[ITK] [slicer-devel] BigTIFF
Gib Bogle
g.bogle at auckland.ac.nz
Wed Sep 17 12:02:43 EDT 2014
Hi Matt,
I don't know what to look for to see what is causing this error in the vtkITK build. Should vtkITK know about ITK_USE_64BITS_IDS?
thanks
Gib
________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Thursday, 18 September 2014 3:55 a.m.
To: Gib Bogle
Cc: Bradley Lowekamp; Steve Pieper; slicer-devel at bwh.harvard.edu; community at itk.org
Subject: Re: [slicer-devel] BigTIFF
Hi Gib,
Getting the builds states to propagate and follow how the get set can
be tricky. A few pointers on where to look for the status:
1) CMakeCache.txt (this file contains the build settings that CMake
recognized from your input when you run CMake)
2) ITKConfig.cmake (this file will exist in the build tree or the
install tree, and it contains CMake varables that may be used by other
projects building against ITK)
3) itkConfigure.h (this is a header that has configured preprocessor
definitions used when building)
HTH,
Matt
On Wed, Sep 17, 2014 at 3:35 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> Hi Bradley, Matt and Steve,
>
> Now for the embarrassing confession. In External_ITK4.cmake I turned
> ITKV3_COMPATIBILITY off and ITK_USE_64BITS_IDS on as suggested, but when I
> finally checked what the code that is being built was using (with #if
> defined ...) I discovered that both ITKV3_COMPATIBILITY and
> ITK_USE_64BITS_IDS were off. How can this be?
>
> It's easy, all it takes is a typo:
> -DITK_USE_64_BITS_IDS:BOOL=ON
> That typo has cost me a couple of days, and caused annoyance to a few
> people, I suspect.
>
> Unfortunately... now Slicer's vtkITK does not build. There are very many
> errors like this:
>
> 3>------ Build started: Project: vtkITK, Configuration: Release x64 ------
> 3>Build started 17/09/2014 7:25:52 p.m..
> 3>InitializeBuildStatus:
> 3> Touching "vtkITK.dir\Release\vtkITK.unsuccessfulbuild".
> 3>CustomBuild:
> 3> Building Custom Rule C:/Slicer/Libs/vtkITK/CMakeLists.txt
> 3> CMake does not need to re-run because
> C:\s\b\Slicer-build\Libs\vtkITK\CMakeFiles\generate.stamp is up-to-date.
> 3>ClCompile:
> 3> vtkITKNumericTraits.cxx
> 3> vtkITKArchetypeDiffusionTensorImageReaderFile.cxx
> 3> vtkITKArchetypeImageSeriesReader.cxx
> 3> vtkITKArchetypeImageSeriesScalarReader.cxx
> 3> vtkITKArchetypeImageSeriesVectorReaderFile.cxx
> 3> vtkITKArchetypeImageSeriesVectorReaderSeries.cxx
> 3> vtkITKImageWriter.cxx
> 3> vtkITKGradientAnisotropicDiffusionImageFilter.cxx
> 3> vtkITKDistanceTransform.cxx
> 3>C:\Slicer\Libs\vtkITK\vtkITKArchetypeImageSeriesScalarReader.cxx(179):
> error C2679: binary '=' : no operator found which takes a right-hand operand
> of type 'itk::ImportImageContainer<TElementIdentifier,TElement> *' (or there
> is no acceptable conversion)
> 3> with
> 3> [
> 3> TElementIdentifier=unsigned __int64,
> 3> TElement=double
> 3> ]
> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(124):
> could be 'itk::SmartPointer<TObjectType>
> &itk::SmartPointer<TObjectType>::operator =(const
> itk::SmartPointer<TObjectType> &)'
> 3> with
> 3> [
> 3> TObjectType=itk::ImportImageContainer<unsigned long,double>
> 3> ]
> 3> c:\s\b\itkv4\modules\core\common\include\itkSmartPointer.h(128):
> or 'itk::SmartPointer<TObjectType>
> &itk::SmartPointer<TObjectType>::operator
> =(itk::ImportImageContainer<TElementIdentifier,TElement> *)'
> 3> with
> 3> [
> 3> TObjectType=itk::ImportImageContainer<unsigned long,double>,
> 3> TElementIdentifier=unsigned long,
> 3> TElement=double
> 3> ]
> 3> while trying to match the argument list
> '(itk::SmartPointer<TObjectType>,
> itk::ImportImageContainer<TElementIdentifier,TElement> *)'
> 3> with
> 3> [
> 3> TObjectType=itk::ImportImageContainer<unsigned long,double>
> 3> ]
> 3> and
> 3> [
> 3> TElementIdentifier=unsigned __int64,
> 3> TElement=double
> 3> ]
>
> I presume these are related to the use of 64-bit integers.
>
> Over to you guys :)
>
> Gib
> ________________________________
> From: Bradley Lowekamp [blowekamp at mail.nih.gov]
> Sent: Tuesday, 16 September 2014 12:45 a.m.
