ImageJ

Problems with DICOM in 1.41b

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

6 messages Options

albertoduina@virgilio.it

Problems with DICOM in 1.41b

Hi all,
today, after the upgrade of ImageJ at 1.41b I have problems
opening some DICOM images, from a MR Siemens machine, here is the
message:
java.lang.NegativeArraySizeException
at ij.plugin.DicomDecoder.getString(DICOM.java:270)
at ij.plugin.DicomDecoder.getHeaderInfo(DICOM.java:743)
at ij.plugin.DicomDecoder.addInfo(DICOM.java:676)
at ij.plugin.DicomDecoder.getFileInfo(DICOM.java:622)
at ij.plugin.DICOM.run(DICOM.java:89)
at ij.IJ.runPlugIn(IJ.java:131)
at ij.IJ.runPlugIn(IJ.java:113)
at ij.io.Opener.openImage(Opener.java:200)
at ij.io.Opener.openImage(Opener.java:253)
at ij.io.Opener.open(Opener.java:117)
at ij.io.Opener.open(Opener.java:56)
at ij.plugin.Commands.run(Commands.java:23)
at ij.IJ.runPlugIn(IJ.java:131)
at ij.Executer.runCommand(Executer.java:104)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(Unknown Source)
the problem not appear with older (>2years) Siemens images.

Another similar problem with images from an HITACHI machine, here the
message is:
<Out of memory>

No problems with images from a GE machine.

With the 1.41a version the problems disappear.

I have tried to investigate, activating the Debug Mode, in the Log window
appear the DicomDecoder output, but it stops somewere into the private
tags, after (0019,1015 FD 24 bytes from 1510) ---: 0.0 and
before the 0019,1016) that must be a DS value (seen with hexWorkShop).
With a BP in Eclipse appear wrong the elementLength = -1067065344

Anybody has similar problems?
Thanks.
Alberto

Johannes Hermen

Re: Problems with DICOM in 1.41b

> Hi all,
> today, after the upgrade of ImageJ at 1.41b I have problems
> opening some DICOM images, from a MR Siemens machine, here is the

We have made some modifications to the DicomDecoder class in the last
Version, to be able to retrieve Float values from the Dicom Header (FD,
FL), which was not implemented before. If you could send me the
problematic images i can try to reproduce and fix the problem.

Thanks
Johannes

-----------------------------------------------------------------
Johannes Hermen - Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor http://www.santec.tudor.lu
29, Avenue John F. Kennedy
L-1855 Luxembourg
-----------------------------------------------------------------

ImageJ Interest Group <[hidden email]> wrote on 08.05.2008 11:14:04:

> Hi all,
> today, after the upgrade of ImageJ at 1.41b I have problems
> opening some DICOM images, from a MR Siemens machine, here is the
> message:
> java.lang.NegativeArraySizeException
> at ij.plugin.DicomDecoder.getString(DICOM.java:270)
> at ij.plugin.DicomDecoder.getHeaderInfo(DICOM.java:743)
> at ij.plugin.DicomDecoder.addInfo(DICOM.java:676)
> at ij.plugin.DicomDecoder.getFileInfo(DICOM.java:622)
> at ij.plugin.DICOM.run(DICOM.java:89)
> at ij.IJ.runPlugIn(IJ.java:131)
> at ij.IJ.runPlugIn(IJ.java:113)
> at ij.io.Opener.openImage(Opener.java:200)
> at ij.io.Opener.openImage(Opener.java:253)
> at ij.io.Opener.open(Opener.java:117)
> at ij.io.Opener.open(Opener.java:56)
> at ij.plugin.Commands.run(Commands.java:23)
> at ij.IJ.runPlugIn(IJ.java:131)
> at ij.Executer.runCommand(Executer.java:104)
> at ij.Executer.run(Executer.java:58)
> at java.lang.Thread.run(Unknown Source)
> the problem not appear with older (>2years) Siemens images.
>
> Another similar problem with images from an HITACHI machine, here the
> message is:
> <Out of memory>
>
> No problems with images from a GE machine.
>
> With the 1.41a version the problems disappear.
>
> I have tried to investigate, activating the Debug Mode, in the Log

window
> appear the DicomDecoder output, but it stops somewere into the private
> tags, after (0019,1015 FD 24 bytes from 1510) ---: 0.0 and
> before the 0019,1016) that must be a DS value (seen with hexWorkShop).
> With a BP in Eclipse appear wrong the elementLength = -1067065344
>
> Anybody has similar problems?
> Thanks.
> Alberto

Wayne Rasband

Re: Problems with DICOM in 1.41b

In reply to this post by albertoduina@virgilio.it

These bugs are fixed in the ImageJ 1.41c daily build, thanks to sample
DICOMs provided by Alberto. The MR Siemens files had an incorrectly
encoded FD (Float Double) private tag with an element length of 24
instead of 8. The "out of memory" errors where the result of ImageJ not
correctly handling UT (Unlimited Text) tags.

