Merge branch 'master' into master

Author: dcwhite

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,50 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: Bug
+assignees: dcwhite
+
+---
+
+## For bugs, follow the template below: fill out all pertinent sections, then delete the rest of the template to reduce clutter. 
+### If all prerequisites are met, just delete that text as well. If they're not all met, the issue will be closed or assigned back to you.
+
+**Prerequisites**
+
+* [ ] Are you running the [latest version of SCIRun](https://github.com/SCIInstitute/SCIRun/releases)?
+* [ ] Are you reporting to the [correct repository](https://github.com/SCIInstitute/SCIRun)?
+* [ ] Did you [perform a cursory search](https://github.com/SCIInstitute/SCIRun/issues) to see if your bug or enhancement is already reported?
+
+For more information on how to write a good [bug report](https://github.com/atom/atom/blob/master/CONTRIBUTING.md#how-do-i-submit-a-good-bug-report) or [enhancement request](https://github.com/atom/atom/blob/master/CONTRIBUTING.md#how-do-i-submit-a-good-enhancement-suggestion), see the `CONTRIBUTING` guide. These links point to another project, but most of the advice holds in general.
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+For Mac crash bugs, please *DO NOT* paste an entire MacOS crash report here. Edit it down to just the stack trace of the thread that crashed, along with the general system info on the top.
+
+**In all bug cases, some combination of screenshots, sample network(s), and input data should be attached. You can use any cloud storage links you want for networks and data.**
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Version**
+
+You can get this information from executing `SCIRun --version` at the command line, or clicking on the version button in the bottom right corner of the GUI (which copies the version to the clipboard). 
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. MacOS, Windows, Linux]
+ - Version [e.g. 10.12, 10, Ubuntu 16.04]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: Enhancement
+assignees: dcwhite
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.travis.yml

@@ -17,18 +17,6 @@ matrix:
       sudo: required
       compiler: clang
       env: PYTHON_VERSION=3.5.6 OSPRAY_BUILD=OFF
-    - os: osx
-      osx_image: xcode7.2
-      env: PYTHON_VERSION=3.4.3 OSPRAY_BUILD=OFF
-    - os: osx
-      osx_image: xcode8.3
-      env: PYTHON_VERSION=3.4.3 OSPRAY_BUILD=OFF
-    - os: osx
-      osx_image: xcode9.3
-      env: PYTHON_VERSION=3.4.3 OSPRAY_BUILD=OFF
-    - os: osx
-      osx_image: xcode10.1
-      env: PYTHON_VERSION=3.4.3 OSPRAY_BUILD=OFF
     - os: osx
       osx_image: xcode7.2
       env: PYTHON_VERSION=3.5.6 OSPRAY_BUILD=OFF
@@ -44,12 +32,6 @@ matrix:
     - os: osx
       osx_image: xcode7.2
       env: PYTHON_VERSION=3.6.7 OSPRAY_BUILD=OFF
-    - os: osx
-      osx_image: xcode8.3
-      env: PYTHON_VERSION=3.6.7 OSPRAY_BUILD=OFF
-    - os: osx
-      osx_image: xcode9.3
-      env: PYTHON_VERSION=3.6.7 OSPRAY_BUILD=OFF
     - os: osx
       osx_image: xcode10.1
       env: PYTHON_VERSION=3.6.7 OSPRAY_BUILD=OFF

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/Field/InterfaceWithCleaver2Algorithm.cc

