RF+TST: refactor various analyze / nifti checks

We want to allow CIFTI2 to be lenient on 0 qfac and pixdims.  Refactor
qfac and pixdims checks into their own functions in analyze and nifti1
test classes.   Write more lenient CIFTI2 checking functions.  Test
CIFTI2 header checks with subclass of NIfTI2 header testing class.

Author: matthew-brett

nibabel/cifti2/parse_cifti2_fast.py

@@ -20,6 +20,7 @@
                      Cifti2Vertices, Cifti2Volume, CIFTI_BrainStructures,
                      CIFTI_MODEL_TYPES, _underscore, CIFTI2HeaderError)
 from .. import xmlutils as xml
+from ..spatialimages import HeaderDataError
 from ..externals.six import BytesIO
 from ..batteryrunners import Report
 from ..nifti1 import Nifti1Extension, extension_codes, intent_codes
@@ -90,24 +91,25 @@ def may_contain_header(klass, binaryblock):
         hdr = klass(binaryblock=binaryblock[:klass.sizeof_hdr])
         return klass._valid_intent_code(hdr.get_intent('code')[0])
 
-    @classmethod
-    def _get_checks(klass):
-        # We need to return our own versions of - e.g. chk_datatype, to
-        # pick up the Nifti datatypes from our class
-        return (klass._chk_sizeof_hdr,
-                klass._chk_datatype,
-                klass._chk_bitpix,
-                klass._chk_pixdims,
-                klass._chk_magic,
-                klass._chk_offset,
-                klass._chk_qform_code,
-                klass._chk_sform_code)
+    @staticmethod
+    def _chk_qfac(hdr, fix=False):
+        # Allow qfac of 0 without complaint for CIFTI2
+        rep = Report(HeaderDataError)
+        if hdr['pixdim'][0] in (-1, 0, 1):
+            return hdr, rep
+        rep.problem_level = 20
+        rep.problem_msg = 'pixdim[0] (qfac) should be 1 (default) or 0 or -1'
+        if fix:
+            hdr['pixdim'][0] = 1
+            rep.fix_msg = 'setting qfac to 1'
+        return hdr, rep
 
+    @staticmethod
     def _chk_pixdims(hdr, fix=False):
-        rep = Report(CIFTI2HeaderError)
+        rep = Report(HeaderDataError)
         pixdims = hdr['pixdim']
         spat_dims = pixdims[1:4]
-        if not np.any(spat_dims <= 0):
+        if not np.any(spat_dims < 0):
             return hdr, rep
         rep.problem_level = 35
         rep.problem_msg = 'pixdim[1,2,3] should be zero or positive'

nibabel/cifti2/tests/test_cifti2io.py

@@ -10,12 +10,16 @@
 
 from os.path import join as pjoin, dirname
 import io
+
 from distutils.version import LooseVersion
 
 import nibabel as nib
 from nibabel import cifti2 as ci
+from nibabel.cifti2.parse_cifti2_fast import _Cifti2AsNiftiHeader
+
 from nibabel.tmpdirs import InTemporaryDirectory
 from nibabel.tests.nibabel_data import get_nibabel_data, needs_nibabel_data
+from nibabel.tests.test_nifti2 import TestNifti2SingleHeader
 
 from numpy.testing import assert_array_almost_equal
 from nose.tools import (assert_true, assert_equal, assert_raises)
@@ -39,6 +43,7 @@
 
 
 def test_read_nifti2():
+    # Error trying to read a CIFTI2 image from a NIfTI2-only image.
     filemap = ci.Cifti2Image.make_file_map()
     for k in filemap:
         filemap[k].fileobj = io.open(NIFTI2_DATA)
@@ -194,3 +199,48 @@ def test_cifti2types():
 
     for klass, count in counter.items():
         assert_true(count > 0, "No exercise of " + klass.__name__)
+
+
+class TestCifti2SingleHeader(TestNifti2SingleHeader):
+    header_class = _Cifti2AsNiftiHeader
+    _pixdim_message = 'pixdim[1,2,3] should be zero or positive'
+
+    def test_pixdim_checks(self):
+        hdr_t = self.header_class()
+        for i in (1, 2, 3):
+            hdr = hdr_t.copy()
+            hdr['pixdim'][i] = -1
+            assert_equal(self._dxer(hdr), self._pixdim_message)
+
+    def test_nifti_qfac_checks(self):
+        # Test qfac is 1 or -1 or 0
+        hdr = self.header_class()
+        # 1, 0, -1 all OK
+        hdr['pixdim'][0] = 1
+        self.log_chk(hdr, 0)
+        hdr['pixdim'][0] = 0
+        self.log_chk(hdr, 0)
+        hdr['pixdim'][0] = -1
+        self.log_chk(hdr, 0)
+        # Anything else is not
+        hdr['pixdim'][0] = 2
+        fhdr, message, raiser = self.log_chk(hdr, 20)
+        assert_equal(fhdr['pixdim'][0], 1)
+        assert_equal(message,
+                     'pixdim[0] (qfac) should be 1 '
+                     '(default) or 0 or -1; setting qfac to 1')
+
+    def test_pixdim_log_checks(self):
+        # pixdim can be zero or positive
+        HC = self.header_class
+        hdr = HC()
+        hdr['pixdim'][1] = -2  # severity 35
+        fhdr, message, raiser = self.log_chk(hdr, 35)
+        assert_equal(fhdr['pixdim'][1], 2)
+        assert_equal(message, self._pixdim_message +
+                     '; setting to abs of pixdim values')
+        assert_raises(*raiser)
+        hdr = HC()
+        hdr['pixdim'][1:4] = 0  # No error or warning
+        fhdr, message, raiser = self.log_chk(hdr, 0)
+        assert_equal(raiser, ())

