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Merged
merged 16 commits into from
Jun 1, 2018
Merged

NF: Functionality for reading AFNI BRIK/HEAD #561

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1890839
NF: Basic functionality for reading AFNI BRIK/HEAD files
rmarkello Oct 2, 2017
f088f51
TEST: Minimal tests for AFNI BRIK/HEAD files
rmarkello Oct 2, 2017
c418a1f
PL: Cleaning up brikhead flake8 errors
rmarkello Oct 9, 2017
c78c786
RF: ArrayProxy and whitespace
rmarkello Jan 22, 2018
8d9e414
TEST: Added BRIK/HEAD doc-tests
rmarkello Jan 23, 2018
aee4f91
TEST: Added tests/files for brikhead.py
rmarkello Jan 24, 2018
dce22dc
TEST: Added broken HEAD files to tests/data
rmarkello Jan 28, 2018
df126dc
TEST: Modified `from_file_map()` in brikhead.py
rmarkello Jan 31, 2018
8107fd4
RF: Responded to brikhead.py reviews
rmarkello Feb 25, 2018
6bd34fe
TEST: Added brikhead to test_image_api.py
rmarkello Mar 3, 2018
a674003
RF: Added brikhead.filespec_to_file_map
rmarkello Mar 6, 2018
477c2ec
RF: Minor brikhead.py refactoring
rmarkello Mar 10, 2018
04df389
FIX: Brikhead doctests
rmarkello Mar 11, 2018
8c7e1eb
TEST: Added testing for errors
rmarkello Mar 19, 2018
6b308bf
RF: some edits / doc extensions to brikhead.py
matthew-brett May 4, 2018
c5f0ecf
RF: Fixed needless list copy in brikhead.py
rmarkello May 7, 2018
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627 changes: 627 additions & 0 deletions nibabel/brikhead.py
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13 changes: 10 additions & 3 deletions nibabel/imageclasses.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
''' Define supported image classes and names '''

from .analyze import AnalyzeImage
from .brikhead import AFNIImage
from .cifti2 import Cifti2Image
from .freesurfer import MGHImage
from .gifti import GiftiImage
Expand All @@ -31,7 +32,7 @@
Cifti2Image, Nifti2Image, # Cifti2 before Nifti2
Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
Minc1Image, Minc2Image, MGHImage,
PARRECImage, GiftiImage]
PARRECImage, GiftiImage, AFNIImage]


# DEPRECATED: mapping of names to classes and class functionality
Expand Down Expand Up @@ -88,7 +89,12 @@ def __getitem__(self, *args, **kwargs):
'ext': '.par',
'has_affine': True,
'makeable': False,
'rw': False})
'rw': False},
afni={'class': AFNIImage,
'ext': '.brik',
'has_affine': True,
'makeable': False,
'rw': False})


class ExtMapRecoder(Recoder):
Expand All @@ -107,14 +113,15 @@ def __getitem__(self, *args, **kwargs):
('mgh', '.mgh'),
('mgz', '.mgz'),
('par', '.par'),
('brik', '.brik')
))

# Image classes known to require spatial axes to be first in index ordering.
# When adding an image class, consider whether the new class should be listed
# here.
KNOWN_SPATIAL_FIRST = (Nifti1Pair, Nifti1Image, Nifti2Pair, Nifti2Image,
Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
MGHImage, PARRECImage)
MGHImage, PARRECImage, AFNIImage)


def spatial_axes_first(img):
Expand Down
133 changes: 133 additions & 0 deletions nibabel/tests/data/bad_attribute+orig.HEAD
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@@ -0,0 +1,133 @@

type = string-attribute
name = DATASET_NAME
count = 5
'none~

type = string-attribute
name = TYPESTRING
count = 15
'3DIM_HEAD_ANAT~

type = string-attribute
name = IDCODE_STRING
count = 27
'AFN_-zxZ0OyZs8eEtm9syGBNdA~

type = string-attribute
name = IDCODE_DATE
count = 25
'Sun Oct 1 21:13:09 2017~

type = integer-attribute
name = SCENE_DATA
count = 8
0 2 0 -999 -999
-999 -999 -999

type = string-attribute
name = LABEL_1
count = 5
'none~

type = string-attribute
name = LABEL_2
count = 5
'none~

type = integer-attribute
name = ORIENT_SPECIFIC
count = 3
0 3 4

type = float-attribute
name = ORIGIN
count = 3
-49.5 -82.312 -52.3511

type = float-attribute
name = DELTA
count = 3
3 3 3

type = float-attribute
name = IJK_TO_DICOM
count = 12
3 0 0 -49.5 0
3 0 -82.312 0 0
3 -52.3511

