The great renaming of '16. Mesh->Arrangement, xiPoint-> TemplatePoint…

…, and all derivatives thereof

CMakeLists.txt

@@ -30,18 +30,18 @@ add_executable (rivet_console
         interface/file_writer.cpp
         interface/file_input_reader.cpp
         interface/input_manager.cpp
-        dcel/mesh.cpp
-        dcel/mesh_builder.cpp
+        dcel/arrangement.cpp
+        dcel/arrangement_builder.cpp
         dcel/anchor.cpp
         dcel/barcode_template.cpp
         dcel/dcel.cpp
-        dcel/mesh_message.cpp
+        dcel/arrangement_message.cpp
         math/map_matrix.cpp
         math/multi_betti.cpp
         math/simplex_tree.cpp
         math/st_node.cpp
-        math/xi_point.cpp
-        math/xi_support_matrix.cpp
+        math/template_point.cpp
+        math/template_points_matrix.cpp
         math/index_matrix.cpp
         math/persistence_updater.cpp
         numerics.cpp
@@ -62,17 +62,17 @@ add_executable(unit_tests
         interface/file_writer.cpp
         interface/file_input_reader.cpp
         interface/input_manager.cpp
-        dcel/mesh.cpp
-        dcel/mesh_builder.cpp
+        dcel/arrangement.cpp
+        dcel/arrangement_builder.cpp
         dcel/anchor.cpp
         dcel/barcode_template.cpp
         dcel/dcel.cpp
         math/map_matrix.cpp
         math/multi_betti.cpp
         math/simplex_tree.cpp
         math/st_node.cpp
-        math/xi_point.cpp
-        math/xi_support_matrix.cpp
+        math/template_point.cpp
+        math/template_points_matrix.cpp
         math/index_matrix.cpp
         math/persistence_updater.cpp
         numerics.cpp

RIVET.pro

@@ -24,7 +24,7 @@ SOURCES	+= main.cpp                         \
 		visualizationwindow.cpp             \
 		dataselectdialog.cpp                \
 		dcel/dcel.cpp                       \
-		dcel/mesh.cpp                       \
+		dcel/arrangement.cpp                       \
 		interface/control_dot.cpp           \
 		#interface/input_manager.cpp         \
 		interface/persistence_bar.cpp       \
@@ -40,10 +40,10 @@ SOURCES	+= main.cpp                         \
 		interface/barcode.cpp               \
 		dcel/barcode_template.cpp           \
 		dcel/anchor.cpp                     \
-		dcel/mesh_message.cpp               \
+		dcel/arrangement_message.cpp               \
 		#math/persistence_updater.cpp        \
-		math/xi_support_matrix.cpp          \
-		math/xi_point.cpp                   \
+		math/template_points_matrix.cpp          \
+		math/template_point.cpp                   \
 		interface/progressdialog.cpp        \
 		computationthread.cpp               \
 		interface/aboutmessagebox.cpp       \
@@ -60,7 +60,7 @@ SOURCES	+= main.cpp                         \
 HEADERS  += visualizationwindow.h			\
 		dataselectdialog.h					\
 		dcel/dcel.h							\
-		dcel/mesh.h							\
+		dcel/arrangement.h							\
 		interface/control_dot.h				\
 		interface/input_manager.h			\
 		interface/persistence_bar.h			\
@@ -77,8 +77,8 @@ HEADERS  += visualizationwindow.h			\
 		dcel/barcode_template.h				\
 		dcel/anchor.h						\
 		math/persistence_updater.h			\
-		math/xi_support_matrix.h			\
-		math/xi_point.h \
+		math/template_points_matrix.h			\
+		math/template_point.h \
     interface/progressdialog.h \
     computationthread.h \
     interface/input_parameters.h \

computation.cpp

@@ -1,6 +1,6 @@
 #include "computation.h"
-#include "dcel/mesh.h"
-#include "dcel/mesh_builder.h"
+#include "dcel/arrangement.h"
+#include "dcel/arrangement_builder.h"
 #include "debug.h"
 #include "math/multi_betti.h"
 #include "timer.h"
@@ -49,9 +49,9 @@ std::unique_ptr<ComputationResult> Computation::compute_raw(ComputationInput& in
     debug() << "  --> xi_i computation took " << timer.elapsed() << " seconds";
 
     //store the xi support points
-    mb.store_support_points(result->xi_support);
+    mb.store_support_points(result->template_points);
 
-    xiSupportReady(XiSupportMessage{ input.x_label, input.y_label, result->xi_support, result->homology_dimensions, input.x_exact, input.y_exact }); //signal that xi support points are ready for visualization
+    template_points_ready(TemplatePointsMessage{ input.x_label, input.y_label, result->template_points, result->homology_dimensions, input.x_exact, input.y_exact }); //signal that xi support points are ready for visualization
     progress.advanceProgressStage(); //update progress box to stage 4
 
