Merge pull request #727 from mglisse/writeoff

New write_points_to_off_file

6 files changed, 75 insertions, 86 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 8f8df138..32ec13bd 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -53,7 +53,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets', ")
 
     # Cython modules
-    set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
+    set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_utils', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'rips_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'cubical_complex', ")
@@ -152,7 +152,7 @@ if(PYTHONINTERP_FOUND)
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
     endif (EIGEN3_FOUND)
 
-    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_reader', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_utils', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'simplex_tree', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'rips_complex', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'cubical_complex', ")
@@ -546,6 +546,7 @@ if(PYTHONINTERP_FOUND)
 
     # Reader utils
     add_gudhi_py_test(test_reader_utils)
+    add_gudhi_py_test(test_off)
 
     # Wasserstein
     if(OT_FOUND)
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst
index 276ac4e2..5491542f 100644
--- a/src/python/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -150,7 +150,7 @@ You shall have something like:
     Cython version 0.29.25 
     Numpy version 1.21.4 
     Boost version 1.77.0
-    + Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
+    + Installed modules are: off_utils;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
         persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;
     + Missing modules are: bottleneck;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex;
         euclidean_strong_witness_complex;
@@ -188,7 +188,7 @@ A complete configuration would be :
     GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so
     MPFR_LIBRARIES = /usr/lib/x86_64-linux-gnu/libmpfr.so
     TBB version 9107 found and used
-    + Installed modules are: bottleneck;off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
+    + Installed modules are: bottleneck;off_utils;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex;
         persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;nerve_gic;subsampling;
         tangential_complex;alpha_complex;euclidean_witness_complex;euclidean_strong_witness_complex;
     + Missing modules are: 
diff --git a/src/python/doc/point_cloud.rst b/src/python/doc/point_cloud.rst
index ffd8f85b..473b303f 100644
--- a/src/python/doc/point_cloud.rst
+++ b/src/python/doc/point_cloud.rst
@@ -13,6 +13,11 @@ File Readers
 
 .. autofunction:: gudhi.read_lower_triangular_matrix_from_csv_file
 
+File Writers
+------------
+
+.. autofunction:: gudhi.write_points_to_off_file
+
 Subsampling
 -----------
 
diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_utils.pyx
index a3200704..9276c7b0 100644
--- a/src/python/gudhi/off_reader.pyx
+++ b/src/python/gudhi/off_utils.pyx
@@ -13,8 +13,10 @@ from __future__ import print_function
 from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.string cimport string
+cimport cython
 import errno
 import os
+import numpy as np
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -24,7 +26,7 @@ cdef extern from "Off_reader_interface.h" namespace "Gudhi":
     vector[vector[double]] read_points_from_OFF_file(string off_file)
 
 def read_points_from_off_file(off_file=''):
-    """Read points from OFF file.
+    """Read points from an `OFF file <fileformats.html#off-file-format>`_.
 
     :param off_file: An OFF file style name.
     :type off_file: string
@@ -39,3 +41,22 @@ def read_points_from_off_file(off_file=''):
             raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
                                     off_file)
 
+@cython.embedsignature(True)
+def write_points_to_off_file(fname, points):
+    """Write points to an `OFF file <fileformats.html#off-file-format>`_.
+
+    A simple wrapper for `numpy.savetxt`.
+
+    :param fname: Name of the OFF file.
+    :type fname: str or file handle
+    :param points: Point coordinates.
+    :type points: numpy array of shape (n, dim)
+    """
+    points = np.array(points, copy=False)
+    assert len(points.shape) == 2
+    dim = points.shape[1]
+    if dim == 3:
+        head = 'OFF\n{} 0 0'.format(points.shape[0])
+    else:
+        head = 'nOFF\n{} {} 0 0'.format(dim, points.shape[0])
+    np.savetxt(fname, points, header=head, comments='')
diff --git a/src/python/test/test_off.py b/src/python/test/test_off.py
new file mode 100644
index 00000000..aea1941b
--- /dev/null
+++ b/src/python/test/test_off.py
@@ -0,0 +1,21 @@
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+    Author(s):       Marc Glisse
+
+    Copyright (C) 2022 Inria
+
+    Modification(s):
+      - YYYY/MM Author: Description of the modification
+"""
+
+import gudhi as gd
+import numpy as np
+import pytest
+
+
+def test_off_rw():
+    for dim in range(2, 6):
+        X = np.random.rand(123, dim)
+        gd.write_points_to_off_file("rand.off", X)
+        Y = gd.read_points_from_off_file("rand.off")
+        assert Y == pytest.approx(X)
diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py
index 3431f372..c1cb4e3f 100755
--- a/src/python/test/test_subsampling.py
+++ b/src/python/test/test_subsampling.py
@@ -16,17 +16,9 @@ __license__ = "MIT"
 
