def process(self, _edObject = None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXdsFastProc.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
self.first_run.dataInput = params
self.first_run.executeSynchronous()
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.second_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG('copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.second_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# increase all the spot ranges end by 20, constrained to
# the data range upper limit
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 20
if range_end > self.end_image_no:
self.DEBUG('End of range {0} would be past the last image {1}'.format(range_end,
self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.second_run.dataInput = params
self.second_run.executeSynchronous()
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.third_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG('copying previously generated files to the new plugin dir')
copy_xds_files(self.second_run.getWorkingDirectory(),
self.third_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 40
if range_end > self.end_image_no:
self.DEBUG('End of range {0} would be past the last image {1}'.format(range_end,
self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.third_run.dataInput = params
self.third_run.executeSynchronous()
EDVerbose.DEBUG('third run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutput")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
self.setFailure()
return
self.dataOutput = parser.dataOutput
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXdsFastProc.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
self.first_run.dataInput = params
self.first_run.executeSynchronous()
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.second_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG(
'copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.second_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# increase all the spot ranges end by 20, constrained to
# the data range upper limit
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 20
if range_end > self.end_image_no:
self.DEBUG(
'End of range {0} would be past the last image {1}'.
format(range_end, self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(
srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.second_run.dataInput = params
self.second_run.executeSynchronous()
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.third_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG(
'copying previously generated files to the new plugin dir')
copy_xds_files(self.second_run.getWorkingDirectory(),
self.third_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 40
if range_end > self.end_image_no:
self.DEBUG(
'End of range {0} would be past the last image {1}'.
format(range_end, self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(
srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.third_run.dataInput = params
self.third_run.executeSynchronous()
EDVerbose.DEBUG('third run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutput")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
self.setFailure()
return
self.dataOutput = parser.dataOutput