> To: Steve Pieper
> Cc: Gib Bogle; slicer-devel at bwh.harvard.edu
> Subject: Re: [slicer-devel] BigTIFF
>
> Hello,
>
> For you slicer build did you also remove the ITKV3_COMPATIBILITY flag here:
> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48
>
> To test for ITK big tiff compatibility, I'd recommend getting python 2.7
> 64-bits then installing SimpleITK (i.e pip install SimpleITK), and try to
> read and write files like these there. More information about getting
> started is here[1].
>
> You should be a able to generate a image with:
>
> import SimpleITK as sitk
> img = sitk.Image( [1250,1250,1250], sitk.sitkUInt8)
> img += 10
> stats = sitk.StatisticsImageFilter()
> stats.Execute(img)
> print stats
>
> This should give you basic access to ITK in python to interactively
> experiment with options with these large images. I have been able to load
> large images with the binaries of SimpleITK on windows 64-bits. I don't know
> if I have tried big tiff though.
>
> A simular test could be done with C++ and ITK directly, but I think
> SimpleITK in python may be quicker for experimentation.
>
> Brad
>
> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted
> [2]
> http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a838017f46860e8a7bc8a9ebc7f3dbfee
>
> On Sep 15, 2014, at 7:37 AM, Steve Pieper <pieper at isomics.com> wrote:
>
> Hi Gib -
>
> Are you testing only on windows? What we would often try to do for this
> kind of debugging is to create a small example that other people can test on
> their configurations. Slicer has a mechanism called a Self Test [1] to
> allow easy replication and debugging across multiple platforms. It's ideal
> if we can hone it down to something like what is described as a 'sscce' [2].
> The self tests will typically download some data from a public web site, run
> some operations, and then print something out saying if it passed or failed
> (or it may crash). Since it's possible to make a small data file that
> expands into a giant tiff image it should be pretty tractable to pose this
> issue in the form of a self test.
>
> Best,
> Steve
>
>
> [1]
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule
>
> [2] http://sscce.org/
>
> On Mon, Sep 15, 2014 at 2:21 AM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>>
>> Hi J-C,
>>
>> Some more info about Slicer with big tiff files.
>>
>> 1250x1250x1250 = 1,953,125,000 bytes loads and displays correctly
>> 1300x1300x1300 = 2,197,000,000 bytes loads but does not display anything
>> 1650x1650x1650 = 4,492,125,000 bytes fails to load (crashes reading page
>> 72)
>>
>> All suggestions will be gratefully received.
>>
>> Cheers
>> Gib
>> ________________________________
>> From: Jean-Christophe Fillion-Robin [jchris.fillionr at kitware.com]
>> Sent: Sunday, 14 September 2014 8:32 p.m.
>> To: Gib Bogle
>> Cc: Steve Pieper; slicer-devel at bwh.harvard.edu
>> Subject: Re: [slicer-devel] BigTIFF
>>
>> Hi Gib,
>>
>> What do you mean by "reinstalled" ? You should not have to install Slicer
>> to be able to execute it from the build directory.
>>
>> After building with "Slicer_BUILD_BRAINSTOOLS" turned off the option
>> "ITK_USE_64_BITS_IDS" added to the ITKv4 external project, it should work
>> out.
>>
>> When done building, make sure to start the Slicer launcher:
>>
>> C:/path/to/project/Slicer-Superbuild/Slicer-build/Slicer.exe
>>
>> and not the Slicer executable:
>>
>>
>> C:/path/to/project/Slicer-Superbuild/Slicer-build/bin/Release/SlicerApp-real.exe
>>
>>
>> By using the launcher, you ensure that the PATH are properly setup and the
>> expected libraries are loaded.
>>
>>
>> Hth
>> Jc
>>
>>
>> On Sat, Sep 13, 2014 at 11:49 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>> wrote:
>>>
>>> I hope I understand correctly. I added the line as shown to
>>> C:\Slicer\SuperBuild\External_ITKv4.cmake:
>>> ...
>>> # ZLIB
>>> -DITK_USE_SYSTEM_ZLIB:BOOL=ON
>>> -DZLIB_ROOT:PATH=${ZLIB_ROOT}
>>> -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR}
>>> -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY}
>>> # Big TIFF
>>> -DITK_USE_64_BITS_IDS:BOOL=ON
>>> ...
>>>
>>> I then did ALL_BUILD in the root of the build directory (C:\s\b). I
>>> presume this is the "superbuild". I then redid ALL_BUILD in
>>> C:\s\b\Slicer-build, and ITKv4-build, and reinstalled. The program still
>>> crashes with the big tiff. Is there somewhere I can check in the project
>>> configuration files to see if setting ITK_USE_64_BITS_IDS actually took
>>> effect?
>>>
>>> Thanks
>>> Gib
>>> ________________________________
>>> From: Steve Pieper [pieper at isomics.com]
>>> Sent: Sunday, 14 September 2014 1:36 p.m.
