Many improvements to RIVET

.gitignore

@@ -25,4 +25,6 @@ ui_progressdialog.h
 ui_visualizationwindow.h
 build
 cmake-build-*
-msgpack
+msgpack
+RIVET.pro.user
+moc_predefs.h

CMakeLists.txt

@@ -21,12 +21,12 @@ externalproject_add(
         msgpack_project
         PREFIX msgpack
         GIT_REPOSITORY https://github.com/msgpack/msgpack-c
-        GIT_TAG 83a4b89818d4ed3b84d69cbf36e782c641ffab53
+        GIT_TAG cpp-3.0.1
         CMAKE_ARGS -D CMAKE_CXX_STANDARD=11 -D CMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
         INSTALL_COMMAND ""
 )
 
-find_package(Boost "1.60")
+find_package(Boost "1.58")
 
 #note this must come before add_executable or it will be ignored
 link_directories(${CMAKE_CURRENT_BINARY_DIR}/docopt/src/docopt_project-build)
@@ -49,58 +49,70 @@ add_library(rivet
         dcel/barcode_template.cpp
         dcel/dcel.cpp
         dcel/arrangement_message.cpp
+	math/bifiltration_data.cpp
+	math/bigraded_matrix.cpp
+	math/firep.cpp
         math/map_matrix.cpp
         math/multi_betti.cpp
-        math/simplex_tree.cpp
-        math/st_node.cpp
         math/template_point.cpp
         math/template_points_matrix.cpp
         math/index_matrix.cpp
         math/persistence_updater.cpp
+        math/presentation.cpp
         numerics.cpp
         timer.cpp
         debug.cpp
         dcel/grades.cpp
         dcel/grades.h
-        math/bool_array.cpp
-        math/bool_array.h
+        #math/bool_array.cpp
+        #math/bool_array.h
         interface/c_api.cpp
+	math/phat_mod/include/phat/representations/vector_heap_mod.h
+	math/phat_mod/include/phat/helpers/misc.h
+	math/phat_mod/include/phat/helpers/thread_local_storage.h
         interface/c_api.h
         api.h
-        api.cpp)
+        api.cpp
+        )
 
 add_dependencies(rivet msgpack_project)
 
 add_executable (rivet_console
         console.cpp
         computation.cpp
-        interface/progress.cpp
+        debug.cpp
         interface/file_writer.cpp
         interface/file_input_reader.cpp
         interface/input_manager.cpp
-        dcel/barcode.cpp
+	interface/progress.cpp
+        numerics.cpp
+        timer.cpp
+        dcel/anchor.cpp
         dcel/arrangement.cpp
         dcel/arrangement_builder.cpp
-        dcel/anchor.cpp
+        dcel/arrangement_message.cpp
+	dcel/barcode.cpp
         dcel/barcode_template.cpp
         dcel/dcel.cpp
-        dcel/arrangement_message.cpp
+        dcel/grades.cpp
+	dcel/grades.h
+	math/bool_array.cpp
+	math/bool_array.h
+	math/bifiltration_data.cpp
+	math/bigraded_matrix.cpp
+	math/firep.cpp
+     	math/index_matrix.cpp
         math/map_matrix.cpp
         math/multi_betti.cpp
-        math/simplex_tree.cpp
-        math/st_node.cpp
+        math/persistence_updater.cpp
+	math/presentation.cpp
         math/template_point.cpp
         math/template_points_matrix.cpp
-        math/index_matrix.cpp
-        math/persistence_updater.cpp
-        numerics.cpp
-        timer.cpp
-        debug.cpp
-        dcel/grades.cpp
-        dcel/grades.h
-        math/bool_array.cpp
-        math/bool_array.h
-        api.cpp)
+	math/phat_mod/include/phat/representations/vector_heap_mod.h
+	math/phat_mod/include/phat/helpers/misc.h
+	math/phat_mod/include/phat/helpers/thread_local_storage.h
+        api.cpp
+        )
 
 add_dependencies(rivet_console docopt_project msgpack_project)
 
@@ -111,34 +123,41 @@ target_link_libraries(rivet_console ${CMAKE_CURRENT_BINARY_DIR}/docopt/src/docop
 
 add_executable(unit_tests
         computation.cpp
-        interface/progress.cpp
+        debug.cpp
         interface/file_writer.cpp
         interface/file_input_reader.cpp
         interface/input_manager.cpp
+	interface/progress.cpp
+        numerics.cpp
+        timer.cpp
+        dcel/anchor.cpp
         dcel/arrangement.cpp
         dcel/arrangement_builder.cpp
-        dcel/anchor.cpp
-        dcel/barcode.cpp
+        dcel/arrangement_message.cpp
+	dcel/barcode.cpp
         dcel/barcode_template.cpp
         dcel/dcel.cpp
+        dcel/grades.cpp
+	dcel/grades.h
+	math/bool_array.cpp
+	math/bool_array.h
+	math/bifiltration_data.cpp
+	math/bigraded_matrix.cpp
+	math/firep.cpp
+     	math/index_matrix.cpp
         math/map_matrix.cpp
         math/multi_betti.cpp
-        math/simplex_tree.cpp
-        math/st_node.cpp
+        math/persistence_updater.cpp
+	math/presentation.cpp
         math/template_point.cpp
         math/template_points_matrix.cpp
-        math/index_matrix.cpp
-        math/persistence_updater.cpp
-        numerics.cpp
-        timer.cpp
-        debug.cpp
+	math/phat_mod/include/phat/representations/vector_heap_mod.h
+	math/phat_mod/include/phat/helpers/misc.h
+	math/phat_mod/include/phat/helpers/thread_local_storage.h
         test/unit_tests.cpp
         dcel/grades.cpp
-        dcel/grades.h
-        math/bool_array.cpp
-        math/bool_array.h
-        dcel/arrangement_message.cpp
-        api.cpp)
+        api.cpp
+)
 
