merging with master. Had a couple of conflicts in SolveInverseProblemWithTikhonov module and the functional tests

Author: jcollfont

.travis.yml

@@ -16,12 +16,12 @@ matrix:
 before_install:
 - date -u
 - uname -a
-- sudo apt-get install mesa-common-dev libgl1-mesa-dev mesa-utils-extra libglapi-mesa ninja-build
+- sudo apt-get install mesa-common-dev libgl1-mesa-dev mesa-utils-extra libglapi-mesa ninja-build libqt4-dev qt4-qmake libqt4-opengl-dev
 
 script:
   - cd bin
   - cmake -GNinja -DTRAVIS_BUILD:BOOL=ON ../Superbuild
-  - travis_wait 40 ninja
+  - travis_wait 80 ninja
   - cd SCIRun
   - ./Algorithm_Layer_Test
   - ./Modules_Factory_Tests --gtest_filter=*HardCodedModuleFactoryTests*

Superbuild/SCIRunDataExternal.cmake

@@ -0,0 +1,47 @@
+#  For more information, please see: http://software.sci.utah.edu
+#
+#  The MIT License
+#
+#  Copyright (c) 2015 Scientific Computing and Imaging Institute,
+#  University of Utah.
+#
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+#  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+#  DEALINGS IN THE SOFTWARE.
+
+SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
+
+SET(data_SVN_URL "https://gforge.sci.utah.edu/svn/CIBCData")
+SET(sci_data_DIR "${CMAKE_BINARY_DIR}/SCIRunData")
+
+ExternalProject_Add(SCI_data_external
+  SVN_REPOSITORY "${data_SVN_URL}"
+  SVN_TRUST_CERT 1
+  SVN_USERNAME "anonymous"
+  SVN_PASSWORD ""
+  DOWNLOAD_DIR "${sci_data_DIR}"
+  PATCH_COMMAND ""
+  INSTALL_DIR ""
+  INSTALL_COMMAND ""
+  CONFIGURE_COMMAND ""
+  CMAKE_COMMAND ""
+  BUILD_COMMAND ""
+)
+
+ExternalProject_Get_Property(SCI_data_external BINARY_DIR)
+SET(SCI_DATA_DIR ${sci_data_DIR} CACHE PATH "")

Superbuild/Superbuild.cmake

@@ -74,6 +74,10 @@ OPTION(BUILD_WITH_PYTHON "Build with python support." ON)
 # Configure tetgen
 OPTION(WITH_TETGEN "Build Tetgen." OFF)
 
+###########################################
+# Configure data
+OPTION(BUILD_WITH_SCIRUN_DATA "Svn checkout data" OFF)
+
 ###########################################
 # Configure Windows executable to run with
 # or without the console
@@ -93,10 +97,16 @@ OPTION(TRAVIS_BUILD "Slim build for Travis CI" OFF)
 MARK_AS_ADVANCED(TRAVIS_BUILD)
 
 IF(TRAVIS_BUILD)
-  SET(BUILD_TESTING OFF)
-  SET(DOWNLOAD_TOOLKITS OFF)
-  SET(BUILD_HEADLESS ON)
-  SET(BUILD_WITH_PYTHON OFF)
+  IF(CMAKE_C_COMPILER_ID MATCHES "GNU")
+    SET(BUILD_TESTING OFF)
+    SET(DOWNLOAD_TOOLKITS OFF)
+    SET(BUILD_HEADLESS ON)
+    SET(BUILD_WITH_PYTHON OFF)
+    SET(BUILD_WITH_SCIRUN_DATA OFF)
+  ELSE()
+    SET(BUILD_WITH_SCIRUN_DATA OFF)
+    # try building everything with clang!
+  ENDIF()
   ADD_DEFINITIONS(-DTRAVIS_BUILD)
 ENDIF()
 
@@ -164,6 +174,14 @@ IF(BUILD_WITH_PYTHON)
   ADD_EXTERNAL( ${SUPERBUILD_DIR}/PythonExternal.cmake Python_external )
 ENDIF()
 
