diff options
author | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-04 10:24:04 +0000 |
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committer | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-04 10:24:04 +0000 |
commit | 73efba37dfcab3f9b8589cb3b0b80f6d7dd7bd0b (patch) | |
tree | 8ed0cf77fafbf47f0cb5bdea97d49b6611a1ef48 | |
parent | f45959484fb85299d9ac60c43de9325e5c06e730 (diff) |
Document utilies in README files using Markdown + move/rename some utilities
Only missing doc for now: Garland_heckbert
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8
19 files changed, 374 insertions, 173 deletions
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..69dbc28a --- /dev/null +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -0,0 +1,37 @@ +cmake_minimum_required(VERSION 2.6) +project(Alpha_complex_utilities) + +if(CGAL_FOUND) + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") + + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence + ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) + target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_alpha_complex_persistence COMMAND $<TARGET_FILE:alpha_complex_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") + add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:periodic_alpha_complex_3d_persistence> + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") + + install(TARGETS alpha_complex_persistence DESTINATION bin) + install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) + + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) +endif(CGAL_FOUND) diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README new file mode 100644 index 00000000..30e1b187 --- /dev/null +++ b/src/Alpha_complex/utilities/README @@ -0,0 +1,131 @@ +# Alpha_complex # + +## `alpha_complex_3d_persistence` ## +This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). + +**Usage** +`alpha_complex_3d_persistence <input OFF file> <p> <min_persistence>` +where +`<input OFF file>` is the path to the input point cloud in OFF format. +`<p>` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer. +`<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. It must be a floating-point number >= -1. + +**Example** +`alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45` + +outputs: +``` +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 +``` + +Here we retrieve expected Betti numbers on a tore 3D: +``` +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 +``` + +N.B.: +* `alpha_complex_3d_persistence` only accepts OFF files in dimension 3. +* Filtration values are alpha square values. + + + + +## `periodic_alpha_complex_3d_persistence` ## +This program computes the persistent homology with coefficient field Z/pZ of the 3D periodic alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). + +**Usage** +`periodic_alpha_complex_3d_persistence <input OFF file> <p> <min_persistence>` +where +`<input OFF file>` is the path to the input point cloud in OFF format. +`<p>` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer. +`<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. It must be a floating-point number >= -1. + +**Example** +`periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off ../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0` + +outputs: +``` +Periodic Delaunay computed. +Simplex_tree dim: 3 +3 0 0 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 2 0.005 inf +3 2 0.005 inf +3 2 0.005 inf +3 3 0.0075 inf +``` + +Here we retrieve expected Betti numbers on an 3D iso-oriented cuboids: +``` +Betti numbers[0] = 1 +Betti numbers[1] = 3 +Betti numbers[2] = 3 +Betti numbers[3] = 1 +``` + +N.B.: +* `periodic_alpha_complex_3d_persistence` only accepts OFF files in dimension 3. +* In this example, the periodic cube is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } +* Filtration values are alpha square values. + + + + + +## `alpha_complex_persistence` ## +This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients). + +**Usage** +`alpha_complex_persistence [options] <OFF input file>` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout. +* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction. +* `-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. + +**Example** +`alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off` + +outputs: +``` +Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 +``` + +Here we retrieve expected Betti numbers on a tore 3D: +``` +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 +``` + +N.B.: +* `alpha_complex_persistence` only accepts OFF files in dimension d. +* Filtration values are alpha square values. diff --git a/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h index 7865e4ec..7865e4ec 100644 --- a/src/Persistent_cohomology/utilities/alpha_complex_3d_helper.h +++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h diff --git a/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index f63ff0f6..f63ff0f6 100644 --- a/src/Persistent_cohomology/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp diff --git a/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index 9e84e91f..9e84e91f 100644 --- a/src/Persistent_cohomology/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp diff --git a/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 8140a3c5..8140a3c5 100644 --- a/src/Persistent_cohomology/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp index 67735ba1..e126caea 100644 --- a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp @@ -32,8 +32,8 @@ #include <cstddef> int main(int argc, char** argv) { - std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " << - "complexes provided in text files in Perseus style (the only numbered in the first line is a dimension D of a" << + std::cout << "This program computes persistent homology, by using the Bitmap_cubical_complex_base class, of cubical " << + "complexes provided in text files in Perseus style. The only number in the first line is a dimension D of a" << "bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let " << "N denote product of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are " << "filtrations of top dimensional cells. We assume that the cells are in the lexicographical order. See " << diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp index 122160a2..7f9296a6 100644 --- a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp +++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp @@ -33,9 +33,9 @@ #include <string> int main(int argc, char** argv) { - std::cout << "This program computes persistent homology, by using " << + std::cout << "This program computes persistent homology, by using the " << "Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in " << - "Perseus style (the only numbered in the first line is a dimension D of a bitmap. In the lines I between 2 " << + "Perseus style. The only number in the first line is a dimension D of a bitmap. In the lines I between 2 " << "and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers " << "in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We " << "assume that the cells are in the lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for" << diff --git a/src/Bitmap_cubical_complex/utilities/README b/src/Bitmap_cubical_complex/utilities/README new file mode 100644 index 00000000..d9085635 --- /dev/null +++ b/src/Bitmap_cubical_complex/utilities/README @@ -0,0 +1,24 @@ +# Bitmap_cubical_complex #
+
+## `Bitmap_cubical_complex` ##
+This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style. The only number in the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the lexicographical order.
