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-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h13
-rw-r--r--src/cmake/modules/GUDHI_third_party_libraries.cmake2
-rw-r--r--src/common/doc/file_formats.h6
-rw-r--r--src/cython/CMakeLists.txt14
-rw-r--r--src/cython/cython/simplex_tree.pyx22
-rw-r--r--src/cython/doc/_templates/layout.html1
-rw-r--r--src/cython/doc/fileformats.rst30
-rw-r--r--src/cython/doc/reader_utils_ref.rst11
8 files changed, 84 insertions, 15 deletions
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 672fda48..e0a147b3 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -591,10 +591,17 @@ class Persistent_cohomology {
std::ofstream diagram_out(diagram_name.c_str());
cmp_intervals_by_length cmp(cpx_);
std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
+ bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity;
for (auto pair : persistent_pairs_) {
- diagram_out << cpx_->dimension(get<0>(pair)) << " "
- << cpx_->filtration(get<0>(pair)) << " "
- << cpx_->filtration(get<1>(pair)) << std::endl;
+ // Special case on windows, inf is "1.#INF"
+ if (has_infinity && cpx_->filtration(get<1>(pair)) == std::numeric_limits<Filtration_value>::infinity()) {
+ diagram_out << cpx_->dimension(get<0>(pair)) << " "
+ << cpx_->filtration(get<0>(pair)) << " inf" << std::endl;
+ } else {
+ diagram_out << cpx_->dimension(get<0>(pair)) << " "
+ << cpx_->filtration(get<0>(pair)) << " "
+ << cpx_->filtration(get<1>(pair)) << std::endl;
+ }
}
}
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 8f486118..e29ba40c 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -117,8 +117,6 @@ if(NOT GUDHI_CYTHON_PATH)
endif(NOT GUDHI_CYTHON_PATH)
if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
- # Unitary tests are available through py.test
- find_program( PYTEST_PATH py.test )
# Default found version 2
if(PYTHON_VERSION_MAJOR EQUAL 2)
# Documentation generation is available through sphinx
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 9d0415b1..d715aa4d 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -26,7 +26,7 @@
namespace Gudhi {
/*! \page fileformats File formats
-
+
\tableofcontents
\section FileFormatsPers Persistence Diagram
@@ -49,6 +49,10 @@ namespace Gudhi {
\endverbatim
Other sample files can be found in the `data/persistence_diagram` folder.
+
+ Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with
+ `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or
+ `Gudhi::read_persistence_intervals_in_dimension()`.
*/
} // namespace Gudhi
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index f427b3c5..a06be008 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -16,7 +16,7 @@ function( add_gudhi_cython_lib THE_LIB )
endfunction( add_gudhi_cython_lib )
if(CYTHON_FOUND)
- message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
+ message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - Sphinx is ${SPHINX_PATH}")
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
@@ -305,13 +305,11 @@ if(CYTHON_FOUND)
set_tests_properties(witness_complex_from_nearest_landmark_table_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
# Unitary tests are available through py.test
- if(PYTEST_PATH)
- add_test(
- NAME gudhi_cython_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${PYTHON_EXECUTABLE} "${PYTEST_PATH}")
- set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
- endif(PYTEST_PATH)
+ add_test(
+ NAME gudhi_cython_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${PYTHON_EXECUTABLE} -m pytest)
+ set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
# Documentation generation is available through sphinx
if(SPHINX_PATH)
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 2acdac3c..9e3b2345 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -61,6 +61,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
vector[int] betti_numbers()
vector[int] persistent_betti_numbers(double from_value, double to_value)
vector[pair[double,double]] intervals_in_dimension(int dimension)
+ void write_output_diagram(string diagram_file_name)
# SimplexTree python interface
cdef class SimplexTree:
@@ -385,7 +386,7 @@ cdef class SimplexTree:
complex in a specific dimension.
:param dimension: The specific dimension.
- :type from_value: int.
+ :type dimension: int.
:returns: The persistence intervals.
:rtype: list of pair of float
@@ -399,3 +400,22 @@ cdef class SimplexTree:
print("intervals_in_dim function requires persistence function"
" to be launched first.")
return intervals_result
+
+ def write_persistence_diagram(self, persistence_file=''):
+ """This function writes the persistence intervals of the simplicial
+ complex in a user given file name.
+
+ :param persistence_file: The specific dimension.
+ :type persistence_file: string.
+
+ :note: intervals_in_dim function requires persistence function to be
+ launched first.
+ """
+ if self.pcohptr != NULL:
+ if persistence_file != '':
+ self.pcohptr.write_output_diagram(str.encode(persistence_file))
+ else:
+ print("persistence_file must be specified")
+ else:
+ print("intervals_in_dim function requires persistence function"
+ " to be launched first.")
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
index b11c1236..243f33c6 100644
--- a/src/cython/doc/_templates/layout.html
+++ b/src/cython/doc/_templates/layout.html
@@ -65,6 +65,7 @@
{#- old style sidebars: using blocks -- should be deprecated #}
{%- block sidebartoc %}
<h2><a href="index.html">GUDHI</a></h2>
+<h2><a href="fileformats.html">File formats</a></h2>
<h2><a href="installation.html">GUDHI installation</a></h2>
<h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
<h2><a href="genindex.html">Index</a></h2>
diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
new file mode 100644
index 00000000..36225b6d
--- /dev/null
+++ b/src/cython/doc/fileformats.rst
@@ -0,0 +1,30 @@
+File formats
+############
+
+To find the correct function to read the files, please refer to :doc:`reader_utils_ref`
+
+Persistence Diagram
+*******************
+
+Such a file, whose extension is usually ``.pers``, contains a list of persistence intervals.
+
+Lines starting with ``#`` are ignored (comments).
+
+Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines)::
+
+ [[field] dimension] birth death
+
+Here is a simple sample file::
+
+ # Persistence diagram example
+ 2 2.7 3.7
+ 2 9.6 14.
+ # Some comments
+ 3 34.2 34.974
+ 4 3. inf
+
+Other sample files can be found in the data/persistence_diagram folder.
+
+Such files can be generated with :meth:`gudhi.SimplexTree.write_persistence_diagram` and read with
+:meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or
+:meth:`gudhi.read_persistence_intervals_in_dimension`.
diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst
new file mode 100644
index 00000000..9c1ea6fc
--- /dev/null
+++ b/src/cython/doc/reader_utils_ref.rst
@@ -0,0 +1,11 @@
+=============================
+Reader utils reference manual
+=============================
+
+.. autofunction:: gudhi.read_off
+
+.. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file
+
+.. autofunction:: gudhi.read_persistence_intervals_grouped_by_dimension
+
+.. autofunction:: gudhi.read_persistence_intervals_in_dimension
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-14 18:19:44 +0000