Fix bus error when saving Nifti data under same name it was loaded from.

See nipy/nibabel#492 for probable explanation

Author: mcraig-ibme

quantiphyse/data/nifti.py

@@ -65,13 +65,13 @@ def __init__(self, fname):
         QpData.__init__(self, fname, grid, nvols, vol_unit=vol_units, vol_scale=vol_scale, fname=fname, metadata=metadata)
 
     def raw(self):
-        # NB: np.asarray convert data to an in-memory array instead of a numpy file memmap.
+        # NB: copy() converts data to an in-memory array instead of a numpy file memmap.
         # Appears to improve speed drastically as well as stop a bug with accessing the subset of the array
         # memmap has been designed to save space on ram by keeping the array on the disk but does
         # horrible things with performance, and analysis especially when the data is on the network.
         if self.rawdata is None:
             nii = nib.load(self.fname)
-            self.rawdata = np.asarray(nii.get_data())
+            self.rawdata = nii.get_data().copy()
             self.rawdata = self._correct_dims(self.rawdata)
 
         self.voldata = None

quantiphyse/test/qpd_test.py

@@ -138,5 +138,15 @@ def testSaveLoadMetadata(self):
             self.assertTrue(key in nifti_data.metadata)
             self.assertEqual(nifti_data.metadata[key], value)
 
+    def testLoadSaveSameName(self):
+        qpd = NumpyData(self.floats4d, grid=self.grid, name="test")
+
+        tempdir = tempfile.mkdtemp(prefix="qp")
+        fname = os.path.join(tempdir, "test.nii")
+        nifti.save(qpd, fname)
+
+        nifti_data = nifti.NiftiData(fname)
+        nifti.save(nifti_data, fname)
+
 if __name__ == '__main__':
     unittest.main()