+
+Examples:
+
+* Create a Cubical Complex from the Perseus style file CubicalOneSphere.txt, computes Persistence cohomology from it and writes the results in a persistence file:
+`Bitmap_cubical_complex data/bitmap/CubicalOneSphere.txt`
+
+* Create a Cubical Complex from the Perseus style file CubicalTwoSphere.txt, computes Persistence cohomology from it and writes the results in a persistence file:
+`Bitmap_cubical_complex data/bitmap/CubicalTwoSphere.txt`
+
+## `Bitmap_cubical_complex_periodic_boundary_conditions` ##
+
+Same as above, but with periodic boundary conditions.
+
+Examples:
+
+* Create a Periodical Cubical Complex from the Perseus style file 2d_torus.txt, computes Persistence cohomology from it and writes the results in a persistence file:
+`Bitmap_cubical_complex_periodic_boundary_conditions.exe data/bitmap/2d_torus.txt`
+
+* Create a Periodical Cubical Complex from the Perseus style file 3d_torus.txt, computes Persistence cohomology from it and writes the results in a persistence file:
+`Bitmap_cubical_complex_periodic_boundary_conditions.exe data/bitmap/3d_torus.txt`
diff --git a/src/Bottleneck_distance/utilities/README b/src/Bottleneck_distance/utilities/README new file mode 100644 index 00000000..4c9b0735 --- /dev/null +++ b/src/Bottleneck_distance/utilities/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 b d`
+
+where `dim` is the dimension of the homological feature, `b` and `d` 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.
\ No newline at end of file diff --git a/src/Persistent_cohomology/utilities/CMakeLists.txt b/src/Persistent_cohomology/utilities/CMakeLists.txt index c2f00da2..5b315801 100644 --- a/src/Persistent_cohomology/utilities/CMakeLists.txt +++ b/src/Persistent_cohomology/utilities/CMakeLists.txt @@ -20,37 +20,4 @@ add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGE install(TARGETS rips_distance_matrix_persistence DESTINATION bin) install(TARGETS rips_persistence DESTINATION bin) -if(CGAL_FOUND) - add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Persistent_cohomology_example_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45") - - install(TARGETS alpha_complex_3d_persistence DESTINATION bin) - - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence - ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Persistent_cohomology_example_alpha_complex COMMAND $<TARGET_FILE:alpha_complex_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:periodic_alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") - - install(TARGETS alpha_complex_persistence DESTINATION bin) - install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) - - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) endif(CGAL_FOUND) diff --git a/src/Persistent_cohomology/utilities/README b/src/Persistent_cohomology/utilities/README index 76e960da..eecee7ee 100644 --- a/src/Persistent_cohomology/utilities/README +++ b/src/Persistent_cohomology/utilities/README @@ -1,114 +1,66 @@ -To build the utilities, run in a Terminal: +# Persistent_cohomology # -cd /path-to-utilities/ -cmake . -make +## `rips_persistence` ## +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: -*********************************************************************************************************************** -Example of use of RIPS: +`p dim b d` -Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points -sampling a 3D torus: +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). -./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 +**Usage** +`rips_persistence [options] <OFF input file>` -output: -2 0 0 inf +**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. + +**Example 1 with Z/2Z coefficients** +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +outputs: +``` +2 0 0 inf 2 1 0.0983494 inf 2 1 0.104347 inf 2 2 0.138335 inf +``` +**Example 2 with Z/3Z coefficients** -Every line is of this format: p1*...*pr dim b d -where - p1*...*pr is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients. - dim is the dimension of the homological feature, - b and d are respectively the birth and death of the feature and - +rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 +outputs: +``` +3 0 0 inf +3 1 0.0983494 inf +3 1 0.104347 inf +3 2 0.138335 inf +``` -with Z/3Z coefficients: -./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 -output: -3 0 0 inf -3 1 0.0983494 inf -3 1 0.104347 inf -3 2 0.138335 inf - -*********************************************************************************************************************** -Example of use of ALPHA: - -For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs. - -1) 3D special case ------------------- -Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points -sampling a torus 3D: - -./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 - -output: -Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 2 -Betti numbers[2] = 1 - -N.B.: - alpha_complex_3d_persistence accepts only OFF files in 3D dimension. - - filtration values are alpha square values - -2) d-Dimension case -------------------- -Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points -sampling a torus 3D: - -./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off - -output: -Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. -Simplex_tree dim: 3 -2 0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 2 -Betti numbers[2] = 1 - -N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension. - - filtration values are alpha square values - -3) 3D periodic special case ---------------------------- -./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off ../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 - -output: -Periodic Delaunay computed. -Simplex_tree dim: 3 + +## `rips_distance_matrix_persistence` ## +Same as `rips_persistence` but taking an distance matrix as input. + +**Example** +`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + +outputs: +``` +The complex contains 46 simplices + and has dimension 3 3 0 0 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 1 0.0025 inf -3 2 0.005 inf -3 2 0.005 inf -3 2 0.005 inf -3 3 0.0075 inf - -Here we retrieve expected Betti numbers on a tore 3D: -Betti numbers[0] = 1 -Betti numbers[1] = 3 -Betti numbers[2] = 3 -Betti numbers[3] = 1 - -N.B.: - periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube -is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } - - filtration values are alpha square values +3 0 0 8.94427 +3 0 0 7.28011 +3 0 0 6.08276 +3 0 0 5.83095 +3 0 0 5.38516 +3 0 0 5 +3 1 11 12.0416 +3 1 6.32456 6.7082 +``` diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index f8527e0f..a8231392 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -14,25 +14,22 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) - - add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) - target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES}) - endif() + + add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_strong_off) add_test(NAME Witness_complex_example_off_test_torus COMMAND $<TARGET_FILE:Witness_complex_example_off> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") add_test(NAME Witness_complex_example_test_sphere_10 COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10") - add_test(NAME Witness_complex_example_test_torus_persistence - COMMAND $<TARGET_FILE:Witness_complex_example_witness_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - + add_test(NAME Witness_complex_example_strong_off_test_torus + COMMAND $<TARGET_FILE:Witness_complex_example_strong_off> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") + install(TARGETS Witness_complex_example_off DESTINATION bin) install(TARGETS Witness_complex_example_sphere DESTINATION bin) - install(TARGETS Witness_complex_example_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_example_strong_off DESTINATION bin) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp index 0ee9ee90..0ee9ee90 100644 --- a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index 918ab864..125a41ff 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -3,24 +3,26 @@ project(Witness_complex_utilities) # CGAL and Eigen3 are required for Euclidean version of Witness if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) - add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) - target_link_libraries(Witness_complex_example_strong_off) + + add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp ) - target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) + target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) - target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) endif() - add_test(NAME Witness_complex_example_strong_off_test_torus - COMMAND $<TARGET_FILE:Witness_complex_example_strong_off> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") - add_test(NAME Witness_complex_example_strong_test_torus_persistence - COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence> + add_test(NAME Witness_complex_strong_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + add_test(NAME Witness_complex_weak_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - install(TARGETS Witness_complex_example_strong_off DESTINATION bin) - install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/README new file mode 100644 index 00000000..d8dc9ca7 --- /dev/null +++ b/src/Witness_complex/utilities/README @@ -0,0 +1,72 @@ +# Witness_complex #
+
+## `weak_witness_persistence` ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+`p dim b d`
+
+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+*Usage*
+`weak_witness_persistence [options] <OFF input file>`
+
+*Allowed options*
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-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.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+*Example*
+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`
+
+outputs:
+```
+Successfully read 1307 points.
+Ambient dimension is 3.
+The complex contains 732 simplices and has dimension 8
+11 0 0 inf
+11 1 0 inf
+11 2 0.0275251 0.0534586
+11 1 0 0.0239952
+```
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
+
+## `strong_witness_persistence` ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+`p dim b d`
+
+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+*Usage*
+`strong_witness_persistence [options] <OFF input file>`
+
+*Allowed options*
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-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.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+*Example*
+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`
+
+outputs:
+```
+Successfully read 1307 points.
+Ambient dimension is 3.
+The complex contains 1836 simplices and has dimension 8
+11 0 0 inf
+11 1 0.00674748 inf
+11 2 0.0937751 0.235354
+```
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
diff --git a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp index f786fe7b..f786fe7b 100644 --- a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp index a1146922..a1146922 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp diff --git a/src/common/utilities/README b/src/common/utilities/README index dc841521..18fa8cc4 100644 --- a/src/common/utilities/README +++ b/src/common/utilities/README @@ -1,19 +1,19 @@ -======================= off_file_from_shape_generator ================================== +# Pointset generator # -Example of use : +## `off_file_from_shape_generator` ## -*** on|in sphere|cube|curve|torus|klein generator +Generates a pointset and save it in an OFF file. Command-line is: +`off_file_from_shape_generator on|in sphere|cube|curve|torus|klein <filename> <num_points> <dimension> <parameter1> <parameter2>...` -./off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2 +Warning: "on cube" generator is not available! - => generates a onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2 +Examples: -./off_file_from_shape_generator in sphere inSphere.off 100 2 +* Generate an onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2: +`off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2` + +* Generate an inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default): +`off_file_from_shape_generator in sphere inSphere.off 100 2` - => generates a inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default) - -./off_file_from_shape_generator in cube inCube.off 10000 3 5.8 - - => generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8 - -!! Warning: hypegenerator on cube is not available !! +* Generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8: +`off_file_from_shape_generator in cube inCube.off 10000 3 5.8` |