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[Fix] buffer_size on ArraySequence #597

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Merged
merged 7 commits into from
Feb 20, 2018
Merged

[Fix] buffer_size on ArraySequence #597

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77a7dc3
fix rows_per_buf definition
skoudoro Feb 16, 2018
3724fcf
add a test to check buffer_size effect
skoudoro Feb 16, 2018
bc96348
adressed @effigies suggestion : get a integer by rounding rows_per_buf
skoudoro Feb 16, 2018
2ace3ef
fix concatenate test
skoudoro Feb 16, 2018
7ce7d0f
addressed matthew comment, and adding shrink to finalize_append step
skoudoro Feb 19, 2018
c7861d2
test_correction
skoudoro Feb 19, 2018
ddd7240
STY: Remove spaces after final newline
effigies Feb 20, 2018
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3 changes: 2 additions & 1 deletion nibabel/streamlines/array_sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ def __init__(self, arr_seq, common_shape, dtype):
self.common_shape = common_shape
n_in_row = reduce(mul, common_shape, 1)
bytes_per_row = n_in_row * dtype.itemsize
self.rows_per_buf = bytes_per_row / self.bytes_per_buf
self.rows_per_buf = max(1, self.bytes_per_buf // bytes_per_row)

def update_seq(self, arr_seq):
arr_seq._offsets = np.array(self.offsets)
Expand Down Expand Up @@ -185,6 +185,7 @@ def finalize_append(self):
return
self._build_cache.update_seq(self)
self._build_cache = None
self.shrink_data()

def _resize_data_to(self, n_rows, build_cache):
""" Resize data array if required """
Expand Down
16 changes: 13 additions & 3 deletions nibabel/streamlines/tests/test_array_sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import sys
import unittest
import tempfile
import itertools
import numpy as np

from nose.tools import assert_equal, assert_raises, assert_true
Expand Down Expand Up @@ -91,11 +92,20 @@ def test_creating_arraysequence_from_list(self):
SEQ_DATA['data'])

def test_creating_arraysequence_from_generator(self):
gen = (e for e in SEQ_DATA['data'])
check_arr_seq(ArraySequence(gen), SEQ_DATA['data'])
gen_1, gen_2 = itertools.tee((e for e in SEQ_DATA['data']))
seq = ArraySequence(gen_1)
seq_with_buffer = ArraySequence(gen_2, buffer_size=256)

# Check buffer size effect
assert_equal(seq_with_buffer.data.shape, seq.data.shape)
assert_true(seq_with_buffer._buffer_size > seq._buffer_size)

# Check generator result
check_arr_seq(seq, SEQ_DATA['data'])
check_arr_seq(seq_with_buffer, SEQ_DATA['data'])

# Already consumed generator
check_empty_arr_seq(ArraySequence(gen))
check_empty_arr_seq(ArraySequence(gen_1))

def test_creating_arraysequence_from_arraysequence(self):
seq = ArraySequence(SEQ_DATA['data'])
Expand Down