ImageJ File->Import->URL Issue, any help appreciated

[Rob Lewis]

While trying to import a dicom file from a URL, (Through the UI or
programatically), i receive the following error in a dialog box named 'Dicom
Decoder':

java.io.IOException
Resetting to invalid mark

I can open the same file locally from the harddisk in imagej using
File->Open. This only happens with some Dicom files.

I have tried 1.41, and the latest daily build of 1.42i.

I am sorry if this already has been discussed, as i have just joined the
mailing list. Any help or pointers would be appreciated!

-Rob

[dscho]

Hi,

On Tue, 10 Feb 2009, Rob Lewis wrote:

> While trying to import a dicom file from a URL, (Through the UI or
> programatically), i receive the following error in a dialog box named 'Dicom
> Decoder':
>
> java.io.IOException
> Resetting to invalid mark

Typically, this error occurs when reading from a stream (which is the
result of opening a URL) but trying to go back to the beginning somewhere
in the middle.

I do not have any experience with the DICOM format, but I imagine that you
have that problem here, and that you need the file locally.  Or you need
to inspect the source (you did not mention which plugin, if any, you use
to open the files) to find out where it tries to "seek" (that is "going
back in a file" is called in computer speak).

Ciao,
Dscho

[John Oreopoulos]

I am trying to use the ImageJ 3D viewer plugin but I'm finding I  
can't load any volume stacks, not even the example stack that is  
provided on the plugin website. I made sure that Java 3D is working  
on my Mac. Does anyone else have any issues getting this plugin to  
work? I'm using the latest version ImageJ, version 1.42h

John Oreopoulos

[dscho]

Hi,

On Tue, 10 Feb 2009, John Oreopoulos wrote:

> I am trying to use the ImageJ 3D viewer plugin but I'm finding I can't
> load any volume stacks, not even the example stack that is provided on
> the plugin website. I made sure that Java 3D is working on my Mac. Does
> anyone else have any issues getting this plugin to work? I'm using the
> latest version ImageJ, version 1.42h

It would be helpful if you described in just a tiny little bit more detail
what exactly is happening.  Nothing?  Does a window pop up with a message?  
What does the Console (/Applications/Utilities/Console) say?  What version
of Java3D do you have?  Does Fiji's 3D viewer work?

Ciao,
Dscho

[Rob Lewis]

So is this expected behavior? It still bothers me it works with some dicom
files and not others. I do not have access to the file locally as i am using
imagej in an applet to view dicom files over the web (which imagej has to
import from a exposed URL).

I am not using any plugins. I am only using ij.jar. I am not sure i have the
experience necessary to debug through the ImageJ code, but i can try (if i
can get the it loaded in eclipse somehow).

-Rob

On Tue, Feb 10, 2009 at 4:35 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Tue, 10 Feb 2009, Rob Lewis wrote:
>
> > While trying to import a dicom file from a URL, (Through the UI or
> > programatically), i receive the following error in a dialog box named
> 'Dicom
> > Decoder':
> >
> > java.io.IOException
> > Resetting to invalid mark
>
> Typically, this error occurs when reading from a stream (which is the
> result of opening a URL) but trying to go back to the beginning somewhere
> in the middle.
>
> I do not have any experience with the DICOM format, but I imagine that you
> have that problem here, and that you need the file locally.  Or you need
> to inspect the source (you did not mention which plugin, if any, you use
> to open the files) to find out where it tries to "seek" (that is "going
> back in a file" is called in computer speak).
>
> Ciao,
> Dscho
>

[Joris FA Meys]

It's pretty easy to debur in Eclipse actually. Check the tutorial of Mica
Kimo Johnson :
http://www.cs.dartmouth.edu/~kimo/blog/computer/imagej_eclipse.html

To debug a plugin, just load the java file into the ImageJ project you made,
and off you go.

