ENH: Added BRAINSABC,BCD,BRAINSFit,BRAINSCommon

BRAINSABC/CMakeLists.txt

@@ -0,0 +1,41 @@
+project(BRAINSABC)
+set(LOCAL_PROJECT_NAME BRAINSABC)
+cmake_minimum_required(VERSION 2.8)
+cmake_policy(VERSION 2.8)
+
+enable_testing()
+include(CTest)
+
+find_package(BRAINSCommonLib NO_MODULE REQUIRED)
+include(${BRAINSCommonLib_USE_FILE})
+
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/PreventInSourceBuilds.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBuildMacros.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMMacroBuildCLI.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBRAINS3BuildMacros.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/IJMacros.txt)
+
+###
+SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+SETIFEMPTY(CMAKE_BUNDLE_OUTPUT_DIRECTORY  ${CMAKE_CURRENT_BINARY_DIR}/bin)
+link_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+
+if(NOT ITK_FOUND)
+    find_package(ITK REQUIRED)
+    include(${ITK_USE_FILE})
+endif(NOT ITK_FOUND)
+
+#-----------------------------------------------------------------------------
+# Output directories.
+#
+#SETOPTIONALDEBUGIMAGEVIEWER()
+
+###
+add_subdirectory(brainseg)
+
+if(1)
+  add_subdirectory(TestSuite)
+endif(1)
+

BRAINSABC/CTestConfig.cmake

@@ -0,0 +1,14 @@
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   enable_testing()
+##   include(CTest)
+set(CTEST_PROJECT_NAME "BRAINSABC")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "testing.psychiatry.uiowa.edu")
+set(CTEST_DROP_LOCATION "/CDash/submit.php?project=BRAINSABC")
+set(CTEST_DROP_SITE_CDASH TRUE)
+set(CTEST_TEST_TIMEOUT 3600)  ## Set timeout to one hour for now.  There is a lot of work to be done.

BRAINSABC/TestSuite/AtlasPVDefinition.xml.md5

@@ -0,0 +1 @@
+24d6e8d67a2fa417853e1b86449c8cfb

BRAINSABC/TestSuite/BRAINSABCTest.cxx

@@ -0,0 +1,22 @@
+//
+// A test driver to append the
+// itk image processing test
+// commands to an
+// the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char * []);
+
+int BRAINSABCTest(int argc, char* * argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}

BRAINSABC/TestSuite/BlendImageFilterTest.cxx

@@ -0,0 +1,53 @@
+#include "itkImage.h"
+#include "itkBlendImageFilter.h"
+#include "itkRandomImageSource.h"
+#include "itkImageRegionConstIterator.h"
+#include "vnl/vnl_math.h"
+
+int main(int, char * *)
+{
+  typedef itk::Image<float, 2> ImageType;
+
+  std::cout << "Create input image using RandomImageSource" << std::endl;
+  ImageType::Pointer images[2];
+  for( unsigned i = 0; i < 2; i++ )
+    {
+    typedef itk::RandomImageSource<ImageType> SourceType;
+    SourceType::Pointer      source = SourceType::New();
+    ImageType::SizeValueType size[2] = {64, 64};
+    source->SetSize( size );
+    source->SetMin(0.0);
+    source->SetMax(1.0);
+    source->Update();
+    images[i] = source->GetOutput();
+    }
+  typedef itk::BlendImageFilter<ImageType, ImageType>
+    BlendImageFilterType;
+  BlendImageFilterType::Pointer filter =
+    BlendImageFilterType::New();
+  filter->SetInput1(images[0]);
+  filter->SetInput2(images[1]);
+  filter->SetBlend1(0.2);
+  filter->SetBlend2(0.8);
+  filter->Update();
+  ImageType::Pointer blendImage = filter->GetOutput();
+  itk::ImageRegionConstIterator<ImageType>
+  it1(images[0],
+      images[0]->GetLargestPossibleRegion() ),
+  it2(images[1],
+      images[1]->GetLargestPossibleRegion() ),
+  itBlend(blendImage,
+          blendImage->GetLargestPossibleRegion() );
+  for( ; !it1.IsAtEnd() && !it2.IsAtEnd() && !itBlend.IsAtEnd();
+       ++it1, ++it2, ++itBlend )
+    {
+    float blend = (it1.Get() * 0.2) + (it2.Get() * 0.8);
+    if( vcl_fabs(blend - itBlend.Get() ) > 0.0001 )
+      {
+      std::cerr << "Expected " << blend << " found " << itBlend.Get()
+                << std::endl;
+      exit(1);
+      }
+    }
+  exit(0);
+}