 add_dependencies(unit_tests msgpack_project)
 

COPYRIGHT

@@ -1,5 +1,4 @@
-RIVET Copyright 2014-2016 The RIVET Developers
-
+RIVET Copyright 2014-2018 The RIVET Developers
 
 Principal contributors to RIVET:
 
@@ -11,6 +10,14 @@ Other contributors to RIVET:
 
   Philip Nadolny
   Abdel-Rahman Madkour
+  Simon Segert
+  Dave Turner
+  Alexander Yu
+  Roy Zhao
+
+This version of RIVET uses some modified code from the PHAT 
+repository for persistence computation by Ulrich Bauer, 
+Michael Kerber, and Jan Reininghaus, Copyright 2013 IST Austria.
 
 
 RIVET is free software: you can redistribute it and/or modify

README.md

@@ -1,35 +1,38 @@
 # RIVET
 
-Program to visualize two-parameter persistent homology. 
-Designed by Michael Lesnick and Matthew Wright. 
-Created December 2013.  
+Program for the visualization and analysis of two-parameter persistent homology.
+
+## Project Founders
+Michael Lesnick  
+Matthew Wright
 
 ## Contributors
-Madkour Abdel-Rahman (St. Olaf)   
-Bryn Keller (Intel Labs)  
-Michael Lesnick (Princeton)  
-Phil Nadolny (St. Olaf)  
-William Wang (UPenn)  
-Matthew Wright (St. Olaf)  
-Alex Yu (Princeton)  
-Roy Zhao (UC Berkeley)
+Madkour Abdel-Rahman   
+Bryn Keller    
+Matthew Wright  
+Phil Nadolny  
+Simon Segert  
+Roy Zhao  
+
+## Dependencies
+RIVET depends on the qt, boost, and msgpack libraries.  In addition, RIVET now incorporates some 
+code from the PHAT repository for persistence computation by Ulrich Bauer, 
+Michael Kerber, Jan Reininghaus.
 
 ## Requirements
 Before starting to build RIVET, you will need to have the following installed:
 
 * A C++ compiler (g++ or clang are what we use)
 * CMake
 * Qt 5
-* Boost (including boost serialization; version 1.60 or newer required)
+* Boost (version 1.58 or newer)
 
 Below we give step-by-step instructions for installing these required dependencies and building RIVET on Ubuntu and Mac OS X.  Building RIVET on Windows is not yet supported (we are working on this), but it is possible to build RIVET using the Bash shell on Windows 10.
 
 ## Building On Ubuntu
 
 ### Installing Dependencies
-To install dependencies on Ubuntu, we suggest that you first upgrade to Ubuntu 16.10; the Ubuntu 16.04 package manager only installs Boost 1.58, whereas RIVET requires Boost version 1.60 or higher.
-
-On Ubuntu 16.10, installation of dependencies should be relatively simple:
+On Ubuntu, installation of dependencies should be relatively simple:
 
     sudo apt-get install cmake qt5-default qt5-qmake qtbase5-dev-tools libboost-all-dev
 

RIVET.pro

@@ -35,6 +35,7 @@ SOURCES	+= main.cpp                         \
 	    math/bool_array.cpp                 \
 		math/index_matrix.cpp               \
 		math/map_matrix.cpp                 \
+		#math/multi_betti.cpp                \
 		dcel/barcode.cpp               \
 		dcel/barcode_template.cpp           \
 		dcel/anchor.cpp                     \
@@ -71,8 +72,6 @@ HEADERS  += visualizationwindow.h			\
 		math/index_matrix.h					\
 		math/map_matrix.h					\
 		math/multi_betti.h					\
-		math/simplex_tree.h					\
-		math/st_node.h						\
 		dcel/barcode.h	    				\
 		dcel/barcode_template.h				\
 		dcel/anchor.h						\
@@ -89,12 +88,13 @@ HEADERS  += visualizationwindow.h			\
     interface/file_input_reader.h \
     #driver.h \
     interface/file_writer.h \
-    cutgraph.h \
     interface/console_interaction.h \
     numerics.h \
+    customspinbox.h
 
 FORMS   += visualizationwindow.ui			\
 		dataselectdialog.ui \
     interface/progressdialog.ui \
     interface/aboutmessagebox.ui \
     interface/configuredialog.ui
+