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[Fix] Manage multiple space delimiter #1450

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merged 2 commits into from
Mar 7, 2018
Merged

[Fix] Manage multiple space delimiter #1450

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7959604
new trick for detecting delimiter
skoudoro Mar 7, 2018
cf93d5d
update tests
skoudoro Mar 7, 2018
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23 changes: 14 additions & 9 deletions dipy/io/gradients.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
from __future__ import division, print_function, absolute_import

from os.path import splitext
import re
from dipy.utils.six import string_types
import numpy as np
import csv
from nibabel.tmpdirs import InTemporaryDirectory


def read_bvals_bvecs(fbvals, fbvecs):
Expand Down Expand Up @@ -32,18 +33,22 @@ def read_bvals_bvecs(fbvals, fbvecs):
# to this list:
vals = []
for this_fname in [fbvals, fbvecs]:
# If the input was None, we don't read anything and move on:
if this_fname is None:
# If the input was None or empty string, we don't read anything and
# move on:
if this_fname is None or not this_fname:
vals.append(None)
else:
if isinstance(this_fname, string_types):
base, ext = splitext(this_fname)
if ext in ['.bvals', '.bval', '.bvecs', '.bvec', '.txt', '.eddy_rotated_bvecs', '']:
with open(this_fname, 'r') as f:
content = f.readline()
sniffer = csv.Sniffer()
detect_delimiter = sniffer.sniff(str(content))
vals.append(np.squeeze(np.loadtxt(this_fname, delimiter=detect_delimiter.delimiter)))
content = f.read()
# We replace coma and tab delimiter by space
with InTemporaryDirectory():
tmp_fname = "tmp_bvals_bvecs.txt"
with open(tmp_fname, 'w') as f:
f.write(re.sub(r'(\t|,)', ' ', content))
vals.append(np.squeeze(np.loadtxt(tmp_fname)))
elif ext == '.npy':
vals.append(np.squeeze(np.load(this_fname)))
else:
Expand All @@ -59,12 +64,12 @@ def read_bvals_bvecs(fbvals, fbvecs):
if bvecs is None:
return bvals, bvecs

if bvecs.shape[1] > bvecs.shape[0]:
bvecs = bvecs.T
if min(bvecs.shape) != 3:
raise IOError('bvec file should have three rows')
if bvecs.ndim != 2:
raise IOError('bvec file should be saved as a two dimensional array')
if bvecs.shape[1] > bvecs.shape[0]:
bvecs = bvecs.T

# If bvals is None, you don't need to check that they have the same shape:
if bvals is None:
Expand Down
144 changes: 74 additions & 70 deletions dipy/io/tests/test_io_gradients.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,7 @@
from __future__ import division, print_function, absolute_import

import os.path as osp
import os
import tempfile
from nibabel.tmpdirs import InTemporaryDirectory

import numpy as np
import numpy.testing as npt
Expand Down Expand Up @@ -31,74 +30,79 @@ def test_read_bvals_bvecs():

# Test for error raising with incorrect file-contents:

# These bvecs only have two rows/columns:
new_bvecs1 = bvecs[:, :2]
# Make a temporary file
bv_file1 = tempfile.NamedTemporaryFile(mode='wt')
# And fill it with these 2-columned bvecs:
for x in range(new_bvecs1.shape[0]):
bv_file1.file.write('%s %s\n' %
(new_bvecs1[x][0], new_bvecs1[x][1]))
bv_file1.close()
npt.assert_raises(IOError, read_bvals_bvecs, fbvals, bv_file1.name)

# These bvecs are saved as one long array:
new_bvecs2 = np.ravel(bvecs)
bv_file2 = tempfile.NamedTemporaryFile()
np.save(bv_file2, new_bvecs2)
bv_file2.close()
npt.assert_raises(IOError, read_bvals_bvecs, fbvals, bv_file2.name)

# There are less bvecs than bvals:
new_bvecs3 = bvecs[:-1, :]
bv_file3 = tempfile.NamedTemporaryFile()
np.save(bv_file3, new_bvecs3)
bv_file3.close()
npt.assert_raises(IOError, read_bvals_bvecs, fbvals, bv_file3.name)

# You entered the bvecs on both sides:
npt.assert_raises(IOError, read_bvals_bvecs, fbvecs, fbvecs)

# All possible delimiters should work
bv_file4 = tempfile.NamedTemporaryFile()
with open(bv_file4.name, 'w') as f:
f.write("66 55 33")
bvals_1, _ = read_bvals_bvecs(bv_file4.name, None)

bv_file5 = tempfile.NamedTemporaryFile()
with open(bv_file5.name, 'w') as f:
f.write("66, 55, 33")
bvals_2, _ = read_bvals_bvecs(bv_file5.name, None)

bv_file6 = tempfile.NamedTemporaryFile()
with open(bv_file6.name, 'w') as f:
f.write("66 \t 55 \t 33")
bvals_3, _ = read_bvals_bvecs(bv_file6.name, None)

