Add read_weights in reader_utils. Add exceptions for file not found and inconsistency in alpha ctor. Add UT accordingly

4 files changed, 139 insertions, 22 deletions

diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx
index 0fea3f37..b7c20f74 100644
--- a/src/python/gudhi/alpha_complex.pyx
+++ b/src/python/gudhi/alpha_complex.pyx
@@ -16,11 +16,12 @@ from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
 from libc.stdint cimport intptr_t
+import errno
 import os
 
 from gudhi.simplex_tree cimport *
 from gudhi.simplex_tree import SimplexTree
-from gudhi import read_points_from_off_file
+from gudhi import read_points_from_off_file, read_weights
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -55,7 +56,7 @@ cdef class AlphaComplex:
     cdef Alpha_complex_interface * this_ptr
 
     # Fake constructor that does nothing but documenting the constructor
-    def __init__(self, points=None, off_file='', precision='safe'):
+    def __init__(self, points=[], off_file='', weights=[], weight_file='', precision='safe'):
         """AlphaComplex constructor.
 
         :param points: A list of points in d-Dimension.
@@ -65,12 +66,24 @@ cdef class AlphaComplex:
             read and overwritten by the points in the `off_file`.
         :type off_file: string
 
+        :param weights: A list of weights. If set, the number of weights must correspond to the
+            number of points.
+        :type weights: list of double
+
+        :param weight_file: A file containing a list of weights (one per line).
+            `weights` are read and overwritten by the weights in the `weight_file`.
+            If set, the number of weights must correspond to the number of points.
+        :type weight_file: string
+
         :param precision: Alpha complex precision can be 'fast', 'safe' or 'exact'. Default is 'safe'.
         :type precision: string
+
+        :raises FileNotFoundError: If `off_file` and/or `weight_file` is set but not found.
+        :raises ValueError: In case of inconsistency between the number of points and weights.
         """
 
     # The real cython constructor
-    def __cinit__(self, points = [], off_file = '', precision = 'safe'):
+    def __cinit__(self, points = [], off_file = '', weights=[], weight_file='', precision = 'safe'):
         assert precision in ['fast', 'safe', 'exact'], "Alpha complex precision can only be 'fast', 'safe' or 'exact'"
         cdef bool fast = precision == 'fast'
         cdef bool exact = precision == 'exact'
@@ -79,12 +92,28 @@ cdef class AlphaComplex:
             if os.path.isfile(off_file):
                 points = read_points_from_off_file(off_file = off_file)
             else:
-                print("file " + off_file + " not found.")
+                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), off_file)
+
+        if weight_file:
+            if os.path.isfile(weight_file):
+                weights = read_weights(weight_file = weight_file)
+            else:
+                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), weight_file)
+
         # need to copy the points to use them without the gil
         cdef vector[vector[double]] pts
+        cdef vector[double] wgts
         pts = points
-        with nogil:
-            self.this_ptr = new Alpha_complex_interface(pts, fast, exact)
+        if len(weights) == 0:
+            with nogil:
+                self.this_ptr = new Alpha_complex_interface(pts, fast, exact)
+        else:
+            if len(weights) == len(points):
+                wgts = weights
+                with nogil:
+                    self.this_ptr = new Alpha_complex_interface(pts, fast, exact)
+            else:
+                raise ValueError("Inconsistency between the number of points and weights")
 
