From b4b84a5934b8a0cebd0eabe52f762889f52a595c Mon Sep 17 00:00:00 2001
From: Michael Wedel <michael.wedel@esss.se>
Date: Fri, 15 Jan 2016 15:48:22 +0100
Subject: [PATCH] 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.
---
.../PythonInterface/plugins/algorithms/LoadCIF.py | 15 +++++++++++++--
.../test/python/plugins/algorithms/LoadCIFTest.py | 11 +++++++----
2 files changed, 20 insertions(+), 6 deletions(-)
diff --git a/Framework/PythonInterface/plugins/algorithms/LoadCIF.py b/Framework/PythonInterface/plugins/algorithms/LoadCIF.py
index f8ebacaca33..74a601627fd 100644
--- a/Framework/PythonInterface/plugins/algorithms/LoadCIF.py
+++ b/Framework/PythonInterface/plugins/algorithms/LoadCIF.py
@@ -6,6 +6,15 @@ from mantid.geometry import SpaceGroupFactory, CrystalStructure
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 @@ class CrystalStructureBuilder(object):
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 @@ class CrystalStructureBuilder(object):
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
index 5c44110e723..816408b3e30 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py
@@ -90,8 +90,11 @@ class CrystalStructureBuilderTestUnitCell(unittest.TestCase):
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 @@ class CrystalStructureBuilderTestAtoms(unittest.TestCase):
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')
--
GitLab