ans = np.array([66., 55., 33.])
npt.assert_array_equal(ans, bvals_1)
npt.assert_array_equal(ans, bvals_2)
npt.assert_array_equal(ans, bvals_3)

bv_file7 = tempfile.NamedTemporaryFile()
with open(bv_file7.name, 'w') as f:
f.write("66 55 33\n45 34 21\n55 32 65\n")
_, bvecs_1 = read_bvals_bvecs(None, bv_file7.name)

bv_file8 = tempfile.NamedTemporaryFile()
with open(bv_file8.name, 'w') as f:
f.write("66, 55, 33\n45, 34, 21 \n 55, 32, 65\n")
_, bvecs_2 = read_bvals_bvecs(None, bv_file8.name)

bv_file9 = tempfile.NamedTemporaryFile()
with open(bv_file9.name, 'w') as f:
f.write("66 \t 55 \t 33\n45 \t 34 \t 21\n55 \t 32 \t 65\n")
_, bvecs_3 = read_bvals_bvecs(None, bv_file9.name)

ans = np.array([[66., 55., 33.], [45., 34., 21.], [55., 32., 65.]])
npt.assert_array_equal(ans, bvecs_1)
npt.assert_array_equal(ans, bvecs_2)
npt.assert_array_equal(ans, bvecs_3)
with InTemporaryDirectory():
# These bvecs only have two rows/columns:
new_bvecs1 = bvecs[:, :2]
# Make a temporary file
with open('test_bv_file1.txt', 'wt') as bv_file1:
# And fill it with these 2-columned bvecs:
for x in range(new_bvecs1.shape[0]):
bv_file1.write('%s %s\n' % (new_bvecs1[x][0],
new_bvecs1[x][1]))
npt.assert_raises(IOError, read_bvals_bvecs, fbvals, 'test_bv_file1.txt')

# These bvecs are saved as one long array:
new_bvecs2 = np.ravel(bvecs)
with open('test_bv_file2.npy', 'w') as bv_file2:
print('FILENAME:', bv_file2.name)
np.save(bv_file2.name, new_bvecs2)
npt.assert_raises(IOError, read_bvals_bvecs, fbvals, 'test_bv_file2.npy')

# There are less bvecs than bvals:
new_bvecs3 = bvecs[:-1, :]
with open('test_bv_file3.txt', 'w') as bv_file3:
np.savetxt(bv_file3.name, new_bvecs3)
npt.assert_raises(IOError, read_bvals_bvecs, fbvals, 'test_bv_file3.txt')

# You entered the bvecs on both sides:
npt.assert_raises(IOError, read_bvals_bvecs, fbvecs, fbvecs)

# All possible delimiters should work
bv_file4 = 'test_space.txt'
with open(bv_file4, 'w') as f:
f.write("66 55 33")
bvals_1, _ = read_bvals_bvecs(bv_file4, '')

bv_file5 = 'test_coma.txt'
with open(bv_file5, 'w') as f:
f.write("66, 55, 33")
bvals_2, _ = read_bvals_bvecs(bv_file5, '')

bv_file6 = 'test_tabs.txt'
with open(bv_file6, 'w') as f:
f.write("66 \t 55 \t 33")
bvals_3, _ = read_bvals_bvecs(bv_file6, '')

ans = np.array([66., 55., 33.])
npt.assert_array_equal(ans, bvals_1)
npt.assert_array_equal(ans, bvals_2)
npt.assert_array_equal(ans, bvals_3)

bv_file7 = 'test_space_2.txt'
with open(bv_file7, 'w') as f:
f.write("66 55 33\n45 34 21\n55 32 65\n")
_, bvecs_1 = read_bvals_bvecs('', bv_file7)

bv_file8 = 'test_coma_2.txt'
with open(bv_file8, 'w') as f:
f.write("66, 55, 33\n45, 34, 21 \n 55, 32, 65\n")
_, bvecs_2 = read_bvals_bvecs('', bv_file8)

bv_file9 = 'test_tabs_2.txt'
with open(bv_file9, 'w') as f:
f.write("66 \t 55 \t 33\n45 \t 34 \t 21\n55 \t 32 \t 65\n")
_, bvecs_3 = read_bvals_bvecs('', bv_file9)

bv_file10 = 'test_multiple_space.txt'
with open(bv_file10, 'w') as f:
f.write("66 55 33\n45, 34, 21 \n 55, 32, 65\n")
_, bvecs_4 = read_bvals_bvecs('', bv_file10)

ans = np.array([[66., 55., 33.], [45., 34., 21.], [55., 32., 65.]])
npt.assert_array_equal(ans, bvecs_1)
npt.assert_array_equal(ans, bvecs_2)
npt.assert_array_equal(ans, bvecs_3)
npt.assert_array_equal(ans, bvecs_4)


if __name__ == '__main__':
Expand Down