+FIND_PACKAGE(Subversion)
+IF(NOT Subversion_FOUND)
+  SET(BUILD_WITH_SCIRUN_DATA OFF)
+ENDIF()
+IF(BUILD_WITH_SCIRUN_DATA)
+  ADD_EXTERNAL( ${SUPERBUILD_DIR}/SCIRunDataExternal.cmake SCI_data_external)
+ENDIF()
+
 IF(WITH_TETGEN)
   MESSAGE(STATUS "Configuring Tetgen library under GPL. The SCIRun InterfaceWithTetGen module can be disabled by setting the CMake build variable WITH_TETGEN to OFF.")
   ADD_EXTERNAL( ${SUPERBUILD_DIR}/TetgenExternal.cmake Tetgen_external )
@@ -201,6 +219,7 @@ SET(SCIRUN_CACHE_ARGS
     "-DTeem_DIR:PATH=${Teem_DIR}"
     "-DTetgen_DIR:PATH=${Tetgen_DIR}"
     "-DFreetype_DIR:PATH=${Freetype_DIR}"
+    "-DSCI_DATA_DIR:PATH=${SCI_DATA_DIR}"
 )
 
 IF(BUILD_WITH_PYTHON)

src/CMakeLists.txt

@@ -770,6 +770,7 @@ SET_PROPERTY(TARGET Core_Containers         PROPERTY FOLDER "Core")
 SET_PROPERTY(TARGET Core_Thread_Legacy         PROPERTY FOLDER "Core")
 SET_PROPERTY(TARGET Core_Serialization_Network         PROPERTY FOLDER "Dataflow/Serialization")
 SET_PROPERTY(TARGET Core_Serialization_Network_Importer         PROPERTY FOLDER "Dataflow/Serialization")
+SET_PROPERTY(TARGET bundle_toolkit         PROPERTY FOLDER "Dataflow/Serialization")
 SET_PROPERTY(TARGET Engine_Network         PROPERTY FOLDER "Dataflow/Engine")
 SET_PROPERTY(TARGET Engine_Scheduler         PROPERTY FOLDER "Dataflow/Engine")
 SET_PROPERTY(TARGET Dataflow_State         PROPERTY FOLDER "Dataflow")

src/Core/Algorithms/Base/AlgorithmBase.cc

@@ -60,8 +60,6 @@ Name::Name(const std::string& name) : name_(name)
   }
 }
 
-AlgorithmBase::~AlgorithmBase() {}
-
 namespace
 {
   // Note: boost::serialization has trouble with NaN values, in addition to the platform differences.
@@ -381,10 +379,10 @@ bool AlgorithmParameterList::checkOption(const AlgorithmParameterName& key, cons
   return boost::iequals(value, currentValue);
 }
 
-void AlgorithmBase::dumpAlgoState() const
+void AlgorithmParameterList::dumpAlgoState() const
 {
   std::ostringstream ostr;
-  ostr << "Algorithm state for " << typeid(*this).name() << " id#" << id() << std::endl;
+  ostr << "Algorithm state for " << typeid(*this).name() << std::endl;
 
   auto range = std::make_pair(paramsBegin(), paramsEnd());
   BOOST_FOREACH(const ParameterMap::value_type& pair, range)
@@ -466,4 +464,4 @@ std::vector<std::string> Core::Algorithms::toNameVector(const Variable::List& li
 std::vector<double> Core::Algorithms::toDoubleVector(const Variable::List& list)
 {
   return toTypedVector<double>(list, [](const Variable& v) { return v.toDouble(); });
-}
+}

src/Core/Algorithms/Base/AlgorithmBase.h

@@ -39,15 +39,15 @@
 namespace SCIRun {
 namespace Core {
 namespace Algorithms {
-  
-  class SCISHARE AlgorithmBase : public AlgorithmInterface, public AlgorithmParameterList, public AlgorithmLogger, public AlgorithmStatusReporter
+
+  class SCISHARE AlgorithmBase :
+    public AlgorithmInterface,
+    public AlgorithmParameterList,
+    public AlgorithmLogger,
+    public AlgorithmStatusReporter
   {
-  public:
-    virtual ~AlgorithmBase();
-  protected:
-    void dumpAlgoState() const;
   };
-  
+
 }}}
 
