Skip zero entries when creating a sparse matrix from numpy (#160) (th…

…anks @alebugariu)

lib/stormpy/storage/__init__.py

@@ -6,53 +6,45 @@
 def build_sparse_matrix(array, row_group_indices=[]):
     """
     Build a sparse matrix from numpy array.
+    Zero entries are skipped.
 
     :param numpy array: The array.
     :param List[double] row_group_indices: List containing the starting row of each row group in ascending order.
     :return: Sparse matrix.
     """
-
-    num_row = array.shape[0]
-    num_col = array.shape[1]
-
-    len_group_indices = len(row_group_indices)
-    if len_group_indices > 0:
-        builder = storage.SparseMatrixBuilder(rows=num_row, columns=num_col, has_custom_row_grouping=True,
-                                              row_groups=len_group_indices)
-    else:
-        builder = storage.SparseMatrixBuilder(rows=num_row, columns=num_col)
-
-    row_group_index = 0
-    for r in range(num_row):
-        # check whether to start a custom row group
-        if row_group_index < len_group_indices and r == row_group_indices[row_group_index]:
-            builder.new_row_group(r)
-            row_group_index += 1
-        # insert values of the current row
-        for c in range(num_col):
-            builder.add_next_value(r, c, array[r, c])
-
-    return builder.build()
+    return _build_sparse_matrix(storage.SparseMatrixBuilder, array, row_group_indices=row_group_indices)
 
 
 def build_parametric_sparse_matrix(array, row_group_indices=[]):
     """
     Build a sparse matrix from numpy array.
+    Zero entries are skipped.
 
     :param numpy array: The array.
     :param List[double] row_group_indices: List containing the starting row of each row group in ascending order.
     :return: Parametric sparse matrix.
     """
+    return _build_sparse_matrix(storage.ParametricSparseMatrixBuilder, array, row_group_indices=row_group_indices)
+
+
+def _build_sparse_matrix(builder_class, array, row_group_indices=[]):
+    """
+    General method to build a sparse matrix from numpy array.
+    Zero entries are skipped.
 
+    :param class builder_class: The class type used to create the matrix builder.
+    :param numpy array: The array.
+    :param List[double] row_group_indices: List containing the starting row of each row group in ascending order.
+    :return: Sparse matrix.
+    """
     num_row = array.shape[0]
     num_col = array.shape[1]
 
     len_group_indices = len(row_group_indices)
     if len_group_indices > 0:
-        builder = storage.ParametricSparseMatrixBuilder(rows=num_row, columns=num_col, has_custom_row_grouping=True,
-                                                        row_groups=len_group_indices)
+        builder = builder_class(rows=num_row, columns=num_col, has_custom_row_grouping=True, row_groups=len_group_indices)
     else:
-        builder = storage.ParametricSparseMatrixBuilder(rows=num_row, columns=num_col)
+        builder = builder_class(rows=num_row, columns=num_col)
 
     row_group_index = 0
     for r in range(num_row):
@@ -62,7 +54,8 @@ def build_parametric_sparse_matrix(array, row_group_indices=[]):
             row_group_index += 1
         # insert values of the current row
         for c in range(num_col):
-            builder.add_next_value(r, c, array[r, c])
+            if array[r, c] != 0:
+                builder.add_next_value(r, c, array[r, c])
 
     return builder.build()
 

tests/storage/test_matrix_builder.py

@@ -211,17 +211,39 @@ def test_matrix_from_numpy(self):
         # Check matrix dimension
         assert matrix.nr_rows == array.shape[0]
         assert matrix.nr_columns == array.shape[1]
-        assert matrix.nr_entries == 8
+        assert matrix.nr_entries == 7
 
         # Check matrix values
         for r in range(array.shape[1]):
             row = matrix.get_row(r)
             for e in row:
-                assert (e.value() == array[r, e.column])
+                assert e.value() == array[r, e.column]
+
+    @numpy_avail
+    def test_matrix_from_numpy_zeros(self):
+        import numpy as np
+        array = np.array([[0, 0, 1, 0],
+                          [0.1, 0, 0, 0.9],
+                          [0, 0, 0, 0],
+                          [1, 0, 0, 0]], dtype='float64')
+
+        matrix = stormpy.build_sparse_matrix(array)
+
+        # Check matrix dimension
+        assert matrix.nr_rows == array.shape[0]
+        assert matrix.nr_columns == array.shape[1]
+        assert matrix.nr_entries == 4
+
+        # Check matrix values
+        for r in range(array.shape[1]):
+            row = matrix.get_row(r)
+            for e in row:
+                assert e.value() == array[r, e.column]
 
     @numpy_avail
     def test_parametric_matrix_from_numpy(self):
         import numpy as np
+        zero = stormpy.RationalRF(0)
         one_pol = stormpy.RationalRF(1)
         one_pol = stormpy.FactorizedPolynomial(one_pol)
         first_val = stormpy.FactorizedRationalFunction(one_pol, one_pol)
@@ -231,22 +253,22 @@ def test_parametric_matrix_from_numpy(self):
         third_val = stormpy.FactorizedRationalFunction(one_pol, two_pol)
 
         array = np.array([[sec_val, first_val],
-                          [first_val, sec_val],
-                          [sec_val, sec_val],
+                          [first_val, zero],
+                          [0, sec_val],
                           [third_val, third_val]])
 
         matrix = stormpy.build_parametric_sparse_matrix(array)
 
         # Check matrix dimension
         assert matrix.nr_rows == array.shape[0]
         assert matrix.nr_columns == array.shape[1]
-        assert matrix.nr_entries == 8
+        assert matrix.nr_entries == 6
 
         # Check matrix values
         for r in range(array.shape[1]):
             row = matrix.get_row(r)
             for e in row:
-                assert (e.value() == array[r, e.column])
+                assert e.value() == array[r, e.column]
 
     @numpy_avail
     def test_matrix_from_numpy_row_grouping(self):
@@ -261,13 +283,13 @@ def test_matrix_from_numpy_row_grouping(self):
         # Check matrix dimension
         assert matrix.nr_rows == array.shape[0]
         assert matrix.nr_columns == array.shape[1]
-        assert matrix.nr_entries == 8
+        assert matrix.nr_entries == 7
 
         # Check matrix values
         for r in range(array.shape[1]):
             row = matrix.get_row(r)
             for e in row:
-                assert (e.value() == array[r, e.column])
+                assert e.value() == array[r, e.column]
 
         # Check row groups
         assert matrix.get_row_group_start(0) == 1
@@ -303,7 +325,7 @@ def test_parametric_matrix_from_numpy_row_grouping(self):
         for r in range(array.shape[1]):
             row = matrix.get_row(r)
             for e in row:
-                assert (e.value() == array[r, e.column])
+                assert e.value() == array[r, e.column]
 
         # Check row groups
         assert matrix.get_row_group_start(0) == 1