@@ -84,9 +84,9 @@ namespace detail
   static const double kDefaultAlpha = 0.4;
   static const double kDefaultAlphaLong = 0.357;
   static const double kDefaultAlphaShort = 0.203;
-  static const double kDefaultScale = 1.0;
+  static const double kDefaultSamplingRate = 1.0;
   static const double kDefaultLipschitz = 0.2;
-  static const double kDefaultMultiplier = 1.0;
+  static const double kDefaultFeatureScaling = 1.0;
   //static const int    kDefaultPadding = 0;
   //static const int    kDefaultMaxIterations = 1000;
   //static const double kDefaultSigma = 1.;
@@ -96,9 +96,9 @@ namespace detail
     cleaver2::MeshType mesh_mode;
     double alphaLong;
     double alphaShort;
-    double scaling;
+    double samplingRate;
     double lipschitz;
-    double multiplier;
+    double featureScaling;
     bool verbose;
     bool simpleMode;
     bool reverseJacobians;
@@ -119,9 +119,9 @@ namespace detail
     Cleaver2Impl(const AlgorithmBase* algo, const Cleaver2Parameters& params, FieldHandle sizingField, FieldHandle backgroundMesh) :
       algo_(algo), params_(params), inputSizingField_(sizingField), inputBackgroundMesh_(backgroundMesh)
     {
-      LOG_DEBUG("Cleaver 2 parameters: \n\tmesh_mode: {}\n\talphaLong: {}\n\talphaShort: {}\n\tscaling: {}\n\tlipschitz: {}\n\tmultiplier: {}\n\tverbose: {}\n\tsimpleMode: {}",
+      LOG_DEBUG("Cleaver 2 parameters: \n\tmesh_mode: {}\n\talphaLong: {}\n\talphaShort: {}\n\tsampling_rate: {}\n\tlipschitz: {}\n\tfeature_scaling: {}\n\tverbose: {}\n\tsimpleMode: {}",
         params_.mesh_mode, params_.alphaLong, params_.alphaShort,
-        params_.scaling, params_.lipschitz, params_.multiplier,
+        params_.samplingRate, params_.lipschitz, params_.featureScaling,
         params_.verbose, params_.simpleMode);
     }
 
@@ -429,8 +429,8 @@ namespace detail
         sizingField_.reset(cleaver2::SizingFieldCreator::createSizingFieldFromVolume(
           volume_.get(),
           (float)(1.0 / params_.lipschitz),
-          (float)params_.scaling,
-          (float)params_.multiplier,
+          (float)params_.samplingRate,
+          (float)params_.featureScaling,
           0, // padding--off
           (params_.mesh_mode != cleaver2::Regular),
           params_.verbose));
@@ -505,11 +505,12 @@ namespace detail
 
 InterfaceWithCleaver2Algorithm::InterfaceWithCleaver2Algorithm()
 {
+  //Cleaver parameters: Scaling = Sampling Rate, Multiplier = Feature Scaling
   addParameter(Parameters::Verbose, true);
   addParameter(Parameters::SimpleMode, false);
   addParameter(Parameters::ReverseJacobians, true);
-  addParameter(Parameters::VolumeScaling, detail::kDefaultScale);
-  addParameter(Parameters::VolumeMultiplier, detail::kDefaultMultiplier);
+  addParameter(Parameters::VolumeScaling, detail::kDefaultSamplingRate);
+  addParameter(Parameters::VolumeMultiplier, detail::kDefaultFeatureScaling);
   addParameter(Parameters::Lipschitz, detail::kDefaultLipschitz);
   //addParameter(Parameters::Padding, detail::kDefaultPadding);
   addParameter(Parameters::AlphaLong, detail::kDefaultAlphaLong);

src/Core/Algorithms/Field/InterfaceWithCleaver2Algorithm.h

@@ -38,6 +38,7 @@ namespace Core {
 namespace Algorithms {
 namespace Fields {
 
+  //Cleaver parameters: Scaling = Sampling Rate, Multiplier = Feature Scaling
   ALGORITHM_PARAMETER_DECL(Verbose);
   ALGORITHM_PARAMETER_DECL(VolumeScaling);
   ALGORITHM_PARAMETER_DECL(VolumeMultiplier);

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

@@ -47,7 +47,7 @@ SET(Core_Algorithms_Legacy_Fields_HEADERS
   FieldData/SetFieldData.h
   FieldData/SetFieldDataToConstantValue.h
   FieldData/SwapFieldDataWithMatrixEntriesAlgo.h
-  #FieldData/SmoothVecFieldMedian.h
+  FieldData/SmoothVecFieldMedianAlgo.h
   Mapping/BuildMappingMatrixAlgo.h
   DomainFields/GetDomainBoundaryAlgo.h
   MeshDerivatives/GetFieldBoundaryAlgo.h
@@ -149,7 +149,7 @@ SET(Core_Algorithms_Legacy_Fields_SRCS
   #FieldData/ConvertMappingMatrixToFieldData.cc
   FieldData/SetFieldData.cc
   FieldData/SetFieldDataToConstantValue.cc
-  #FieldData/SmoothVecFieldMedian.cc
+  FieldData/SmoothVecFieldMedianAlgo.cc
   #FilterFieldData/DilateFieldData.cc
   #FilterFieldData/ErodeFieldData.cc
   #FilterFieldData/TriSurfPhaseFilter.cc