multipers 2.5.0b3__tar.gz → 2.5.0b4__tar.gz

{multipers-2.5.0b3 → multipers-2.5.0b4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.5.0b3
+Version: 2.5.0b4
 Summary: Multiparameter Topological Persistence for Machine Learning
 Keywords: TDA,Persistence,Multiparameter,sklearn,autodiff
 Author-Email: David Loiseaux <david.lapous@proton.me>, Hannah Schreiber <hannah.schreiber@inria.fr>

{multipers-2.5.0b3 → multipers-2.5.0b4}/THIRD_PARTY_NOTICES.md

@@ -24,6 +24,12 @@ As a result, distributed `multipers` artifacts built with these components are l
   - Commit used in this workspace: `a481f8d90af7a97795c467d81fb3db2cf952a58e`
   - License: GPL-3.0-or-later (see upstream `COPYING`)
 
+- `rhomboidtiling_newer_cgal_version`
+  - Upstream: https://github.com/DavidLapous/rhomboidtiling_newer_cgal_version
+  - Header/source path used at build time: `ext/rhomboidtiling_newer_cgal_version`
+  - Commit used in this workspace: `c414cdc60f30196ffd3ce5cda1817368655905f0`
+  - License: MIT (see `ext/rhomboidtiling_newer_cgal_version/LICENSE.md`)
+
 - `mpfree`
   - Upstream: https://bitbucket.org/mkerber/mpfree/
   - Header source path used at build time: `ext/mpfree`

{multipers-2.5.0b3 → multipers-2.5.0b4}/cmake/MultipersBuild.cmake

@@ -16,6 +16,23 @@ function(multipers_apply_common_build_flags target_name)
         MULTIPERS_DISABLE_MPFREE_INTERFACE=1
         MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE=1
         MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE=1
+        MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE=1
+    )
+  endif()
+
+  if(NOT MULTIPERS_HAS_FLAT_FILTRATION_CONTAINER)
+    target_compile_definitions(
+      ${target_name}
+      PRIVATE
+        MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE=1
+    )
+  endif()
+
+  if(NOT CGAL_FOUND)
+    target_compile_definitions(
+      ${target_name}
+      PRIVATE
+        MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE=1
     )
   endif()
 
@@ -53,8 +70,12 @@ endfunction()
 set(MULTIPERS_SHARED_CORE_MODULES
   simplex_tree_multi
   slicer
+  mma_structures
   multiparameter_module_approximation
+  _mpfree_interface
   _function_delaunay_interface
+  _multi_critical_interface
+  _rhomboid_tiling_interface
 )
 
 set(MULTIPERS_BOOST_MODULES
@@ -69,6 +90,7 @@ set(MULTIPERS_GMP_MODULE
   _mpfree_interface
   _multi_critical_interface
   _function_delaunay_interface
+  _rhomboid_tiling_interface
 )
 
 set(MULTIPERS_GMP_MODULES ${MULTIPERS_GMP_MODULE})
@@ -88,7 +110,10 @@ set(MULTIPERS_TBB_MODULES
   point_measure
   grids
   slicer
+  _mpfree_interface
   _function_delaunay_interface
+  _multi_critical_interface
+  _rhomboid_tiling_interface
 )
 
 set(MULTIPERS_MODULE_INCLUDE_DIR_MAP
@@ -96,6 +121,7 @@ set(MULTIPERS_MODULE_INCLUDE_DIR_MAP
   _mpfree_interface MULTIPERS_MPFREE_INCLUDE_DIRS
   _multi_critical_interface MULTIPERS_MULTI_CRITICAL_INCLUDE_DIRS
   _function_delaunay_interface MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS
+  _rhomboid_tiling_interface MULTIPERS_RHOMBOID_TILING_INCLUDE_DIRS
 )
 
 set(MULTIPERS_FORKED_PHAT_MODULES
@@ -206,6 +232,7 @@ function(multipers_configure_extension_include_dirs module_name target_name)
   if(uses_forked_phat EQUAL -1)
     target_include_directories(${target_name} BEFORE PRIVATE ${MULTIPERS_PHAT_INCLUDE_DIRS})
   endif()
+  set_target_properties(${target_name} PROPERTIES COMPILE_FLAGS "--no-warnings")
 endfunction()
 
 function(multipers_configure_extension_backend module_name target_name)
@@ -227,6 +254,26 @@ function(multipers_configure_extension_backend module_name target_name)
     target_link_libraries(${target_name} PRIVATE multipers_aida_static)
   endif()
 