     def __dealloc__(self):
         if self.this_ptr != NULL:
diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx
index fe1c3a2e..f997ad3e 100644
--- a/src/python/gudhi/reader_utils.pyx
+++ b/src/python/gudhi/reader_utils.pyx
@@ -84,3 +84,19 @@ def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=-
                 'utf-8'), only_this_dim))
     print("file " + persistence_file + " not set or not found.")
     return []
+
+def read_weights(weight_file=''):
+    """Reads a file containing weights. Only one float value per line is read and stored.
+    The return value is a `list(weight)`.
+
+    :param weight_file: A weight file style name (one weight per line).
+    :type weight_file: string
+
+    :returns:  A list of weights.
+    :rtype: List[float]
+    """
+    weights=[]
+    with open(weight_file, 'r') as wfile:
+        weights = [float(wline) for wline in wfile if wline.strip()]
+    return weights
+
diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py
index 8f1424ec..35059339 100755
--- a/src/python/test/test_alpha_complex.py
+++ b/src/python/test/test_alpha_complex.py
@@ -261,3 +261,58 @@ def _3d_tetrahedrons(precision):
 def test_3d_tetrahedrons():
     for precision in ['fast', 'safe', 'exact']:
         _3d_tetrahedrons(precision)
+
+def test_non_existing_off_file():
+    with pytest.raises(FileNotFoundError):
+        alpha = gd.AlphaComplex(off_file="pouetpouettralala.toubiloubabdou")
+
+def test_non_existing_weight_file():
+    off_file = open("alphacomplexdoc.off", "w")
+    off_file.write("OFF         \n" \
+                   "7 0 0       \n" \
+                   "1.0 1.0  0.0\n" \
+                   "7.0 0.0  0.0\n" \
+                   "4.0 6.0  0.0\n" \
+                   "9.0 6.0  0.0\n" \
+                   "0.0 14.0 0.0\n" \
+                   "2.0 19.0 0.0\n" \
+                   "9.0 17.0 0.0\n"  )
+    off_file.close()
+
+    with pytest.raises(FileNotFoundError):
+        alpha = gd.AlphaComplex(off_file="alphacomplexdoc.off",
+                                weight_file="pouetpouettralala.toubiloubabdou")
+
+
+def test_inconsistency_off_weight_file():
+    off_file = open("alphacomplexdoc.off", "w")
+    off_file.write("OFF         \n" \
+                   "7 0 0       \n" \
+                   "1.0 1.0  0.0\n" \
+                   "7.0 0.0  0.0\n" \
+                   "4.0 6.0  0.0\n" \
+                   "9.0 6.0  0.0\n" \
+                   "0.0 14.0 0.0\n" \
+                   "2.0 19.0 0.0\n" \
+                   "9.0 17.0 0.0\n"  )
+    off_file.close()
+    # 7 points, 8 weights, on purpose
+    weight_file = open("alphacomplexdoc.wgt", "w")
+    weight_file.write("5.0\n" \
+                   "2.0\n" \
+                   "7.0\n" \
+                   "4.0\n" \
+                   "9.0\n" \
+                   "0.0\n" \
+                   "2.0\n" \
+                   "9.0\n"  )
+    weight_file.close()
+
+    with pytest.raises(ValueError):
+        alpha = gd.AlphaComplex(off_file="alphacomplexdoc.off",
+                                weight_file="alphacomplexdoc.wgt")
+
+    # 7 points, 6 weights, on purpose
+    with pytest.raises(ValueError):
+        alpha = gd.AlphaComplex(off_file="alphacomplexdoc.off",
+                                weights=[1., 2., 3., 4., 5., 6.])
diff --git a/src/python/test/test_reader_utils.py b/src/python/test/test_reader_utils.py
index 90da6651..91de9ba0 100755
--- a/src/python/test/test_reader_utils.py
+++ b/src/python/test/test_reader_utils.py
@@ -8,8 +8,9 @@
       - YYYY/MM Author: Description of the modification
 """
 
