Merge remote-tracking branch 'upstream/master'

Author: jessdtate

README.md

@@ -12,10 +12,8 @@ https://github.com/SCIInstitute/SCIRun
 	- [Summary](#user-content-summary)
 	- [Goals](#user-content-goals)
 	- [Documentation](#user-content-documentation)
-	- [Platform Notes](#user-content-platform-notes)
-		- [Build requirements](#user-content-build-requirements)
-		- [CMake Build Generators](#user-content-cmake-build-generators)
-		- [Unix Makefiles notes](#user-content-unix-makefiles-notes)
+ 	  - [Build](#user-content-build)
+ 	  - [Python API](#user-content-python-api)
 	- [Questions and Answers](#user-content-questions-and-answers)
 	- [License and Credits](#user-content-license-and-credits)
 
@@ -24,49 +22,18 @@ https://github.com/SCIInstitute/SCIRun
 | Warning! |  SCIRun 5 is alpha software, you may use for real science but beware of instability.  |
 |:--------:|:-------------------------------------------------------------------------------------:|
 
-###Goals
+### Goals
 SCIRun 5 is a complete rewrite of the GUI front end and graphical components of SCIRun 4, including a more stable and
 efficient middle layer, with support for Python scripting.
 
 ### Documentation
-For documentation, please see: http://sciinstitute.github.io/SCIRun/
-
-### Platform Notes
-#### Build requirements
-* OS X (tested on 10.7-10.11)
-  - Apple clang 5.1
-  - Qt 4.8
-    + Download from http://releases.qt-project.org/qt4/source/qt-mac-opensource-4.8.4.dmg.
-    + The above dmg will not work if using OS X 10.11. In this case Qt 4.8 can be acquired through macports using the command 'sudo port install qt4-mac' - more on macports here: https://www.macports.org/install.php
-* Windows (tested on Windows 7, 8, 10)
-  - Visual Studio 2013, 2015
-  - Qt 4.8
-    + Build from source (see http://scirundocwiki.sci.utah.edu/SCIRunDocs/index.php/CIBC:Seg3D2:Building_Releases#Installing_Qt_on_your_system_and_building_from_scratch for instructions), but be sure to download http://releases.qt-project.org/qt4/source/qt-everywhere-opensource-src-4.8.4.tar.gz.
-* Linux (tested on Ubuntu 12.10, OpenSUSE Leap)
-  - gcc 4.6, 4.7, 4.8
-  - Qt 4.8
-    + Build from source (http://releases.qt-project.org/qt4/source/qt-everywhere-opensource-src-4.8.4.tar.gz), or use system libraries if available.
-* All platforms
-  - CMake 2.8
-    + Root cmake file is SCIRun/Superbuild/CMakeLists.txt.
-    + Building in the source directory is not permitted.
-    + Make sure BUILD_SHARED_LIBS is on (default setting).
-
-#### CMake Build Generators
-* Windows
-  - Visual Studio 2013
-* OS X (tested on 10.7 and 10.8 and 10.10)
-  - Unix Makefiles
-  - Xcode
-* Linux (tested on Ubuntu 12.10)
-  - Unix Makefiles
-
-#### Unix Makefiles notes
-* Build Superbuild first (src/Superbuild), then subsequently, SCIRun can be built by itself (src/).
-* Included `build.sh` takes care of all this for you.
-
-### Tagging releases
-On an OSX system, run script `release.sh` in the `src` directory with the release name in format `alpha.XX` as a parameter.
+For documentation, please see: http://sciinstitute.github.io/scirun.pages
+
+#### Build
+Please see http://sciinstitute.github.io/scirun.pages/build.html
+
+#### Python API
+Please see http://sciinstitute.github.io/scirun.pages/python.html
 