+  if(module_name STREQUAL "_rhomboid_tiling_interface")
+    if(NOT MSVC)
+      target_compile_options(
+        ${target_name}
+        PRIVATE
+          -fno-associative-math
+          -fno-unsafe-math-optimizations
+      )
+    endif()
+    if(TARGET multipers_rhomboid_tiling_static)
+      target_link_libraries(${target_name} PRIVATE multipers_rhomboid_tiling_static)
+    endif()
+    if(TARGET CGAL::CGAL)
+      target_link_libraries(${target_name} PRIVATE CGAL::CGAL)
+    endif()
+    if(TARGET CGAL::CGAL_Core)
+      target_link_libraries(${target_name} PRIVATE CGAL::CGAL_Core)
+    endif()
+  endif()
+
   list(FIND MULTIPERS_OPENMP_MODULES "${module_name}" uses_openmp)
   if(NOT uses_openmp EQUAL -1)
     multipers_link_openmp(${target_name})
@@ -346,6 +393,7 @@ set(MULTIPERS_MODULES
   _aida_interface
   _function_delaunay_interface
   _multi_critical_interface
+  _rhomboid_tiling_interface
 )
 
 if(WIN32)

{multipers-2.5.0b3 → multipers-2.5.0b4}/cmake/MultipersCodegen.cmake

@@ -8,6 +8,7 @@ set(MULTIPERS_TEMPLATE_FILES
   "${CMAKE_SOURCE_DIR}/multipers/filtration_conversions.pxd.tp"
   "${CMAKE_SOURCE_DIR}/multipers/slicer.pxd.tp"
   "${CMAKE_SOURCE_DIR}/multipers/mma_structures.pyx.tp"
+  "${CMAKE_SOURCE_DIR}/multipers/multiparameter_module_approximation.pyx.tp"
   "${CMAKE_SOURCE_DIR}/multipers/simplex_tree_multi.pyx.tp"
   "${CMAKE_SOURCE_DIR}/multipers/slicer.pyx.tp"
 )
@@ -17,6 +18,7 @@ set(MULTIPERS_GENERATED_FILES
   "${MULTIPERS_GENERATED_ROOT}/multipers/filtration_conversions.pxd"
   "${MULTIPERS_GENERATED_ROOT}/multipers/slicer.pxd"
   "${MULTIPERS_GENERATED_ROOT}/multipers/mma_structures.pyx"
+  "${MULTIPERS_GENERATED_ROOT}/multipers/multiparameter_module_approximation.pyx"
   "${MULTIPERS_GENERATED_ROOT}/multipers/simplex_tree_multi.pyx"
   "${MULTIPERS_GENERATED_ROOT}/multipers/slicer.pyx"
 )
@@ -32,6 +34,33 @@ set(MULTIPERS_CORE_GENERATED_FILES
 
 set(MULTIPERS_TEMPITA_GRID_GEN "${CMAKE_SOURCE_DIR}/tools/tempita_grid_gen.py")
 
+execute_process(
+  COMMAND
+    "${Python3_EXECUTABLE}" "-c"
+    "import importlib.util, pathlib; spec = importlib.util.spec_from_file_location('multipers_user_options', pathlib.Path(r'${CMAKE_SOURCE_DIR}') / 'options.py'); mod = importlib.util.module_from_spec(spec); spec.loader.exec_module(mod); print('1' if 'Degree_rips_bifiltration' in getattr(mod, 'FILTRATION_CONTAINERS', ()) else '0')"
+  RESULT_VARIABLE MULTIPERS_FLAT_CONTAINER_DETECT_RESULT
+  OUTPUT_VARIABLE MULTIPERS_HAS_FLAT_CONTAINER_RAW
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+  ERROR_VARIABLE MULTIPERS_FLAT_CONTAINER_DETECT_ERROR
+)
+
+if(NOT MULTIPERS_FLAT_CONTAINER_DETECT_RESULT EQUAL 0)
+  message(
+    FATAL_ERROR
+      "Failed to detect FILTRATION_CONTAINERS from options.py: ${MULTIPERS_FLAT_CONTAINER_DETECT_ERROR}"
+  )
+endif()
+
+set(MULTIPERS_HAS_FLAT_FILTRATION_CONTAINER OFF)
+if(MULTIPERS_HAS_FLAT_CONTAINER_RAW STREQUAL "1")
+  set(MULTIPERS_HAS_FLAT_FILTRATION_CONTAINER ON)
+endif()
+
+message(
+  STATUS
+    "MULTIPERS_HAS_FLAT_FILTRATION_CONTAINER=${MULTIPERS_HAS_FLAT_FILTRATION_CONTAINER}"
+)
+
 option(
   MULTIPERS_TEMPITA_GRID_VERBOSE
   "Enable verbose Tempita grid generation logs"