 #endif

src/Core/Algorithms/Base/AlgorithmData.h

@@ -55,7 +55,7 @@ namespace Algorithms {
     {
       auto it = data_.find(name);
       /// @todo: log incorrect type if present but wrong type
-      return it == data_.end() ? boost::shared_ptr<T>() : boost::dynamic_pointer_cast<T>(it->second[0]);
+      return it == data_.end() ? nullptr : boost::dynamic_pointer_cast<T>(it->second[0]);
     }
 
     template <typename T>
@@ -81,11 +81,11 @@ namespace Algorithms {
     boost::any transient_;
   };
 
-  class SCISHARE AlgorithmInput : public AlgorithmData 
+  class SCISHARE AlgorithmInput : public AlgorithmData
   {
   public:
     AlgorithmInput() {}
-    AlgorithmInput(const Map& m) : AlgorithmData(m) {}
+    explicit AlgorithmInput(const Map& m) : AlgorithmData(m) {}
   };
 
   class SCISHARE AlgorithmOutput : public AlgorithmData
@@ -97,9 +97,9 @@ namespace Algorithms {
     VariableHandle additionalAlgoOutput_;
   };
 
-  typedef Datatypes::SharedPointer<AlgorithmInput> AlgorithmInputHandle;
-  typedef Datatypes::SharedPointer<AlgorithmOutput> AlgorithmOutputHandle;
-  
+  typedef SharedPointer<AlgorithmInput> AlgorithmInputHandle;
+  typedef SharedPointer<AlgorithmOutput> AlgorithmOutputHandle;
+
 }}}
 
 #endif

src/Core/Algorithms/Base/AlgorithmFwd.h

@@ -30,18 +30,19 @@
 #define ALGORITHMS_BASE_ALGORITHMFWD_H
 
 #include <Core/Datatypes/DatatypeFwd.h>
+#include <Core/Utils/SmartPointers.h>
 #include <Core/Algorithms/Base/share.h>
 
 namespace SCIRun {
 namespace Core {
 namespace Algorithms {
 
   class AlgorithmBase;
-  typedef Datatypes::SharedPointer<AlgorithmBase> AlgorithmHandle;
+  typedef SharedPointer<AlgorithmBase> AlgorithmHandle;
 
   class AlgorithmFactory;
-  typedef Datatypes::SharedPointer<AlgorithmFactory> AlgorithmFactoryHandle;
+  typedef SharedPointer<AlgorithmFactory> AlgorithmFactoryHandle;
 
 }}}
 
-#endif
+#endif

src/Core/Algorithms/Base/AlgorithmInterfaces.h

@@ -36,22 +36,11 @@
 namespace SCIRun {
 namespace Core {
 namespace Algorithms {
-  
+
   class SCISHARE AlgorithmInterface : public HasIntegerId
   {
   public:
     virtual ~AlgorithmInterface() {}
-    
-    /*
- @todo idea: make it mockable
-  
-    virtual OutputDatatypeHandleOptions run(InputDatatypeHandleOptions, ModuleParameterState) = 0;
-
-      ModuleParameterState: essentially a map of GuiVars. but need hooks for undo/redo and serialization
-      Input: tuple/heterogeneous vector of Datatypes
-      Output: tuple of Datatypes, possibly delay-executed
-    */
-
     virtual AlgorithmOutput run(const AlgorithmInput& input) const = 0;
   };
 

src/Core/Algorithms/Base/AlgorithmParameterList.h

@@ -73,10 +73,11 @@ namespace Algorithms {
     typedef std::map<AlgorithmParameterName, AlgorithmParameter> ParameterMap;
     ParameterMap::const_iterator paramsBegin() const { return parameters_.begin(); }
     ParameterMap::const_iterator paramsEnd() const { return parameters_.end(); }
+    void dumpAlgoState() const;
   private:
     ParameterMap parameters_;
   };
-  
+
 }}}
 
 #endif