TEST: Added tests/files for brikhead.py

Created new tests for brikhead.py and added/modified datafiles to support them.
Notably, added scaled+tlrc.BRIK/HEAD to test inclusion of data scaling factors
and gzipped exampled4d+orig.BRIK to accommodate loading gzipped files.

Author: rmarkello

nibabel/brikhead.py

@@ -51,15 +51,6 @@
     5: 'D',
 }
 
-_orient_dict = {
-    0: 'R',
-    1: 'L',
-    2: 'P',
-    3: 'A',
-    4: 'I',
-    5: 'S'
-}
-
 space_codes = Recoder((
     (0, 'unknown', ''),
     (1, 'scanner', 'ORIG'),
@@ -222,15 +213,15 @@ def scaling(self):
 
     def __array__(self):
         raw_data = self.get_unscaled()
-        # apply volume specific scaling
+        # apply volume specific scaling (may change datatype!)
         if self._scaling is not None:
-            return raw_data * self._scaling.astype(self.dtype)
+            return raw_data * self._scaling
 
         return raw_data
 
     def __getitem__(self, slicer):
         raw_data = super(AFNIArrayProxy, self).__getitem__(slicer)
-        # apply volume specific scaling
+        # apply volume specific scaling (may change datatype!)
         if self._scaling is not None:
             scaling = self._scaling.copy()
             fake_data = strided_scalar(self._shape)
@@ -312,20 +303,6 @@ def _calc_zooms(self):
 
         return xyz_step + t_step
 
-    def get_orient(self):
-        """Returns orientation of data
-
-        Three letter string of {('L','R'), ('P','A'), ('I','S')} specifying
-        data orientation
-
-        Returns
-        -------
-        orient : str
-        """
-        orient = [_orient_dict[f] for f in self.info['ORIENT_SPECIFIC']]
-
-        return ''.join(orient)
-
     def get_space(self):
         """Returns space of dataset
 
@@ -334,7 +311,7 @@ def get_space(self):
         space : str
         """
         listed_space = self.info.get('TEMPLATE_SPACE', 0)
-        space = space_codes.label[listed_space]
+        space = space_codes.space[listed_space]
 
         return space
 
@@ -363,14 +340,15 @@ def get_data_scaling(self):
 
         Examples
         --------
-        >>> header = AFNIHeader(parse_AFNI_header('example4d+orig.HEAD'))
+        >>> header = AFNIHeader(parse_AFNI_header('scaled+tlrc.HEAD'))
         >>> header.get_data_scaling()
+        array([  3.88336300e-08])
         """
         floatfacs = self.info.get('BRICK_FLOAT_FACS', None)
         if floatfacs is None or not np.any(floatfacs):
             return None
         scale = np.ones(self.info['DATASET_RANK'][1])
-        floatfacs = np.asarray(floatfacs)
+        floatfacs = np.atleast_1d(floatfacs)
         scale[floatfacs.nonzero()] = floatfacs[floatfacs.nonzero()]
 
         return scale
@@ -419,7 +397,7 @@ class AFNIImage(SpatialImage):
            [  0.    ,   0.    ,   3.    , -52.3511],
            [  0.    ,   0.    ,   0.    ,   1.    ]])
     >>> head = load('example4d+orig.HEAD')
-    >>> (head.get_data() == brik.get_data()).all()
+    >>> np.array_equal(head.get_data(), brik.get_data())
     True
     """
 

nibabel/tests/data/example4d+orig.BRIK

@@ -0,0 +1,121 @@
+
+type = string-attribute
+name = HISTORY_NOTE
+count = 304
+'[rossmarkello@rossdm.local: Tue Jan 23 20:04:42 2018] {AFNI_18.0.09:macosx_10.7_Intel_64} 3dcalc -short -a 'mreg/subj-020_task-rest_bold.nii.gz[0]' -expr a -prefix scaled\n[rossmarkello@rossdm.local: Tue Jan 23 20:05:10 2018] {AFNI_18.0.09:macosx_10.7_Intel_64} 3dAutobox -prefix scaled+tlrc scaled+tlrc~
+
+type = string-attribute
+name = TYPESTRING
+count = 15
+'3DIM_HEAD_ANAT~
+
+type = string-attribute
+name = IDCODE_STRING
+count = 27
+'AFN_vLKn9e5VumKelWXNeq4SWA~
+
+type = string-attribute
+name = IDCODE_DATE
+count = 25
+'Tue Jan 23 20:05:10 2018~
+
+type = integer-attribute
+name = SCENE_DATA
+count = 8
+ 2 2 0 -999 -999
+ -999 -999 -999
+
+type = string-attribute
+name = LABEL_1
+count = 5
+'zyxt~
+
+type = string-attribute
+name = LABEL_2
+count = 5
+'zyxt~
+
+type = string-attribute
+name = DATASET_NAME
+count = 5
+'zyxt~
+
+type = integer-attribute
+name = ORIENT_SPECIFIC
+count = 3
+ 1 2 4
+
+type  = float-attribute
+name  = ORIGIN
+count = 3
+             66             87            -54
+
+type  = float-attribute
+name  = DELTA
+count = 3
+             -3             -3              3
+
+type  = float-attribute
+name  = IJK_TO_DICOM
+count = 12
+             -3              0              0             66              0
+             -3              0             87              0              0
+              3            -54
+
+type  = float-attribute
+name  = IJK_TO_DICOM_REAL
+count = 12
+             -3              0              0             66              0
+             -3              0             87              0              0
+              3            -54
+
+type  = float-attribute
+name  = BRICK_STATS
+count = 2
+   1.941682e-07    0.001272461
+
+type = integer-attribute
+name = DATASET_RANK
+count = 8
+ 3 1 0 0 0
+ 0 0 0
+
+type = integer-attribute
+name = DATASET_DIMENSIONS
+count = 5
+ 47 54 43 0 0
+
+type = integer-attribute
+name = BRICK_TYPES
+count = 1
+ 1
+
+type  = float-attribute
+name  = BRICK_FLOAT_FACS
+count = 1
+   3.883363e-08
+
+type = string-attribute
+name = BRICK_LABS
+count = 3
+'#0~
+
+type = string-attribute
+name = BRICK_KEYWORDS
+count = 1
+'~
+
+type = string-attribute
+name = TEMPLATE_SPACE
+count = 5
+'TLRC~
+
+type = integer-attribute
+name = INT_CMAP
+count = 1
+ 0
+
+type = string-attribute
+name = BYTEORDER_STRING
+count = 10
+'LSB_FIRST~

