Merge master

3 files changed, 267 insertions, 12 deletions

diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index f15284f3..f81e6137 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -286,3 +286,30 @@ def _weighted_doc_example(precision):
 def test_weighted_doc_example():
     for precision in ['fast', 'safe', 'exact']:
         _weighted_doc_example(precision)
+
+def test_float_relative_precision():
+    assert AlphaComplex.get_float_relative_precision() == 1e-5
+    # Must be > 0.
+    with pytest.raises(ValueError):
+        AlphaComplex.set_float_relative_precision(0.)
+    # Must be < 1.
+    with pytest.raises(ValueError):
+        AlphaComplex.set_float_relative_precision(1.)
+
+    points = [[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]]
+    st = AlphaComplex(points=points).create_simplex_tree()
+    filtrations = list(st.get_filtration())
+
+    # Get a better precision
+    AlphaComplex.set_float_relative_precision(1e-15)
+    assert AlphaComplex.get_float_relative_precision() == 1e-15
+
+    st = AlphaComplex(points=points).create_simplex_tree()
+    filtrations_better_resolution = list(st.get_filtration())
+
+    assert len(filtrations) == len(filtrations_better_resolution)
+    for idx in range(len(filtrations)):
+        # check simplex is the same
+        assert filtrations[idx][0] == filtrations_better_resolution[idx][0]
+        # check filtration is about the same with a relative precision of the worst case
+        assert filtrations[idx][1] == pytest.approx(filtrations_better_resolution[idx][1], rel=1e-5)
diff --git a/src/python/test/test_persistence_graphical_tools.py b/src/python/test/test_persistence_graphical_tools.py
new file mode 100644
index 00000000..c19836b7
--- /dev/null
+++ b/src/python/test/test_persistence_graphical_tools.py
@@ -0,0 +1,121 @@
+""" 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):       Vincent Rouvreau
+
+    Copyright (C) 2021 Inria
+
+    Modification(s):
+      - YYYY/MM Author: Description of the modification
+"""
+
+import gudhi as gd
+import numpy as np
+import matplotlib as plt
+import pytest
+
+
+def test_array_handler():
+    diags = np.array([[1, 2], [3, 4], [5, 6]], float)
+    arr_diags = gd.persistence_graphical_tools._array_handler(diags)
+    for idx in range(len(diags)):
+        assert arr_diags[idx][0] == 0
+        np.testing.assert_array_equal(arr_diags[idx][1], diags[idx])
+
+    diags = [(1.0, 2.0), (3.0, 4.0), (5.0, 6.0)]
+    arr_diags = gd.persistence_graphical_tools._array_handler(diags)
+    for idx in range(len(diags)):
+        assert arr_diags[idx][0] == 0
+        assert arr_diags[idx][1] == diags[idx]
+
+    diags = [(0, (1.0, 2.0)), (0, (3.0, 4.0)), (0, (5.0, 6.0))]
+    assert gd.persistence_graphical_tools._array_handler(diags) == diags
+
+
+def test_min_birth_max_death():
+    diags = [
+        (0, (0.0, float("inf"))),
+        (0, (0.0983494, float("inf"))),
+        (0, (0.0, 0.122545)),
+        (0, (0.0, 0.12047)),
+        (0, (0.0, 0.118398)),
+        (0, (0.118398, 1.0)),
+        (0, (0.0, 0.117908)),
+        (0, (0.0, 0.112307)),
+        (0, (0.0, 0.107535)),