     //STAGES 4 and 5: BUILD THE LINE ARRANGEMENT AND COMPUTE BARCODE TEMPLATES
@@ -62,18 +62,18 @@ std::unique_ptr<ComputationResult> Computation::compute_raw(ComputationInput& in
     }
 
     timer.restart();
-    MeshBuilder builder(verbosity);
-    auto arrangement = builder.build_arrangement(mb, input.x_exact, input.y_exact, result->xi_support, progress); ///TODO: update this -- does not need to store list of xi support points in xi_support
+    ArrangementBuilder builder(verbosity);
+    auto arrangement = builder.build_arrangement(mb, input.x_exact, input.y_exact, result->template_points, progress); ///TODO: update this -- does not need to store list of xi support points in xi_support
     //NOTE: this also computes and stores barcode templates in the arrangement
 
     debug() << "   building the line arrangement and computing all barcode templates took"
             << timer.elapsed() << "milliseconds";
 
     //send (a pointer to) the arrangement back to the VisualizationWindow
-    arrangementReady(arrangement);
+    arrangement_ready(arrangement);
     //re-send xi support and other anchors
-    debug() << "Sending" << result->xi_support.size() << "anchors";
-    xiSupportReady(XiSupportMessage{ input.x_label, input.y_label, result->xi_support, result->homology_dimensions, input.x_exact, input.y_exact });
+    debug() << "Sending" << result->template_points.size() << "anchors";
+    template_points_ready(TemplatePointsMessage{ input.x_label, input.y_label, result->template_points, result->homology_dimensions, input.x_exact, input.y_exact });
     arrangement->test_consistency();
     result->arrangement = std::move(arrangement);
     return result;

computation.h

@@ -5,7 +5,7 @@
 #include "interface/input_manager.h"
 #include "interface/input_parameters.h"
 #include "math/simplex_tree.h"
-#include "math/xi_point.h"
+#include "math/template_point.h"
 #include "numerics.h"
 
 #include "boost/multi_array.hpp"
@@ -42,16 +42,16 @@ class ComputationInput {
 
 struct ComputationResult {
     unsigned_matrix homology_dimensions;
-    std::vector<xiPoint> xi_support;
-    std::shared_ptr<Mesh> arrangement;
+    std::vector<TemplatePoint> template_points;
+    std::shared_ptr<Arrangement> arrangement;
     std::shared_ptr<SimplexTree> bifiltration;
 };
 
 class Computation {
 public:
     //TODO: these signals are a little strange, they should go away soon
-    boost::signals2::signal<void(std::shared_ptr<Mesh>)> arrangementReady;
-    boost::signals2::signal<void(XiSupportMessage)> xiSupportReady;
+    boost::signals2::signal<void(std::shared_ptr<Arrangement>)> arrangement_ready;
+    boost::signals2::signal<void(TemplatePointsMessage)> template_points_ready;
     Computation(InputParameters& params, Progress& progress);
     ~Computation();
 

computationthread.cpp

@@ -1,13 +1,13 @@
 #include "computationthread.h"
 
-#include "dcel/mesh.h"
-#include "dcel/mesh_message.h"
+#include "dcel/arrangement.h"
+#include "dcel/arrangement_message.h"
 #include "dcel/serialization.h"
 #include "interface/input_manager.h"
 #include "interface/input_parameters.h"
 #include "math/multi_betti.h"
 #include "math/simplex_tree.h"
-#include "math/xi_point.h"
+#include "math/template_point.h"
 
 #include "interface/console_interaction.h"
 
@@ -28,7 +28,7 @@
 ComputationThread::ComputationThread(InputParameters& params, QObject* parent)
     : QThread(parent)
     , params(params)
-    , xi_support()
+    , template_points()
     , x_exact()
     , y_exact()
     , x_label()
@@ -77,11 +77,11 @@ void ComputationThread::load_from_file()
     assert(type == "RIVET_1");
     boost::archive::binary_iarchive archive(file);
 
-    arrangement.reset(new MeshMessage());
+    arrangement.reset(new ArrangementMessage());
     archive >> params;
     archive >> message;
     unpack_message_fields();
-    emit xiSupportReady();
+    emit templatePointsReady();
     archive >> *arrangement;
     emit arrangementReady(&*arrangement);
 }
@@ -90,7 +90,7 @@ void ComputationThread::load_from_file()
 void ComputationThread::unpack_message_fields()
 {
 
