Merge branch 'master' into dependabot/pip/notebook-6.4.12

Author: akenmorris

Applications/shapeworks/Commands.cpp

@@ -230,13 +230,17 @@ void AnalyzeCommand::buildParser() {
 
   parser.add_option("--name").action("store").type("string").set_default("").help("Path to project file.");
   parser.add_option("--output").action("store").type("string").set_default("").help("Path to output file.");
+  parser.add_option("--range").action("store").type("float").set_default(3.0f).help("Standard deviation range for PCA [default: 3.0].");
+  parser.add_option("--steps").action("store").type("int").set_default(21).help("Number of steps to use for PCA [default: 21].");
 
   Command::buildParser();
 }
 
 bool AnalyzeCommand::execute(const optparse::Values& options, SharedCommandData& sharedData) {
   const std::string& projectFile(static_cast<std::string>(options.get("name")));
   const std::string& outputFile(static_cast<std::string>(options.get("output")));
+  const float range = static_cast<float>(options.get("range"));
+  const int steps = static_cast<int>(options.get("steps"));
 
   if (projectFile.length() == 0) {
     std::cerr << "Must specify project name with --name <project.xlsx|.swproj>\n";
@@ -268,7 +272,7 @@ bool AnalyzeCommand::execute(const optparse::Values& options, SharedCommandData&
     boost::filesystem::path dir(oldBasePath);
     boost::filesystem::path file(outputFile);
     boost::filesystem::path full_output = dir / file;
-    analyze.run_offline_analysis(full_output.string());
+    analyze.run_offline_analysis(full_output.string(), range, steps);
 
     boost::filesystem::current_path(oldBasePath);
 

Libs/Analyze/Analyze.cpp

@@ -130,7 +130,7 @@ Analyze::Analyze(ProjectHandle project) : project_(project), mesh_manager_(new M
 }
 
 //---------------------------------------------------------------------------
-void Analyze::run_offline_analysis(std::string outfile) {
+void Analyze::run_offline_analysis(std::string outfile, float range, float steps) {
   SW_LOG("ShapeWorks Offline Analysis");
   if (!project_->get_particles_present()) {
     throw std::runtime_error("Project has not been optimized, please run optimize first");
@@ -140,8 +140,6 @@ void Analyze::run_offline_analysis(std::string outfile) {
 
   json j;
 
-  double range = 2.0;  // TODO: make this configurable
-  double steps = 11;   // TODO: make this configurable
   int half_steps = (steps / 2.0);
   double increment = range / half_steps;
 

Libs/Analyze/Analyze.h

@@ -18,7 +18,7 @@ class Analyze {
   Analyze(ProjectHandle project);
 
   /// Run offline analysis, saving results to outfile
-  void run_offline_analysis(std::string outfile);
+  void run_offline_analysis(std::string outfile, float range, float steps);
 
   /// Return the list of shapes
   ShapeList get_shapes();