Switch to PyBind11

Author: derohde

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "pybind11"]
+	path = pybind11
+	url = https://github.com/pybind/pybind11.git

CMakeLists.txt

@@ -3,7 +3,7 @@ project(Fred LANGUAGES CXX C)
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Ofast")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -shared")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libgcc -static-libstdc++")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fpermissive") #supress error in older gcc
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
@@ -12,24 +12,14 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-trapping-math")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ftree-vectorize")
 #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopt-info-vec")
 #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopt-info-loop")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wl,--no-undefined")
-#set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static-libgcc -static-libstdc++ -static")
 
 include_directories(${CMAKE_SOURCE_DIR}/include)
 
-find_package(PythonInterp REQUIRED)
-find_package(PythonLibs REQUIRED)
-find_package(Boost 1.63 COMPONENTS system chrono ${BPY} ${BNPY} REQUIRED)
 find_package(OpenMP REQUIRED)
 
 add_definitions(-D_GLIBCXX_PARALLEL)
 
-include_directories(${Boost_INCLUDE_DIRS})
-include_directories(${PYTHON_INCLUDE_DIRS})
-
-link_libraries(${Boost_LIBRARIES})
-link_libraries(${PYTHON_LIBRARIES})
-
+find_package(OpenMP)
 if(OpenMP_CXX_FOUND)
     link_libraries(OpenMP::OpenMP_CXX)
 endif()
@@ -40,10 +30,13 @@ if(NOT TARGET OpenMP::OpenMP_CXX)
                  PROPERTY INTERFACE_COMPILE_OPTIONS ${OpenMP_CXX_FLAGS})
     set_property(TARGET OpenMP::OpenMP_CXX
                  PROPERTY INTERFACE_LINK_LIBRARIES ${OpenMP_CXX_FLAGS} Threads::Threads)
-    link_libraries(OpenMP::OpenMP_CXX)
+
 endif()
+link_libraries(OpenMP::OpenMP_CXX)
+
+add_subdirectory(pybind11)
 
-PYTHON_ADD_MODULE(backend
+pybind11_add_module(backend
             src/fred_python_wrapper.cpp
             src/curve.cpp
             src/point.cpp

py/Fred/__init__.py Fred/__init__.pypy/Fred/__init__.py renamed to Fred/__init__.py

@@ -1,14 +1,12 @@
+all: pre install
+
 pre:
-	sudo apt install -y libboost-all-dev
-	sudo apt-get install -y python3-setuptools
-	sudo apt-get install -y python3-numpy
-	sudo apt-get install -y python3-matplotlib
-	sudo apt-get install -y cmake
+	git submodule init
+	git submodule update
 
 install:
-	cd py && /usr/bin/python3 ./setup.py install --user
+	python setup.py install --user
 
 clean:
-	rm -r py/dist py/build/ py/Fred.egg-info/
-	pip3 uninstall Fred -y
+	rm -r dist build/ Fred_Frechet.egg-info/ & pip uninstall Fred-Frechet -y
 

Fred/__pycache__/__init__.cpython-39.pyc

@@ -1,6 +1,8 @@
 # Fred ![alt text](https://raw.githubusercontent.com/derohde/Fred/master/logo/logo.png "Fred logo")
 A fast, scalable and light-weight C++ Fréchet distance library, exposed to python and focused on (k,l)-clustering of polygonal curves.
 
+### NOW USING PYBIND11 INSTEAD OF BOOST!
+
 ## Ingredients C++ Backend
 `import Fred.backend as fred`
 
@@ -52,55 +54,31 @@ By default, Fred will automatically determine the number of threads to use. If y
 
 A `fred.Distance_Matrix()` can be used to speed up consecutive calls of `fred.discrete_klcenter` and `fred.discrete_klmedian`. As the name suggests, it stores the distances already computed.
 