nibabel/tests/data/example4d+orig.BRIK.gz

@@ -15,7 +15,7 @@
 from .. import load, Nifti1Image
 from .. import brikhead
 
-from nose.tools import (assert_true, assert_equal)
+from nose.tools import (assert_true, assert_equal, assert_raises)
 from numpy.testing import assert_array_equal
 from ..testing import data_path
 
@@ -24,41 +24,80 @@
 
 EXAMPLE_IMAGES = [
     dict(
-        fname=pjoin(data_path, 'example4d+orig.BRIK'),
+        head=pjoin(data_path, 'example4d+orig.HEAD'),
+        brik=pjoin(data_path, 'example4d+orig.BRIK.gz'),
         shape=(33, 41, 25, 3),
         dtype=np.int16,
         affine=np.array([[-3.0,0,0,49.5],
                          [0,-3.0,0,82.312],
                          [0,0,3.0,-52.3511],
                          [0,0,0,1.0]]),
         zooms=(3., 3., 3., 3.),
-        # These values from SPM2
         data_summary=dict(
             min=0,
             max=13722,
             mean=4266.76024636),
-        is_proxy=True)
+        is_proxy=True,
+        space='ORIG',
+        labels=['#0', '#1', '#2'],
+        scaling=None),
+    dict(
+        head=pjoin(data_path, 'scaled+tlrc.HEAD'),
+        brik=pjoin(data_path, 'scaled+tlrc.BRIK'),
+        shape=(47, 54, 43),
+        dtype=np.int16,
+        affine=np.array([[3.0,0,0,-66.],
+                         [0,3.0,0,-87.],
+                         [0,0,3.0,-54.],
+                         [0,0,0,1.0]]),
+        zooms=(3., 3., 3.),
+        data_summary=dict(
+            min=1.9416814999999998e-07,
+            max=0.0012724615542099998,
+            mean=0.00023919645351876782),
+        is_proxy=True,
+        space='TLRC',
+        labels=['#0'],
+        scaling=np.array([  3.88336300e-08]),
+    )
 ]
 
 
+class TestAFNIHeader(object):
+    module = brikhead
+    test_files = EXAMPLE_IMAGES
+
+    def test_makehead(self):
+        for tp in self.test_files:
+            head1 = self.module.AFNIHeader.from_fileobj(tp['head'])
+            head2 = self.module.AFNIHeader.from_header(head1)
+            assert_equal(head1, head2)
+            with assert_raises(self.module.AFNIError):
+                self.module.AFNIHeader.from_header(header=None)
+            with assert_raises(self.module.AFNIError):
+                self.module.AFNIHeader.from_header(tp['brik'])
+
+
 class TestAFNIImage(object):
     module = brikhead
     test_files = EXAMPLE_IMAGES
 
     def test_brikheadfile(self):
         for tp in self.test_files:
-            brik = self.module.load(tp['fname'])
+            brik = self.module.load(tp['brik'])
             assert_equal(brik.get_data_dtype().type, tp['dtype'])
             assert_equal(brik.shape, tp['shape'])
             assert_equal(brik.header.get_zooms(), tp['zooms'])
             assert_array_equal(brik.affine, tp['affine'])
+            assert_equal(brik.header.get_space(), tp['space'])
             data = brik.get_data()
             assert_equal(data.shape, tp['shape'])
+            assert_array_equal(brik.dataobj.scaling, tp['scaling'])
 
     def test_load(self):
         # Check highest level load of brikhead works
         for tp in self.test_files:
-            img = load(tp['fname'])
+            img = load(tp['brik'])
             data = img.get_data()
             assert_equal(data.shape, tp['shape'])
             # min, max, mean values
@@ -71,7 +110,7 @@ def test_load(self):
     def test_array_proxy_slicing(self):
         # Test slicing of array proxy
         for tp in self.test_files:
-            img = load(tp['fname'])
+            img = load(tp['brik'])
             arr = img.get_data()
             prox = img.dataobj
             assert_true(prox.is_proxy)