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Merged
merged 32 commits into from
Apr 18, 2017
Merged

ENH: Support TCK streamlines file format #486

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46b1de9
Initial support for TCK
MarcCote Feb 25, 2016
7648d3c
FIX: check for eof
MarcCote Feb 25, 2016
306dc6e
Support Python 3
MarcCote Feb 25, 2016
9c9cb5d
More Python3 supports
MarcCote Mar 31, 2016
86dc54c
Send streamlines to world space before saving in a TCK file
MarcCote Apr 1, 2016
2b87c36
Added unit test that make sure we handle affine_to_rasmm correctly in…
MarcCote Apr 1, 2016
317b1cc
RF+DOC+TEST: tck format.
MarcCote Sep 13, 2016
7a5532f
BF: Supports Python 3
MarcCote Sep 13, 2016
1df9501
PEP8
MarcCote Sep 13, 2016
893fa44
TST: added unit test for TCK files written in big-endian
MarcCote Sep 13, 2016
96d555b
BF: Python 3
MarcCote Sep 14, 2016
e9ab875
BF: fixed TCK buferring and added a unit test
MarcCote Sep 21, 2016
b4cbbcc
BF: Was saving unwanted information in a TCK's header.
MarcCote Oct 4, 2016
21158e1
Added TCK version of the standard test.
MarcCote Nov 4, 2016
de8ee31
Typos
MarcCote Nov 4, 2016
570b37d
BF: Assume identity affine when loading TCK files.
MarcCote Dec 22, 2016
0f63e7c
PEP8
MarcCote Feb 13, 2017
72d146a
DOC+PEP8: Finish addressing @matthew-brett's comments.
MarcCote Feb 28, 2017
ea84c9d
RF: refactor tck read for speed
matthew-brett Mar 27, 2017
a4bda85
MAINT: update numpy dependency to 1.7
matthew-brett Mar 27, 2017
2df7518
Merge pull request #12 from matthew-brett/refactor-tck-read
MarcCote Mar 29, 2017
029f853
PEP8 + addressed's @matthew-brett's comments
MarcCote Mar 29, 2017
9228075
Convert MagicNumber to bytes
MarcCote Mar 30, 2017
4d93676
Addressed's @jchoude's comments
MarcCote Mar 31, 2017
aacf014
Increase test coverage
MarcCote Mar 31, 2017
c6117fe
PEP8
MarcCote Mar 31, 2017
bac044b
Update docstring and addressed @Matthew-brett's last comments
MarcCote Apr 7, 2017
3dc3d71
RF: move create_empty_header logic to top level
matthew-brett Apr 13, 2017
9511327
RF: make default trk structured array a scalar
matthew-brett Apr 13, 2017
0bacbf5
BF: adapt tests to new TractogramFile interface
matthew-brett Apr 13, 2017
0d0ece1
[DOC] mentioned that the file needs to be opened in binary mode if pr…
MarcCote Apr 18, 2017
d2e08da
Merge pull request #13 from matthew-brett/refactor-create-empty-header
MarcCote Apr 18, 2017
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6 changes: 3 additions & 3 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,19 +33,19 @@ matrix:
# Absolute minimum dependencies
- python: 2.7
env:
- DEPENDS="numpy==1.6.0" PYDICOM=0
- DEPENDS="numpy==1.7.1" PYDICOM=0
# Absolute minimum dependencies plus oldest MPL
# Check these against:
# nibabel/info.py
# doc/source/installation.rst
# requirements.txt
- python: 2.7
env:
- DEPENDS="numpy==1.6.0 matplotlib==1.3.1" PYDICOM=0
- DEPENDS="numpy==1.7.1 matplotlib==1.3.1" PYDICOM=0
# Minimum pydicom dependency
- python: 2.7
env:
- DEPENDS="numpy==1.6.0 pydicom==0.9.7 pillow==2.6"
- DEPENDS="numpy==1.7.1 pydicom==0.9.7 pillow==2.6"
# test against numpy 1.7
- python: 2.7
env:
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2 changes: 1 addition & 1 deletion doc/source/installation.rst
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Expand Up @@ -87,7 +87,7 @@ Requirements
.travis.yml

* Python_ 2.7, or >= 3.4
* NumPy_ 1.6 or greater
* NumPy_ 1.7 or greater
* Six_ 1.3 or greater
* SciPy_ (optional, for full SPM-ANALYZE support)
* PyDICOM_ 0.9.7 or greater (optional, for DICOM support)
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2 changes: 1 addition & 1 deletion nibabel/info.py
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Expand Up @@ -186,7 +186,7 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
# doc/source/installation.rst
# requirements.txt
# .travis.yml
NUMPY_MIN_VERSION = '1.6.0'
NUMPY_MIN_VERSION = '1.7.1'
PYDICOM_MIN_VERSION = '0.9.7'
SIX_MIN_VERSION = '1.3'

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5 changes: 4 additions & 1 deletion nibabel/streamlines/__init__.py
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Expand Up @@ -10,9 +10,12 @@
from .tractogram_file import ExtensionWarning

from .trk import TrkFile
from .tck import TckFile

# List of all supported formats
FORMATS = {".trk": TrkFile}
FORMATS = {".trk": TrkFile,
".tck": TckFile
}


def is_supported(fileobj):
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