{multipers-2.5.0b3 → multipers-2.5.0b4}/cmake/MultipersDependencies.cmake

@@ -8,6 +8,7 @@ find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module NumPy)
 find_package(Boost REQUIRED COMPONENTS system timer chrono)
 find_package(OpenMP REQUIRED COMPONENTS CXX)
 find_package(TBB CONFIG REQUIRED COMPONENTS tbb)
+find_package(CGAL QUIET COMPONENTS Core)
 
 find_library(MULTIPERS_GMP_LIBRARY REQUIRED NAMES gmp)
 
@@ -67,6 +68,28 @@ set(MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS
   "${CMAKE_SOURCE_DIR}/ext/function_delaunay/scc_mod/include"
 )
 
+set(MULTIPERS_RHOMBOID_TILING_INCLUDE_DIRS
+  "${CMAKE_SOURCE_DIR}/ext/rhomboidtiling_newer_cgal_version/src"
+)
+
+if(CGAL_FOUND)
+  list(APPEND MULTIPERS_RHOMBOID_TILING_INCLUDE_DIRS ${CGAL_INCLUDE_DIRS})
+endif()
+
+if(CGAL_FOUND AND EXISTS "${CMAKE_SOURCE_DIR}/ext/rhomboidtiling_newer_cgal_version/src/rhomboid.cpp" AND EXISTS "${CMAKE_SOURCE_DIR}/ext/rhomboidtiling_newer_cgal_version/src/utils.cpp")
+  add_library(
+    multipers_rhomboid_tiling_static
+    STATIC
+    "${CMAKE_SOURCE_DIR}/ext/rhomboidtiling_newer_cgal_version/src/rhomboid.cpp"
+    "${CMAKE_SOURCE_DIR}/ext/rhomboidtiling_newer_cgal_version/src/utils.cpp"
+  )
+  target_include_directories(multipers_rhomboid_tiling_static PUBLIC ${MULTIPERS_RHOMBOID_TILING_INCLUDE_DIRS})
+  target_link_libraries(multipers_rhomboid_tiling_static PUBLIC CGAL::CGAL)
+  if(TARGET CGAL::CGAL_Core)
+    target_link_libraries(multipers_rhomboid_tiling_static PUBLIC CGAL::CGAL_Core)
+  endif()
+endif()
+
 if(NOT WIN32)
   add_library(
     multipers_aida_static
@@ -81,4 +104,6 @@ if(NOT WIN32)
   )
   target_include_directories(multipers_aida_static PUBLIC ${MULTIPERS_AIDA_INCLUDE_DIRS})
   target_link_libraries(multipers_aida_static PUBLIC Boost::timer Boost::chrono)
+  set_target_properties(multipers_aida_static PROPERTIES COMPILE_FLAGS "--no-warnings")
 endif()
+