nibabel/tests/test_analyze.py

@@ -130,6 +130,9 @@ def test_checks(self):
         hdr = hdr_t.copy()
         hdr['bitpix'] = 0
         assert_equal(self._dxer(hdr), 'bitpix does not match datatype')
+
+    def test_pixdim_checks(self):
+        hdr_t = self.header_class()
         for i in (1, 2, 3):
             hdr = hdr_t.copy()
             hdr['pixdim'][i] = -1
@@ -176,7 +179,10 @@ def test_log_checks(self):
         assert_equal(message, 'bitpix does not match datatype; '
                      'setting bitpix to match datatype')
         assert_raises(*raiser)
+
+    def test_pixdim_log_checks(self):
         # pixdim positive
+        HC = self.header_class
         hdr = HC()
         hdr['pixdim'][1] = -2  # severity 35
         fhdr, message, raiser = self.log_chk(hdr, 35)
@@ -232,18 +238,21 @@ def test_logger_error(self):
         # Make a new logger
         str_io = StringIO()
         logger = logging.getLogger('test.logger')
-        logger.setLevel(30)  # defaultish level
         logger.addHandler(logging.StreamHandler(str_io))
-        # Prepare an error
-        hdr['pixdim'][1] = 0  # severity 30
+        # Prepare a defect: bitpix not matching data type
+        hdr['datatype'] = 16  # float32
+        hdr['bitpix'] = 16  # severity 10
+        logger.setLevel(10)
         log_cache = imageglobals.logger, imageglobals.error_level
         try:
             # Check log message appears in new logger
             imageglobals.logger = logger
             hdr.copy().check_fix()
-            assert_equal(str_io.getvalue(), PIXDIM0_MSG + '\n')
+            assert_equal(str_io.getvalue(),
+                         'bitpix does not match datatype; '
+                         'setting bitpix to match datatype\n')
             # Check that error_level in fact causes error to be raised
-            imageglobals.error_level = 30
+            imageglobals.error_level = 10
             assert_raises(HeaderDataError, hdr.copy().check_fix)
         finally:
             imageglobals.logger, imageglobals.error_level = log_cache

nibabel/tests/test_nifti1.py

@@ -186,17 +186,25 @@ def test_slope_inter(self):
             assert_array_equal([hdr['scl_slope'], hdr['scl_inter']],
                                raw_values)
 
-    def test_nifti_qsform_checks(self):
-        # qfac, qform, sform checks
-        # qfac
-        HC = self.header_class
-        hdr = HC()
+    def test_nifti_qfac_checks(self):
+        # Test qfac is 1 or -1
+        hdr = self.header_class()
+        # 1, -1 OK
+        hdr['pixdim'][0] = 1
+        self.log_chk(hdr, 0)
+        hdr['pixdim'][0] = -1
+        self.log_chk(hdr, 0)
+        # 0 is not
         hdr['pixdim'][0] = 0
         fhdr, message, raiser = self.log_chk(hdr, 20)
         assert_equal(fhdr['pixdim'][0], 1)
         assert_equal(message,
                      'pixdim[0] (qfac) should be 1 '
                      '(default) or -1; setting qfac to 1')
+
+    def test_nifti_qsform_checks(self):
+        # qform, sform checks
+        HC = self.header_class
         # qform, sform
         hdr = HC()
         hdr['qform_code'] = -1

nibabel/tests/test_nifti2.py

@@ -78,11 +78,6 @@ class TestNifti2Image(TestNifti1Image):
     image_class = Nifti2Image
 
 
-class TestNifti2Image(TestNifti1Image):
-    # Run analyze-flavor spatialimage tests
-    image_class = Nifti2Image
-
-
 class TestNifti2Pair(TestNifti1Pair):
     # Run analyze-flavor spatialimage tests
     image_class = Nifti2Pair