-#### discrete (k,l)-center clustering (continuous Fréchet) -- multiple calls
+#### discrete (k,l)-center clustering (continuous Fréchet)
 - from [**Approximating (k,l)-center clustering for curves**](https://dl.acm.org/doi/10.5555/3310435.3310616)
 - signature: `fred.discrete_klcenter_multi(k, l, curves, distances, center_domain, random_first_center)` with parameters 
     - `k`: number of centers
     - `l`: maximum complexity of the centers, only used when center_domain is default value
-    - `distances`: `fred.Distance_Matrix`
+    - `distances`: `fred.Distance_Matrix`, defaults to empty `fred.Distance_Matrix`
     - `center_domain`: possible centers, defaults to empty `fred.Curves()`, in this case the input is simplified and used as center domain
     - `random_first_center`: determines if first center is chosen uniformly at random or first curve is used as first center, optional, defaults to true
 - returns: `fred.Clustering_Result` with mebers 
     - `value`: objective value 
     - `time`: running-time 
     - `assignment`: empty if compute_assignment has not been called
 
-#### discrete (k,l)-median clustering (continuous Fréchet) -- multiple calls
+#### discrete (k,l)-median clustering (continuous Fréchet)
 - Algorithm 6 in [**Coresets for (k,l)-Clustering under the Fréchet distance**](https://arxiv.org/pdf/1901.01870.pdf) + simplification
 - signature: `fred.discrete_klmedian_multi(k, l, curves, distances, center_domain)` with parameters 
     - `k`: number of centers
     - `l`: maximum complexity of the centers, only used when center_domain is default value
-    - `distances`: `fred.Distance_Matrix`
-    - `center_domain`: possible centers, optional parameter, if not given the input is simplified and used as center domain
-- returns: `fred.Clustering_Result` with mebers 
-    - `value`: objective value 
-    - `time`: running-time 
-    - `assignment`: empty if compute_assignment has not been called
-    
-#### discrete (k,l)-center clustering (continuous Fréchet) -- oneshot
-- from [**Approximating (k,l)-center clustering for curves**](https://dl.acm.org/doi/10.5555/3310435.3310616)
-- signature: `fred.discrete_klcenter(k, l, curves, center_domain, random_first_center)` with parameters 
-    - `k`: number of centers
-    - `l`: maximum complexity of the centers, only used when center_domain is default value
-    - `center_domain`: possible centers, optional parameter, if not given the input is simplified and used as center domain
-    - `random_first_center`: determines if first center is chosen uniformly at random or first curve is used as first center, optional, defaults to true
-- returns: `fred.Clustering_Result` with mebers 
-    - `value`: objective value 
-    - `time`: running-time 
-    - `assignment`: empty if compute_assignment has not been called
-
-#### discrete (k,l)-median clustering (continuous Fréchet) -- oneshot
-- Algorithm 6 in [**Coresets for (k,l)-Clustering under the Fréchet distance**](https://arxiv.org/pdf/1901.01870.pdf) + simplification
-- signature: `fred.discrete_klmedian(k, l, curves, center_domain)` with parameters
-    - `k`: number of centers
-    - `l`: maximum complexity of the centers, only used when center_domain is default value
+    - `distances`: `fred.Distance_Matrix`, defaults to empty `fred.Distance_Matrix`
     - `center_domain`: possible centers, optional parameter, if not given the input is simplified and used as center domain
 - returns: `fred.Clustering_Result` with mebers 
     - `value`: objective value 
     - `time`: running-time 
     - `assignment`: empty if compute_assignment has not been called
 
-
 #### Clustering Result
 - signature: `fred.Clustering_Result`
 - methods: `len(fred.Clustering_Result)`: number of centers, `fred.Clustering_Result[i]`: get ith center, `fred.Clustering_Result.compute_assignment(fred.Curves)`: assigns every curve to its nearest center
@@ -112,27 +90,23 @@ A `fred.Distance_Matrix()` can be used to speed up consecutive calls of `fred.di
 
 ### Dimension Reduction via Gaussian Random Projection 
 - [Section 2 in **Random Projections and Sampling Algorithms for Clustering of High Dimensional Polygonal Curves**](https://papers.nips.cc/paper/9443-random-projections-and-sampling-algorithms-for-clustering-of-high-dimensional-polygonal-curves)
-- signature: `fred.dimension_reduction(curves, epsilon, empirical_constant)` with parameters `epsilon`: (1+epsilon) approximation parameter, `empirical_constant`: use constant of empirical study (faster, but less accurate)
+- signature: `fred.dimension_reduction(curves, epsilon, empirical_constant)` with parameters `epsilon`: (1+epsilon) approximation parameter, `empirical_constant`: use constant of empirical study (faster, but less accurate), defaults to `True`
 - returns: `fred.Curves` collection of curves
 
 ## Installation
-Get requirements under Ubuntu: `make pre`
-
-Python3 installation into userdir: `make install`
 
-### If something does not work with Boost
+### Requirements
 
-Manual installation of Boost
+You have to have installed:
+ - git
+ - openmp available (should be a part of your compiler)
+ 
+Thats it!
 