Kind regards
Joris


On Wed, Feb 11, 2009 at 12:48 AM, Rob Lewis <[hidden email]> wrote:

> So is this expected behavior? It still bothers me it works with some dicom
> files and not others. I do not have access to the file locally as i am
> using
> imagej in an applet to view dicom files over the web (which imagej has to
> import from a exposed URL).
>
> I am not using any plugins. I am only using ij.jar. I am not sure i have
> the
> experience necessary to debug through the ImageJ code, but i can try (if i
> can get the it loaded in eclipse somehow).
>
> -Rob
>
> On Tue, Feb 10, 2009 at 4:35 PM, Johannes Schindelin <
> [hidden email]> wrote:
>
> > Hi,
> >
> > On Tue, 10 Feb 2009, Rob Lewis wrote:
> >
> > > While trying to import a dicom file from a URL, (Through the UI or
> > > programatically), i receive the following error in a dialog box named
> > 'Dicom
> > > Decoder':
> > >
> > > java.io.IOException
> > > Resetting to invalid mark
> >
> > Typically, this error occurs when reading from a stream (which is the
> > result of opening a URL) but trying to go back to the beginning somewhere
> > in the middle.
> >
> > I do not have any experience with the DICOM format, but I imagine that
> you
> > have that problem here, and that you need the file locally.  Or you need
> > to inspect the source (you did not mention which plugin, if any, you use
> > to open the files) to find out where it tries to "seek" (that is "going
> > back in a file" is called in computer speak).
> >
> > Ciao,
> > Dscho
> >
>

[Christopher Yip]

Figured it out - looks like you need Java3D1.5 to get this to work _at  
least on my OS X machine running 10.5.6

I had Java3D 1.3 running but following the instructions here:

http://blogs.sun.com/mart/entry/installing_java3d_1_5_on

the ImageJ 3D viewer plug-in now appears to be working


On Feb 10, 2009, at 6:26 PM, Johannes Schindelin wrote:

> Hi,
>
> On Tue, 10 Feb 2009, John Oreopoulos wrote:
>
>> I am trying to use the ImageJ 3D viewer plugin but I'm finding I  
>> can't
>> load any volume stacks, not even the example stack that is provided  
>> on
>> the plugin website. I made sure that Java 3D is working on my Mac.  
>> Does
>> anyone else have any issues getting this plugin to work? I'm using  
>> the
>> latest version ImageJ, version 1.42h
>
> It would be helpful if you described in just a tiny little bit more  
> detail
> what exactly is happening.  Nothing?  Does a window pop up with a  
> message?
> What does the Console (/Applications/Utilities/Console) say?  What  
> version
> of Java3D do you have?  Does Fiji's 3D viewer work?
>
> Ciao,
> Dscho

Christopher M. Yip Ph.D., P.Eng
Professor - Canada Research Chair in Molecular Imaging
Department of Chemical Engineering and Applied Chemistry
Department of Biochemistry
Institute of Biomaterials and Biomedical Engineering
The Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto
Room 404 160 College St.
Toronto, ON, CANADA M5S 3E1
[phone]
[phone] (fax)
[hidden email]
http://bigten.med.utoronto.ca

[Wayne Rasband]

On Feb 10, 2009, at 3:22 PM, Rob Lewis wrote:

> While trying to import a dicom file from a URL, (Through the UI or
> programatically), i receive the following error in a dialog box named
> 'Dicom
> Decoder':
>
> java.io.IOException
> Resetting to invalid mark
>
> I can open the same file locally from the harddisk in imagej using
> File->Open. This only happens with some Dicom files.
>
> I have tried 1.41, and the latest daily build of 1.42i.
>
> I am sorry if this already has been discussed, as i have just joined
> the
> mailing list. Any help or pointers would be appreciated!

The latest 1.42i daily build increases the size of the mark/reset input
steam buffer from 200,000 to 400,000 bytes, allowing DICOMs with
headers up to 400,000 bytes to by opened using a URL.

-wayne