Merge pull request #1919 from SCIInstitute/module-deprecate

Module deprecation and bug fixes

Author: dcwhite

src/CMakeLists.txt

@@ -207,6 +207,18 @@ IF(BUILD_TESTING)
   ADD_DEFINITIONS(-DTEST_RESOURCE_ROOT_DIR="${SCIRUN_TEST_RESOURCE_DIR}" -DBUILD_TESTING)
 ENDIF()
 
+#########################################################################
+# Configure Spdlog
+set (cxxfeaturelist ${CMAKE_CXX_COMPILE_FEATURES})
+
+list (FIND cxxfeaturelist "cxx_thread_local" _index)
+if (${_index} GREATER -1)
+  message("Found cxx_thread_local")
+else()
+  message(WARNING "Did NOT find cxx_thread_local--turning off feature of spdlog")
+  add_definitions(-DDISABLE_SPDLOG_TLS=1)
+endif()
+
 #########################################################################
 # External projects
 

src/Core/Algorithms/Math/ResizeMatrixAlgo.cc

@@ -27,7 +27,6 @@ DEALINGS IN THE SOFTWARE.
 
 
 #include <Core/Algorithms/Math/ResizeMatrixAlgo.h>
-#include<Core/Datatypes/Matrix.h>
 #include <Core/Datatypes/DenseMatrix.h>
 #include <Core/Datatypes/MatrixTypeConversions.h>
 #include <Core/Algorithms/Base/AlgorithmVariableNames.h>
@@ -51,7 +50,6 @@ ResizeMatrixAlgo::ResizeMatrixAlgo()
   addParameter(Parameters::NoOfRows, 1);
   addParameter(Parameters::NoOfColumns, 1);
   addOption(Parameters::Major,"Row","Row|Column");
-
 }
 
 AlgorithmOutput ResizeMatrixAlgo::run(const AlgorithmInput& input) const
@@ -64,7 +62,7 @@ AlgorithmOutput ResizeMatrixAlgo::run(const AlgorithmInput& input) const
   std::string major=getOption(Parameters::Major);
   DenseMatrixHandle dense=castMatrix::toDense(inputMatrix);
   DenseMatrixHandle denseMat(new DenseMatrix(*dense));
-  
+
   if(major=="Column")
   {
     denseMat->transposeInPlace();
@@ -73,9 +71,9 @@ AlgorithmOutput ResizeMatrixAlgo::run(const AlgorithmInput& input) const
 
   Map<MatrixXd> result(denseMat->data(),columns,rows);
   DenseMatrixHandle outputArray(new DenseMatrix(result.matrix()));
-  
+
   outputArray->transposeInPlace();
-  
+
   if(denseMat->rows()*denseMat->cols() != rows*columns)
   {
     warning("Input size does not match the size of the Output Matrix, Matrix will be padded with zeros or cropped up.");
@@ -86,10 +84,10 @@ AlgorithmOutput ResizeMatrixAlgo::run(const AlgorithmInput& input) const
       resultMatrix[i]=0;
     }
   }
-  
+
   if(major=="Column")
     outputArray->transposeInPlace();
-  
+
   AlgorithmOutput output;
   output[Variables::OutputMatrix]=outputArray;
   return output;

src/Core/Algorithms/Math/ResizeMatrixAlgo.h

@@ -28,40 +28,27 @@
 #ifndef CORE_ALGORITHMS_MATH_ResizeMatrixALGO_H
 #define CORE_ALGORITHMS_MATH_ResizeMatrixALGO_H
 
-#include<Core/Datatypes/Matrix.h>
-#include<Core/Datatypes/DenseMatrix.h>
-#include<Core/Datatypes/DenseColumnMatrix.h>
-#include <Dataflow/Network/Module.h>
-#include <Eigen/Dense>
-
-#include<string>
-#include<sstream>
-#include<vector>
-#include<algorithm>
-
-#include<Core/Algorithms/Base/AlgorithmVariableNames.h>
 #include<Core/Algorithms/Base/AlgorithmBase.h>
 #include<Core/Algorithms/Math/share.h>
 
-namespace SCIRun{
-    namespace Core{
-        namespace Algorithms{
-            namespace Math{
-                
-                ALGORITHM_PARAMETER_DECL(NoOfRows);
-                ALGORITHM_PARAMETER_DECL(NoOfColumns);
-                ALGORITHM_PARAMETER_DECL(Major);
-                
-                
-                class SCISHARE ResizeMatrixAlgo : public AlgorithmBase
-                {
-                public:
-                  ResizeMatrixAlgo();
-                    
-                  AlgorithmOutput run(const AlgorithmInput& input) const;
-                    
-                    
-                };
+namespace SCIRun
+{
+    namespace Core
+    {
+        namespace Algorithms
+        {
+            namespace Math
+            {
+              ALGORITHM_PARAMETER_DECL(NoOfRows);
+              ALGORITHM_PARAMETER_DECL(NoOfColumns);
+              ALGORITHM_PARAMETER_DECL(Major);
+
+              class SCISHARE ResizeMatrixAlgo : public AlgorithmBase
+              {
+              public:
+                ResizeMatrixAlgo();
+                AlgorithmOutput run(const AlgorithmInput& input) const;
+              };
             }
         }
     }