-import gudhi
+import gudhi as gd
 import numpy as np
+from pytest import raises
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2017 Inria"
@@ -18,7 +19,7 @@ __license__ = "MIT"
 
 def test_non_existing_csv_file():
     # Try to open a non existing file
-    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(
+    matrix = gd.read_lower_triangular_matrix_from_csv_file(
         csv_file="pouetpouettralala.toubiloubabdou"
     )
     assert matrix == []
@@ -29,7 +30,7 @@ def test_full_square_distance_matrix_csv_file():
     test_file = open("full_square_distance_matrix.csv", "w")
     test_file.write("0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;")
     test_file.close()
-    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(
+    matrix = gd.read_lower_triangular_matrix_from_csv_file(
         csv_file="full_square_distance_matrix.csv"
     )
     assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]]
@@ -40,7 +41,7 @@ def test_lower_triangular_distance_matrix_csv_file():
     test_file = open("lower_triangular_distance_matrix.csv", "w")
     test_file.write("\n1,\n2,3,\n4,5,6,\n7,8,9,10,")
     test_file.close()
-    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(
+    matrix = gd.read_lower_triangular_matrix_from_csv_file(
         csv_file="lower_triangular_distance_matrix.csv", separator=","
     )
     assert matrix == [[], [1.0], [2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0, 10.0]]
@@ -48,11 +49,11 @@ def test_lower_triangular_distance_matrix_csv_file():
 
 def test_non_existing_persistence_file():
     # Try to open a non existing file
-    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(
+    persistence = gd.read_persistence_intervals_grouped_by_dimension(
         persistence_file="pouetpouettralala.toubiloubabdou"
     )
     assert persistence == []
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="pouetpouettralala.toubiloubabdou", only_this_dim=1
     )
     np.testing.assert_array_equal(persistence, [])
@@ -65,21 +66,21 @@ def test_read_persistence_intervals_without_dimension():
         "# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf"
     )
     test_file.close()
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_without_dimension.pers"
     )
     np.testing.assert_array_equal(
         persistence, [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float("Inf"))]
     )
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_without_dimension.pers", only_this_dim=0
     )
     np.testing.assert_array_equal(persistence, [])
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_without_dimension.pers", only_this_dim=1
     )
     np.testing.assert_array_equal(persistence, [])
-    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(
+    persistence = gd.read_persistence_intervals_grouped_by_dimension(
         persistence_file="persistence_intervals_without_dimension.pers"
     )
     assert persistence == {
@@ -94,29 +95,29 @@ def test_read_persistence_intervals_with_dimension():
         "# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf"
     )
     test_file.close()
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_with_dimension.pers"
     )
     np.testing.assert_array_equal(
         persistence, [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float("Inf"))]
     )
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=0
     )
     np.testing.assert_array_equal(persistence, [(2.7, 3.7)])
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=1
     )
     np.testing.assert_array_equal(persistence, [(9.6, 14.0), (3.0, float("Inf"))])
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=2
     )
     np.testing.assert_array_equal(persistence, [])
-    persistence = gudhi.read_persistence_intervals_in_dimension(
+    persistence = gd.read_persistence_intervals_in_dimension(
         persistence_file="persistence_intervals_with_dimension.pers", only_this_dim=3
     )
     np.testing.assert_array_equal(persistence, [(34.2, 34.974)])
-    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(
+    persistence = gd.read_persistence_intervals_grouped_by_dimension(
         persistence_file="persistence_intervals_with_dimension.pers"
     )
     assert persistence == {
@@ -124,3 +125,19 @@ def test_read_persistence_intervals_with_dimension():
         1: [(9.6, 14.0), (3.0, float("Inf"))],
         3: [(34.2, 34.974)],
     }
+
+
+def test_non_existing_weights_file():
+    with raises(FileNotFoundError):
+        # Try to open a non existing file
+        persistence = gd.read_weights(weight_file="pouetpouettralala.toubiloubabdou")
+
+def test_read_weights():
+    # Create test file
+    test_file = open("test_read_weights.wgt", "w")
+    test_file.write(
+        "2.7\n 9.6 \n\t34.2\n3.\t\n\n"
+    )
+    test_file.close()
+    weights = gd.read_weights(weight_file = "test_read_weights.wgt")
+    assert weights == [2.7, 9.6, 34.2, 3.]