Relative data file path printing (#79)

Add argument `relative_data_path` to `nrrd.write` for specifying whether to save the 'data file' field in the header relative or absolute.

Fixes #78

nrrd/tests/test_writing.py

@@ -158,7 +158,8 @@ def test_write_detached_raw_as_nrrd(self):
         output_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.nhdr')
         output_data_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.nrrd')
 
-        nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True)
+        nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True,
+                   relative_data_path=False)
 
         # Read back the same file
         data, header = nrrd.read(output_filename)
@@ -198,7 +199,8 @@ def test_write_detached_gz(self):
         output_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.nhdr')
         output_data_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.raw.gz')
 
-        nrrd.write(output_filename, self.data_input, {u'encoding': 'gz'}, detached_header=False)
+        nrrd.write(output_filename, self.data_input, {u'encoding': 'gz'}, detached_header=False,
+                   relative_data_path=False)
 
         # Read back the same file
         data, header = nrrd.read(output_filename)
@@ -208,27 +210,25 @@ def test_write_detached_gz(self):
 
     def test_write_detached_bz2(self):
         output_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.nhdr')
-        output_data_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.raw.bz2')
 
         nrrd.write(output_filename, self.data_input, {u'encoding': 'bz2'}, detached_header=False)
 
         # Read back the same file
         data, header = nrrd.read(output_filename)
         self.assertEqual(self.expected_data, data.tostring(order='F'))
         self.assertEqual(header['encoding'], 'bz2')
-        self.assertEqual(header['data file'], output_data_filename)
+        self.assertEqual(header['data file'], 'testfile_detached_raw.raw.bz2')
 
     def test_write_detached_ascii(self):
         output_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.nhdr')
-        output_data_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.txt')
 
         nrrd.write(output_filename, self.data_input, {u'encoding': 'txt'}, detached_header=False)
 
         # Read back the same file
         data, header = nrrd.read(output_filename)
         self.assertEqual(self.expected_data, data.tostring(order='F'))
         self.assertEqual(header['encoding'], 'txt')
-        self.assertEqual(header['data file'], output_data_filename)
+        self.assertEqual(header['data file'], 'testfile_detached_raw.txt')
 
 
 if __name__ == '__main__':

nrrd/writer.py

@@ -93,7 +93,7 @@ def _format_field_value(value, field_type):
         raise NRRDError('Invalid field type given: %s' % field_type)
 
 
-def write(filename, data, header={}, detached_header=False, custom_field_map=None,
+def write(filename, data, header={}, detached_header=False, relative_data_path=True, custom_field_map=None,
                           compression_level = 9):
     """Write :class:`numpy.ndarray` to NRRD file
 
@@ -121,6 +121,9 @@ def write(filename, data, header={}, detached_header=False, custom_field_map=Non
         Data to save to the NRRD file
     detached_header : :obj:`bool`, optional
         Whether the header and data should be saved in separate files. Defaults to :obj:`False`
+    relative_data_path : :class:`bool`
+        Whether the data filename in detached header is saved with a relative path or absolute path.
+        This parameter is ignored if there is no detached header. Defaults to :obj:`True`
     custom_field_map : :class:`dict` (:class:`str`, :class:`str`), optional
         Dictionary used for parsing custom field types where the key is the custom field name and the value is a
         string identifying datatype for the custom field.
@@ -183,12 +186,14 @@ def write(filename, data, header={}, detached_header=False, custom_field_map=Non
             else:
                 raise NRRDError('Invalid encoding specification while writing NRRD file: %s' % header['encoding'])
 
-            header['data file'] = data_filename
+            header['data file'] = os.path.basename(data_filename) \
+                if relative_data_path else os.path.abspath(data_filename)
         else:
             data_filename = header['data file']
     elif filename.endswith('.nrrd') and detached_header:
         data_filename = filename
-        header['data file'] = data_filename
+        header['data file'] = os.path.basename(data_filename) \
+            if relative_data_path else os.path.abspath(data_filename)
         filename = '%s.nhdr' % os.path.splitext(filename)[0]
     else:
         # Write header & data as one file