multipers-2.5.0b4/ext/rhomboidtiling_newer_cgal_version/README.md

@@ -0,0 +1,117 @@
+# Rhomboid Tiling and Order-k Delaunay Mosaics
+
+For a given d-dimensional finite set of input points, the rhomboid tiling,
+introduced in [The Multi-cover Persistence of Euclidean
+Balls](http://pub.ist.ac.at/~edels/Papers/2018-P-01-MultiCover.pdf),
+is a (d+1)-dimensional geometric structure consisting of rhomboids, which
+are parallelpipeds and their analogues in dimensions other than 3.
+From the rhomboid tiling one can obtain order-k Delaunay mosaics (dual to
+order-k Voronoi tesselations), degree-k Delaunay mosaics (dual to degree-k
+Voronoi tesselations, which decompose the space into k-th Brillouin zones),
+and a discrete version of the filtration of multi-covers of Euclidean balls.
+
+This is a C++ implementation of an algorithm to compute the rhomboid tiling
+for a given input point set, based on the paper 
+[A Simple Algorithm for Computing Higher Order Delaunay
+Mosaics](http://pub.ist.ac.at/~edels/Papers/2020-P-01-SimpleAlgorithm.pdf).
+Currently, the input point set can be 2- or 3-dimensional.
+The implementation uses the [CGAL](https://www.cgal.org/)
+library for Delaunay triangulations and exact arithmetics and includes
+some unit tests using [Catch2](https://github.com/catchorg/Catch2),
+and mostly makes an earlier implementation from 
+https://github.com/geoo89/orderkdelaunay obsolete.
+
+
+## Prerequisites
+
+_Prerequisites:_ cmake, CGAL version <= 4.9, Catch2 (included);
+to work with CGAL version >= 4.10, some typedefs need to be changed,
+see `src/dimensional_traits_2.h` and `src/dimensional_traits_3.h`.
+
+The build setup builds a commandline tool and tests. To build, run:
+```
+cmake .
+make
+```
+
+The unit tests use Catch2 which is included as a header and comes
+with its own licence.
+
+
+## Interface
+
+The class representing the rhomboid tiling is RhomboidTiling<Dt> as defined in
+`src/rhomboid_tiling.h`. It is templated with a dimensional traits class that
+contains dimension specific functionality. For 2D computations use 
+DimensionalTraits_2 from `src/dimensional_traits_2.h`; for 3D use
+DimensionalTraits_3 from `src/dimensional_traits_3.h`.
+
+Upon construction, the rhomboid tiling is computed from the provided input
+points, up to the specified highest order. It provides access methods
+for various combinatorial structures:
+
+- The rhomboids themselves: `get_rhomboids`
+- The order-k Delaunay mosaic: `get_slice_mosaic`
+- The degree-k Delaunay mosaic: `get_halfint_slice_mosaic`
+- Delaunay _slabs_: `get_slab_mosaic`
+
+The order-k Delaunay mosaic is obtained as the intersection of the rhomboid
+tiling with a hyperplane at depth k; degree-k Delaunay mosaic as the
+intersection with a hyperplane at depth k+0.5; a Delaunay slab is the
+intersection of the space between the hyperplanes at depth k and k+1 and
+the rhomboid tiling.
+
+The rhomboid tiling is equipped with a radius function on its rhomboids,
+which allows for the computation of a discrete version of the 2-parameter
+filtration (radius r and depth k) of multi-covers of Euclidean balls.
+The related filtration on the order-k Delaunay mosaics is a discrete version
+of the filtration by parameter r of k-covers of Euclidean balls for a fixed k.
+Access methods for these filtration are:
+
+- Filtration of the rhomboid tiling: `get_rhomboid_filtration`
+- Filtration of the order-k Delaunay mosaic: `get_slice_filtration` and `get_delaunay_filtration`
+- 2-parameter filtration of sliced rhomboids: `get_bifiltration`
+- 2-parameter filtration of unsliced rhomboids: `get_rhomboid_bifiltration`
+
+See the documentation in `src/rhomboid_tiling.h` for details.
+
+
+## Commandline tool
+
+The commandline tool accepts an input filename, output filename, dimension
+parameter, order up to which to compute the mosaics, and an optional parameter
+indicating the desired output data.
+
+Example usage:
+```
+./main example_data/example_input.txt example_data/example_output.txt 3 4 slices
+```
+Input and output are text files. The input is one point per line,
+each with d coordinates separated by spaces, where d is the provided dimension
+parameter (currently only 2 and 3 dimensional data is supported).
+Options for the output data are:
+
+- bifi: [default] Boundary matrix of the 2-parameter discrete sliced rhomboid bifiltration.
+- cbifi: A combinatorial representation of bifi (a cell is represented by its vertices rather than its ID).
+- ubifi: boundary matrix of (unsliced) rhomboid bifiltration.
+- rhomboids: The rhomboids of the rhomboid tiling (top dimensional cells only).
+- slices: All order-k Delaunay slices (top dimensional cells only).
+- halfint: All degree-k Delaunay half-integer slices (top dimensional cells only).
+- slabs: All Delaunay slabs, i.e. cells between order-k and order-(k+1) Delaunay slices (top dimensional cells only).
+- frhomboids: The filtration on the rhomboid tiling.
+- fslices: Filtrations on the order-k Delaunay slices for each k.
+- fslabs: Filtrations on the order-k Delaunay slices for each k and intermediate Delaunay slabs.
+- bslices: Boundary matrices for order-k Delaunay slice filtration for each k.
+- firep: free implicit representation of bifi.
+- ufirep: free implicit representation of ubifi.
+
+The output format depends on the output data. For bifi and ubifi, each cell is
+assigned an ID, and in the output file, each cell is line of space separated
+values, consisting of its ID, its dimension, its order *k*, its radius value
+*r*, and the IDs of its boundary cells.
+For the other output formats, the output meaning and data type
+are documented in `src/rhomboid_tiling.h`. The formatting of each output data
+type is defined in the respective class definition, with the exception of
+CCell, which is a `std::vector` of `std::vector` of `int`s and is output in 
+the list format used in python, i.e. comma separated values wrapped in square
+brackets.