Merge branch 'extensions-in-hdr' into main-master

* extensions-in-hdr:
  RF - clean up stuff left over from previous extensions management
  DOC - whitespace edits and added comment

Author: matthew-brett

nibabel/analyze.py

@@ -261,7 +261,7 @@ def __init__(self,
             Default is True.
 
         Examples
-	--------
+        --------
         >>> hdr1 = AnalyzeHeader() # an empty header
         >>> hdr1.endianness == native_code
         True
@@ -366,6 +366,8 @@ def from_header(klass, header=None, check=True):
                 # the presence of the mapping certifies the fields as
                 # being of the same meaning as for Analyze types
                 pass
+        # set any fields etc that are specific to this format (overriden by
+        # sub-classes)
         obj._set_format_specifics()
         if check:
             obj.check_fix()
@@ -957,7 +959,7 @@ def _getter(obj, key):
                 return obj.get_value_label(key)
             except ValueError:
                 return obj[key]
-        
+
         return '\n'.join(
             [summary,
              pretty_mapping(self, _getter)])

nibabel/nifti1.py

@@ -357,8 +357,7 @@ def get_codes(self):
     def get_sizeondisk(self):
         """Return the size of the complete header extensions in the NIfTI file.
         """
-        # add four bytes for the NIfTI extension flag!
-        return np.sum([e.get_sizeondisk() for e in self]) + 4
+        return np.sum([e.get_sizeondisk() for e in self])
 
     def __repr__(self):
         s = "Nifti1Extensions(%s)" \
@@ -534,9 +533,15 @@ def from_fileobj(klass, fileobj, endianness=None, check=True):
         return hdr
 
     def write_to(self, fileobj):
+        # First check that vox offset is large enough
+        if self.is_single:
+            vox_offset = self._header_data['vox_offset']
+            min_vox_offset = 352 + self.extensions.get_sizeondisk()
+            if vox_offset < min_vox_offset:
+                raise HeaderDataError('vox offset of %d, but need at least %d'
+                                      % (vox_offset, min_vox_offset))
         super(Nifti1Header, self).write_to(fileobj)
-        n_exts = len(self.extensions)
-        if n_exts == 0:
+        if len(self.extensions) == 0:
             # If single file, write required 0 stream to signal no extensions
             if self.is_single:
                 fileobj.write('\x00' * 4)
@@ -1408,11 +1413,7 @@ def update_header(self):
         # make sure that there is space for the header.  If any
         # extensions, figure out necessary vox_offset for extensions to
         # fit
-        if (self.extra.has_key('extensions') and
-            len(self.extra['extensions'])):
-            min_vox_offset = 348 + self.extra['extensions'].get_sizeondisk()
-        else:
-            min_vox_offset = 352
+        min_vox_offset = 352 + hdr.extensions.get_sizeondisk()
         if hdr['vox_offset'] < min_vox_offset:
             hdr['vox_offset'] = min_vox_offset
 

nibabel/tests/test_nifti1.py

@@ -429,7 +429,7 @@ def test_nifti_extensions():
     assert_true(exts_container.count('comment') == 2)
     assert_true(exts_container.count('afni') == 0)
     assert_true(exts_container.get_codes() == [6, 6])
-    assert_true((exts_container.get_sizeondisk() - 4) % 16 == 0)
+    assert_true((exts_container.get_sizeondisk()) % 16 == 0)
     # first extension should be short one
     assert_true(exts_container[0].get_content() == 'extcomment1')
     # add one
@@ -438,7 +438,7 @@ def test_nifti_extensions():
     assert_true(exts_container.get_codes() == [6, 6, 4])
     assert_true(exts_container.count('comment') == 2)
     assert_true(exts_container.count('afni') == 1)
-    assert_true((exts_container.get_sizeondisk() - 4) % 16 == 0)
+    assert_true((exts_container.get_sizeondisk()) % 16 == 0)
     # delete one
     del exts_container[1]
     assert_true(exts_container.get_codes() == [6, 4])