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-rw-r--r--src/python/CMakeLists.txt43
-rwxr-xr-xsrc/python/example/alpha_complex_diagram_persistence_from_off_file_example.py23
-rwxr-xr-xsrc/python/example/alpha_complex_from_points_example.py2
-rw-r--r--src/python/gudhi/clustering/tomato.py4
-rw-r--r--src/python/gudhi/point_cloud/knn.py2
-rw-r--r--src/python/gudhi/simplex_tree.pyx2
-rw-r--r--src/python/setup.py.in5
-rwxr-xr-xsrc/python/test/test_tomato.py2
8 files changed, 41 insertions, 42 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 5c1402a6..73303a24 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -276,6 +276,7 @@ if(PYTHONINTERP_FOUND)
install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
+ set(GUDHI_PYTHON_PATH_ENV "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")
# Documentation generation is available through sphinx - requires all modules
# Make it first as sphinx test is by far the longest test which is nice when testing in parallel
if(SPHINX_PATH)
@@ -295,14 +296,14 @@ if(PYTHONINTERP_FOUND)
# sphinx target requires gudhi.so, because conf.py reads gudhi version from it
add_custom_target(sphinx
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
add_test(NAME sphinx_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
# Set missing or not modules
@@ -346,13 +347,13 @@ if(PYTHONINTERP_FOUND)
# Bottleneck and Alpha
add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
-f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
# Tangential
add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
--no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
@@ -361,13 +362,13 @@ if(PYTHONINTERP_FOUND)
# Witness complex
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}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${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}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${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)
@@ -379,7 +380,7 @@ if(PYTHONINTERP_FOUND)
# Bottleneck
add_test(NAME bottleneck_basic_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
if (PYBIND11_FOUND)
@@ -392,26 +393,26 @@ if(PYTHONINTERP_FOUND)
file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
add_test(NAME cover_complex_nerve_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
-f human.off -c 2 -r 10 -g 0.3)
add_test(NAME cover_complex_coordinate_gic_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
-f human.off -c 0 -v)
add_test(NAME cover_complex_functional_gic_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
-o lucky_cat.off
-f lucky_cat_PCA1 -v)
add_test(NAME cover_complex_voronoi_gic_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
-f human.off -n 700 -v)
@@ -422,13 +423,13 @@ if(PYTHONINTERP_FOUND)
# Alpha
add_test(NAME alpha_complex_from_points_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
add_test(NAME alpha_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}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
- --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+ --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
add_gudhi_py_test(test_alpha_complex)
endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
@@ -441,13 +442,13 @@ if(PYTHONINTERP_FOUND)
# Cubical
add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
--no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
add_test(NAME random_cubical_complex_persistence_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
10 10 10)
@@ -456,19 +457,19 @@ if(PYTHONINTERP_FOUND)
# Rips
add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
--no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
add_test(NAME rips_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}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3)
add_test(NAME rips_complex_from_points_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
add_gudhi_py_test(test_rips_complex)
@@ -476,7 +477,7 @@ if(PYTHONINTERP_FOUND)
# Simplex tree
add_test(NAME simplex_tree_example_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
add_gudhi_py_test(test_simplex_tree)
@@ -485,7 +486,7 @@ if(PYTHONINTERP_FOUND)
# Witness
add_test(NAME witness_complex_from_nearest_landmark_table_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
add_gudhi_py_test(test_witness_complex)
diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 1e0273b3..fe03be31 100755
--- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -25,12 +25,12 @@ parser = argparse.ArgumentParser(
description="AlphaComplex creation from " "points read in a OFF file.",
epilog="Example: "
"example/alpha_complex_diagram_persistence_from_off_file_example.py "
- "-f ../data/points/tore3D_300.off -a 0.6"
+ "-f ../data/points/tore3D_300.off"
"- Constructs a alpha complex with the "
"points from the given OFF file.",
)
parser.add_argument("-f", "--file", type=str, required=True)
-parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5)
+parser.add_argument("-a", "--max_alpha_square", type=float, required=False)
parser.add_argument("-b", "--band", type=float, default=0.0)
parser.add_argument(
"--no-diagram",
@@ -47,21 +47,20 @@ with open(args.file, "r") as f:
print("##############################################################")
print("AlphaComplex creation from points read in a OFF file")
- message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square)
- print(message)
-
alpha_complex = gudhi.AlphaComplex(off_file=args.file)
- simplex_tree = alpha_complex.create_simplex_tree(
- max_alpha_square=args.max_alpha_square
- )
+ if args.max_alpha_square is not None:
+ print("with max_edge_length=", args.max_alpha_square)
+ simplex_tree = alpha_complex.create_simplex_tree(
+ max_alpha_square=args.max_alpha_square
+ )
+ else:
+ simplex_tree = alpha_complex.create_simplex_tree()
- message = "Number of simplices=" + repr(simplex_tree.num_simplices())
- print(message)
+ print("Number of simplices=", simplex_tree.num_simplices())
diag = simplex_tree.persistence()
- print("betti_numbers()=")
- print(simplex_tree.betti_numbers())
+ print("betti_numbers()=", simplex_tree.betti_numbers())
if args.no_diagram == False:
import matplotlib.pyplot as plot
diff --git a/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py
index 465632eb..5d5ca66a 100755
--- a/src/python/example/alpha_complex_from_points_example.py
+++ b/src/python/example/alpha_complex_from_points_example.py
@@ -19,7 +19,7 @@ __license__ = "MIT"
print("#####################################################################")
print("AlphaComplex creation from points")
alpha_complex = AlphaComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]])
-simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=60.0)
+simplex_tree = alpha_complex.create_simplex_tree()
if simplex_tree.find([0, 1]):
print("[0, 1] Found !!")