-- `mkdir $HOME/boost` (This folder is hardcoded in setup.py, another location won't work.)
-- `cd /tmp`
-- `wget https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.gz`
-- `tar -xzf boost_1_73_0.tar.gz`
-- `cd boost_1_73_0`
-- `./bootstrap.sh --with-python=/usr/bin/python3`
-- `./b2 install --prefix=$HOME/boost`
+### Installation Procedure
 
-After that, go back to Freds folder and run `make clean` and then `make install`
+ - Variant 1: simply run `pip install git+https://github.com/derohde/Fred`
+ - Variant 2: clone repository and run `make` for installation into userdir
 
 ## Test
 Just run `python py/test.py`.
@@ -213,10 +187,10 @@ dm = fred.Distance_Matrix() # computing the Fréchet distance is costly,
 
 for k in range(2, 6):
 
-    clustering = fred.discrete_klcenter_multi(k, 10, curves, dm)
+    clustering = fred.discrete_klcenter(k, 10, curves, dm)
     print("clustering cost is {}".format(clustering.value))
 
-    clustering = fred.discrete_klmedian_multi(k, 10, curves, dm)
+    clustering = fred.discrete_klmedian(k, 10, curves, dm)
     print("clustering cost is {}".format(clustering.value))
 
 clustering.compute_assignment(curves)

py/Fred/hd_fs.py Fred/hd_fs.pypy/Fred/hd_fs.py renamed to Fred/hd_fs.py

@@ -11,8 +11,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #pragma once
 
 #include <unordered_map>
-
-#include <boost/chrono/include.hpp>
+#include <chrono>
 
 #include "random.hpp"
 #include "curve.hpp"
@@ -132,7 +131,7 @@ struct Clustering_Result {
 
 Clustering_Result gonzalez(const curve_number_t num_centers, const curve_size_t ell, const Curves &in, Distance_Matrix &distances, const bool arya = false, const Curves &center_domain = Curves(), const bool random_start_center = true) {
 
-    const auto start = boost::chrono::process_real_cpu_clock::now();
+    const auto start = std::chrono::high_resolution_clock::now();
     Clustering_Result result;
 
     if (in.empty()) return result;
@@ -233,10 +232,10 @@ Clustering_Result gonzalez(const curve_number_t num_centers, const curve_size_t
     Curves simpl_centers;
     for (const auto center: centers) simpl_centers.push_back(simplified_in[center]);
 
-    auto end = boost::chrono::process_real_cpu_clock::now();
+    auto end = std::chrono::high_resolution_clock::now();
     result.centers = simpl_centers;
     result.value = curr_maxdist;
-    result.running_time = (end-start).count() / 1000000000.0;
+    result.running_time = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
     return result;
 }
 
@@ -245,7 +244,7 @@ Clustering_Result arya(const curve_number_t num_centers, const curve_size_t ell,
 }
 
 Clustering_Result one_median_sampling(const curve_size_t ell, const Curves &in, const double epsilon, const Curves &center_domain = Curves()) {
-    const auto start = boost::chrono::process_real_cpu_clock::now();
+    const auto start = std::chrono::high_resolution_clock::now();
     Clustering_Result result;
     std::vector<curve_number_t> centers;
     const Curves &simplified_in = center_domain;
@@ -296,15 +295,15 @@ Clustering_Result one_median_sampling(const curve_size_t ell, const Curves &in,
     }
     centers.push_back(best_candidate);
 
-    auto end = boost::chrono::process_real_cpu_clock::now();
+    auto end = std::chrono::high_resolution_clock::now();
     result.centers.push_back(simplified_in[centers[0]]);
     result.value = _center_cost_sum(in, simplified_in, centers, distances);
-    result.running_time = (end-start).count() / 1000000000.0;
+    result.running_time = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
     return result;
 }
 
 Clustering_Result one_median_exhaustive(const curve_size_t ell, const Curves &in, const Curves &center_domain = Curves()) {
-    const auto start = boost::chrono::process_real_cpu_clock::now();
+    const auto start = std::chrono::high_resolution_clock::now();
     Clustering_Result result;
     std::vector<curve_number_t> centers;
     const Curves &simplified_in = center_domain;
@@ -344,15 +343,15 @@ Clustering_Result one_median_exhaustive(const curve_size_t ell, const Curves &in
     }
     centers.push_back(best_candidate);
 
