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Merged
merged 8 commits into from
Mar 9, 2018
Merged

tst: explicitly set intent codes to allow proper loading #604

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b560da6
fix: explicitly set intent codes to allow proper loading
mgxd Feb 23, 2018
8d5d70d
fix: do not allow saving of images without intent
mgxd Feb 23, 2018
fc619c0
fix: use unknown CIFTI type, raise ValueError if incorrect intent code
mgxd Feb 26, 2018
4ab086b
enh: move cifti intent check into to_file_map
mgxd Mar 4, 2018
0036e0c
enh: set default intent code when saving CIFTI images
mgxd Mar 6, 2018
e995d50
STY: remove unused import
mgxd Mar 6, 2018
5f6b64f
sty: utilize assert_equals
mgxd Mar 6, 2018
ba81e30
fix: use correct CIFTI intent names
mgxd Mar 8, 2018
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3 changes: 3 additions & 0 deletions nibabel/cifti2/cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1384,6 +1384,9 @@ def to_file_map(self, file_map=None):
header = self._nifti_header
extension = Cifti2Extension(content=self.header.to_xml())
header.extensions.append(extension)
# if intent code is not set, default to unknown CIFTI
if header.get_intent()[0] == 'none':
header.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
data = reshape_dataobj(self.dataobj,
(1, 1, 1, 1) + self.dataobj.shape)
# If qform not set, reset pixdim values so Nifti2 does not complain
Expand Down
24 changes: 12 additions & 12 deletions nibabel/cifti2/parse_cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,27 +52,27 @@ def _mangle(self, value):
# The codes below appear on the CIFTI-2 standard
# http://www.nitrc.org/plugins/mwiki/index.php/cifti:ConnectivityMatrixFileFormats
# https://www.nitrc.org/forum/attachment.php?attachid=341&group_id=454&forum_id=1955
(3000, 'dense fiber/fan samples', (), 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN'),
(3001, 'dense connectivity', (), 'NIFTI_INTENT_CONNECTIVITY_DENSE'),
(3002, 'dense data series/fiber fans', (),
(3000, 'ConnUnknown', (), 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN'),
(3001, 'ConnDense', (), 'NIFTI_INTENT_CONNECTIVITY_DENSE'),
(3002, 'ConnDenseSeries', (),
'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES'),
(3003, 'parcellated connectivity', (),
(3003, 'ConnParcels', (),
'NIFTI_INTENT_CONNECTIVITY_PARCELLATED'),
(3004, 'parcellated data series', (),
(3004, 'ConnParcelSries', (),
"NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES"),
(3006, 'dense scalar', (),
(3006, 'ConnDenseScalar', (),
'NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS'),
(3007, 'dense label', (),
(3007, 'ConnDenseLabel', (),
'NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS'),
(3008, 'parcellated scalar', (),
(3008, 'ConnParcelScalr', (),
'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR'),
(3009, 'parcellated dense connectivity', (),
(3009, 'ConnParcelDense', (),
'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE'),
(3010, 'dense parcellated connectivity', (),
(3010, 'ConnDenseParcel', (),
'NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED'),
(3011, 'parcellated connectivity series', (),
(3011, 'ConnPPSr', (),
'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES'),
(3012, 'parcellated connectivity scalar', (),
(3012, 'ConnPPSc', (),
'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR')))


Expand Down
51 changes: 45 additions & 6 deletions nibabel/cifti2/tests/test_new_cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
"""
import numpy as np

import nibabel as nib
from nibabel import cifti2 as ci
from nibabel.tmpdirs import InTemporaryDirectory

Expand Down Expand Up @@ -212,10 +213,14 @@ def test_dtseries():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(13, 9)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES')

with InTemporaryDirectory():
ci.save(img, 'test.dtseries.nii')
img2 = ci.load('test.dtseries.nii')
img2 = nib.load('test.dtseries.nii')
assert_equal(img2.nifti_header.get_intent()[0],
'ConnDenseSeries')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_series_map(img2.header.matrix.get_index_map(0))
check_geometry_map(img2.header.matrix.get_index_map(1))
Expand All @@ -231,10 +236,13 @@ def test_dscalar():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 9)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS')

with InTemporaryDirectory():
ci.save(img, 'test.dscalar.nii')
img2 = ci.load('test.dscalar.nii')
img2 = nib.load('test.dscalar.nii')
assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseScalar')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_scalar_map(img2.header.matrix.get_index_map(0))
check_geometry_map(img2.header.matrix.get_index_map(1))
Expand All @@ -250,10 +258,13 @@ def test_dlabel():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 9)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS')

with InTemporaryDirectory():
ci.save(img, 'test.dlabel.nii')
img2 = ci.load('test.dlabel.nii')
img2 = nib.load('test.dlabel.nii')
assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseLabel')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_label_map(img2.header.matrix.get_index_map(0))
check_geometry_map(img2.header.matrix.get_index_map(1))
Expand All @@ -267,10 +278,13 @@ def test_dconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(9, 9)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE')

with InTemporaryDirectory():
ci.save(img, 'test.dconn.nii')
img2 = ci.load('test.dconn.nii')
img2 = nib.load('test.dconn.nii')
assert_equal(img2.nifti_header.get_intent()[0], 'ConnDense')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
assert_equal(img2.header.matrix.get_index_map(0),
img2.header.matrix.get_index_map(1))
Expand All @@ -287,10 +301,13 @@ def test_ptseries():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(13, 3)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES')

