BF+TST - update header from affines when needed

The update routine updates the header information from the affine only
if the affine differs from the current estimate of the affine stored in
the header.

Add tests for header updating on save

Author: matthew-brett

nibabel/analyze.py

@@ -1053,12 +1053,20 @@ def update_header(self):
         (1.0, 2.0, 3.0)
         '''
         hdr = self._header
+        # We need to update the header if the data shape has changed.  It's a
+        # bit difficult to change the data shape using the standard API, but
+        # maybe it happened
         if not self._data is None:
             hdr.set_data_shape(self._data.shape)
-        if not self._affine is None:
-            RZS = self._affine[:3, :3]
-            vox = np.sqrt(np.sum(RZS * RZS, axis=0))
-            hdr['pixdim'][1:4] = vox
+        # If the affine is not None, and it is different from the main affine in
+        # the header, update the heaader
+        if self._affine is None:
+            return
+        if np.all(self._affine == hdr.get_best_affine()):
+            return
+        RZS = self._affine[:3, :3]
+        vox = np.sqrt(np.sum(RZS * RZS, axis=0))
+        hdr['pixdim'][1:4] = vox
 
 
 load = AnalyzeImage.load

nibabel/nifti1.py

@@ -1428,14 +1428,16 @@ def update_header(self):
         super(Nifti1Pair, self).update_header()
         hdr = self._header
         hdr['magic'] = 'ni1'
-        if not self._affine is None:
-            # Set affine into sform
-            hdr.set_sform(self._affine, code='aligned')
-            # Make qform 'unknown', set voxel sizes from affine
-            hdr['qform_code'] = 0
-            RZS = self._affine[:3, :3]
-            zooms = np.sqrt(np.sum(RZS * RZS, axis=0))
-            hdr['pixdim'][1:4] = zooms
+        # If the affine is not None, and it is different from the main affine in
+        # the header, update the heaader
+        if self._affine is None:
+            return
+        if np.all(self._affine == hdr.get_best_affine()):
+            return
+        # Set affine into sform with default code
+        hdr.set_sform(self._affine, code='aligned')
+        # Make qform 'unknown'
+        hdr.set_qform(self._affine, code='unknown')
 
 
 class Nifti1Image(Nifti1Pair):

nibabel/tests/test_analyze.py

@@ -532,6 +532,37 @@ def test_affine_44(self):
         # Not OK - affine wrong shape
         assert_raises(ValueError, IC, data, np.diag([2, 3, 4]))
 
+    def test_header_updating(self):
+        # Only update on changes
+        img_klass = self.image_class
+        # With a None affine - don't overwrite zooms
+        img = img_klass(np.zeros((2,3,4)), None)
+        hdr = img.get_header()
+        hdr.set_zooms((4,5,6))
+        # Save / reload using bytes IO objects
+        for key, value in img.file_map.items():
+            value.fileobj = BytesIO()
+        img.to_file_map()
+        hdr_back = img.from_file_map(img.file_map).get_header()
+        assert_array_equal(hdr_back.get_zooms(), (4,5,6))
+        # With a real affine, update zooms
+        img = img_klass(np.zeros((2,3,4)), np.diag([2,3,4,1]), hdr)
+        hdr = img.get_header()
+        assert_array_equal(hdr.get_zooms(), (2, 3, 4))
+        # Modify affine in-place? Update on save.
+        img.get_affine()[0,0] = 9
+        for key, value in img.file_map.items():
+            value.fileobj = BytesIO()
+        img.to_file_map()
+        hdr_back = img.from_file_map(img.file_map).get_header()
+        assert_array_equal(hdr.get_zooms(), (9, 3, 4))
+        # Modify data in-place?  Update on save
+        data = img.get_data()
+        data.shape = (3, 2, 4)
+        img.to_file_map()
+        img_back = img.from_file_map(img.file_map)
+        assert_array_equal(img_back.shape, (3, 2, 4))
+
 
 def test_unsupported():
     # analyze does not support uint32

nibabel/tests/test_nifti1.py

@@ -174,11 +174,46 @@ def test_binblock_is_file(self):
 
 
 class TestNifti1Image(tana.TestAnalyzeImage):
-    # class for testing images
+    # Run analyze-flavor spatialimage tests
     image_class = Nifti1Image
 
-
-class TestNifti1Pair(tana.TestAnalyzeImage):
+    def _qform_rt(self, img):
+        # Round trip image after setting qform, sform codes
+        hdr = img.get_header()
+        hdr['qform_code'] = 3
+        hdr['sform_code'] = 4
+        # Save / reload using bytes IO objects
+        for key, value in img.file_map.items():
+            value.fileobj = BytesIO()
+        img.to_file_map()
+        return img.from_file_map(img.file_map)
+
+    def test_qform_cycle(self):
+        # Qform load save cycle
+        img_klass = self.image_class
+        # None affine
+        img = img_klass(np.zeros((2,3,4)), None)
+        hdr_back = self._qform_rt(img).get_header()
+        assert_equal(hdr_back['qform_code'], 3)
+        assert_equal(hdr_back['sform_code'], 4)
+        # Try non-None affine
+        img = img_klass(np.zeros((2,3,4)), np.eye(4))
+        hdr_back = self._qform_rt(img).get_header()
+        assert_equal(hdr_back['qform_code'], 3)
+        assert_equal(hdr_back['sform_code'], 4)
+        # Modify affine in-place - does it hold?
+        img.get_affine()[0,0] = 9
+        img.to_file_map()
+        img_back = img.from_file_map(img.file_map)
+        exp_aff = np.diag([9,1,1,1])
+        assert_array_equal(img_back.get_affine(), exp_aff)
+        hdr_back = img.get_header()
+        assert_array_equal(hdr_back.get_sform(), exp_aff)
+        assert_array_equal(hdr_back.get_qform(), exp_aff)
+
+
+class TestNifti1Pair(TestNifti1Image):
+    # Run analyze-flavor spatialimage tests
     image_class = Nifti1Pair
 
 

nibabel/tests/test_spm99analyze.py

@@ -105,6 +105,10 @@ class TestSpm99AnalyzeImage(test_analyze.TestAnalyzeImage):
         test_analyze.TestAnalyzeImage.test_data_hdr_cache
     ))
 
+    test_header_updating = (scipy_skip(
+        test_analyze.TestAnalyzeImage.test_header_updating
+    ))
+
     @scipy_skip
     def test_mat_read(self):
         # Test mat file reading and writing for the SPM analyze types