+        (0, (0.0, 0.106382)),
+    ]
+    assert gd.persistence_graphical_tools.__min_birth_max_death(diags) == (0.0, 1.0)
+    assert gd.persistence_graphical_tools.__min_birth_max_death(diags, band=4.0) == (0.0, 5.0)
+
+
+def test_limit_min_birth_max_death():
+    diags = [
+        (0, (2.0, float("inf"))),
+        (0, (2.0, float("inf"))),
+    ]
+    assert gd.persistence_graphical_tools.__min_birth_max_death(diags) == (2.0, 3.0)
+    assert gd.persistence_graphical_tools.__min_birth_max_death(diags, band=4.0) == (2.0, 6.0)
+
+
+def test_limit_to_max_intervals():
+    diags = [
+        (0, (0.0, float("inf"))),
+        (0, (0.0983494, float("inf"))),
+        (0, (0.0, 0.122545)),
+        (0, (0.0, 0.12047)),
+        (0, (0.0, 0.118398)),
+        (0, (0.118398, 1.0)),
+        (0, (0.0, 0.117908)),
+        (0, (0.0, 0.112307)),
+        (0, (0.0, 0.107535)),
+        (0, (0.0, 0.106382)),
+    ]
+    # check no warnings if max_intervals equals to the diagrams number
+    with pytest.warns(None) as record:
+        truncated_diags = gd.persistence_graphical_tools._limit_to_max_intervals(
+            diags, 10, key=lambda life_time: life_time[1][1] - life_time[1][0]
+        )
+        # check diagrams are not sorted
+        assert truncated_diags == diags
+    assert len(record) == 0
+
+    # check warning if max_intervals lower than the diagrams number
+    with pytest.warns(UserWarning) as record:
+        truncated_diags = gd.persistence_graphical_tools._limit_to_max_intervals(
+            diags, 5, key=lambda life_time: life_time[1][1] - life_time[1][0]
+        )
+        # check diagrams are truncated and sorted by life time
+        assert truncated_diags == [
+            (0, (0.0, float("inf"))),
+            (0, (0.0983494, float("inf"))),
+            (0, (0.118398, 1.0)),
+            (0, (0.0, 0.122545)),
+            (0, (0.0, 0.12047)),
+        ]
+    assert len(record) == 1
+
+
+def _limit_plot_persistence(function):
+    pplot = function(persistence=[])
+    assert isinstance(pplot, plt.axes.SubplotBase)
+    pplot = function(persistence=[], legend=True)
+    assert isinstance(pplot, plt.axes.SubplotBase)
+    pplot = function(persistence=[(0, float("inf"))])
+    assert isinstance(pplot, plt.axes.SubplotBase)
+    pplot = function(persistence=[(0, float("inf"))], legend=True)
+    assert isinstance(pplot, plt.axes.SubplotBase)
+
+
+def test_limit_plot_persistence():
+    for function in [gd.plot_persistence_barcode, gd.plot_persistence_diagram, gd.plot_persistence_density]:
+        _limit_plot_persistence(function)
+
+
+def _non_existing_persistence_file(function):
+    with pytest.raises(FileNotFoundError):
+        function(persistence_file="pouetpouettralala.toubiloubabdou")
+
+
+def test_non_existing_persistence_file():
+    for function in [gd.plot_persistence_barcode, gd.plot_persistence_diagram, gd.plot_persistence_density]:
+        _non_existing_persistence_file(function)
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 31c46213..688f4fd6 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -8,7 +8,7 @@
       - YYYY/MM Author: Description of the modification
 """
 