-    xi_support = message.xi_support;
+    template_points = message.template_points;
     std::vector<unsigned> dims(message.homology_dimensions.shape(),
         message.homology_dimensions.shape() + message.homology_dimensions.num_dimensions());
     assert(dims.size() == 2);
@@ -141,7 +141,7 @@ void ComputationThread::compute_from_file()
                 }
                 unpack_message_fields();
                 reading_xi = false;
-                emit xiSupportReady();
+                emit templatePointsReady();
             } else {
                 ss << line.toStdString();
             }
@@ -157,17 +157,17 @@ void ComputationThread::compute_from_file()
                 if (type != "RIVET_1") {
                     throw std::runtime_error("Unsupported file format");
                 }
-                qDebug() << "ComputationThread::compute_from_file() : checkpoint A -- xi_support.size() = " << xi_support.size();
+                qDebug() << "ComputationThread::compute_from_file() : checkpoint A -- template_points.size() = " << template_points.size();
                 boost::archive::binary_iarchive archive(input);
-                arrangement.reset(new MeshMessage());
+                arrangement.reset(new ArrangementMessage());
                 InputParameters p;
                 archive >> p;
                 archive >> message;
                 unpack_message_fields();
                 archive >> *arrangement;
-                qDebug() << "ComputationThread::compute_from_file() : checkpoint B -- xi_support.size() = " << xi_support.size();
+                qDebug() << "ComputationThread::compute_from_file() : checkpoint B -- template_points.size() = " << template_points.size();
             }
-            //                qDebug() << "Mesh received: " << arrangement->x_exact.size() << " x " << arrangement->y_exact.size();
+            //                qDebug() << "Arrangement received: " << arrangement->x_exact.size() << " x " << arrangement->y_exact.size();
             emit arrangementReady(&*arrangement);
             return;
         } else if (line.startsWith("PROGRESS ")) {
@@ -182,22 +182,22 @@ void ComputationThread::compute_from_file()
         }
     }
 
-    qDebug() << "Mesh was not delivered";
+    qDebug() << "Arrangement was not delivered";
 
 } //end run()
 
 //TODO: this doesn't really belong here, look for a better place.
 //NOTE this is a copy of a function in the console
 //It has to be here because we get duplicate symbol errors when we use binary_oarchive in a different compilation
 //unit in addition to this one.
-void write_boost_file(QString file_name, InputParameters const& params, XiSupportMessage const& message, MeshMessage const& mesh)
+void write_boost_file(QString file_name, InputParameters const& params, TemplatePointsMessage const& message, ArrangementMessage const& arrangement)
 {
     std::ofstream file(file_name.toStdString(), std::ios::binary);
     if (!file.is_open()) {
         throw std::runtime_error("Could not open " + file_name.toStdString() + " for writing");
     }
     file << "RIVET_1\n";
     boost::archive::binary_oarchive oarchive(file);
-    oarchive& params& message& mesh;
+    oarchive& params& message& arrangement;
     file.flush();
 }

computationthread.h

@@ -4,11 +4,11 @@
 //forward declarations
 class InputManager;
 struct InputParameters;
-class Mesh;
+class Arrangement;
 
 #include "dcel/barcode_template.h"
 #include "math/simplex_tree.h"
-#include "math/xi_point.h"
+#include "math/template_point.h"
 
 #include <QObject>
 #include <QThread>
@@ -18,7 +18,7 @@ typedef boost::multiprecision::cpp_rational exact;
 #include "boost/multi_array.hpp"
 typedef boost::multi_array<unsigned, 2> unsigned_matrix;
 
-#include "dcel/mesh_message.h"
+#include "dcel/arrangement_message.h"
 #include <vector>
 
 class ComputationThread : public QThread {
@@ -34,8 +34,8 @@ class ComputationThread : public QThread {
     void compute();
 
     //TODO: these really ought to be delivered via signal rather than read by other classes
-    XiSupportMessage message;
-    std::vector<xiPoint> xi_support;
+    TemplatePointsMessage message;
+    std::vector<TemplatePoint> template_points;
     std::vector<exact> x_exact;
     std::vector<exact> y_exact;
     unsigned_matrix hom_dims;
@@ -46,16 +46,16 @@ class ComputationThread : public QThread {
     void advanceProgressStage();
     void setProgressMaximum(unsigned max);
     void setCurrentProgress(unsigned current);
-    void xiSupportReady();
-    void arrangementReady(MeshMessage* arrangement);
+    void templatePointsReady();
+    void arrangementReady(ArrangementMessage* arrangement);
 
 protected:
     void run() Q_DECL_OVERRIDE;
 
 private:
     InputParameters& params;
 
-    std::shared_ptr<MeshMessage> arrangement;
+    std::shared_ptr<ArrangementMessage> arrangement;
 
     void compute_from_file();
     void unpack_message_fields();
@@ -64,5 +64,5 @@ class ComputationThread : public QThread {
 };
 
 //TODO: Move this somewhere. See comments on implementation for details.
-void write_boost_file(QString file_name, InputParameters const& params, XiSupportMessage const& message, MeshMessage const& mesh);
+void write_boost_file(QString file_name, InputParameters const& params, TemplatePointsMessage const& message, ArrangementMessage const& arrangement);
 #endif // COMPUTATIONTHREAD_H