Refs #11268. Errors are removed from numbers.

The numbers in CIFs may contain error estimates, indicated like this: 0.03(1), the strings are cut off starting with ( now.
mantidproject · Jan 15, 2016 · b4b84a5 · b4b84a5
1 parent c99b141
commit b4b84a5
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Showing 2 changed files with 20 additions and 6 deletions.
diff --git a/Framework/PythonInterface/plugins/algorithms/LoadCIF.py b/Framework/PythonInterface/plugins/algorithms/LoadCIF.py
@@ -6,6 +6,15 @@
 
 import re
 
+# pylint: disable=invalid-name
+def removeErrorEstimateFromNumber(numberString):
+    errorBegin = numberString.find('(')
+
+    if errorBegin == -1:
+        return numberString
+
+    return numberString[:errorBegin]
+
 
 class CrystalStructureBuilder(object):
     '''
@@ -80,7 +89,8 @@ def _getUnitCell(self, cifData):
         unitCellComponents = [u'_cell_length_a', u'_cell_length_b', u'_cell_length_c',
                               u'_cell_angle_alpha', u'_cell_angle_beta', u'_cell_angle_gamma']
 
-        unitCellValueMap = dict([(str(x), str(cifData[x])) if x in cifData.keys() else (str(x), None) for x in
+        unitCellValueMap = dict([(str(x), removeErrorEstimateFromNumber(str(cifData[x]))) if x in cifData.keys()
+                                 else (str(x), None) for x in
                                  unitCellComponents])
 
         if unitCellValueMap['_cell_length_a'] is None:
@@ -123,7 +133,8 @@ def _getAtoms(self, cifData):
         for atomLine in zip(*atomLists):
             stringAtomLine = [str(x) for x in atomLine]
 
-            cleanLine = [self._getCleanAtomSymbol(stringAtomLine[0])] + list(stringAtomLine[1:])
+            cleanLine = [self._getCleanAtomSymbol(stringAtomLine[0])] + [removeErrorEstimateFromNumber(x) for x in
+                                                                         list(stringAtomLine[1:])]
             atomLines.append(' '.join(cleanLine))
 
         return ';'.join(atomLines)

diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py
@@ -90,8 +90,11 @@ def test_getUnitCell_orthorhombic(self):
 
     def test_getUnitCell_hexagonal(self):
         cell = {u'_cell_length_a': u'5.6', u'_cell_length_c': u'2.3', u'_cell_angle_gamma': u'120.0'}
+        cell_errors = {u'_cell_length_a': u'5.6(1)', u'_cell_length_c': u'2.3(1)', u'_cell_angle_gamma': u'120.0'}
 
         self.assertEqual(self.builder._getUnitCell(cell), '5.6 5.6 2.3 90.0 90.0 120.0')
+        self.assertEqual(self.builder._getUnitCell(cell_errors), '5.6 5.6 2.3 90.0 90.0 120.0')
+
 
 
 class CrystalStructureBuilderTestAtoms(unittest.TestCase):
@@ -111,10 +114,10 @@ def test_getAtoms_required_keys(self):
 
     def test_getAtoms_correct(self):
         data = dict([(u'_atom_site_label', [u'Si', u'Al']),
-                     (u'_atom_site_fract_x', [u'1/8', u'0.34']),
-                     (u'_atom_site_fract_y', [u'1/8', u'0.56']),
-                     (u'_atom_site_fract_z', [u'1/8', u'0.23']),
-                     (u'_atom_site_occupancy', [u'1.0', u'1.0']),
+                     (u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
+                     (u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
+                     (u'_atom_site_fract_z', [u'1/8', u'0.23(2)']),
+                     (u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
                      (u'_atom_site_U_iso_or_equiv', [u'0.01', u'0.02'])])
 
         self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')