[ITK] [slicer-devel] BigTIFF

Thu Sep 18 16:32:19 EDT 2014

Gib,

I have continued to work on refactoring ITK's TIFFImageIO, fixing some bugs along the way:
http://review.source.kitware.com/#/c/17111/

If you have some specific images that are problematic, it would be good if you could run "tiffinfo"[1] on them to look at the tags or provide a copy of them.

Thanks,
Brad

[1] http://www.libtiff.org/tools.html
________________________________________
From: Gib Bogle [g.bogle at auckland.ac.nz]
Sent: Thursday, September 18, 2014 3:47 PM
To: Lowekamp, Bradley (NIH/NLM/LHC) [C]; Jean-Christophe Fillion-Robin
Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper
Subject: RE: [ITK] [slicer-devel] BigTIFF

Hi Bradley,

I am using your itkTIFFImageIO.cxx.  It does not seem to have any effect on the problem I'm having.  I will check again that I am really compiling with this fix.

I wonder whether the failure to display tiffs with size between 2^31 and 2^32 could be caused by the use of a 'long' somewhere instead of an 'unsigned long'.  Just grasping at straws.

Best
Gib
________________________________________
From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov]
Sent: Friday, 19 September 2014 1:02 a.m.
To: Gib Bogle; Jean-Christophe Fillion-Robin
Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper
Subject: RE: [ITK] [slicer-devel] BigTIFF

Hello,

I thought I sent this message last nigh, regarding the tiff reading issue.

Did you update the ITK version to ITK master?

I just committed a fix to ITK this week to likely address this issue:
https://github.com/InsightSoftwareConsortium/ITK/commit/a7d9a4405c693b935a02339e67762ea750a04e1c

You will need to modify the repository to:
git://itk.org/ITK.git and the hash to: a7d9a4405c693b935a02339e67762ea750a04e1c in the Superbuild/External_ITKv4.cmake file.

Brad

________________________________
From: Gib Bogle [g.bogle at auckland.ac.nz]
Sent: Wednesday, September 17, 2014 11:07 PM
To: Jean-Christophe Fillion-Robin
Cc: community at itk.org; slicer-devel at bwh.harvard.edu; Steve Pieper
Subject: Re: [ITK] [slicer-devel] BigTIFF

Hi J-C,

OK, now that I know it's the Network drives I can easily take care of it.

What do I need to do to ensure that the Python code is found?  Is it just a matter of adding a directory to the PATH?

Do you have any insights into the weird situation that I can display tiff files < 2^31 GB and > 2^32 GB but not those of intermediate size?

Another observation:  When I load the 4 GB file the memory usage (in Task Manager) increases by 8 GB, then immediately drops back to 4 GB, and after some time I see a slice of the image.  But when I load a 2 GB file (I mean slightly more than 2 GB) the memory usage climbs by 2 GB (then the display screen remains blank).

Thanks
Gib
________________________________
From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com]
Sent: Thursday, 18 September 2014 2:51 p.m.
To: Gib Bogle
Cc: Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org
Subject: Re: [ITK] [slicer-devel] BigTIFF

Hi Gib,

On Wed, Sep 17, 2014 at 8:36 PM, Gib Bogle <g.bogle at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> wrote:
Correction!  You were right.  There was a network drive that I could not see until I right-clicked on Network, then Disconnect network drive.  Now it's responsive :)

There is indeed known issue with network drive and file dialog.
See https://bugreports.qt-project.org/browse/QTBUG-13182

If you would like to by pass the file dialog, the next time, you could directly load the file from the "File -> Recently loaded"

There is another wrinkle that I'm not concerned about right now.  When I execute the installed program, C:\Program files\Slicer.exe, the console shows this error message:

Traceback (most recent call last):
  File "<string>", line 7, in <module>
  File "C:/Program Files/Slicer/bin/Python/slicer/slicerqt.py", line 1, in <module>
    import vtk, qt, ctk
ImportError: No module named vtk

but the program runs.  I don't see that message when I run the executable in Slicer-build.  The files in both places are the same, also the SlicerApp-real.exe files - of course, since INSTALL just copies them.  I have seen any difference in the ability to display the tiff files.

This is explained by the fact you installed Slicer instead of creating a package or running the launcher from the build tree. In that case, the python path are not setup by the launcher and the Slicer executable fails to locate its dependent python packages ...

Hth
JC

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