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 67 Mobile Fax 68 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. HiI 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 listwhereas 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 67 Mobile Fax 68 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.

HiI 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 listwhereas 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 FileGetInfo 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 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! On Jan 18, 2008, at 12:17 AM, Goldsmith, Noel wrote: HiI 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 listwhereas 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 HelloMy 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 FileGetInfo 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 helpfulBen P.S.

Hi to Andrew Cool if you know him! Ben Tupper 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!. 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). 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. 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. 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.' 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. 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 etcI 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. 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.

Re: (ping: Roy Xfce Applet For Mac Pro

I next tried Ubuntu: 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. 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. Or the widget set? It is possible that knoppix may not have set the best possible graphics mode. The Knoppix KDE desktop seems very old fashioned.

Think again:-): 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: 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. 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?

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. 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 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?

It is possible that knoppix may not have set the best possible graphics mode. The Knoppix KDE desktop seems very old fashioned. Think again:-): 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: 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. 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? It is possible that knoppix may not have set the best possible graphics mode.

The Knoppix KDE desktop seems very old fashioned. Think again:-): 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: 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.

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) 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. 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? 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 1.