 ### Questions and Answers
 For help, email the testing mailing list at [email protected].

src/Core/Algorithms/Legacy/Fields/CMakeLists.txt

@@ -30,6 +30,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
   ClipMesh/ClipMeshBySelection.h
   ClipMesh/ClipMeshByIsovalue.h
   ConvertMeshType/ConvertMeshToPointCloudMeshAlgo.h
+  ConvertMeshType/ConvertMeshToUnstructuredMesh.h
   DistanceField/CalculateSignedDistanceField.h
   DistanceField/CalculateDistanceField.h
   Mapping/ApplyMappingMatrix.h
@@ -98,6 +99,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
   RegisterWithCorrespondences.h
   SampleField/GeneratePointSamplesFromField.h
   DistanceField/CalculateIsInsideField.h
+  MeshData/GetMeshQualityFieldAlgo.h
 )
 
 SET(Core_Algorithms_Legacy_Fields_SRCS
@@ -112,7 +114,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
   ConvertMeshType/ConvertMeshToPointCloudMeshAlgo.cc
   ConvertMeshType/ConvertMeshToTetVolMesh.cc
   ConvertMeshType/ConvertMeshToTriSurfMeshAlgo.cc
-  #ConvertMeshType/ConvertMeshToUnstructuredMesh.cc
+  ConvertMeshType/ConvertMeshToUnstructuredMesh.cc
   ConvertMeshType/ConvertMeshToIrregularMesh.cc
   #ConvertMeshType/ConvertLatVolDataFromElemToNode.cc
   #ConvertMeshType/ConvertLatVolDataFromNodeToElem.cc
@@ -179,7 +181,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
   Mapping/ApplyMappingMatrix.cc
   #MeshData/GetSurfaceNodeNormals.cc
   #MeshData/GetSurfaceElemNormals.cc
-  #MeshData/GetMeshQualityField.cc
+  MeshData/GetMeshQualityFieldAlgo.cc
   #MeshDerivatives/CalculateMeshConnector.cc
   #MeshDerivatives/CalculateMeshCenter.cc
   #MeshDerivatives/GetCentroids.cc

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToIrregularMesh.cc

@@ -42,7 +42,7 @@ using namespace SCIRun::Core::Algorithms;
 using namespace SCIRun::Core::Datatypes;
 
 bool 
-ConvertMeshToIrregularMeshAlgo::run(FieldHandle input, FieldHandle& output) const
+ConvertMeshToIrregularMeshAlgo::runImpl(FieldHandle input, FieldHandle& output) const
 {
   // Mark that we are starting the algorithm, but do not report progress
   ScopedAlgorithmStatusReporter asr(this, "ConvertMeshToIrregularMesh");
@@ -188,17 +188,15 @@ ConvertMeshToIrregularMeshAlgo::run(FieldHandle input, FieldHandle& output) cons
   return (true);
 }
 
-AlgorithmOutputName ConvertMeshToIrregularMeshAlgo::OutputField("OutputField");
-
 AlgorithmOutput ConvertMeshToIrregularMeshAlgo::run(const AlgorithmInput& input) const
 {
   auto ifield = input.get<Field>(Variables::InputField);
 
   FieldHandle ofield;
-  if (!run(ifield, ofield))
+  if (!runImpl(ifield, ofield))
     THROW_ALGORITHM_PROCESSING_ERROR("False returned on legacy run call.");
 
   AlgorithmOutput output;
-  output[OutputField] = ofield;
+  output[Variables::OutputField] = ofield;
   return output;
 }

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToIrregularMesh.h

@@ -31,8 +31,6 @@
 #define CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTTOIRREGULARMESH_H 1
 
 #include <Core/Algorithms/Base/AlgorithmBase.h>
-
-// for Windows support
 #include <Core/Algorithms/Legacy/Fields/share.h>
 
 namespace SCIRun {
@@ -47,11 +45,9 @@ class SCISHARE ConvertMeshToIrregularMeshAlgo : public AlgorithmBase
     {
     }
 