src/Core/Datatypes/Color.cc

@@ -91,3 +91,9 @@ std::ostream& SCIRun::Core::Datatypes::operator<<(std::ostream& out, const Color
   out << "Color(" << color.r() << "," << color.g() << "," << color.b() << ")";
   return out;
 }
+
+bool ViewSceneFeedback::matchesWithModuleId(const std::string& modId) const
+{
+  auto toMatch = GeometryObject::delimiter + modId + GeometryObject::delimiter;
+  return selectionName.find(toMatch) != std::string::npos;
+}

src/Core/Datatypes/Color.h

@@ -84,6 +84,8 @@ namespace Datatypes {
     Geometry::Transform transform;
     std::string selectionName;
     std::tuple<int,int> windowSize;
+
+    bool matchesWithModuleId(const std::string& modId) const;
   };
 
   struct SCISHARE MeshComponentSelectionFeedback : ModuleFeedback

src/Core/Datatypes/Legacy/Color/Color.cc

@@ -35,7 +35,13 @@
 #ifndef Q_MOC_RUN
 #include <Core/Utils/Singleton.h>
 #include <boost/filesystem/path.hpp>
+
+// older Mac compiler does not support thread-local storage
+#if defined(__APPLE__) && defined(DISABLE_SPDLOG_TLS)
+#define SPDLOG_NO_TLS
+#endif
 #include <spdlog/spdlog.h>
+
 #endif
 #include <Core/Logging/share.h>
 

src/Core/Datatypes/Legacy/Color/Color.h

@@ -53,7 +53,7 @@ void DynamicPortManager::connectionAddedNeedToCloneAPort(const SCIRun::Dataflow:
     {
       ModuleBuilder builder;
       auto newPortId = builder.cloneInputPort(moduleIn, cd.in_.portId_);
-      portAdded_(moduleIn->get_id(), newPortId);
+      portAdded_(moduleIn->id(), newPortId);
     }
   }
 }
@@ -70,7 +70,7 @@ void DynamicPortManager::connectionRemovedNeedToRemoveAPort(const SCIRun::Datafl
       {
         ModuleBuilder builder;
         builder.removeInputPort(moduleIn, desc.in_.portId_);
-        portRemoved_(moduleIn->get_id(), desc.in_.portId_);
+        portRemoved_(moduleIn->id(), desc.in_.portId_);
       }
     }
   }

src/Core/Logging/Log.h

@@ -141,10 +141,10 @@ namespace
           uiVisible = true;
         }
         auto mod = nec_.addModule(m);
-        if (mod->has_ui())
+        if (mod->hasUI())
           mod->setUiVisible(uiVisible);
         mods_.push_back(mod);
-        positions.modulePositions[mod->get_id().id_] =
+        positions.modulePositions[mod->id().id_] =
           { snippetSpacer + numSnips * MODULE_HORIZONTAL_SPACING,
             snippetSpacer + MODULE_VERTICAL_SPACING * i++ };
       }
@@ -280,9 +280,9 @@ void NetworkEditorController::interruptModule(const ModuleId& id)
 ModuleHandle NetworkEditorController::duplicateModule(const ModuleHandle& module)
 {
   ENSURE_NOT_NULL(module, "Cannot duplicate null module");
-  auto id(module->get_id());
-  auto newModule = addModuleImpl(module->get_info());
-  newModule->set_state(module->get_state()->clone());
+  auto id(module->id());
+  auto newModule = addModuleImpl(module->info());
+  newModule->setState(module->get_state()->clone());
   static ModuleCounter dummy;
   moduleAdded_(id.name_, newModule, dummy);
 
@@ -485,7 +485,7 @@ void NetworkEditorController::loadNetwork(const NetworkFileHandle& xml)
       for (size_t i = 0; i < theNetwork_->nmodules(); ++i)
       {
         auto module = theNetwork_->module(i);
-        moduleAdded_(module->get_module_name(), module, modulesDone);
+        moduleAdded_(module->name(), module, modulesDone);
         networkDoneLoading_(static_cast<int>(i));
       }
 
@@ -562,7 +562,7 @@ void NetworkEditorController::appendToNetwork(const NetworkFileHandle& xml)
       for (size_t i = startIndex; i < theNetwork_->nmodules(); ++i)
       {
         auto module = theNetwork_->module(i);
-        moduleAdded_(module->get_module_name(), module, modulesDone);
+        moduleAdded_(module->name(), module, modulesDone);
       }
 
       {