>>>
>>> To: Gib Bogle
>>> Cc: slicer-devel at bwh.harvard.edu
>>> Subject: Re: [slicer-devel] BigTIFF
>>>
>>> Hey Gib -
>>>
>>> Sounds like progress - the ITK_USE_64_BITS_IDS should be set to ON in the
>>> ITK build process [1] during the superbuild. I don't think much else was
>>> required except turning off the IKTv3 parts.
>>>
>>> [1]
>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L32-L68
>>>
>>> -Steve
>>>
>>> p.s. I hear the ABs beat the Boks recently in a close match (we don't get
>>> it on TV). So the Jo'berg game should be a great rematch!
>>>
>>> On Sat, Sep 13, 2014 at 9:11 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>> wrote:
>>>>
>>>> You did warn me.
>>>>
>>>> Here is the list of options not ticked:
>>>>
>>>> Slicer_BUILD_BRAINSTOOLS
>>>> _LEGACY_CLI
>>>> _LandmarkRegistration
>>>> _TESTING_EXTENSIONS
>>>> _UPDATE_TRANSLATION
>>>> _USE_GIT_PROTOCOL
>>>> _OpenIGTLink
>>>> _PYTHONQT_WITH_OPENSSL
>>>> _PYTHONQT_WITH_TCL
>>>> _QtTesting
>>>> _SimpleITK
>>>> _VTK_DEBUG_LINKS
>>>> Slicer_WITH_LIBRARY_VERSION
>>>>
>>>> USE_BRAINS*
>>>> USE_ConvertBetweenFileFormats
>>>> USE_DWIConvert
>>>> USE_DebugImageViewer
>>>> USE_GTRACT
>>>> USE_ICCDEF
>>>> USE_ImageCalculator
>>>> USE_ReferenceAtlas
>>>>
>>>> -------
>>>>
>>>> Progress! Process Monitor showed me that the exit code was C0000139,
>>>> which means a DLL was not found. I then realized that I have different
>>>> occurrences of many of the DLLs on my disk (QT, ITK and VTK) and this
>>>> prompted me to look more carefully at the PATH environment variable. I just
>>>> tested with all the new paths at the start of the PATH string, and Slicer
>>>> starts successfully! I can load a tiff! But ... it still crashes when I
>>>> attempt to load a 4 GB tiff.
>>>>
>>>> I am now wondering (belatedly!) about the way I tried to build with big
>>>> tiff capability. I guessed, and added the entry ITK_USE_64BITS_IDS as
>>>> 'bool'. It appears ticked in Ungrouped Entries. I really should have asked
>>>> for directions before doing this - now I'm wondering if that switch actually
>>>> had any effect. Is that the right thing to do, and if not, what is?
>>>>
>>>> Thanks
>>>> Gib
>>>> ________________________________
>>>> From: Steve Pieper [pieper at isomics.com]
>>>> Sent: Sunday, 14 September 2014 10:02 a.m.
>>>>
>>>> To: Gib Bogle
>>>> Cc: slicer-devel at bwh.harvard.edu
>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>
>>>> Yes, well, don't say I didn't warn you! ; )
>>>>
>>>> You do need loadable modules and you probably do want python (a lot of
>>>> core stuff is in python, like the editor).
>>>>
>>>> BRAINSTools should be off for now, since it needs ITKv3.
>>>>
>>>> I'm not sure either what to do next, but I suggest maybe trying the
>>>> Process Monitor from microsoft (sysinternals) and see what it was doing when
>>>> it exited. But that may be a longshot.
>>>>
>>>> -Steve
>>>>
>>>> On Sat, Sep 13, 2014 at 4:39 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>> wrote:
>>>>>
>>>>> Hi Steve,
>>>>>
>>>>> That was an interesting exercise. I managed to build Slicer without
>>>>> Qtloadablemodules. As you might expect, it was not much use. The program
>>>>> started up but without any capabilities, just an empty shell. (I'm a bit
>>>>> handicapped by not knowing anything about how Slicer is constructed.) So I
>>>>> built it again, this time selecting most things except BRAINTools. The
>>>>> build took a long time, partly because I turned on the Python option, which
>>>>> I don't need. This time there were no errors, except for a couple of
>>>>> occasions where the attempt to create a directory failed - this was because
>>>>> the directory already existed, and was easily solved by deleting the
>>>>> directory and building again. I installed everything that wanted to be
>>>>> installed, and modified the environment variables to suit.
>>>>>
>>>>> My sense of satisfaction was short-lived, however. When Slicer is
>>>>> invoked the Acknowledgements screen flashes up briefly then the program
>>>>> exits. There are no error messages. Dependency Walker shows that all the
>>>>> DLLs are being found. I am assuming that BRAINTools is not needed (not
>>>>> knowing what it is).
>>>>>
>>>>> I sense that I must be close to getting it working, but I'm not sure
>>>>> what to do next.
>>>>>
>>>>> Cheers
>>>>> Gib
>>>>> ________________________________
>>>>> From: Steve Pieper [pieper at isomics.com]
>>>>> Sent: Sunday, 14 September 2014 12:36 a.m.