-    bool run(FieldHandle input, FieldHandle& output) const;
-
-    static AlgorithmOutputName OutputField;
+    bool runImpl(FieldHandle input, FieldHandle& output) const;
 
-    virtual AlgorithmOutput run(const AlgorithmInput& input) const; 
+    virtual AlgorithmOutput run(const AlgorithmInput& input) const override; 
 };
 
 }}}}

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToPointCloudMeshAlgo.h

@@ -6,7 +6,7 @@
    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
@@ -24,7 +24,7 @@
    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.
-*/
+   */
 
 
 #ifndef CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTTOPOINTCLOUDMESH_H
@@ -39,18 +39,21 @@ namespace SCIRun {
     namespace Algorithms {
       namespace Fields {
 
-class SCISHARE ConvertMeshToPointCloudMeshAlgo : public AlgorithmBase
-{
-  public:
-    ConvertMeshToPointCloudMeshAlgo();
+        class SCISHARE ConvertMeshToPointCloudMeshAlgo : public AlgorithmBase
+        {
+        public:
+          ConvertMeshToPointCloudMeshAlgo();
 
-    bool runImpl(FieldHandle input, FieldHandle& output) const;
-    virtual AlgorithmOutput run(const AlgorithmInput& input) const override;
+          bool runImpl(FieldHandle input, FieldHandle& output) const;
+          virtual AlgorithmOutput run(const AlgorithmInput& input) const override;
 
-    static AlgorithmParameterName Location;
-};
+          static AlgorithmParameterName Location;
+        };
 
-      }}}}
+      }
+    }
+  }
+}
 
 #endif 
 

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.cc

@@ -27,39 +27,30 @@
 */
 
 // Get all the class definitions. 
-#include <Core/Algorithms/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.h>
-#include <Core/Datatypes/FieldInformation.h>
-
-// As we already included DynamicAlgorithm.h in the header we do not need to
-// include it again here.
-
-namespace SCIRunAlgo {
+#include <Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.h>
+#include <Core/Datatypes/Legacy/Field/FieldInformation.h>
+#include <Core/Datatypes/Legacy/Field/VMesh.h>
+#include <Core/Datatypes/Legacy/Field/VField.h>
+#include <Core/Datatypes/PropertyManagerExtensions.h>
+#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
+#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
 
 using namespace SCIRun;
+using namespace SCIRun::Core::Algorithms::Fields;
+using namespace SCIRun::Core::Geometry;
+using namespace SCIRun::Core::Utility;
+using namespace SCIRun::Core::Algorithms;
+using namespace SCIRun::Core::Datatypes;
 
-// Implementation of the actual access point to the algorithm
-
-bool 
-ConvertMeshToUnstructuredMeshAlgo::
-run(FieldHandle input, FieldHandle& output)
+bool ConvertMeshToUnstructuredMeshAlgo::runImpl(FieldHandle input, FieldHandle& output) const
 {
-  // Mark that we are starting the algorithm, but do not report progress
-  algo_start("ConvertMeshToUnstructuredMesh");
-
-  // Step 0:
-  // Safety test:
-  // Test whether we received actually a field. A handle can point to no object.
-  // Using a null handle will cause the program to crash. Hence it is a good
-  // policy to check all incoming handles and to see whether they point to actual
-  // objects.
-  
-  // Handle: the function get_rep() returns the pointer contained in the handle
-  if (input.get_rep() == 0)
+  ScopedAlgorithmStatusReporter asr(this, "ConvertMeshToUnstructuredMesh");
+
+  // Null check
+  if (!input)
   {
-    // If we encounter a null pointer we return an error message and return to
-    // the program to deal with this error. 
     error("No input field");
-    algo_end(); return (false);
+    return (false);
   }
 
  // Step 1: determine the type of the input fields and determine what type the
@@ -91,7 +82,7 @@ run(FieldHandle input, FieldHandle& output)
    if (fi.is_nonlinear())
   {
     error("This function has not yet been defined for non-linear elements");
-    algo_end(); return (false);
+    return (false);
   }
 
