Merge pull request #494 from MarcCote/enh_concatenate_array_sequences

MRG: function to concatenate multiple ArraySequence objects

Adds the function `nibabel.streamlines.array_sequence.concatenate(seqs, axis)` that can concatenate multiple `ArraySequence` objects along the provided axis.

Author: matthew-brett

nibabel/streamlines/array_sequence.py

@@ -380,3 +380,31 @@ def create_arraysequences_from_generator(gen, n):
     for seq in seqs:
         seq.finalize_append()
     return seqs
+
+
+def concatenate(seqs, axis):
+    """ Concatenates multiple :class:`ArraySequence` objects along an axis.
+
+    Parameters
+    ----------
+    seqs: iterable of :class:`ArraySequence` objects
+        Sequences to concatenate.
+    axis : int
+        Axis along which the sequences will be concatenated.
+
+    Returns
+    -------
+    new_seq: :class:`ArraySequence` object
+        New :class:`ArraySequence` object which is the result of
+        concatenating multiple sequences along the given axis.
+    """
+    new_seq = seqs[0].copy()
+    if axis == 0:
+        # This is the same as an extend.
+        for seq in seqs[1:]:
+            new_seq.extend(seq)
+
+        return new_seq
+
+    new_seq._data = np.concatenate([seq._data for seq in seqs], axis=axis)
+    return new_seq

nibabel/streamlines/tests/test_array_sequence.py

@@ -8,7 +8,7 @@
 from nibabel.testing import assert_arrays_equal
 from numpy.testing import assert_array_equal
 
-from ..array_sequence import ArraySequence, is_array_sequence
+from ..array_sequence import ArraySequence, is_array_sequence, concatenate
 
 
 SEQ_DATA = {}
@@ -299,3 +299,18 @@ def test_save_and_load_arraysequence(self):
 
             # Make sure we can add new elements to it.
             loaded_seq.append(SEQ_DATA['data'][0])
+
+
+def test_concatenate():
+    seq = SEQ_DATA['seq'].copy()  # In case there is in-place modification.
+    seqs = [seq[:, [i]] for i in range(seq.common_shape[0])]
+    new_seq = concatenate(seqs, axis=1)
+    seq._data += 100  # Modifying the 'seq' shouldn't change 'new_seq'.
+    check_arr_seq(new_seq, SEQ_DATA['data'])
+    assert_true(not new_seq._is_view)
+
+    seq = SEQ_DATA['seq']
+    seqs = [seq[:, [i]] for i in range(seq.common_shape[0])]
+    new_seq = concatenate(seqs, axis=0)
+    assert_true(len(new_seq), seq.common_shape[0] * len(seq))
+    assert_array_equal(new_seq._data, seq._data.T.reshape((-1, 1)))