with InTemporaryDirectory():
ci.save(img, 'test.ptseries.nii')
img2 = ci.load('test.ptseries.nii')
img2 = nib.load('test.ptseries.nii')
assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelSries')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_series_map(img2.header.matrix.get_index_map(0))
check_parcel_map(img2.header.matrix.get_index_map(1))
Expand All @@ -306,10 +323,13 @@ def test_pscalar():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 3)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR')

with InTemporaryDirectory():
ci.save(img, 'test.pscalar.nii')
img2 = ci.load('test.pscalar.nii')
img2 = nib.load('test.pscalar.nii')
assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelScalr')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_scalar_map(img2.header.matrix.get_index_map(0))
check_parcel_map(img2.header.matrix.get_index_map(1))
Expand All @@ -325,10 +345,13 @@ def test_pdconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 3)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE')

with InTemporaryDirectory():
ci.save(img, 'test.pdconn.nii')
img2 = ci.load('test.pdconn.nii')
assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelDense')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_geometry_map(img2.header.matrix.get_index_map(0))
check_parcel_map(img2.header.matrix.get_index_map(1))
Expand All @@ -344,10 +367,13 @@ def test_dpconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 3)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED')

with InTemporaryDirectory():
ci.save(img, 'test.dpconn.nii')
img2 = ci.load('test.dpconn.nii')
assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseParcel')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_parcel_map(img2.header.matrix.get_index_map(0))
check_geometry_map(img2.header.matrix.get_index_map(1))
Expand All @@ -367,6 +393,8 @@ def test_plabel():
with InTemporaryDirectory():
ci.save(img, 'test.plabel.nii')
img2 = ci.load('test.plabel.nii')
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is this a valid CIFTI type? I cannot find *plabel.nii in the specifications
https://www.nitrc.org/forum/attachment.php?attachid=341&group_id=454&forum_id=1955

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there is a plabel: https://github.com/Washington-University/workbench/blob/master/src/Commands/CommandParser.cxx#L661

but indeed i don't see it in the spec.

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also here: https://github.com/Washington-University/workbench/blob/6c7414d9ba379604c10673d6d68eeeb68f1332e9/src/Common/DataFileTypeEnum.cxx#L207

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If we will raise an exception upon saving, we have some options

  • remove the plabel test
  • alter ci.save's signature to include a new parameter, force=False, that can be switched on to allow saving without intent codes

WDYT?

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how about skipping the plabel test for now till we find the INTENT code. i would rather not have a parameter.

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@effigies i had no luck finding it as well
https://github.com/Washington-University/workbench/blob/1b79e569e8b8277f4abf71fabd4afc2889849362/src/FilesBase/nifti2.h#L32-L49

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@coalsont coalsont Mar 6, 2018 •
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plabel is not in the cifti-2 spec. We didn't see it being useful at the time, so it was not in the draft. We later found that the information needed to reorder parcellated files to group certain parcels together in matrix display could be stored as a parcels by labels file, and decided to use that extention, matching the previous pattern of extension naming.

Per the "unknown" special cifti intent (main cifti-2 document, top of page 13, middle of paragraph), it is in fact valid to make such a file, and its extension is technically open to be anything that ends in ".<something>.nii". Feel free to write a test that loads and/or saves a cifti mapping combination that is not in the spec, this is an expected use case.

assert_equal(img.nifti_header.get_intent()[0], 'ConnUnknown')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
check_label_map(img2.header.matrix.get_index_map(0))
check_parcel_map(img2.header.matrix.get_index_map(1))
Expand All @@ -380,10 +408,13 @@ def test_pconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(3, 3)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED')

with InTemporaryDirectory():
ci.save(img, 'test.pconn.nii')
img2 = ci.load('test.pconn.nii')
assert_equal(img.nifti_header.get_intent()[0], 'ConnParcels')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
assert_equal(img2.header.matrix.get_index_map(0),
img2.header.matrix.get_index_map(1))
Expand All @@ -401,10 +432,14 @@ def test_pconnseries():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(3, 3, 13)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_'
'PARCELLATED_SERIES')

with InTemporaryDirectory():
ci.save(img, 'test.pconnseries.nii')
img2 = ci.load('test.pconnseries.nii')
assert_equal(img.nifti_header.get_intent()[0], 'ConnPPSr')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
assert_equal(img2.header.matrix.get_index_map(0),
img2.header.matrix.get_index_map(1))
Expand All @@ -423,10 +458,14 @@ def test_pconnscalar():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(3, 3, 13)
img = ci.Cifti2Image(data, hdr)
img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_'
'PARCELLATED_SCALAR')

with InTemporaryDirectory():
ci.save(img, 'test.pconnscalar.nii')
img2 = ci.load('test.pconnscalar.nii')
assert_equal(img.nifti_header.get_intent()[0], 'ConnPPSc')
assert_true(isinstance(img2, ci.Cifti2Image))
assert_true((img2.get_data() == data).all())
assert_equal(img2.header.matrix.get_index_map(0),
img2.header.matrix.get_index_map(1))
Expand Down