>>>>>
>>>>> To: Gib Bogle
>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>
>>>>> Hi Gib -
>>>>>
>>>>> A lot of the building goes on in parallel so you need to review the
>>>>> whole build log to see what is going on. I'm guessing ITK didn't build
>>>>> correctly. Typically I do a Control-A Control-C in the visual studio output
>>>>> window and then paste it into a text editor to look for issues. Definitely
>>>>> you don't want to be editing any of the visual studio files, since they are
>>>>> generated by cmake every configure -- much better to sort out what is going
>>>>> on at the cmake flag level.
>>>>>
>>>>> Best,
>>>>> Steve
>>>>>
>>>>> On Fri, Sep 12, 2014 at 9:27 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>>> wrote:
>>>>>>
>>>>>> Looking at the Project Properties for qSlicerBaseQTCore I notice
>>>>>> something odd. Here is a snippet from the list of Linker > Input >
>>>>>> Additional Dependencies:
>>>>>>
>>>>>> ...
>>>>>> C:\s\b\ITKv4-build\lib\Release\itktiff-4.6.lib
>>>>>> C:\s\b\ITKv4-build\lib\Release\itkjpeg-4.6.lib
>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOMRC-4.6.lib
>>>>>> C:\s\b\ITKv4-build\lib\Release\ITKIOImageBase-4.6.lib
>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkInfovis.lib
>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkWidgets.lib
>>>>>> C:\s\b\VTKv5-build\bin\Release\vtkVolumeRendering.lib
>>>>>> ..\..\lib\Slicer-4.3\Release\FreeSurfer.lib
>>>>>> ITKCommon.lib
>>>>>> C:\Qt64\4.8.1\lib\QtOpenGL4.lib
>>>>>> ...
>>>>>>
>>>>>> For some reason ITKCommon.lib is treated differently from all the
>>>>>> other (at first sight) ITK libraries. Any ideas about how I might fix this?
>>>>>> If I edit the linker configuration for qSlicerBaseQTCore to point correctly
>>>>>> to the ITKCommon library it builds OK, but I'd rather not have to do this
>>>>>> 40+ times.
>>>>>>
>>>>>> Thanks again
>>>>>> Gib
>>>>>> ________________________________
>>>>>> From: slicer-devel-bounces at bwh.harvard.edu
>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Gib Bogle
>>>>>> [g.bogle at auckland.ac.nz]
>>>>>> Sent: Saturday, 13 September 2014 12:59 p.m.
>>>>>>
>>>>>> To: Steve Pieper
>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>
>>>>>> Hi Steve,
>>>>>>
>>>>>> All goes well until the point where the qSlicer*.lib get made. The
>>>>>> first error, while building qSlicerBaseQTCore.lib, is:
>>>>>>
>>>>>> LINK : fatal error LNK1181: cannot open input file 'ITKCommon.lib'
>>>>>>
>>>>>> I don't know how to interpret this. I am guessing that it wants to
>>>>>> link the ITK library that was just built, i.e.:
>>>>>> \s\b\ITKv4-build\lib\Release\ITKCommon-4.6.lib
>>>>>> This is the first of about 40 such link errors.
>>>>>>
>>>>>> I'm not sure if ITK really needed to be built, since it is already
>>>>>> installed (64-bit) on my system, but I didn't see any option for skipping
>>>>>> that step (same for VTK). Is an INSTALL step for ITK needed? Should I set
>>>>>> ITK_DIR appropriately?
>>>>>>
>>>>>> Thanks
>>>>>> Gib
>>>>>> ________________________________
>>>>>> From: Steve Pieper [pieper at isomics.com]
>>>>>> Sent: Saturday, 13 September 2014 9:02 a.m.
>>>>>> To: Gib Bogle
>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>
>>>>>> Hi Gib -
>>>>>>
>>>>>> I'd give a qualified 'yes' answer. Technically what you propose is
>>>>>> quite reasonable, and would be workable. But if you haven't built a big
>>>>>> package on windows before there are quite a few prerequites (qt, cmake, git,
>>>>>> visual studio...) and odd things can go wrong if it isn't all done just
>>>>>> right. That said, slicer is actually quite well supported on windows,
>>>>>> better, IMHO, than many cross-platform systems. But windows is really the
>>>>>> trickiest platform in my experience.
>>>>>>
>>>>>> -Steve
>>>>>>
>>>>>>
>>>>>> On Fri, Sep 12, 2014 at 4:32 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Steve,
>>>>>>>
>>>>>>> Do you think I would be able to build Slicer myself, with
>>>>>>> ITK_USE_64BITS_IDS and leaving out BRAINSTools and anything else that
>>>>>>> depends on either ITKDeprecated or ITKV3Compatibility? My need at this
>>>>>>> point is simply for a 3D viewer that can handle big images.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Gib
>>>>>>> ________________________________
>>>>>>> From: Gib Bogle
>>>>>>> Sent: Wednesday, 10 September 2014 10:34 a.m.