-wayne

On May 8, 2008, at 5:14 AM, Alberto Duina wrote:

Hao Jiang-3

Mouse point

There is a problem here, usually after an image was opened, user move
the mouse on that image, from the status bar will show the point value
of cursor.

Now because the image is very big, I don't want to open with actual
size, so a "decimation" has been set, for example, an image of
1000X1000, set "decimation" as 10, then the image will be opened as
100X100.

Now the problem is, after that when move the mouse, will only show
actual cursor point, but the user want to multiply this point with
"decimation" to reflect original image size.

How can I do this?

*************************************************************************
PRIVILEGE AND CONFIDENTIALITY NOTICE:

The information in this email is intended for the named recipients only.
It may contain privileged and confidential information. If you have
received this communication in error, any use, copying or dissemination
of its contents is strictly prohibited. Please erase all copies of the
message along with any included attachments and notify Intermap
Technologies or the sender immediately by telephone at the number
indicated on this page.

*************************************************************************

Fco. Javier Merino Guardiola

Re: Mouse point

Hi,

Here you can find an example of a mouse listener (http://rsb.info.nih.gov/ij/plugins/download/Mouse_Listener.java
), I think you could do that using a listener.

The method you should implement is the mouseMoved(), and use the
IJ.ShowStatus(...) function to write the rescaled value.

El 10/05/2008, a las 0:53, Hao Jiang escribió:

> There is a problem here, usually after an image was opened, user move
> the mouse on that image, from the status bar will show the point value
> of cursor.
>
> Now because the image is very big, I don't want to open with actual
> size, so a "decimation" has been set, for example, an image of
> 1000X1000, set "decimation" as 10, then the image will be opened as
> 100X100.
>
> Now the problem is, after that when move the mouse, will only show
> actual cursor point, but the user want to multiply this point with
> "decimation" to reflect original image size.
>
> How can I do this?
>
>
>
> *************************************************************************
> PRIVILEGE AND CONFIDENTIALITY NOTICE:
>
> The information in this email is intended for the named recipients
> only.
> It may contain privileged and confidential information. If you have
> received this communication in error, any use, copying or
> dissemination
> of its contents is strictly prohibited. Please erase all copies of
> the
> message along with any included attachments and notify Intermap
> Technologies or the sender immediately by telephone at the number
> indicated on this page.
>
> *************************************************************************

Hao Jiang-3

Re: Mouse point

Thanks, now I'm able to solve my problem.

Hao Jiang

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Fco. Javier Merino Guardiola
Sent: Saturday, May 10, 2008 5:19 PM
To: [hidden email]
Subject: Re: Mouse point

Hi,

Here you can find an example of a mouse listener (http://rsb.info.nih.gov/ij/plugins/download/Mouse_Listener.java
), I think you could do that using a listener.

The method you should implement is the mouseMoved(), and use the
IJ.ShowStatus(...) function to write the rescaled value.

El 10/05/2008, a las 0:53, Hao Jiang escribió:

> There is a problem here, usually after an image was opened, user move
> the mouse on that image, from the status bar will show the point value
> of cursor.
>
> Now because the image is very big, I don't want to open with actual
> size, so a "decimation" has been set, for example, an image of
> 1000X1000, set "decimation" as 10, then the image will be opened as
> 100X100.
>
> Now the problem is, after that when move the mouse, will only show
> actual cursor point, but the user want to multiply this point with
> "decimation" to reflect original image size.
>
> How can I do this?
>
>
>
> **********************************************************************
> ***
> PRIVILEGE AND CONFIDENTIALITY NOTICE:
>
> The information in this email is intended for the named recipients
> only.
> It may contain privileged and confidential information. If you have
> received this communication in error, any use, copying or
> dissemination of its contents is strictly prohibited. Please erase
> all copies of the message along with any included attachments and
> notify Intermap Technologies or the sender immediately by telephone at
> the number indicated on this page.
>
> **********************************************************************
> ***

*************************************************************************
PRIVILEGE AND CONFIDENTIALITY NOTICE:

The information in this email is intended for the named recipients only.
It may contain privileged and confidential information. If you have
received this communication in error, any use, copying or dissemination
of its contents is strictly prohibited. Please erase all copies of the
message along with any included attachments and notify Intermap
Technologies or the sender immediately by telephone at the number
indicated on this page.

*************************************************************************