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Slicer4 - DICOM many problems

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Slicer4 - DICOM many problems

S. EDAH-TALLY
Hello,

With latest 2013-03-05 nightly build, Linux x86_84.

Can't load a DICOM volume in an ISO file ripped from CD and mounted locally.

The "Load Scalar and Tensor Volume" in the Data Module has disappeared.

Using the DICOM module, there's first of all an error with Python's ASCII codec
failure with UTF-8 characters. After a little web search, got my hands dirty
with the following patch :



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

*** DICOMScalarVolumePlugin.py 2013-03-06 17:07:45.418064312 +0100
--- /tmp/DICOMScalarVolumePlugin.py 2013-03-06 17:08:26.244744813 +0100
***************
*** 259,266 ****
      """
      if not (hasattr(x,'name') and hasattr(y,'name')):
          return 0
!     xName = str(x.name)
!     yName = str(y.name)
      try:
        xNumber = int(xName[:xName.index(':')])
        yNumber = int(yName[:yName.index(':')])
--- 259,268 ----
      """
      if not (hasattr(x,'name') and hasattr(y,'name')):
          return 0
!     #xName = str(x.name)
!     #yName = str(y.name)
!     xName = (x.name).encode('utf-8')
!     yName = (y.name).encode('utf-8')
      try:
        xNumber = int(xName[:xName.index(':')])
        yNumber = int(yName[:yName.index(':')])
***************
*** 293,299 ****
      for f in files:
        fileList.InsertNextValue(f)
      volumesLogic = slicer.modules.volumes.logic()
!     return(volumesLogic.AddArchetypeScalarVolume(files[0],name,0,fileList))
 
    def load(self,loadable):
      """Load the select as a scalar volume
--- 295,301 ----
      for f in files:
        fileList.InsertNextValue(f)
      volumesLogic = slicer.modules.volumes.logic()
!    
return(volumesLogic.AddArchetypeScalarVolume(files[0],name.encode('utf-8'),0,fileList))
 
    def load(self,loadable):
      """Load the select as a scalar volume

*****************************************************************************
DISCLAIMER : I really don't know Python and even less Slicer's internals !
*****************************************************************************

So after asking DICOMScalarVolumePlugin to use UTF-8 in three places, the
DICOM module doesn't complain to load data, BUT, it show tens of volumes !
Loading any of these many volumes, the visualizer shows only one slice at a
time in the red panel, the yellow and green panels show a horizontal line. The
data actually is a single CT study with 1118 images.

So I really can't see how to load, display and work with a CT study presented
as a DICOM series. It's all so easy with 3.3.6. I understand there's still
work in progress.

I would be grateful if someone can just tell me how to do that, or tell me
that we may expect a working 'Load scalar and tensor volume' as in the good
old days.

Thank you.

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Re: Slicer4 - DICOM many problems

Steve Pieper
Hi - 

First question: do you have files that you can share which replicate this issue?  that is, files that do not contain patient identifying information?  If so it would be a big help and we could doublecheck you patch.  

Second, you should be able to load the data using the Add Data interface and selecting one of the volumes from the CT series (be sure to show the options and unclick the SingleFile option).

Best,
-Steve



On Wed, Mar 6, 2013 at 11:29 AM, <[hidden email]> wrote:
Hello,

With latest 2013-03-05 nightly build, Linux x86_84.

Can't load a DICOM volume in an ISO file ripped from CD and mounted locally.

The "Load Scalar and Tensor Volume" in the Data Module has disappeared.

Using the DICOM module, there's first of all an error with Python's ASCII codec
failure with UTF-8 characters. After a little web search, got my hands dirty
with the following patch :



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

*** DICOMScalarVolumePlugin.py  2013-03-06 17:07:45.418064312 +0100
--- /tmp/DICOMScalarVolumePlugin.py     2013-03-06 17:08:26.244744813 +0100
***************
*** 259,266 ****
      """
      if not (hasattr(x,'name') and hasattr(y,'name')):
          return 0
!     xName = str(x.name)
!     yName = str(y.name)
      try:
        xNumber = int(xName[:xName.index(':')])
        yNumber = int(yName[:yName.index(':')])
--- 259,268 ----
      """
      if not (hasattr(x,'name') and hasattr(y,'name')):
          return 0
!     #xName = str(x.name)
!     #yName = str(y.name)
!     xName = (x.name).encode('utf-8')
!     yName = (y.name).encode('utf-8')
      try:
        xNumber = int(xName[:xName.index(':')])
        yNumber = int(yName[:yName.index(':')])
***************
*** 293,299 ****
      for f in files:
        fileList.InsertNextValue(f)
      volumesLogic = slicer.modules.volumes.logic()
!     return(volumesLogic.AddArchetypeScalarVolume(files[0],name,0,fileList))

    def load(self,loadable):
      """Load the select as a scalar volume
--- 295,301 ----
      for f in files:
        fileList.InsertNextValue(f)
      volumesLogic = slicer.modules.volumes.logic()
!
return(volumesLogic.AddArchetypeScalarVolume(files[0],name.encode('utf-8'),0,fileList))

    def load(self,loadable):
      """Load the select as a scalar volume

*****************************************************************************
DISCLAIMER : I really don't know Python and even less Slicer's internals !
*****************************************************************************

So after asking DICOMScalarVolumePlugin to use UTF-8 in three places, the
DICOM module doesn't complain to load data, BUT, it show tens of volumes !
Loading any of these many volumes, the visualizer shows only one slice at a
time in the red panel, the yellow and green panels show a horizontal line. The
data actually is a single CT study with 1118 images.