>>>>>>> To: Jean-Christophe Fillion-Robin; Steve Pieper
>>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>> Subject: RE: [slicer-devel] BigTIFF
>>>>>>>
>>>>>>> Hi Jean-Christophe,
>>>>>>>
>>>>>>> Any idea when 4.5 will enter the world?
>>>>>>>
>>>>>>> Cheers
>>>>>>> Gib
>>>>>>> ________________________________
>>>>>>> From: slicer-devel-bounces at bwh.harvard.edu
>>>>>>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Jean-Christophe
>>>>>>> Fillion-Robin [jchris.fillionr at kitware.com]
>>>>>>> Sent: Wednesday, 10 September 2014 10:31 a.m.
>>>>>>> To: Steve Pieper
>>>>>>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>
>>>>>>> Hi Folks,
>>>>>>>
>>>>>>> Thanks to Brad Lowekamp, Slicer core (r23663) does NOT depend on
>>>>>>> either ITKDeprecated or ITKV3Compatibility.
>>>>>>>
>>>>>>> That said, BRAINSTools and some extensions are still depending on
>>>>>>> these module. All details are captured here:
>>>>>>>
>>>>>>> http://na-mic.org/Mantis/view.php?id=3825#c12486
>>>>>>>
>>>>>>> Note also that this will NOT be addressed for Slicer 4.4 release. The
>>>>>>> enabling of ITK_USE_64BITS_IDS that will allow BigTiff to be loaded is
>>>>>>> planned for 4.5.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Jc
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Sep 5, 2014 at 10:26 AM, Steve Pieper <pieper at isomics.com>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi Matt -
>>>>>>>>
>>>>>>>> Thanks, that's helpful.
>>>>>>>>
>>>>>>>> I suspect that for slicer, the only real issues will be in vtkITK,
>>>>>>>> which includes all the file IO adapters. But I think it will be pretty
>>>>>>>> straightforward.
>>>>>>>>
>>>>>>>> But there's no reason to start that until we know that BRAINSTools
>>>>>>>> will work - right now at least some of them depend on ITKDeprecated.
>>>>>>>>
>>>>>>>> -Steve
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Sep 5, 2014 at 10:06 AM, Matt McCormick
>>>>>>>> <matt.mccormick at kitware.com> wrote:
>>>>>>>>>
>>>>>>>>> Here is what the process would look like:
>>>>>>>>>
>>>>>>>>> 0) Start with a clean software quality dashboard.
>>>>>>>>> 1) Set ITKV3_COMPATIBILITY to OFF in
>>>>>>>>> Superbuild/External_ITKv4.cmake
>>>>>>>>> 2) Rebuild and encounter errors and test failures.
>>>>>>>>> 3) Fix the errors with the help of the ITK migration guide [1] and
>>>>>>>>> the
>>>>>>>>> ITK mailing list [2]. They usually fairly strait forward changes
>>>>>>>>> (minor modifications to the API, etc).
>>>>>>>>> 4) Set ITK_USE_64BITS_IDS to ON.
>>>>>>>>> 5) Profit.
>>>>>>>>>
>>>>>>>>> HTH,
>>>>>>>>> Matt
>>>>>>>>>
>>>>>>>>> [1] http://itk.org/migrationv4/
>>>>>>>>>
>>>>>>>>> [2] http://www.itk.org/ITK/help/mailing.html
>>>>>>>>>
>>>>>>>>> On Thu, Sep 4, 2014 at 4:52 PM, Steve Pieper <pieper at isomics.com>
>>>>>>>>> wrote:
>>>>>>>>> > Yes, agreed it's a good goal and I believe the expertise exists,
>>>>>>>>> > but it's
>>>>>>>>> > looking like there's a fair amount of code to retrofit.
>>>>>>>>> >
>>>>>>>>> > Maybe Hans, Brad, Matt or others could provide some idea just
>>>>>>>>> > what is
>>>>>>>>> > involved?
>>>>>>>>> >
>>>>>>>>> > -Steve
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> > On Thu, Sep 4, 2014 at 4:50 PM, Gib Bogle
>>>>>>>>> > <g.bogle at auckland.ac.nz> wrote:
>>>>>>>>> >>
>>>>>>>>> >> :( I imagine that people are increasingly working with very
>>>>>>>>> >> large
>>>>>>>>> >> datasets, so the number of people who would like to have this
>>>>>>>>> >> capability
>>>>>>>>> >> will grow. I, alas, am not an ITK expert.
>>>>>>>>> >> ________________________________
>>>>>>>>> >> From: Steve Pieper [pieper at isomics.com]
>>>>>>>>> >> Sent: Friday, 5 September 2014 8:42 a.m.
>>>>>>>>> >>
>>>>>>>>> >> To: Gib Bogle
>>>>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu
>>>>>>>>> >> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>> >>
>>>>>>>>> >> Alas the build where I enabled 64 bit id's failed to even
>>>>>>>>> >> configure
>>>>>>>>> >> properly. Lots of key code depends on the ITKDeprecated module,
>>>>>>>>> >> like vtkITK
>>>>>>>>> >> and various components of BRAINSTools. So I would say some ITK
>>>>>>>>> >> experts are
>>>>>>>>> >> going to need to dig in before this mode can be enabled.