   // If the mesh is already unstructured, we only need to copy the input to the
@@ -102,7 +93,7 @@ run(FieldHandle input, FieldHandle& output)
     remark("Mesh already is unstructured; copying input to output");
     // Copy input to output (output is a reference to the input)
     output = input;
-    algo_end(); return (true);
+    return (true);
   }
 
   // Define the output type of the data
@@ -121,19 +112,19 @@ run(FieldHandle input, FieldHandle& output)
   else
   {
     error("No unstructure method available for mesh: " + fi.get_mesh_type());
-    algo_end(); return (false);
+    return (false);
   }
 
   // Create a new output field
   output = CreateField(fo);
 
-  if (output.get_rep() == 0)
+  if (!output)
   { 
     // Error reporting:
     // we forward the specific message to the ProgressReporter and return a
     // false to indicate that an error has occured.
     error("Could not obtain input field");
-    algo_end(); return (false);
+    return (false);
   }  
 
   // Get the virtual interface of the objects
@@ -169,16 +160,23 @@ run(FieldHandle input, FieldHandle& output)
     omesh->add_elem(nodes);
   }
 
-  // Resize the data
-  // and copy the data
   ofield->resize_values();
   ofield->copy_values(ifield);
 
-  /// Copy properties of the property manager
-	output->copy_properties(input.get_rep());
+  CopyProperties(*input, *output);
 
-  // Success:
-  algo_end(); return (true);
+  return (true);
 }
 
-} // End namespace SCIRunAlgo
+AlgorithmOutput ConvertMeshToUnstructuredMeshAlgo::run(const AlgorithmInput& input) const
+{
+  auto ifield = input.get<Field>(Variables::InputField);
+
+  FieldHandle ofield;
+  if (!runImpl(ifield, ofield))
+    THROW_ALGORITHM_PROCESSING_ERROR("False returned on legacy run call.");
+
+  AlgorithmOutput output;
+  output[Variables::OutputField] = ofield;
+  return output;
+}

src/Core/Algorithms/Legacy/Fields/ConvertMeshType/ConvertMeshToUnstructuredMesh.h

@@ -30,32 +30,29 @@
 #ifndef CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTMESHTOUNSTRUCTUREDMESH_H
 #define CORE_ALGORITHMS_FIELDS_CONVERTMESHTYPE_CONVERTMESHTOUNSTRUCTUREDMESH_H 1
 
-// Datatypes that the algorithm uses
-#include <Core/Datatypes/Mesh.h>
-#include <Core/Datatypes/Field.h>
+#include <Core/Algorithms/Base/AlgorithmBase.h>
+#include <Core/Algorithms/Legacy/Fields/share.h>
 
-// Base class for algorithm
-#include <Core/Algorithms/Util/AlgoBase.h>
+namespace SCIRun {
+  namespace Core {
+    namespace Algorithms {
+      namespace Fields {
 
-// for Windows support
-#include <Core/Algorithms/Fields/share.h>
+        class SCISHARE ConvertMeshToUnstructuredMeshAlgo : public AlgorithmBase
+        {
+        public:
+          ConvertMeshToUnstructuredMeshAlgo()
+          {
+          }
 
-namespace SCIRunAlgo {
+          bool runImpl(FieldHandle input, FieldHandle& output) const;
 
-using namespace SCIRun;
+          virtual AlgorithmOutput run(const AlgorithmInput& input) const override;
+        };
 
-class SCISHARE ConvertMeshToUnstructuredMeshAlgo : public AlgoBase
-{
-  public:
-    /// Set defaults
-    ConvertMeshToUnstructuredMeshAlgo()
-    {
+      }
     }
+  }
+}
 
-    /// run the algorithm
-    bool run(FieldHandle input, FieldHandle& output);};
-
-} // end namespace SCIRunAlgo
-
-#endif
-
+#endif