Refactor (#4)

* get rid of double/float, improve naming

* Remove sorted_id_to_value_ vector from Filtration

* Use combinatorial enumeration as simplex Uid (as in Ripser)

* Check for Ctrl-C in Python

* Add threading to boundary matrix computation

* Breaking: id of cell is always reset to its position in vector
To allow multi-threaded filtration initialization.
Also add multithreading to more places (copying matrix in parallel reduction,
setting pivots, etc).

README.md

@@ -13,10 +13,20 @@ from
 arXiv preprint arXiv:2203.16748 (2022)."*](https://arxiv.org/abs/2203.16748)
 
 Currently it supports computation of lower-star persistence
-of scalar functions on regular grids or of user-defined
+of scalar functions on regular grids, Vietoris-Rips filtrations or of user-defined
 filtrations (where each simplex needs to be created manually).
+It can compute image, kernel and cokernel persistence.
+Oineus provides differentiable filtrations to simplify topological
+optimization. It can compute zero-persistence diagrams. It provides
+a convenience function for mapping cylinder construction.
 It is written in C++ with python bindings (pybind11).
 
+## Installation
+
+```shell
+pip install oineus
+```
+
 ## Compilation
 
 Oineus requires C++17 standard and python3.

bindings/python/CMakeLists.txt

@@ -13,17 +13,23 @@ add_custom_target           (oineus ALL ${CMAKE_COMMAND} -E copy_directory
                                        ${CMAKE_CURRENT_SOURCE_DIR}/oineus ${MODULE_OUTPUT_DIRECTORY}/oineus
                                        DEPENDS ${OINEUS_PYTHON})
 
+set(OINEUS_PYTHON_INT "long int" CACHE STRING "Choose the Int type in Python bindings, options are: int, long int, long long int." FORCE)
+set_property(CACHE OINEUS_PYTHON_INT PROPERTY STRINGS "int" "long int" "long long int")
+
+set(OINEUS_PYTHON_REAL "double" CACHE STRING "Choose the Real type in Python bindings, options are: float, double." FORCE)
+set_property(CACHE OINEUS_PYTHON_REAL PROPERTY STRINGS "float" "double")
 
 pybind11_add_module         (_oineus oineus.cpp
                                      oineus_common.cpp
                                      oineus_decomposition.cpp
-                                     oineus_index_diagram.cpp
-                                     oineus_fil_dgm_simplex_double.cpp
-                                     oineus_fil_dgm_simplex_float.cpp
-                                     oineus_functions_double.cpp
-                                     oineus_functions_float.cpp
+                                     oineus_diagram.cpp
+                                     oineus_cells.cpp
+                                     oineus_filtration.cpp
+                                     oineus_kicr.cpp
+                                     oineus_functions.cpp
                                      oineus_top_optimizer.cpp
                             )
+target_compile_definitions(_oineus PRIVATE OINEUS_PYTHON_REAL=${OINEUS_PYTHON_REAL} OINEUS_PYTHON_INT=${OINEUS_PYTHON_INT})
 target_link_libraries       (_oineus PRIVATE ${libraries})
 target_include_directories  (_oineus PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/../../include"
                                               "${CMAKE_CURRENT_SOURCE_DIR}/../../extern")

bindings/python/oineus.cpp

@@ -8,19 +8,12 @@ PYBIND11_MODULE(_oineus, m)
 {
     m.doc() = "Oineus python bindings";
 
-//    std::string float_suffix = "_float";
-    std::string double_suffix = "_double";
-//    std::string double_suffix = "";
-
-    init_oineus_common_int(m);
-    init_oineus_common_diagram_int(m);
-    init_oineus_common_decomposition_int(m);
-
-//    init_oineus_functions_float(m, float_suffix);
-//    init_oineus_fil_dgm_simplex_float(m, float_suffix);
-
-    init_oineus_functions_double(m, double_suffix);
-    init_oineus_fil_dgm_simplex_double(m, double_suffix);
-
+    init_oineus_common(m);
+    init_oineus_cells(m);
+    init_oineus_filtration(m);
+    init_oineus_common_decomposition(m);
+    init_oineus_diagram(m);
+    init_oineus_functions(m);
+    init_oineus_kicr(m);
     init_oineus_top_optimizer(m);
 }