>>>>>>>>> >>
>>>>>>>>> >> -Steve
>>>>>>>>> >>
>>>>>>>>> >>
>>>>>>>>> >> On Thu, Sep 4, 2014 at 4:08 PM, Gib Bogle
>>>>>>>>> >> <g.bogle at auckland.ac.nz> wrote:
>>>>>>>>> >>>
>>>>>>>>> >>> I await the results with interest...
>>>>>>>>> >>> ________________________________
>>>>>>>>> >>> From: slicer-devel-bounces at bwh.harvard.edu
>>>>>>>>> >>> [slicer-devel-bounces at bwh.harvard.edu] on behalf of Steve
>>>>>>>>> >>> Pieper
>>>>>>>>> >>> [pieper at isomics.com]
>>>>>>>>> >>> Sent: Friday, 5 September 2014 1:32 a.m.
>>>>>>>>> >>> To: Bradley Lowekamp
>>>>>>>>> >>>
>>>>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>> >>>
>>>>>>>>> >>> Makes sense, thanks for clarifying Brad. Jc recently moved out
>>>>>>>>> >>> a lot of
>>>>>>>>> >>> legacy CLI code - perhaps those were the main places
>>>>>>>>> >>> ITKV3_COMPATIBILITY was
>>>>>>>>> >>> required? I kicked off a build to see what will happen.
>>>>>>>>> >>>
>>>>>>>>> >>> -Steve
>>>>>>>>> >>>
>>>>>>>>> >>>
>>>>>>>>> >>> On Thu, Sep 4, 2014 at 8:36 AM, Bradley Lowekamp
>>>>>>>>> >>> <blowekamp at mail.nih.gov>
>>>>>>>>> >>> wrote:
>>>>>>>>> >>>>
>>>>>>>>> >>>> Steve,
>>>>>>>>> >>>>
>>>>>>>>> >>>> Yes, this is certainly an issue with how ITK has been
>>>>>>>>> >>>> configured in
>>>>>>>>> >>>> Slicer.
>>>>>>>>> >>>>
>>>>>>>>> >>>> To turn on the 64-bit IDs for windows 64, ITKV3_COMPATIBILITY
>>>>>>>>> >>>> needs to
>>>>>>>>> >>>> be disabled, and then the ITKDeprecated module can no longer
>>>>>>>>> >>>> be used. I have
>>>>>>>>> >>>> brought these issue up before and offered assistance but no
>>>>>>>>> >>>> one wanted to
>>>>>>>>> >>>> champion changing these configuration flags.
>>>>>>>>> >>>>
>>>>>>>>> >>>> Brad
>>>>>>>>> >>>>
>>>>>>>>> >>>> On Sep 3, 2014, at 6:30 PM, Steve Pieper <pieper at isomics.com>
>>>>>>>>> >>>> wrote:
>>>>>>>>> >>>>
>>>>>>>>> >>>> Hi Brad -
>>>>>>>>> >>>>
>>>>>>>>> >>>> Right, this is not tiff specific but is ITK specific. I was
>>>>>>>>> >>>> able to
>>>>>>>>> >>>> create a 1650^3 volume (of doubles) in VTK, save with slicer's
>>>>>>>>> >>>> vtkNRRDWriter
>>>>>>>>> >>>> and reload with vtkNRRDReader. Could not read the same file
>>>>>>>>> >>>> with ITK's NRRD
>>>>>>>>> >>>> reader. This was all on a slicer current trunk build with
>>>>>>>>> >>>> default options
>>>>>>>>> >>>> on win7 64bit.
>>>>>>>>> >>>>
>>>>>>>>> >>>> So are we out of luck enabling 64bit IDs or is it just
>>>>>>>>> >>>> something nobody
>>>>>>>>> >>>> has tried?
>>>>>>>>> >>>>
>>>>>>>>> >>>> -Steve
>>>>>>>>> >>>>
>>>>>>>>> >>>>
>>>>>>>>> >>>> On Wed, Sep 3, 2014 at 11:17 AM, Bradley Lowekamp
>>>>>>>>> >>>> <blowekamp at mail.nih.gov> wrote:
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> Steve,
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> Can you usr/load any image greater that 2GB into Slicer on
>>>>>>>>> >>>>> windows 64?
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> There should be some image source filters in the
>>>>>>>>> >>>>> SimpleFilters modules
>>>>>>>>> >>>>> to generate images. I don't think this issue is tiff
>>>>>>>>> >>>>> specific.
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> Bread
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> On Sep 3, 2014, at 11:03 AM, Steve Pieper
>>>>>>>>> >>>>> <pieper at isomics.com> wrote:
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> I was able to replicate the crash - Thanks for the data, Gib!
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> I happens in the itk tiff reader. I created a bug report and
>>>>>>>>> >>>>> pasted in
>>>>>>>>> >>>>> a stack trace and put a link to the data.