 
 def test_write_off_file_for_tests():
-    file = open("subsample.off", "w")
-    file.write("nOFF\n")
-    file.write("2 7 0 0\n")
-    file.write("1.0 1.0\n")
-    file.write("7.0 0.0\n")
-    file.write("4.0 6.0\n")
-    file.write("9.0 6.0\n")
-    file.write("0.0 14.0\n")
-    file.write("2.0 19.0\n")
-    file.write("9.0 17.0\n")
-    file.close()
+    gudhi.write_points_to_off_file(
+        "subsample.off", [[1.0, 1.0], [7.0, 0.0], [4.0, 6.0], [9.0, 6.0], [0.0, 14.0], [2.0, 19.0], [9.0, 17.0]]
+    )
 
 
 def test_simple_choose_n_farthest_points_with_a_starting_point():
@@ -34,54 +26,29 @@ def test_simple_choose_n_farthest_points_with_a_starting_point():
     i = 0
     for point in point_set:
         # The iteration starts with the given starting point
-        sub_set = gudhi.choose_n_farthest_points(
-            points=point_set, nb_points=1, starting_point=i
-        )
+        sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=1, starting_point=i)
         assert sub_set[0] == point_set[i]
         i = i + 1
 
     # The iteration finds then the farthest
-    sub_set = gudhi.choose_n_farthest_points(
-        points=point_set, nb_points=2, starting_point=1
-    )
+    sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=1)
     assert sub_set[1] == point_set[3]
-    sub_set = gudhi.choose_n_farthest_points(
-        points=point_set, nb_points=2, starting_point=3
-    )
+    sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=3)
     assert sub_set[1] == point_set[1]
-    sub_set = gudhi.choose_n_farthest_points(
-        points=point_set, nb_points=2, starting_point=0
-    )
+    sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=0)
     assert sub_set[1] == point_set[2]
-    sub_set = gudhi.choose_n_farthest_points(
-        points=point_set, nb_points=2, starting_point=2
-    )
+    sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=2, starting_point=2)
     assert sub_set[1] == point_set[0]
 
     # Test the limits
-    assert (
-        gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=0) == []
-    )
-    assert (
-        gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=0) == []
-    )
-    assert (
-        gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=1) == []
-    )
-    assert (
-        gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=1) == []
-    )
+    assert gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=0) == []
+    assert gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=0) == []
+    assert gudhi.choose_n_farthest_points(points=[], nb_points=0, starting_point=1) == []
+    assert gudhi.choose_n_farthest_points(points=[], nb_points=1, starting_point=1) == []
 
     # From off file test
     for i in range(0, 7):
-        assert (
-            len(
-                gudhi.choose_n_farthest_points(
-                    off_file="subsample.off", nb_points=i, starting_point=i
-                )
-            )
-            == i
-        )
+        assert len(gudhi.choose_n_farthest_points(off_file="subsample.off", nb_points=i, starting_point=i)) == i
 
 
 def test_simple_choose_n_farthest_points_randomed():
@@ -104,10 +71,7 @@ def test_simple_choose_n_farthest_points_randomed():
 
     # From off file test
     for i in range(0, 7):
-        assert (
-            len(gudhi.choose_n_farthest_points(off_file="subsample.off", nb_points=i))
-            == i
-        )
+        assert len(gudhi.choose_n_farthest_points(off_file="subsample.off", nb_points=i)) == i
 
 
 def test_simple_pick_n_random_points():
@@ -130,9 +94,7 @@ def test_simple_pick_n_random_points():
 
     # From off file test
     for i in range(0, 7):
-        assert (
-            len(gudhi.pick_n_random_points(off_file="subsample.off", nb_points=i)) == i
-        )
+        assert len(gudhi.pick_n_random_points(off_file="subsample.off", nb_points=i)) == i
 
 
 def test_simple_sparsify_points():
@@ -152,31 +114,10 @@ def test_simple_sparsify_points():
     ]
     assert gudhi.sparsify_point_set(points=point_set, min_squared_dist=2.001) == [[0, 1]]
 
-    assert (
-        len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=0.0))
-        == 7
-    )
-    assert (
-        len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=30.0))
-        == 5
-    )
-    assert (
-        len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=40.1))
-        == 4
-    )
-    assert (
-        len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=89.9))
-        == 3
-    )
-    assert (
-        len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=100.0))
-        == 2
-    )
-    assert (
-        len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=324.9))
-        == 2
-    )
-    assert (
-        len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=325.01))
-        == 1
-    )
+    assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=0.0)) == 7
+    assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=30.0)) == 5
+    assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=40.1)) == 4
+    assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=89.9)) == 3
+    assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=100.0)) == 2
+    assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=324.9)) == 2
+    assert len(gudhi.sparsify_point_set(off_file="subsample.off", min_squared_dist=325.01)) == 1