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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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2 changes: 2 additions & 0 deletions nibabel/cifti2/cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1442,4 +1442,6 @@ def save(img, filename):
filename : str
filename to which to save image
"""
if img.nifti_header.get_intent()[0] == 'none':
raise AttributeError("CIFTI image has an invalid intent code.")
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Actually, I think I would rather set the intent by default to 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN', and I think we should do this in Cifti2Image.to_file_map(), maybe after resetting pixdim.

if header.get_intent()[0] == 'none':
    header.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')

This feels a little cleaner to me, as the CIFTI equivalent of saving a NIFTI without setting an intent code, which we also allow.

Cifti2Image.instance_to_filename(img, filename)
76 changes: 51 additions & 25 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 +213,12 @@ 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_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 +234,12 @@ 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_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 +255,12 @@ 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_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 +274,12 @@ 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_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 +296,12 @@ 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_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 +317,12 @@ 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_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 +338,12 @@ 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_DENSE_PARCELLATED')

with InTemporaryDirectory():
ci.save(img, 'test.pdconn.nii')
img2 = ci.load('test.pdconn.nii')
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 @@ -344,33 +359,38 @@ 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_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))
del img2


def test_plabel():
label_map = create_label_map((0, ))
parcel_map = create_parcel_map((1, ))
matrix = ci.Cifti2Matrix()
matrix.append(label_map)
matrix.append(parcel_map)
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 3)
img = ci.Cifti2Image(data, hdr)

with InTemporaryDirectory():
ci.save(img, 'test.plabel.nii')
img2 = ci.load('test.plabel.nii')
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))
del img2
# SKIP until intent code is specified
# https://www.nitrc.org/forum/attachment.php?attachid=341&group_id=454&forum_id=1955
# def test_plabel():
# label_map = create_label_map((0, ))
# parcel_map = create_parcel_map((1, ))
# matrix = ci.Cifti2Matrix()
# matrix.append(label_map)
# matrix.append(parcel_map)
# hdr = ci.Cifti2Header(matrix)
# data = np.random.randn(2, 3)
# img = ci.Cifti2Image(data, hdr)
#
# with InTemporaryDirectory():
# ci.save(img, 'test.plabel.nii')
# img2 = ci.load('test.plabel.nii')
# 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))
# del img2


def test_pconn():
Expand All @@ -380,10 +400,12 @@ 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_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 @@ -394,17 +416,19 @@ def test_pconn():
def test_pconnseries():
parcel_map = create_parcel_map((0, 1))
series_map = create_series_map((2, ))

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I'd re-add this line to clean the diff.

matrix = ci.Cifti2Matrix()
matrix.append(parcel_map)
matrix.append(series_map)
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_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 @@ -416,17 +440,19 @@ def test_pconnseries():
def test_pconnscalar():
parcel_map = create_parcel_map((0, 1))
scalar_map = create_scalar_map((2, ))

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Re-add.

matrix = ci.Cifti2Matrix()
matrix.append(parcel_map)
matrix.append(scalar_map)
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_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