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> http://na-mic.org/Bug/view.php?id=3825
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> -Steve
>>>>>>>>> >>>>>
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> On Tue, Sep 2, 2014 at 5:24 PM, Bradley Lowekamp
>>>>>>>>> >>>>> <blowekamp at mail.nih.gov> wrote:
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> Matt, I was just about to point that out.
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> The other things is the compatibility flag:
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv4.cmake#L48
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> I think the prevents the 64-bit IDs being used. That is it's
>>>>>>>>> >>>>>> still
>>>>>>>>> >>>>>> long not long long, so that it's "compatible" with ITKv3.
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkIntTypes.h#L122
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> Brad
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> On Sep 2, 2014, at 5:15 PM, Steve Pieper
>>>>>>>>> >>>>>> <pieper at isomics.com> wrote:
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> Thanks Matt - that looks logical! Let's see if we can
>>>>>>>>> >>>>>> replicate the
>>>>>>>>> >>>>>> issue and then we can see if that has any side effects.
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>>
>>>>>>>>> >>>>>> On Tue, Sep 2, 2014 at 4:44 PM, Matt McCormick
>>>>>>>>> >>>>>> <matt.mccormick at kitware.com> wrote:
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>> Here is an untested patch that may fix the problem:
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>> https://github.com/thewtex/Slicer/commit/24d571c970d012015a95ac6063e3b0a3fede96fb
>>>>>>>>> >>>>>>>
>>>>>>>>> >>>>>>> On Tue, Sep 2, 2014 at 4:42 PM, Gib Bogle
>>>>>>>>> >>>>>>> <g.bogle at auckland.ac.nz>
>>>>>>>>> >>>>>>> wrote:
>>>>>>>>> >>>>>>> > I have to do something else for a while now. I'll get
>>>>>>>>> >>>>>>> > back to this
>>>>>>>>> >>>>>>> > later.
>>>>>>>>> >>>>>>> > ________________________________
>>>>>>>>> >>>>>>> > From: Steve Pieper [pieper at isomics.com]
>>>>>>>>> >>>>>>> > Sent: Wednesday, 3 September 2014 8:41 a.m.
>>>>>>>>> >>>>>>> >
>>>>>>>>> >>>>>>> > To: Gib Bogle
>>>>>>>>> >>>>>>> > Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu
>>>>>>>>> >>>>>>> > Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>> >>>>>>> >
>>>>>>>>> >>>>>>> > Sure, if that works that's fine. Or maybe Brad knows how
>>>>>>>>> >>>>>>> > to
>>>>>>>>> >>>>>>> > generate a big
>>>>>>>>> >>>>>>> > file with SimpleITK. Or a statically linked executable
>>>>>>>>> >>>>>>> > for any
>>>>>>>>> >>>>>>> > standard
>>>>>>>>> >>>>>>> > platform should be fine too.
>>>>>>>>> >>>>>>> >
>>>>>>>>> >>>>>>> >
>>>>>>>>> >>>>>>> > On Tue, Sep 2, 2014 at 4:40 PM, Gib Bogle
>>>>>>>>> >>>>>>> > <g.bogle at auckland.ac.nz>
>>>>>>>>> >>>>>>> > wrote:
>>>>>>>>> >>>>>>> >>
>>>>>>>>> >>>>>>> >> On second thoughts a very simple image will compress to
>>>>>>>>> >>>>>>> >> a
>>>>>>>>> >>>>>>> >> reasonable size.
>>>>>>>>> >>>>>>> >> Slicer seems to handle the compression modes used by ITK
>>>>>>>>> >>>>>>> >> without
>>>>>>>>> >>>>>>> >> problems.
>>>>>>>>> >>>>>>> >> ________________________________
>>>>>>>>> >>>>>>> >> From: Steve Pieper [pieper at isomics.com]
>>>>>>>>> >>>>>>> >> Sent: Wednesday, 3 September 2014 8:31 a.m.
>>>>>>>>> >>>>>>> >> To: Gib Bogle
>>>>>>>>> >>>>>>> >> Cc: Bradley Lowekamp; slicer-devel at bwh.harvard.edu
>>>>>>>>> >>>>>>> >> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>> >>>>>>> >>
>>>>>>>>> >>>>>>> >> Hi -
>>>>>>>>> >>>>>>> >>
>>>>>>>>> >>>>>>> >> Is there an easy way to generate a big tiff like this,
>>>>>>>>> >>>>>>> >> for example
>>>>>>>>> >>>>>>> >> with a
>>>>>>>>> >>>>>>> >> few lines of SimpleITK code? (Easier than trying to
>>>>>>>>> >>>>>>> >> transfer a
>>>>>>>>> >>>>>>> >> 4.5GB file
>>>>>>>>> >>>>>>> >> from NZ).
>>>>>>>>> >>>>>>> >>
>>>>>>>>> >>>>>>> >> -Steve
>>>>>>>>> >>>>>>> >>
>>>>>>>>> >>>>>>> >>
>>>>>>>>> >>>>>>> >> On Tue, Sep 2, 2014 at 4:26 PM, Gib Bogle
>>>>>>>>> >>>>>>> >> <g.bogle at auckland.ac.nz>
>>>>>>>>> >>>>>>> >> wrote:
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> Hi Brad,
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> I installed Slicer-4.3.1 64-bit version on Windows 7.
