Skip to content

fix: unicode problem with MRTrix2TrackVis #1804

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 5 commits into from
Apr 29, 2017
Merged

fix: unicode problem with MRTrix2TrackVis #1804

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
53c62c0
fix: removed file in different PR
mgxd Feb 11, 2017
a30b884
undo
mgxd Feb 11, 2017
c5d5f06
Merge branch 'fix/mrtrix' of github.com:mgxd/nipype into fix/mrtrix
mgxd Mar 15, 2017
bb2b08a
Merge branch 'master' of git://github.com/nipy/nipype into fix/mrtrix
mgxd Apr 28, 2017
29512c7
fix: streamlines less than 100
mgxd Apr 28, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 12 additions & 9 deletions nipype/interfaces/mrtrix/convert.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,9 @@
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(datadir)

"""
from __future__ import print_function, division, unicode_literals, absolute_import
from builtins import open
from io import open

import os.path as op
import nibabel as nb
Expand Down Expand Up @@ -55,10 +54,11 @@ def read_mrtrix_tracks(in_file, as_generator=True):


def read_mrtrix_header(in_file):
fileobj = open(in_file, 'r')
fileobj = open(in_file, 'rb')
header = {}
iflogger.info('Reading header data...')
for line in fileobj:
line = line.decode()
if line == 'END\n':
iflogger.info('Reached the end of the header!')
break
Expand All @@ -78,7 +78,7 @@ def read_mrtrix_header(in_file):
def read_mrtrix_streamlines(in_file, header, as_generator=True):
offset = header['offset']
stream_count = header['count']
fileobj = open(in_file, 'r')
fileobj = open(in_file, 'rb')
fileobj.seek(offset)
endianness = native_code
f4dt = np.dtype(endianness + 'f4')
Expand Down Expand Up @@ -138,9 +138,14 @@ def track_gen(track_points):
if n_streams == stream_count:
iflogger.info('100% : {n} tracks read'.format(n=n_streams))
raise StopIteration
if n_streams % int(stream_count / 100) == 0:
percent = int(float(n_streams) / float(stream_count) * 100)
iflogger.info('{p}% : {n} tracks read'.format(p=percent, n=n_streams))
try:
if n_streams % int(stream_count / 100) == 0:
percent = int(float(n_streams) / float(stream_count) * 100)
iflogger.info('{p}% : {n} tracks read'.format(p=percent,
n=n_streams))
except ZeroDivisionError:
iflogger.info('{} stream read out of {}'.format(n_streams,
stream_count))
track_points, nonfinite_list = points_per_track(offset)
fileobj.seek(offset)
streamlines = track_gen(track_points)
Expand All @@ -166,10 +171,8 @@ class MRTrix2TrackVis(BaseInterface):
"""
Converts MRtrix (.tck) tract files into TrackVis (.trk) format
using functions from dipy

Example
-------

>>> import nipype.interfaces.mrtrix as mrt
>>> tck2trk = mrt.MRTrix2TrackVis()
>>> tck2trk.inputs.in_file = 'dwi_CSD_tracked.tck'
Expand Down