-    auto end = boost::chrono::process_real_cpu_clock::now();
+    auto end = std::chrono::high_resolution_clock::now();
     result.centers.push_back(simplified_in[centers[0]]);
     result.value = best_objective_value;
-    result.running_time = (end-start).count() / 1000000000.0;
+    result.running_time = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
     return result;
 }
 
 Clustering_Result two_two_dtw_one_two_median(const Curves &in, const bool with_assignment = false) {
-    const auto start = boost::chrono::process_real_cpu_clock::now();
+    const auto start = std::chrono::high_resolution_clock::now();
     Clustering_Result result;
 
     const auto n = in.size();
@@ -431,15 +430,15 @@ Clustering_Result two_two_dtw_one_two_median(const Curves &in, const bool with_a
     for (const auto &p : S1) cost += p.dist(mu1);
     for (const auto &p : S2) cost += p.dist(mu2);
 
-    auto end = boost::chrono::process_real_cpu_clock::now();
+    auto end = std::chrono::high_resolution_clock::now();
     result.centers.push_back(center_curve);
     result.value = cost;
-    result.running_time = (end-start).count() / 1000000000.0;
+    result.running_time = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
     return result;
 }
 
 Clustering_Result two_two_dtw_one_two_median_exact(const Curves &in, const bool with_assignment = false) {
-    const auto start = boost::chrono::process_real_cpu_clock::now();
+    const auto start = std::chrono::high_resolution_clock::now();
     Clustering_Result result;
     Curve best_center(in.dimensions());
     const auto infty = std::numeric_limits<distance_t>::infinity();
@@ -508,10 +507,10 @@ Clustering_Result two_two_dtw_one_two_median_exact(const Curves &in, const bool
         }
     }
 
-    auto end = boost::chrono::process_real_cpu_clock::now();
+    auto end = std::chrono::high_resolution_clock::now();
     result.centers.push_back(best_center);
     result.value = best;
-    result.running_time = (end-start).count() / 1000000000.0;
+    result.running_time = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
     return result;
 }
 

py/Fred/median.py Fred/median.pypy/Fred/median.py renamed to Fred/median.py

@@ -9,16 +9,10 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 */
 #pragma once
 
-#include <boost/python.hpp>
-#include <boost/python/numpy.hpp>
-
 #include "types.hpp"
 #include "clustering.hpp"
 #include "frechet.hpp"
 
-namespace np = boost::python::numpy;
-namespace p = boost::python;
-
 namespace Coreset {
 
 class Onemedian_Coreset {
@@ -62,31 +56,31 @@ class Onemedian_Coreset {
         }
     }
 
-    inline np::ndarray get_lambda() const {
-        np::dtype dt = np::dtype::get_builtin<distance_t>();
-        p::list l;
-        np::ndarray result = np::array(l, dt);
-        for (const auto &elem: lambda) {
-            l.append(elem);
-        }
-        result = np::array(l, dt);
-        return result;
-    }
+//     inline np::ndarray get_lambda() const {
+//         np::dtype dt = np::dtype::get_builtin<distance_t>();
+//         p::list l;
+//         np::ndarray result = np::array(l, dt);
+//         for (const auto &elem: lambda) {
+//             l.append(elem);
+//         }
+//         result = np::array(l, dt);
+//         return result;
+//     }
 
     inline distance_t get_Lambda() const {
         return Lambda;
     }
 
-    inline np::ndarray get_curves() const {
-        np::dtype dt = np::dtype::get_builtin<curve_number_t>();
-        p::list l;
-        np::ndarray result = np::array(l, dt);
-        for (const auto &elem: coreset) {
-            l.append(elem);
-        }
-        result = np::array(l, dt);
-        return result;
-    }
+//     inline np::ndarray get_curves() const {
+//         np::dtype dt = np::dtype::get_builtin<curve_number_t>();
+//         p::list l;
+//         np::ndarray result = np::array(l, dt);
+//         for (const auto &elem: coreset) {
+//             l.append(elem);
+//         }
+//         result = np::array(l, dt);
+//         return result;
+//     }
 
     inline distance_t get_cost() const {
         return cost;