrospect I think they are really OK, just something I was not used
> to.

In old versions of suse linux, there were various problems with the fonts in
java apps (so I have agree with you). More recently (the last 2 or 3 versions
I used)  they seem to have resolved all of that.

But have in mind that you can change quite drastically the way the windows
manager looks. There is one very lightweight calle Xfce (you can get ubuntu
with Xfce [xubuntu]) http://www.xubuntu.org/ that would be good for running
from a usb stick.

About fonts, Dscho wrote a little plugin that allows to change the IJ menu
font size (and which I use because the font is too small for me). Just ask if
you need it.

Cheers,

G.

[dscho]

Hi,

On Mon, 21 Jan 2008, Gabriel Landini wrote:

> For some time I have been thinking that it would be ideal to have a
> ImageJ live CD. But for this one needs to carefully choose what to put
> in and then maintain it! It is certainly not a job to do alone.

Heh, you are certainly not the only one thinking about such a thing.  Stay
tuned; I think it'll take about 3-4 weeks until we announce something.

(Yes, this is meant to make you curious...)

Ciao,
Dscho
 

[dscho]

Hi,

On Mon, 21 Jan 2008, Curtis Rueden wrote:

> Sun's Java is now open source, and I have not kept up on any recent
> ramifications of that (Will gij continue to be developed? Can gij
> legally use any of Sun's code? Etc.).

AFAICT Sun's Java (the official distribution, at least) has still this
slightly mind-amputated license.  At least you can redistribute it freely
now.

Only the development versions are GPL (v2 if I remember correctly), but if
you hope to get your changes in, you'll have to sign away your soul.

Having said that, it is much better than it used to be 10 years ago (it
really seemed that they _wanted_ to kill off java; they certainly
succeeded with the Java CPU).

And as I know the GNU people, they will not allow gij to stay GPLv2, but
force it to v3, which is incompatible with GPLv2.  So no, I fully expect
gij to die a slow and painful death, because they failed to be pragmatic
about it and keep GPLv2 so that they could take parts of Sun's Java.

Ciao,
Dscho