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-rw-r--r--src/cython/CMakeLists.txt25
-rw-r--r--src/cython/doc/citation.rst2
-rw-r--r--src/cython/doc/cubical_complex_user.rst12
-rw-r--r--src/cython/doc/installation.rst23
-rwxr-xr-xsrc/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py69
-rwxr-xr-xsrc/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py4
-rwxr-xr-xsrc/cython/example/simplex_tree_example.py2
-rw-r--r--src/cython/include/Tangential_complex_interface.h2
-rwxr-xr-xsrc/cython/test/test_simplex_tree.py11
9 files changed, 111 insertions, 39 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ec8589f0..afca9d60 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -185,6 +185,19 @@ if(CYTHON_FOUND)
add_gudhi_py_test(test_tangential_complex)
+ # Witness complex AND Subsampling
+ add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+ add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
# Subsampling
add_gudhi_py_test(test_subsampling)
@@ -218,18 +231,6 @@ if(CYTHON_FOUND)
if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
# Euclidean witness
- add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
- add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
add_gudhi_py_test(test_euclidean_witness_complex)
endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst
index 6cdfb7cc..f4fdf83b 100644
--- a/src/cython/doc/citation.rst
+++ b/src/cython/doc/citation.rst
@@ -12,4 +12,4 @@ Manual, as well as for publications directly related to the GUDHI library.
GUDHI bibtex
************
-.. literalinclude:: how_to_cite_gudhi.bib
+.. literalinclude:: ../../biblio/how_to_cite_gudhi.bib
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 36fa3ba9..2bfac62a 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -59,7 +59,7 @@ directions, allows to determine, dimension, neighborhood, boundary and coboundar
:math:`C \in \mathcal{K}`.
.. figure::
- img/Cubical_complex_representation.png
+ ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png
:alt: Cubical complex.
:figclass: align-center
@@ -87,7 +87,7 @@ in the example below). Next, in lexicographical order, the filtration of top dim
20 4 7 6 5 in the example below).
.. figure::
- img/exampleBitmap.png
+ ../../doc/Bitmap_cubical_complex/exampleBitmap.png
:alt: Example of a input data.
:figclass: align-center
@@ -95,9 +95,9 @@ in the example below). Next, in lexicographical order, the filtration of top dim
The input file for the following complex is:
-.. literalinclude:: cubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt
-.. centered:: data/bitmap/cubicalcomplexdoc.txt
+.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt
.. testcode::
@@ -128,9 +128,9 @@ complex with periodic boundary conditions. One can also use Perseus style input
conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1.
For instance:
-.. literalinclude:: periodiccubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
-.. centered:: data/bitmap/periodiccubicalcomplexdoc.txt
+.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index f98a5039..c182f176 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -68,31 +68,32 @@ The :doc:`Alpha complex </alpha_complex_user>`,
C++ library which provides easy access to efficient and reliable geometric
algorithms.
-Having CGAL version 4.6.0 or higher installed is recommended. The procedure to
-install this library according to your operating system is detailed
+Having CGAL, the Computational Geometry Algorithms Library, version 4.7.0 or
+higher installed is recommended. The procedure to install this library
+according to your operating system is detailed
`here <http://doc.cgal.org/latest/Manual/installation.html>`_.
-The following examples require the Computational Geometry Algorithms Library:
-
-.. only:: builder_html
-
- * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
- * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
-
-The following example requires CGAL version ≥ 4.7.0:
+The following examples requires CGAL version ≥ 4.7.0:
.. only:: builder_html
* :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
* :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
-The following example requires CGAL version ≥ 4.8.0:
+The following examples requires CGAL version ≥ 4.8.0:
.. only:: builder_html
* :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
* :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
+The following examples requires CGAL version ≥ 4.8.1:
+
+.. only:: builder_html
+
+ * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+ * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
Eigen3
======
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
new file mode 100755
index 00000000..79f6df75
--- /dev/null
+++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""This file is part of the Gudhi Library. The Gudhi library
+ (Geometric Understanding in Higher Dimensions) is a generic C++
+ library for computational topology.
+
+ Author(s): Vincent Rouvreau
+
+ Copyright (C) 2017 INRIA
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+parser = argparse.ArgumentParser(description='RipsComplex creation from '
+ 'a correlation matrix read in a csv file.',
+ epilog='Example: '
+ 'example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py '
+ '-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3'
+ '- Constructs a Rips complex with the '
+ 'correlation matrix from the given csv file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
+parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+args = parser.parse_args()
+
+print("#####################################################################")
+print("RipsComplex creation from correlation matrix read in a csv file")
+
+message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+print(message)
+
+correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file)
+# Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix:
+distance_matrix = [[1-correlation_matrix[i][j] for j in range(len(correlation_matrix[0]))] for i in range(len(correlation_matrix))]
+rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=args.max_edge_length)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+
+message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+print(message)
+
+diag = simplex_tree.persistence()
+
+print("betti_numbers()=")
+print(simplex_tree.betti_numbers())
+
+if args.no_diagram == False:
+ pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+ pplot.show()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index fa82a2f3..c8aac240 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -30,12 +30,12 @@ __copyright__ = "Copyright (C) 2016 INRIA"
__license__ = "GPL v3"
parser = argparse.ArgumentParser(description='RipsComplex creation from '
- 'a distance matrix read in a OFF file.',
+ 'a distance matrix read in a csv file.',
epilog='Example: '
'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py '
'-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3'
'- Constructs a Rips complex with the '
- 'points from the given OFF file.')
+ 'distance matrix from the given csv file.')
parser.add_argument("-f", "--file", type=str, required=True)
parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
parser.add_argument("-d", "--max_dimension", type=int, default=1)
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index 831d9da8..51a60e73 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -48,8 +48,6 @@ if st.insert([0, 1, 2], filtration=4.0):
else:
print("Not inserted...")
-# FIXME: Remove this line
-st.set_dimension(3)
print("dimension=", st.dimension())
st.initialize_filtration()
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 5e9dc0e4..ecf014b3 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -106,8 +106,6 @@ class Tangential_complex_interface {
void create_simplex_tree(Simplex_tree<>* simplex_tree) {
int max_dim = tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
- // FIXME
- simplex_tree->set_dimension(max_dim);
simplex_tree->initialize_filtration();
}
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index 4d452d7d..801d52b7 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -34,9 +34,13 @@ def test_insertion():
# insert test
assert st.insert([0, 1]) == True
+
+ assert st.dimension() == 1
+
assert st.insert([0, 1, 2], filtration=4.0) == True
- # FIXME: Remove this line
- st.set_dimension(2)
+
+ assert st.dimension() == 2
+
assert st.num_simplices() == 7
assert st.num_vertices() == 3
@@ -86,8 +90,9 @@ def test_insertion():
assert st.find([2]) == True
st.initialize_filtration()
- assert st.persistence() == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
+ assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
assert st.__is_persistence_defined() == True
+
assert st.betti_numbers() == [1, 1]
assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-09 19:48:06 +0000