Teem fix #5
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Teem fix #5
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bugfix for fibertractdispersion
In a heirarchial build, it is unnecessary to recursively include the find_package options in subdirectories.
Since calling 'cmake_minimum_required' with version X.Y.Z implies that policy associated with version X.Y.Z will be set, this commit removes the redundant call to "cmake_policy". For more details, see [1] [1] http://www.cmake.org/cmake/help/v2.8.9/cmake.html#command:cmake_minimum_required
Since the checks are already done in "Common.cmake" that is included from both "SuperBuild.cmake" and "UKFTractography.cmake", this commit removed the duplicate code.
Since the variable MODULE_INCLUDE_DIRECTORIES is passed to the macro SEMMacroBuildCLI, there are no need to manually include the directories. This commit removes the "redundant" call.
The top-level CMakeLists.cmake, based on the value of the UKFTractography_SUPERBUILD variable, already conditionally includes either UKFTractography.cmake or SuperBuild.cmake. This commit removes the SuperBuild/CMakeLists.txt file that contain code already existing in SuperBuild.cmake.
Since the project makes use of SEMMacroBuildCLI macro, there is no need to selectively integrate "GenerateCLP" and then manually include the macro. By simply looking up the SlicerExecutionModel package and including the associated *_USE_FILE, all required macro will be available.
…rentiated This commits enables the following cases: * By default the extension will be built as a standalone project using superbuild to download the required dependencies. * Slicer extension can simply be built specifying -DUKFTractography_BUILD_SLICER_EXTENSION:BOOL=ON -DSlicer_DIR:PATH=/path/to/Slicer-SuperBuild/Slicer-build -DEigen_DIR:PATH=/path/to/Eigen-build
Since the teem library provides a TeemConfig.cmake file if it is either
build as part of Superbuild or install on the system, it is sufficient
to use the "find_package()" call.
This commit fixes a configure error [1] by removing the extra call to
"find_library" that ended up finding the teem library installed on the
system.
More specifically, in the Slicer case, the Teem_DIR was used by the
previous call to "find_package(teem)" to find the teem library built by
Slicer.
Modules ended up referencing a mix of system teem library and Slicer teem
library.
[1] Configure rrror fixed by this commit:
8<----8<----8<----8<----8<----8<----8<----8<----
Cannot generate a safe linker search path for target ConvertVTK because
files in some directories may conflict with libraries in implicit
directories:
link library [libteem.so] in /usr/lib may be hidden by files in:
/home/jchris/Projects/Slicer-2-SuperBuild-Release/teem-build/bin
8<----8<----8<----8<----8<----8<----8<----8<----
On system without Qt development libraries installed in a default system location, Eigen couldn't be built. This commit removed the Qt dependency by disabling the test depending on Qt.
This commit update the external project so that it conditionally download and build teem.
This commit remove the Slicer specific settings from SlicerExectionModel and ensure the project will be configured with the expected values. Then, it is not needed anymore to overwrite the SlicerExecutionModel_DEFAULT_* variable in the current scope. This has been tested for both a SlicerExtension and a standalone built. In both case the libraries are built where expected.
Instead of manually creating list of option to give to each project, this commits removed redundant code and leverage the "mark_as_superbuild" macro. By specifying the ALL_PROJECTS value, we ensure that the option will be passed down to all external projects. By using "ExternalProject_Include_Dependencies", the CMAKE_GENERATOR option will be automatically passed to each project using it. This commit removed the explicit management of this parameter. Finally, since the passing of the _DIR variable is already set by calling "mark_as_superbuild" in each external project, this commit removed the explicit management of these.
…onfigure-errors Simplify buildsystem and fix configure errors
Due to Artichoke bug pnlbwh#6 [1], it is required to set the value in the cache so that they can be considered when configuring the external projects. This commit will fix the build error reported below: // ---- /usr/bin/ld: /projects/pnl/home/petersv/testukf/build/lib/libitksys-4.6.a(SystemTools.cxx.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /projects/pnl/home/petersv/testukf/build/lib/libitksys-4.6.a: could not read symbols: Bad value collect2: ld returned 1 exit status // ---- [1] commontk/Artichoke#6
COMP: Ensure CMAKE flags are passed down to all external project.
Fixing some bugs in computedispersion.cxx that probably resulted from typos. In addition, I changed the line if(inDiskPlaneCount > 0) to > 10 for speed up. There is no need to perform the computations inside this if statement if inDiskPlaneCount < 10, as the function will return false in this case - see the following if statement.
COMP: remove obsolete --simpleTensorModel flag from tests COMP: fixed path for teem libraries
COMP: Fix vtk fiber bundle writer This was work done by Kent Williams
…scalar-value-per-point data gets written as FieldData.
BUG: always write out DDF as THE scalar data for a fiber bundleOther sca...
…e XML Added grant numbers to acknowledgements, added some names to contributors list, and changed some default settings in the UI as suggested by Ron.
Reverting some of the changes to teem library paths made in commit cf25b45, July 11th 2014, which were causing the Slicer Extension build to crash.
COMP: Make CompressedSensing and fibertractdisperssion optional The default is not to build either
The existing code works to build the UKF slicer extension and the new search code might not work when built as a slicer extension, so use the old behavior if the extension is being built.
Fix teem link
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Hi Kent, I don't have write access to the BRAINSia repositories, I only have Peter On 08/18/2014 02:13 PM, Kent Williams wrote:
The information in this e-mail is intended only for the person to whom it is |
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I didn’t know you needed access to the pulled-from repo to merge a pull request. Why don’t you just make this change? index 0ced8c2..ac39e35 100644 From: petersv2 <[email protected]mailto:[email protected]> Hi Kent, I don't have write access to the BRAINSia repositories, I only have Peter On 08/18/2014 02:13 PM, Kent Williams wrote:
The information in this e-mail is intended only for the person to whom it is — Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. |
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I didn't know either, but I just tried and it didn't work :-) OK, I'll Thanks, On 08/18/2014 02:23 PM, Kent Williams wrote:
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This should fix the UKF standalone build