TEST: Add more BV tests.

Author: thomastweets

nibabel/brainvoyager/bv.py

@@ -672,7 +672,7 @@ def get_base_affine(self):
         if not self.get_xflip():
             # make the BV internal Z axis neurological (left-is-left);
             # not default in BV files!
-            zooms[0] *= -1
+            zooms = (-zooms[0], zooms[1], zooms[2])
 
         # compute the rotation
         rot = np.zeros((3, 3))

nibabel/brainvoyager/bv_vmr.py

@@ -163,7 +163,7 @@ def get_base_affine(self):
         if not self.get_xflip():
             # make the BV internal Z axis neurological (left-is-left);
             # not default in BV files!
-            zooms[0] *= -1
+            zooms = (-zooms[0], zooms[1], zooms[2])
 
         # compute the rotation
         rot = np.zeros((3, 3))

nibabel/brainvoyager/tests/test_bv.py

@@ -15,10 +15,10 @@
 from ..bv import (readCString, parse_BV_header, pack_BV_header, BvFileHeader,
                   calc_BV_header_size, _proto2default, update_BV_header,
                   parse_st, combine_st, BvError)
-from ..bv_vtc import VTC_HDR_DICT_PROTO
+from ..bv_vtc import VTC_HDR_DICT_PROTO, BvVtcHeader
 from ..bv_vmr import BvVmrImage
 from ...testing import (assert_equal, assert_array_equal, data_path,
-                        assert_true, assert_false, assert_raises)
+                        assert_true, assert_raises)
 from . import BV_EXAMPLE_IMAGES, BV_EXAMPLE_HDRS
 from ...externals import OrderedDict
 
@@ -270,13 +270,44 @@ def test_BvFileHeader_xflip():
     # should only return
     bv.set_xflip(True)
 
+    # cannot flip most BV images
     assert_raises(BvError, bv.set_xflip, False)
 
 
 def test_BvFileHeader_endianness():
     assert_raises(BvError, BvFileHeader, endianness='>')
 
 
+def test_BvFileHeader_not_implemented():
+    bv = BvFileHeader()
+    assert_raises(NotImplementedError, bv.get_data_shape)
+    assert_raises(NotImplementedError, bv.set_data_shape, (1, 2, 3))
+
+
+def test_BvVtcHeader_from_header():
+    vtc = load(vtc_file)
+    vtc_data = vtc.get_data()
+
+    # try the same load through the header
+    fread = open(vtc_file, 'rb')
+    header = BvVtcHeader.from_fileobj(fread)
+    image = header.data_from_fileobj(fread)
+    assert_array_equal(vtc_data, image)
+    fread.close()
+
+
+def test_BvVtcHeader_data_from_fileobj():
+    vtc = load(vtc_file)
+    vtc_data = vtc.get_data()
+
+    # try the same load through the header
+    fread = open(vtc_file, 'rb')
+    header = BvVtcHeader.from_fileobj(fread)
+    image = header.data_from_fileobj(fread)
+    assert_array_equal(vtc_data, image)
+    fread.close()
+
+
 def test_parse_all_BV_headers():
     for images, headers in zip(BV_EXAMPLE_IMAGES, BV_EXAMPLE_HDRS):
         for i in range(len(images)):

nibabel/brainvoyager/tests/test_bv_vmr.py

@@ -13,7 +13,7 @@
 from ..bv import BvError
 from ..bv_vmr import BvVmrImage, BvVmrHeader
 from ...testing import (assert_equal, assert_true, assert_false, assert_raises,
-                        data_path)
+                        assert_array_equal, data_path)
 from ...externals import OrderedDict
 
 vmr_file = pjoin(data_path, 'test.vmr')
@@ -130,9 +130,22 @@ def test_BvVmrHeader_xflip():
     assert_true(vmr.get_xflip())
     vmr.set_xflip(False)
     assert_false(vmr.get_xflip())
+    assert_equal(vmr._hdr_dict['lr_convention'], 2)
+    vmr.set_xflip(True)
+    assert_true(vmr.get_xflip())
+    assert_equal(vmr._hdr_dict['lr_convention'], 1)
     vmr.set_xflip(0)
+    assert_equal(vmr._hdr_dict['lr_convention'], 0)
     assert_raises(BvError, vmr.get_xflip)
 
+    vmr = BvVmrImage.from_filename(vmr_file)
+    vmr.header.set_xflip(False)
+    expected_affine = [[1., 0., 0., 0.],
+                       [0., 0., -1., -1.],
+                       [0., -1., 0., 1.],
+                       [0., 0., 0., 1.]]
+    assert_array_equal(vmr.header.get_affine(), expected_affine)
+
 
 def test_BvVmrHeader_set_zooms():
     vmr = BvVmrHeader()

nibabel/brainvoyager/tests/test_bv_vtc.py

@@ -115,6 +115,31 @@ def test_BvVtcHeader_xflip():
     assert_raises(BvError, vtc.get_xflip)
 
 
+def test_BvVtcHeader_guess_framing_cube():
+    vtc = BvVtcHeader()
+    assert_equal(vtc._guess_framing_cube(), (256, 256, 256))
+    vtc._hdr_dict['x_end'] = 400
+    vtc._hdr_dict['y_end'] = 400
+    vtc._hdr_dict['z_end'] = 400
+    assert_equal(vtc._guess_framing_cube(), (512, 512, 512))
+
+
+def test_BvVtcHeader_zooms():
+    vtc = BvVtcHeader()
+    assert_equal(vtc.get_zooms(), (3.0, 3.0, 3.0))
+
+    # set all zooms to one value (default for VTC files)
+    vtc.set_zooms(2)
+    assert_equal(vtc.get_zooms(), (2.0, 2.0, 2.0))
+    vtc.set_zooms((1.0, 1.0, 1.0))
+    assert_equal(vtc.get_zooms(), (1.0, 1.0, 1.0))
+    vtc.set_zooms((4, 4, 4))
+    assert_equal(vtc.get_zooms(), (4.0, 4.0, 4.0))
+
+    # set zooms to different values for the three dimensions (not possible)
+    assert_raises(BvError, vtc.set_zooms, (1.0, 2.0, 3.0))
+
+
 def test_BvVtcHeader_fileversion_error():
     vtc = BvVtcHeader()
     vtc._hdr_dict['version'] = 4