RF+BF - check whether image and header are same file when saving

Author: matthew-brett

nibabel/analyze.py

@@ -1377,14 +1377,21 @@ def to_file_map(self, file_map=None):
         hdr = self.get_header()
         slope, inter, mn, mx = hdr.scaling_from_data(data)
         hdr_fh, img_fh = self._get_fileholders(file_map)
+        # Check if hdr and img refer to same file; this can happen with odd
+        # analyze images but most often this is because it's a single nifti file
+        hdr_img_same = hdr_fh.same_file_as(img_fh)
         hdrf = hdr_fh.get_prepare_fileobj(mode='wb')
-        imgf = img_fh.get_prepare_fileobj(mode='wb')
+        if hdr_img_same:
+            imgf = hdrf
+        else:
+            imgf = img_fh.get_prepare_fileobj(mode='wb')
         self._write_header(hdrf, hdr, slope, inter)
         self._write_image(imgf, data, hdr, slope, inter, mn, mx)
         if hdr_fh.fileobj is None: # was filename
             hdrf.close()
-        if img_fh.fileobj is None: # was filename
-            imgf.close()
+        if not hdr_img_same:
+            if img_fh.fileobj is None: # was filename
+                imgf.close()
         self._header = hdr
         self.file_map = file_map
 

nibabel/fileholders.py

@@ -73,6 +73,23 @@ def get_prepare_fileobj(self, *args, **kwargs):
             raise FileHolderError('No filename or fileobj present')
         return obj
 
+    def same_file_as(self, other):
+        """ Test if `self` refers to same files / fileobj as `other`
+
+        Parameters
+        ----------
+        other : object
+            object with `filename` and `fileobj` attributes
+
+        Returns
+        -------
+        tf : bool
+            True if `other` has the same filename (or both have None) and the
+            same fileobj (or both have None
+        """
+        return ((self.filename == other.filename) and
+                (self.fileobj == other.fileobj))
+
 
 def copy_file_map(file_map):
     ''' Copy mapping of fileholders given by `file_map`

nibabel/tests/test_fileholders.py

@@ -0,0 +1,53 @@
+""" Testing fileholders
+"""
+
+from StringIO import StringIO
+
+import numpy as np
+
+from ..fileholders import FileHolder, FileHolderError, copy_file_map
+from ..tmpdirs import InTemporaryDirectory
+
+from numpy.testing import (assert_array_almost_equal,
+                           assert_array_equal)
+
+from nose.tools import assert_true, assert_false, assert_equal, assert_raises
+
+
+def test_init():
+    fh = FileHolder('a_fname')
+    assert_equal(fh.filename, 'a_fname')
+    assert_true(fh.fileobj is None)
+    assert_equal(fh.pos, 0)
+    sio0 = StringIO()
+    fh = FileHolder('a_test', sio0)
+    assert_equal(fh.filename, 'a_test')
+    assert_true(fh.fileobj is sio0)
+    assert_equal(fh.pos, 0)
+    fh = FileHolder('a_test_2', sio0, 3)
+    assert_equal(fh.filename, 'a_test_2')
+    assert_true(fh.fileobj is sio0)
+    assert_equal(fh.pos, 3)
+
+
+def test_same_file_as():
+    fh = FileHolder('a_fname')
+    assert_true(fh.same_file_as(fh))
+    fh2 = FileHolder('a_test')
+    assert_false(fh.same_file_as(fh2))
+    sio0 = StringIO()
+    fh3 = FileHolder('a_fname', sio0)
+    fh4 = FileHolder('a_fname', sio0)
+    assert_true(fh3.same_file_as(fh4))
+    assert_false(fh3.same_file_as(fh))
+    fh5 = FileHolder(fileobj=sio0)
+    fh6 = FileHolder(fileobj=sio0)
+    assert_true(fh5.same_file_as(fh6))
+    # Not if the filename is the same
+    assert_false(fh5.same_file_as(fh3))
+    # pos doesn't matter
+    fh4_again = FileHolder('a_fname', sio0, pos=4)
+    assert_true(fh3.same_file_as(fh4_again))
+
+
+

nibabel/tests/test_nifti1.py

@@ -368,28 +368,27 @@ def test_set_slice_times():
     yield assert_equal(hdr['slice_code'], 6)
 
 
-@parametric
 def test_nifti1_images():
     shape = (2, 4, 6)
     npt = np.float32
     data = np.arange(np.prod(shape), dtype=npt).reshape(shape)
     affine = np.diag([1, 2, 3, 1])
     img = Nifti1Image(data, affine)
-    yield assert_equal(img.get_shape(), shape)
+    assert_equal(img.get_shape(), shape)
     img.set_data_dtype(npt)
     stio = StringIO()
     img.file_map['image'].fileobj = stio
     img.to_file_map()
     img2 = Nifti1Image.from_file_map(img.file_map)
-    yield assert_array_equal(img2.get_data(), data)
+    assert_array_equal(img2.get_data(), data)
     with InTemporaryDirectory() as tmpdir:
         for ext in ('.gz', '.bz2'):
             fname = os.path.join(tmpdir, 'test.nii' + ext)
             img.to_filename(fname)
             img3 = Nifti1Image.load(fname)
-            yield assert_true(isinstance(img3, img.__class__))
-            yield assert_array_equal(img3.get_data(), data)
-            yield assert_equal(img3.get_header(), img.get_header())
+            assert_true(isinstance(img3, img.__class__))
+            assert_array_equal(img3.get_data(), data)
+            assert_equal(img3.get_header(), img.get_header())
             # del to avoid windows errors of form 'The process cannot
             # access the file because it is being used'
             del img3