Author: bugman
Date: Tue Dec 2 21:57:15 2014
New Revision: 26905
URL: http://svn.gna.org/viewcvs/relax?rev=26905&view=rev
Log:
Merged revisions 26901-26902 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26901 | bugman | 2014-12-02 21:39:10 +0100 (Tue, 02 Dec 2014) | 9 lines
Created the State.test_bug_23017_ieee_754_multidim_numpy_arrays system test.
This is to catch bug #23017 (https://gna.org/bugs/?23017), the
multidimensional numpy arrays are not
being stored as IEEE 754 arrays in the XML state and results files.
This test checks a rank-2 float64 numpy array stored in the current data
pipe against what the IEEE
754 int list should be for it.
........
r26902 | bugman | 2014-12-02 21:42:14 +0100 (Tue, 02 Dec 2014) | 9 lines
Simple fix for bug #23017 (https://gna.org/bugs/?23017).
This is the multidimensional numpy arrays are not being stored as IEEE 754
arrays in the XML state
and results files. The problem was a relatively recent regression caused
by a change to the
is_float_matrix() function of the lib.arg_check module. It was simply that
the default dims keyword
argument value was changed from None to (3, 3). Therefore any call to the
function without
supplying the dims argument would fail if the matrix was not of the (3, 3)
shape.
........
Modified:
branches/space_mapping_refactor/ (props changed)
branches/space_mapping_refactor/lib/arg_check.py
branches/space_mapping_refactor/test_suite/system_tests/state.py
Propchange: branches/space_mapping_refactor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Dec 2 21:57:15 2014
@@ -1 +1 @@
-/trunk:1-26871,26874-26885
+/trunk:1-26904
Modified: branches/space_mapping_refactor/lib/arg_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/arg_check.py?rev=26905&r1=26904&r2=26905&view=diff
==============================================================================
--- branches/space_mapping_refactor/lib/arg_check.py (original)
+++ branches/space_mapping_refactor/lib/arg_check.py Tue Dec 2 21:57:15
2014
@@ -150,7 +150,7 @@
return True
-def is_float_matrix(arg, name=None, dim=(3, 3), can_be_none=False,
none_elements=False, raise_error=True):
+def is_float_matrix(arg, name=None, dim=None, can_be_none=False,
none_elements=False, raise_error=True):
"""Test if the argument is a matrix of floats.
@param arg: The argument.
Modified: branches/space_mapping_refactor/test_suite/system_tests/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/state.py?rev=26905&r1=26904&r2=26905&view=diff
==============================================================================
--- branches/space_mapping_refactor/test_suite/system_tests/state.py
(original)
+++ branches/space_mapping_refactor/test_suite/system_tests/state.py Tue
Dec 2 21:57:15 2014
@@ -21,7 +21,9 @@
# Python module imports.
from copy import deepcopy
+from numpy import array, float64
from os import sep
+from re import search
from tempfile import mktemp
# relax module imports.
@@ -51,6 +53,86 @@
if not dep_check.C_module_exp_fn and methodName in
['test_write_read_pipes']:
# Store in the status object.
status.skipped_tests.append([methodName, 'Relax curve-fitting C
module', self._skip_type])
+
+
+ def get_ieee_754(self, lines=None):
+ """Find and convert the IEEE 754 int list from the list of text
lines.
+
+ @keyword lines: The lines of XML text to extract the IEEE 754 array
from.
+ @type lines: list of str
+ @return: The IEEE 754 array, if it exists.
+ @rtype: list of int
+ """
+
+ # Loop over the lines, finding the IEEE 754 lines.
+ ieee_754 = ""
+ in_tag = False
+ for line in lines:
+ # The tag start line, so switch the flag.
+ if search("<ieee_754", line):
+ in_tag = True
+
+ # The tag end line, so store the line and switch the flag.
+ if search("</ieee_754", line):
+ ieee_754 += line
+ in_tag = False
+
+ # Store the line.
+ if in_tag:
+ ieee_754 += line
+
+ # Strip the tags and newlines.
+ ieee_754 = ieee_754.replace('<ieee_754_byte_array>', '')
+ ieee_754 = ieee_754.replace('</ieee_754_byte_array>', '')
+ ieee_754 = ieee_754.replace('\n', '')
+
+ # Nothing left.
+ if ieee_754 == '':
+ return None
+
+ # Convert the remaining text to an int list.
+ ieee_754 = eval(ieee_754)
+
+ # Return the array.
+ return ieee_754
+
+
+
+ def get_xml_tag(self, file=None, name=None):
+ """Extract the text lines for the given XML tag.
+
+ @keyword file: The file name top open.
+ @type file: str
+ @keyword name: The XML tag name to isolate.
+ @type name: str
+ @return: The list of lines corresponding to the XML tag.
+ @rtype: list of str
+ """
+
+ # Read the contents of the file.
+ file = open(file)
+ lines = file.readlines()
+ file.close()
+
+ # Loop over the lines, finding all corresponding tags.
+ tag_lines = []
+ in_tag = False
+ for line in lines:
+ # The tag start line, so switch the flag.
+ if search("<%s "%name, line):
+ in_tag = True
+
+ # The tag end line, so store the line and switch the flag.
+ if search("</%s>"%name, line):
+ tag_lines.append(line)
+ in_tag = False
+
+ # Store the line.
+ if in_tag:
+ tag_lines.append(line)
+
+ # Return the lines.
+ return tag_lines
def setUp(self):
@@ -118,6 +200,28 @@
self.interpreter.state.save(self.tmpfile, force=True)
+ def test_bug_23017_ieee_754_multidim_numpy_arrays(self):
+ """Test catching U{bug #23017<https://gna.org/bugs/?23017>}, the
multidimensional numpy arrays are not being stored as IEEE 754 arrays in the
XML state and results files."""
+
+ # Create a data pipe.
+ self.interpreter.pipe.create('test', 'mf')
+
+ # The numpy structure.
+ cdp.test = array([[1, 2, 3], [4, 5, 6]], float64)
+
+ # Save the state.
+ self.interpreter.state.save(self.tmpfile, compress_type=0,
force=True)
+
+ # Get the tag lines.
+ lines = self.get_xml_tag(file=self.tmpfile, name='test')
+
+ # Extract the IEEE 754 array as an int list.
+ ieee_754 = self.get_ieee_754(lines=lines)
+
+ # Check.
+ self.assertEqual(ieee_754, [[[0, 0, 0, 0, 0, 0, 240, 63], [0, 0, 0,
0, 0, 0, 0, 64], [0, 0, 0, 0, 0, 0, 8, 64]], [[0, 0, 0, 0, 0, 0, 16, 64], [0,
0, 0, 0, 0, 0, 20, 64], [0, 0, 0, 0, 0, 0, 24, 64]]])
+
+
def test_state_xml(self):
"""Test the saving, loading, and second saving and loading of the
program state in XML format."""
r26905 - in /branches/space_mapping_refactor: ./ lib/arg_check.py test_suite/system_tests/state.py