def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
output = plugin.dataOutput
reference = XSDataXdsOutput.parseFile(self.getReferenceDataOutputFile())
EDAssert.strAlmostEqual(output.marshal(),
reference.marshal(),
"output looks good")
def process(self, _edObject = None):
EDPlugin.process(self)
output = XSDataXdsOutput()
# get all the file's contents, find where the info is and then
# use helper functions to retrieve stuff and put it in the
# data model
try:
f = open(self.dataInput.correct_lp.path.value, 'r')
lines = f.readlines()
except IOError:
EDVerbose.ERROR('Could not open the specified XDS output file for reading')
self.setFailure()
return
# look for the "big piece of information"
info_begin = None
info_end = None
for lineno, line in enumerate(lines):
if info_begin is None:
if line.find('REFINEMENT OF DIFFRACTION PARAMETERS USING ALL IMAGES') != -1:
info_begin = lineno
else:
if line.find('MEAN INTENSITY AS FUNCTION OF SPINDLE POSITION WITHIN DATA IMAGE') != -1:
info_end = lineno
break
if info_begin is None or info_end is None:
EDVerbose.ERROR('could not find the refined parameters')
self.setFailure()
return
_extract_infos(lines[info_begin:info_end], output)
# second pass, look for the interesting table
info_begin = None
info_end = None
started = False
for line_no, line in enumerate(lines):
if line.find('REFLECTIONS OF TYPE H,0,0 0,K,0 0,0,L OR EXPECTED TO BE ABSENT (*)') != -1:
# the table will start shortly after
started = True
continue
if started:
# look if we are at the table yet
if line.find('LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected') != -1:
# there's an empty line after the header
info_begin = line_no + 2
if info_begin is not None and line.find('total') != -1:
# we're at the last table line
info_end = line_no
if info_begin is None or info_end is None:
EDVerbose.ERROR('could not find the completeness table')
self.setFailure()
return
_extract_completeness_entries(lines[info_begin:info_end+1], output)
# now for the last bit: check if we were given a path to the
# gxparm file and if it exists get the space group and unit
# cell constants from it
if self.dataInput.gxparm is not None:
gxparm_path = self.dataInput.gxparm.path.value
if os.path.exists(gxparm_path):
with open(gxparm_path, 'r') as f:
lines = f.readlines()
for line in lines:
# the one we want has 7 floats
chunks = line.split()
if len(chunks) == 7:
output.sg_number = XSDataInteger(int(chunks[0]))
output.unit_cell_constants = [XSDataFloat(float(x)) for x in chunks[1:]]
input_file = self.dataInput.correct_lp.path.value
output.xds_run_directory = XSDataString(os.path.dirname(input_file))
self.dataOutput = output
def process(self, _edObject=None):
EDPlugin.process(self)
output = XSDataXdsOutput()
# get all the file's contents, find where the info is and then
# use helper functions to retrieve stuff and put it in the
# data model
try:
f = open(self.dataInput.correct_lp.path.value, 'r')
lines = f.readlines()
except IOError:
EDVerbose.ERROR(
'Could not open the specified XDS output file for reading')
self.setFailure()
return
# look for the "big piece of information"
info_begin = None
info_end = None
for lineno, line in enumerate(lines):
if info_begin is None:
if line.find(
'REFINEMENT OF DIFFRACTION PARAMETERS USING ALL IMAGES'
) != -1:
info_begin = lineno
else:
if line.find(
'MEAN INTENSITY AS FUNCTION OF SPINDLE POSITION WITHIN DATA IMAGE'
) != -1:
info_end = lineno
break
if info_begin is None or info_end is None:
EDVerbose.ERROR('could not find the refined parameters')
self.setFailure()
return
_extract_infos(lines[info_begin:info_end], output)
# second pass, look for the interesting table
info_begin = None
info_end = None
started = False
for line_no, line in enumerate(lines):
if line.find(
'REFLECTIONS OF TYPE H,0,0 0,K,0 0,0,L OR EXPECTED TO BE ABSENT (*)'
) != -1:
# the table will start shortly after
started = True
continue
if started:
# look if we are at the table yet
if line.find(
'LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected'
) != -1:
# there's an empty line after the header
info_begin = line_no + 2
if info_begin is not None and line.find('total') != -1:
# we're at the last table line
info_end = line_no
if info_begin is None or info_end is None:
EDVerbose.ERROR('could not find the completeness table')
self.setFailure()
return
_extract_completeness_entries(lines[info_begin:info_end + 1], output)
# now for the last bit: check if we were given a path to the
# gxparm file and if it exists get the space group and unit
# cell constants from it
if self.dataInput.gxparm is not None:
gxparm_path = self.dataInput.gxparm.path.value
if os.path.exists(gxparm_path):
with open(gxparm_path, 'r') as f:
lines = f.readlines()
for line in lines:
# the one we want has 7 floats
chunks = line.split()
if len(chunks) == 7:
output.sg_number = XSDataInteger(int(chunks[0]))
output.unit_cell_constants = [
XSDataFloat(float(x)) for x in chunks[1:]
]
input_file = self.dataInput.correct_lp.path.value
output.xds_run_directory = XSDataString(os.path.dirname(input_file))
self.dataOutput = output