-from gudhi import SimplexTree, __GUDHI_USE_EIGEN3
+from gudhi import SimplexTree
 import numpy as np
 import pytest
 
@@ -354,16 +354,11 @@ def test_collapse_edges():
 
     assert st.num_simplices() == 10
 
-    if __GUDHI_USE_EIGEN3:
-        st.collapse_edges()
-        assert st.num_simplices() == 9
-        assert st.find([1, 3]) == False
-        for simplex in st.get_skeleton(0):
-            assert simplex[1] == 1.
-    else:
-        # If no Eigen3, collapse_edges throws an exception
-        with pytest.raises(RuntimeError):
-            st.collapse_edges()
+    st.collapse_edges()
+    assert st.num_simplices() == 9
+    assert st.find([0, 2]) == False # [1, 3] would be fine as well
+    for simplex in st.get_skeleton(0):
+        assert simplex[1] == 1.
 
 def test_reset_filtration():
     st = SimplexTree()
@@ -447,4 +442,116 @@ def test_persistence_intervals_in_dimension():
     assert np.array_equal(H2, np.array([[ 0., float("inf")]]))
     # Test empty case
     assert st.persistence_intervals_in_dimension(3).shape == (0, 2)
-    
\ No newline at end of file
+
+def test_equality_operator():
+    st1 = SimplexTree()
+    st2 = SimplexTree()
+
+    assert st1 == st2
+
+    st1.insert([1,2,3], 4.)
+    assert st1 != st2
+
+    st2.insert([1,2,3], 4.)
+    assert st1 == st2
+
+def test_simplex_tree_deep_copy():
+    st = SimplexTree()
+    st.insert([1, 2, 3], 0.)
+    # compute persistence only on the original
+    st.compute_persistence()
+
+    st_copy = st.copy()
+    assert st_copy == st
+    st_filt_list = list(st.get_filtration())
+
+    # check persistence is not copied
+    assert st.__is_persistence_defined() == True
+    assert st_copy.__is_persistence_defined() == False
+
+    # remove something in the copy and check the copy is included in the original
+    st_copy.remove_maximal_simplex([1, 2, 3])
+    a_filt_list = list(st_copy.get_filtration())
+    assert len(a_filt_list) < len(st_filt_list)
+
+    for a_splx in a_filt_list:
+        assert a_splx in st_filt_list
+    
+    # test double free
+    del st
+    del st_copy
+
+def test_simplex_tree_deep_copy_constructor():
+    st = SimplexTree()
+    st.insert([1, 2, 3], 0.)
+    # compute persistence only on the original
+    st.compute_persistence()
+
+    st_copy = SimplexTree(st)
+    assert st_copy == st
+    st_filt_list = list(st.get_filtration())
+
+    # check persistence is not copied
+    assert st.__is_persistence_defined() == True
+    assert st_copy.__is_persistence_defined() == False
+
+    # remove something in the copy and check the copy is included in the original
+    st_copy.remove_maximal_simplex([1, 2, 3])
+    a_filt_list = list(st_copy.get_filtration())
+    assert len(a_filt_list) < len(st_filt_list)
+
+    for a_splx in a_filt_list:
+        assert a_splx in st_filt_list
+    
+    # test double free
+    del st
+    del st_copy
+
+def test_simplex_tree_constructor_exception():
+    with pytest.raises(TypeError):
+        st = SimplexTree(other = "Construction from a string shall raise an exception")
+
+def test_expansion_with_blocker():
+    st=SimplexTree()
+    st.insert([0,1],0)
+    st.insert([0,2],1)
+    st.insert([0,3],2)
+    st.insert([1,2],3)
+    st.insert([1,3],4)
+    st.insert([2,3],5)
+    st.insert([2,4],6)
+    st.insert([3,6],7)
+    st.insert([4,5],8)
+    st.insert([4,6],9)
+    st.insert([5,6],10)
+    st.insert([6],10)
+
+    def blocker(simplex):
+        try:
+            # Block all simplices that countains vertex 6
+            simplex.index(6)
+            print(simplex, ' is blocked')
+            return True
+        except ValueError:
+            print(simplex, ' is accepted')
+            st.assign_filtration(simplex, st.filtration(simplex) + 1.)
+            return False
+
+    st.expansion_with_blocker(2, blocker)
+    assert st.num_simplices() == 22
+    assert st.dimension() == 2
+    assert st.find([4,5,6]) == False
+    assert st.filtration([0,1,2]) == 4.
+    assert st.filtration([0,1,3]) == 5.
+    assert st.filtration([0,2,3]) == 6.
+    assert st.filtration([1,2,3]) == 6.
+
+    st.expansion_with_blocker(3, blocker)
+    assert st.num_simplices() == 23
+    assert st.dimension() == 3
+    assert st.find([4,5,6]) == False
+    assert st.filtration([0,1,2]) == 4.
+    assert st.filtration([0,1,3]) == 5.
+    assert st.filtration([0,2,3]) == 6.
+    assert st.filtration([1,2,3]) == 6.
+    assert st.filtration([0,1,2,3]) == 7.