diff options
Diffstat (limited to 'src')
-rw-r--r-- | src/Alpha_complex/utilities/README | 10 | ||||
-rw-r--r-- | src/Bottleneck_distance/example/CMakeLists.txt | 12 | ||||
-rw-r--r-- | src/Bottleneck_distance/example/README | 19 | ||||
-rw-r--r-- | src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp (renamed from src/Bottleneck_distance/utilities/alpha_rips_persistence_bottleneck_distance.cpp) | 0 | ||||
-rw-r--r-- | src/Bottleneck_distance/utilities/CMakeLists.txt | 11 | ||||
-rw-r--r-- | src/Bottleneck_distance/utilities/README | 19 | ||||
-rw-r--r-- | src/Bottleneck_distance/utilities/bottleneck_read_file_example.cpp (renamed from src/Bottleneck_distance/example/bottleneck_read_file_example.cpp) | 2 | ||||
-rw-r--r-- | src/Rips_complex/utilities/README | 2 |
8 files changed, 42 insertions, 33 deletions
diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README index 30e1b187..abb17bf7 100644 --- a/src/Alpha_complex/utilities/README +++ b/src/Alpha_complex/utilities/README @@ -5,14 +5,14 @@ This program computes the persistent homology with coefficient field Z/pZ of the `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). +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` must be a prime number). **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. +`<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. **Example** `alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45` @@ -45,14 +45,14 @@ This program computes the persistent homology with coefficient field Z/pZ of the `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). +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` must be a prime number). **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. +`<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. **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` @@ -93,7 +93,7 @@ This program computes the persistent homology with coefficient field Z/pZ of the `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). +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` must be a prime number). **Usage** `alpha_complex_persistence [options] <OFF input file>` diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 6a602dbb..9677f5c5 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -3,15 +3,15 @@ project(Bottleneck_distance_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) - add_executable (bottleneck_read_file_example bottleneck_read_file_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}) add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>) + 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") - 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) + install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) 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..0e314608 --- /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 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.
diff --git a/src/Bottleneck_distance/utilities/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp index fd164b22..fd164b22 100644 --- a/src/Bottleneck_distance/utilities/alpha_rips_persistence_bottleneck_distance.cpp +++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt index 634b2479..decdc789 100644 --- a/src/Bottleneck_distance/utilities/CMakeLists.txt +++ b/src/Bottleneck_distance/utilities/CMakeLists.txt @@ -2,16 +2,15 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_utilities) 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_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) if (TBB_FOUND) target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) endif(TBB_FOUND) - 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") + 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 alpha_rips_persistence_bottleneck_distance DESTINATION bin) + install(TARGETS bottleneck_read_file_example DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/utilities/README b/src/Bottleneck_distance/utilities/README index 4c9b0735..cfdccf0b 100644 --- a/src/Bottleneck_distance/utilities/README +++ b/src/Bottleneck_distance/utilities/README @@ -1,19 +1,10 @@ # 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.
+## `bottleneck_read_file_example` ##
+This program computes the Bottleneck distance between two persistence diagram files.
Usage:
-`alpha_rips_persistence_bottleneck_distance [options] <OFF input file>`
-
-Allowed options:
+`bottleneck_read_file_example <file_1.pers> <file_2.pers> [<tolerance>]`
-* `-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 +<file_1.pers> and <file_2.pers> must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers).
+<tolerance> is an error bound on the bottleneck distance (set by default to the smallest positive double value).
diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/utilities/bottleneck_read_file_example.cpp index 24d73c57..9dd52b31 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/utilities/bottleneck_read_file_example.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/Rips_complex/utilities/README b/src/Rips_complex/utilities/README index ddb7860f..93ec3658 100644 --- a/src/Rips_complex/utilities/README +++ b/src/Rips_complex/utilities/README @@ -5,7 +5,7 @@ This program computes the persistent homology with coefficient field *Z/pZ* of a `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). +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` must be a prime number). **Usage** `rips_persistence [options] <OFF input file>` |