So I really can't see how to load, display and work with a CT study presented
as a DICOM series. It's all so easy with 3.3.6. I understand there's still
work in progress.

I would be grateful if someone can just tell me how to do that, or tell me
that we may expect a working 'Load scalar and tensor volume' as in the good
old days.

Thank you.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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Re: Slicer4 - DICOM many problems

S. EDAH-TALLY
In reply to this post by S. EDAH-TALLY

Le samedi 9 mars 2013 17:05:50 vous avez écrit :

Hi -  Thanks for providing the data - I'll delete it once we've sorted this out. Oddly enough I cannot replicate what you see.  I was able to get the attached image by loading via the dicom module in the normal way.  Note that I also see the multiple load options like you do in 03.png, but like yours only the first is selected by default and when I load it all of the images are loaded. I wonder if you are having the same trouble that is being discussed on the developer list: http://slicer-devel.65872.n3.nabble.com/Problem-with-DICOM-module-tt4027815.html#a4027927 we'd only seen this on a mac, but maybe you also have it.  Are you you using a build downloaded from slicer.org or one you built your self?  If you haven't, could you try the slicer.org nightly and see if you have the same issue? I also had no problem with the text encoding, perhaps because I'm using a mac instead of linux? -Steve



Hi,

 

I used latest nightly r21787 from slicer.org, I do not build Slicer myself.

I'll keep trying next nightly builds and hope I can use them.

 

Thanks for investigating.

 

SET


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Re: Slicer4 - DICOM many problems

Steve Pieper
Let us know if it starts working.  I still suspect there's a text encoding issue, perhaps a native language localization configuration difference on your linux system that impacts the parsing.

-Steve


On Sun, Mar 10, 2013 at 9:51 AM, SET <[hidden email]> wrote:

Le samedi 9 mars 2013 17:05:50 vous avez écrit :

Hi -  Thanks for providing the data - I'll delete it once we've sorted this out. Oddly enough I cannot replicate what you see.  I was able to get the attached image by loading via the dicom module in the normal way.  Note that I also see the multiple load options like you do in 03.png, but like yours only the first is selected by default and when I load it all of the images are loaded. I wonder if you are having the same trouble that is being discussed on the developer list: http://slicer-devel.65872.n3.nabble.com/Problem-with-DICOM-module-tt4027815.html#a4027927 we'd only seen this on a mac, but maybe you also have it.  Are you you using a build downloaded from slicer.org or one you built your self?  If you haven't, could you try the slicer.org nightly and see if you have the same issue? I also had no problem with the text encoding, perhaps because I'm using a mac instead of linux? -Steve



Hi,

 

I used latest nightly r21787 from slicer.org, I do not build Slicer myself.

I'll keep trying next nightly builds and hope I can use them.

 

Thanks for investigating.

 

SET



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Re: Slicer4 - DICOM many problems

Steve Pieper
Nothing exotic.

We're pretty provincial here in America - France counts as very exotic :)  

Kidding aside, we have lots of francophones (and linux users) in the project so hopefully someone will have an idea.

-Steve


On Sun, Mar 10, 2013 at 11:48 AM, SET <[hidden email]> wrote:

Le dimanche 10 mars 2013 11:46:30 vous avez écrit :

Let us know if it starts working.  I still suspect there's a text encoding issue, perhaps a native language localization configuration difference on your linux system that impacts the parsing. -Steve



For the rocord :

 

Here's the output of the locale command :

 

LANG=fr_FR.UTF-8

LC_CTYPE="fr_FR.UTF-8"

LC_NUMERIC="fr_FR.UTF-8"

LC_TIME="fr_FR.UTF-8"

LC_COLLATE="fr_FR.UTF-8"

LC_MONETARY="fr_FR.UTF-8"

LC_MESSAGES="fr_FR.UTF-8"

LC_PAPER="fr_FR.UTF-8"

LC_NAME="fr_FR.UTF-8"

LC_ADDRESS="fr_FR.UTF-8"

LC_TELEPHONE="fr_FR.UTF-8"

LC_MEASUREMENT="fr_FR.UTF-8"

LC_IDENTIFICATION="fr_FR.UTF-8"

LC_ALL=

 

Nothing exotic.

 

Regards.

 

SET

 



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Re: Slicer4 - DICOM many problems

S. EDAH-TALLY

Le dimanche 10 mars 2013 12:04:27 vous avez écrit :

We're pretty provincial here in America - France counts as very exotic :)   Kidding aside, we have lots of francophones (and linux users) in the project so hopefully someone will have an idea. -Steve


Hello,

 

Some updates. Concerns loading a DICOM CT via the DICOM module.

 

1. Using nightly 2013-03-13 on MacOSX, the series gets loaded straight away !

 

2. Using nightly 2013-03-13 on Linux x86_64, the series cannot be loaded correctly.

 

3. Built Slicer 4 from SVN on Linux x86_64 according to the instructions on slicer.org. The series is not loaded correctly on first try, only a single slice is displayed. If I uncheck and check again the first line in the volume list, then the series gets loaded and displayed normally in all three panels.

 

4. DICOMScalarVolumePlugin still complains about non ASCII characters with some studies. Applying the patch (cf first mail of this thread) is still relevant and working successfully. Unfortunately, it happens with nominative patient data, I can't forward you these. Anonymous data always load flawlessly.

 

Regards.

SET


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