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-rw-r--r--src/Bottleneck_distance/example/CMakeLists.txt34
-rw-r--r--src/Bottleneck_distance/example/README19
-rw-r--r--src/Bottleneck_distance/include/gudhi/Bottleneck.h4
-rw-r--r--src/Bottleneck_distance/include/gudhi/Neighbors_finder.h3
-rw-r--r--src/Bottleneck_distance/utilities/CMakeLists.txt16
-rw-r--r--src/Bottleneck_distance/utilities/bottleneck_distance.cpp (renamed from src/Bottleneck_distance/example/bottleneck_read_file_example.cpp)2
-rw-r--r--src/Bottleneck_distance/utilities/bottleneckdistance.md18
7 files changed, 67 insertions, 29 deletions
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index eac617db..6095d6eb 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -2,37 +2,21 @@ cmake_minimum_required(VERSION 2.6)
project(Bottleneck_distance_examples)
if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
- add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
+ add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+ target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
if (TBB_FOUND)
- target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES})
+ target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
endif(TBB_FOUND)
-
+
add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
-
- add_test(NAME Bottleneck_read_file_example
- COMMAND $<TARGET_FILE:bottleneck_read_file_example>
- "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
-
- install(TARGETS bottleneck_read_file_example DESTINATION bin)
- install(TARGETS bottleneck_basic_example DESTINATION bin)
-
-endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-
-# Eigen3 and CGAL > 4.7.0 is required for alpha complex
-# CGAL > 4.8.1 is required for bottleneck distance =>
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
- add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
- target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
- COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
+ COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
+ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
+ install(TARGETS bottleneck_basic_example DESTINATION bin)
install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
- if (TBB_FOUND)
- target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
- endif(TBB_FOUND)
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/README b/src/Bottleneck_distance/example/README
new file mode 100644
index 00000000..01bcd74a
--- /dev/null
+++ b/src/Bottleneck_distance/example/README
@@ -0,0 +1,19 @@
+# Bottleneck_distance #
+
+## `alpha_rips_persistence_bottleneck_distance` ##
+This program computes the persistent homology with coefficient field Z/pZ of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+`p dim birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+Usage:
+`alpha_rips_persistence_bottleneck_distance [options] <OFF input file>`
+
+Allowed options:
+
+* `-h [ --help ]` Produce help message
+* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.`
+* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.`
+* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
index 8c97dce9..7aee07bb 100644
--- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h
+++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
@@ -46,7 +46,7 @@ double bottleneck_distance_approx(Persistence_graph& g, double e) {
if (step <= b_lower_bound || step >= b_upper_bound) // Avoid precision problem
break;
m.set_r(step);
- while (m.multi_augment()) {}; // compute a maximum matching (in the graph corresponding to the current r)
+ while (m.multi_augment()) {} // compute a maximum matching (in the graph corresponding to the current r)
if (m.perfect()) {
m = biggest_unperfect;
b_upper_bound = step;
@@ -68,7 +68,7 @@ double bottleneck_distance_exact(Persistence_graph& g) {
while (lower_bound_i != upper_bound_i) {
long step = lower_bound_i + static_cast<long> ((upper_bound_i - lower_bound_i - 1) / alpha);
m.set_r(sd.at(step));
- while (m.multi_augment()) {}; // compute a maximum matching (in the graph corresponding to the current r)
+ while (m.multi_augment()) {} // compute a maximum matching (in the graph corresponding to the current r)
if (m.perfect()) {
m = biggest_unperfect;
upper_bound_i = step;
diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
index a6b9b021..87c7cee5 100644
--- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
@@ -32,6 +32,7 @@
#include <unordered_set>
#include <vector>
+#include <algorithm> // for std::max
namespace Gudhi {
@@ -44,7 +45,7 @@ struct Square_query {
typedef Internal_point Point_d;
typedef double FT;
bool contains(Point_d p) const {
- return std::abs(p.x()-c.x()) <= size && std::abs(p.y()-c.y()) <= size;
+ return std::max(std::abs(p.x()-c.x()), std::abs(p.y()-c.y())) <= size;
}
bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT, D> const&r) const {
return
diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt
new file mode 100644
index 00000000..d19e3b1c
--- /dev/null
+++ b/src/Bottleneck_distance/utilities/CMakeLists.txt
@@ -0,0 +1,16 @@
+cmake_minimum_required(VERSION 2.6)
+project(Bottleneck_distance_utilities)
+
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+ add_executable (bottleneck_distance bottleneck_distance.cpp)
+ if (TBB_FOUND)
+ target_link_libraries(bottleneck_distance ${TBB_LIBRARIES})
+ endif(TBB_FOUND)
+
+ add_test(NAME Bottleneck_distance_utilities_Bottleneck_read_file
+ COMMAND $<TARGET_FILE:bottleneck_distance>
+ "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
+
+ install(TARGETS bottleneck_distance DESTINATION bin)
+
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/utilities/bottleneck_distance.cpp
index 24d73c57..9dd52b31 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/utilities/bottleneck_distance.cpp
@@ -31,7 +31,7 @@
int main(int argc, char** argv) {
if (argc < 3) {
std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" <<
- " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
+ " should contain a birth-death pair per line. Third, optional parameter is an error bound on the bottleneck" <<
" distance (set by default to the smallest positive double value). If you set the error bound to 0, be" <<
" aware this version is exact but expensive. The program will now terminate \n";
return -1;
diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md
new file mode 100644
index 00000000..526f5822
--- /dev/null
+++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md
@@ -0,0 +1,18 @@
+
+
+# Bottleneck distance #
+
+## bottleneck_read_file_example ##
+
+This program computes the Bottleneck distance between two persistence diagram files.
+
+**Usage**
+
+```
+ bottleneck_read_file_example <file_1.pers> <file_2.pers> [<tolerance>]
+```
+
+where
+
+* `<file_1.pers>` and `<file_2.pers>` must be in the format described [here](/doc/latest/fileformats.html#FileFormatsPers).
+* `<tolerance>` is an error bound on the bottleneck distance (set by default to the smallest positive double value).
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-28 01:03:49 +0000