type = float-attribute
name = IJK_TO_DICOM_REAL
count = 12
3 0 0 -49.5 0
3 0 -82.312 0 0
3 -52.3511

type = float-attribute
name = BRICK_STATS
count = 6
0 13722 0 10051 0
9968

type = integer-attribute
name = TAXIS_NUMS
count = 8
3 25 77002 -999 -999
-999 -999 -999

type = float-attribute
name = TAXIS_FLOATS
count = 8
0 3 0 -52.3511 3
-999999 -999999 -999999

type = float-attribute
name = TAXIS_OFFSETS
count = 25
0.3260869 1.826087 0.3913043 1.891304 0.4565217
1.956521 0.5217391 2.021739 0.5869564 2.086956
0.6521738 2.152174 0.7173912 2.217391 0.7826086
2.282609 0.8478259 2.347826 0.9130433 2.413044
0.9782607 2.478261 1.043478 2.543479 1.108696

type = integer-attribute
name = DATASET_RANK
count = 8
3 3 0 0 0
0 0 0

type = integer-attribute
name = DATASET_DIMENSIONS
count = 5
33 41 25 0 0

type = integer-attribute
name = BRICK_TYPES
count = 3
1 1 1

type = float-attribute
name = BRICK_FLOAT_FACS
count = 3
0 0 0

type = string-attribute
name = TEMPLATE_SPACE
count = 5
'ORIG~

type = integer-attribute
name = INT_CMAP
count = 1
0

type = integer-attribute
name = BYTEORDER_STRING
count = 10
'LSB_FIRST~

type = string-attribute
name = BRICK_LABS
count = 9
'#0~#1~#2~
133 changes: 133 additions & 0 deletions nibabel/tests/data/bad_datatype+orig.HEAD
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@@ -0,0 +1,133 @@

type = string-attribute
name = DATASET_NAME
count = 5
'none~

type = string-attribute
name = TYPESTRING
count = 15
'3DIM_HEAD_ANAT~

type = string-attribute
name = IDCODE_STRING
count = 27
'AFN_-zxZ0OyZs8eEtm9syGBNdA~

type = string-attribute
name = IDCODE_DATE
count = 25
'Sun Oct 1 21:13:09 2017~

type = integer-attribute
name = SCENE_DATA
count = 8
0 2 0 -999 -999
-999 -999 -999

type = string-attribute
name = LABEL_1
count = 5
'none~

type = string-attribute
name = LABEL_2
count = 5
'none~

type = integer-attribute
name = ORIENT_SPECIFIC
count = 3
0 3 4

type = float-attribute
name = ORIGIN
count = 3
-49.5 -82.312 -52.3511

type = float-attribute
name = DELTA
count = 3
3 3 3

type = float-attribute
name = IJK_TO_DICOM
count = 12
3 0 0 -49.5 0
3 0 -82.312 0 0
3 -52.3511

type = float-attribute
name = IJK_TO_DICOM_REAL
count = 12
3 0 0 -49.5 0
3 0 -82.312 0 0
3 -52.3511

type = float-attribute
name = BRICK_STATS
count = 6
0 13722 0 10051 0
9968

type = integer-attribute
name = TAXIS_NUMS
count = 8
3 25 77002 -999 -999
-999 -999 -999

type = float-attribute
name = TAXIS_FLOATS
count = 8
0 3 0 -52.3511 3
-999999 -999999 -999999

type = float-attribute
name = TAXIS_OFFSETS
count = 25
0.3260869 1.826087 0.3913043 1.891304 0.4565217
1.956521 0.5217391 2.021739 0.5869564 2.086956
0.6521738 2.152174 0.7173912 2.217391 0.7826086
2.282609 0.8478259 2.347826 0.9130433 2.413044
0.9782607 2.478261 1.043478 2.543479 1.108696

type = integer-attribute
name = DATASET_RANK
count = 8
3 3 0 0 0
0 0 0

type = integer-attribute
name = DATASET_DIMENSIONS
count = 5
33 41 25 0 0

type = integer-attribute
name = BRICK_TYPES
count = 3
1 3 5

type = float-attribute
name = BRICK_FLOAT_FACS
count = 3
0 0 0

type = string-attribute
name = TEMPLATE_SPACE
count = 5
'ORIG~

type = integer-attribute
name = INT_CMAP
count = 1
0

type = string-attribute
name = BYTEORDER_STRING
count = 10
'LSB_FIRST~

type = string-attribute
name = BRICK_LABS
count = 9
'#0~#1~#2~
Binary file added nibabel/tests/data/example4d+orig.BRIK.gz
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