diff --git a/src/python/gudhi/clustering/tomato.py b/src/python/gudhi/clustering/tomato.py
index fbba3cc8..d0e9995c 100644
--- a/src/python/gudhi/clustering/tomato.py
+++ b/src/python/gudhi/clustering/tomato.py
@@ -271,7 +271,7 @@ class Tomato:
l = self.max_weight_per_cc_.min()
r = self.max_weight_per_cc_.max()
if self.diagram_.size > 0:
- plt.plot(self.diagram_[:, 0], self.diagram_[:, 1], "ro")
+ plt.plot(self.diagram_[:, 0], self.diagram_[:, 1], "o", color="red")
l = min(l, self.diagram_[:, 1].min())
r = max(r, self.diagram_[:, 0].max())
if l == r:
@@ -283,7 +283,7 @@ class Tomato:
l, r = -1.0, 1.0
plt.plot([l, r], [l, r])
plt.plot(
- self.max_weight_per_cc_, numpy.full(self.max_weight_per_cc_.shape, 1.1 * l - 0.1 * r), "ro", color="green"
+ self.max_weight_per_cc_, numpy.full(self.max_weight_per_cc_.shape, 1.1 * l - 0.1 * r), "o", color="green"
)
plt.show()
diff --git a/src/python/gudhi/point_cloud/knn.py b/src/python/gudhi/point_cloud/knn.py
index 994be3b6..829bf1bf 100644
--- a/src/python/gudhi/point_cloud/knn.py
+++ b/src/python/gudhi/point_cloud/knn.py
@@ -111,7 +111,7 @@ class KNearestNeighbors:
nargs = {
k: v for k, v in self.params.items() if k in {"p", "n_jobs", "metric_params", "algorithm", "leaf_size"}
}
- self.nn = NearestNeighbors(self.k, metric=self.metric, **nargs)
+ self.nn = NearestNeighbors(n_neighbors=self.k, metric=self.metric, **nargs)
self.nn.fit(X)
if self.params["implementation"] == "hnsw":
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index d7991417..be08a3a1 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -11,7 +11,7 @@ from cython.operator import dereference, preincrement
from libc.stdint cimport intptr_t
import numpy
from numpy import array as np_array
-cimport simplex_tree
+cimport gudhi.simplex_tree
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 98d058fc..65f5446e 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -41,10 +41,9 @@ for module in cython_modules:
libraries=libraries,
library_dirs=library_dirs,
include_dirs=include_dirs,
- runtime_library_dirs=runtime_library_dirs,
- cython_directives = {'language_level': str(sys.version_info[0])},))
+ runtime_library_dirs=runtime_library_dirs,))
-ext_modules = cythonize(ext_modules)
+ext_modules = cythonize(ext_modules, compiler_directives={'language_level': str(sys.version_info[0])})
for module in pybind11_modules:
my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)]
diff --git a/src/python/test/test_tomato.py b/src/python/test/test_tomato.py
index ecab03c4..c571f799 100755
--- a/src/python/test/test_tomato.py
+++ b/src/python/test/test_tomato.py
@@ -37,7 +37,7 @@ def test_tomato_1():
t = Tomato(metric="euclidean", graph_type="radius", r=4.7, k=4)
t.fit(a)
assert t.max_weight_per_cc_.size == 2
- assert np.array_equal(t.neighbors_, [[0, 1, 2], [0, 1, 2], [0, 1, 2], [3, 4, 5, 6], [3, 4, 5], [3, 4, 5], [3, 6]])
+ assert t.neighbors_ == [[0, 1, 2], [0, 1, 2], [0, 1, 2], [3, 4, 5, 6], [3, 4, 5], [3, 4, 5], [3, 6]]
t.plot_diagram()
t = Tomato(graph_type="radius", r=4.7, k=4, symmetrize_graph=True)
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-07 00:53:25 +0000