BRAINSABC/TestSuite/CMakeLists.txt

@@ -0,0 +1,60 @@
+list(APPEND ExternalData_URL_TEMPLATES
+  # Local data store populated by the ITK pre-commit hook
+  "file:///${CMAKE_SOURCE_DIR}/.ExternalData/%(algo)/%(hash)"
+  # Data published by Iowa Psychiatry web interface
+  "http://www.psychiatry.uiowa.edu/users/brainstestdata/ctestdata/%(algo)/%(hash)"
+
+  # Data published by MIDAS
+  "http://midas.kitware.com/api/rest/midas.bitstream.by.hash?hash=%(hash)&algorithm=%(algo)"
+
+  # Data published by developers using git-gerrit-push.
+  "http://www.itk.org/files/ExternalData/%(algo)/%(hash)"
+  )
+
+# Tell ExternalData commands to transform raw files to content links.
+# TODO: Condition this feature on presence of our pre-commit hook.
+set(ExternalData_LINK_CONTENT MD5)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/ExternalData.cmake)
+
+include_directories(
+  ${BRAINSABC_SOURCE_DIR}/brainseg
+  ${BRAINSABC_SOURCE_DIR}/common
+  ${BRAINSABC_BINARY_DIR}/brainseg
+)
+
+
+
+MakeTestDriverFromSEMTool(BRAINSABC BRAINSABCTest.cxx)
+
+ExternalData_add_test( FetchData NAME BRAINSABCLongTest
+  COMMAND ${LAUNCH_EXE} $<TARGET_FILE:BRAINSABCTestDriver>
+    --compare DATA{test_data/refResults/labels.nii.gz}
+               ${CMAKE_CURRENT_BINARY_DIR}/labels.nii.gz
+    --compareIntensityTolerance 1
+    --compareRadiusTolerance 1
+    --compareNumberOfPixelsTolerance 10000
+  BRAINSABCTest
+  --inputVolumes DATA{test_data/small_ISO_T1_REP0.nii.gz} --inputVolumes DATA{test_data/small_ISO_T2_REP0.nii.gz}
+  --outputVolumes ${CMAKE_CURRENT_BINARY_DIR}/T1_cleaned.nii.gz,${CMAKE_CURRENT_BINARY_DIR}/T2_cleaned.nii.gz
+  --outputLabels ${CMAKE_CURRENT_BINARY_DIR}/labels.nii.gz
+  --outputDirtyLabels ${CMAKE_CURRENT_BINARY_DIR}/dirty_labels.nii.gz
+  --posteriorTemplate ${CMAKE_CURRENT_BINARY_DIR}/POST_%s.nii.gz
+  --inputVolumeTypes T1,T2
+  --filterIteration 3
+  --maxIterations 2
+  --maxBiasDegree 2
+  --debuglevel 0
+  --outputFormat NIFTI
+  --outputDir ${CMAKE_CURRENT_BINARY_DIR}
+  --gridSize  5,3,4
+  --atlasDefinition ${CMAKE_CURRENT_BINARY_DIR}/../../src/bin/Atlas/Atlas_20110607/AtlasPVDefinition.xml
+)
+set_tests_properties(BRAINSABCLongTest PROPERTIES TIMEOUT 6500)
+
+if(0) # This should be restored after fixing.
+add_executable(BlendImageFilterTest BlendImageFilterTest.cxx)
+target_link_libraries(BlendImageFilterTest ${ITK_LIBRARIES})
+ExternalData_add_test( FetchData NAME BlendImageFilterTest COMMAND ${LAUNCH_EXE}  $<TARGET_FILE:BlendImageFilterTest> )
+endif()
+
+ExternalData_Add_Target( FetchData )  # Name of data management target