>>>>>>>>> >>>>>>> >>> I can load
>>>>>>>>> >>>>>>> >>> a tiff
>>>>>>>>> >>>>>>> >>> file that is about 1 GB (grey-scale 1000x1000x1000),
>>>>>>>>> >>>>>>> >>> but a couple
>>>>>>>>> >>>>>>> >>> of bigger
>>>>>>>>> >>>>>>> >>> files fail. When I try to open a file that is about
>>>>>>>>> >>>>>>> >>> 4.5 GB
>>>>>>>>> >>>>>>> >>> (actually when I
>>>>>>>>> >>>>>>> >>> try to add data to the scene) the program crashes
>>>>>>>>> >>>>>>> >>> immediately,
>>>>>>>>> >>>>>>> >>> exception
>>>>>>>>> >>>>>>> >>> code c0000005. The result with an image of about half
>>>>>>>>> >>>>>>> >>> this size
>>>>>>>>> >>>>>>> >>> is the
>>>>>>>>> >>>>>>> >>> same. Sometimes the behaviour is slightly different -
>>>>>>>>> >>>>>>> >>> I see the
>>>>>>>>> >>>>>>> >>> "Loading..." popup, but it's stuck on 15% and the
>>>>>>>>> >>>>>>> >>> windows greys
>>>>>>>>> >>>>>>> >>> out.
>>>>>>>>> >>>>>>> >>> Nothing happens after that, until I click the x button
>>>>>>>>> >>>>>>> >>> on the
>>>>>>>>> >>>>>>> >>> popup, and the
>>>>>>>>> >>>>>>> >>> program crashes.
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> These files were all written with ITK. The reason I
>>>>>>>>> >>>>>>> >>> installed
>>>>>>>>> >>>>>>> >>> Slicer is
>>>>>>>>> >>>>>>> >>> simply to be able to view big files - Irfanview is very
>>>>>>>>> >>>>>>> >>> good but
>>>>>>>>> >>>>>>> >>> BigTIFFs
>>>>>>>>> >>>>>>> >>> are not enabled.
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> Is it a case of having to build Slicer myself, with
>>>>>>>>> >>>>>>> >>> different
>>>>>>>>> >>>>>>> >>> build
>>>>>>>>> >>>>>>> >>> options?
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> Thanks
>>>>>>>>> >>>>>>> >>> Gib
>>>>>>>>> >>>>>>> >>> ________________________________
>>>>>>>>> >>>>>>> >>> From: Bradley Lowekamp [blowekamp at mail.nih.gov]
>>>>>>>>> >>>>>>> >>> Sent: Wednesday, 3 September 2014 1:00 a.m.
>>>>>>>>> >>>>>>> >>> To: Gib Bogle
>>>>>>>>> >>>>>>> >>> Cc: slicer-devel at bwh.harvard.edu
>>>>>>>>> >>>>>>> >>> Subject: Re: [slicer-devel] BigTIFF
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> Hello,
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> I believe Slicer is using ITK's libtiff library 4.0.3,
>>>>>>>>> >>>>>>> >>> and the
>>>>>>>>> >>>>>>> >>> associated
>>>>>>>>> >>>>>>> >>> ITK ImageIO. This should support BigTIFFs. Could you
>>>>>>>>> >>>>>>> >>> please
>>>>>>>>> >>>>>>> >>> provide more
>>>>>>>>> >>>>>>> >>> detail about your issue?
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> Brad
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> On Sep 1, 2014, at 5:14 PM, Gib Bogle
>>>>>>>>> >>>>>>> >>> <g.bogle at auckland.ac.nz>
>>>>>>>>> >>>>>>> >>> wrote:
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> Hi,
>>>>>>>>> >>>>>>> >>> It seems that Slicer (the Windows version, anyway) does
>>>>>>>>> >>>>>>> >>> not
>>>>>>>>> >>>>>>> >>> handle
>>>>>>>>> >>>>>>> >>> BigTIFFs. Is there a plan to add this capability?
>>>>>>>>> >>>>>>> >>> Thanks
>>>>>>>>> >>>>>>> >>> Gib
>>>>>>>>> >>>>>>> >>> _______________________________________________
>>>>>>>>> >>>>>>> >>> slicer-devel mailing list
>>>>>>>>> >>>>>>> >>> slicer-devel at bwh.harvard.edu
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
>>>>>>>>> >>>>>>> >>> To unsubscribe: send email to
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>>>>>>>>> >>>>>>> >>> unsubscribe as
>>>>>>>>> >>>>>>> >>> the
>>>>>>>>> >>>>>>> >>> subject
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>>>>>>>>> >>>>>>> >>>
>>>>>>>>> >>>>>>> >>>
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>>>>>>>>> >
>>>>>>>>> > _______________________________________________
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> +1 919 869 8849
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
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