def _showEmanCtf(self, paramName=None):
program = eman2.Plugin.getProgram('e2ctf.py')
args = '--allparticles --minptcl=0 --minqual=0'
args += ' --gui --constbfactor=-1.0 --sf=auto'
hostConfig = self.protocol.getHostConfig()
# Create the steps executor
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
# Finally run the protocol
self.protocol.runJob(program,
args,
cwd=self.protocol._getExtraPath(),
numberOfMpi=1,
numberOfThreads=1)
# Open dialog to request confirmation to overwrite output
saveChanges = askYesNo(
"Save output changes?",
"Do you want to overwrite output particles with new CTF values?\n"
"This may take a while depending on the set size.",
self.getTkRoot())
if saveChanges:
self.protocol.createOutputStep()
showInfo("Output updated",
"Output particles were updated with new CTF values.",
self.getTkRoot())
def _showBfactorVols(self, paramName=None):
volsBfactor = []
guinierPlots = []
volumes = self._volFileNames('reconstructedFileNamesIters')
for vol in volumes:
volBfactor = vol + '.bfactor'
volsBfactor.append(volBfactor)
args = '-i %(vol)s --sampling %(samplingRate)s --maxres %(maxRes)s -o %(volBfactor)s ' + self.correctBfactorExtraCommand.get(
)
maxRes = self.maxRes.get()
samplingRate = self.protocol.resolSam
args = args % locals()
hostConfig = self.protocol.getHostConfig()
# Create the steps executor
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
# Finally run the protocol
self.protocol.runJob("xmipp_volume_correct_bfactor",
args,
numberOfMpi=1)
guinierPlots.append(self._showGuinier(volBfactor))
return self._showVolumes(volsBfactor) + guinierPlots
def _runEulerXplor(self, paramName=None):
program = Plugin.getProgram('e2eulerxplor.py')
hostConfig = self.protocol.getHostConfig()
# Create the steps executor
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
# Finally run the protocol
self.protocol.runJob(program,
"",
cwd=self.protocol._getExtraPath(),
numberOfMpi=1,
numberOfThreads=1)
return []
def _runAnalysis(self, paramName=None):
program = Plugin.getProgram('analyze')
args = ' %s %d --Apix %0.3f' % (
self.protocol._getFileName("output_dir"),
self._epoch,
self.protocol._getSampling())
hostConfig = self.protocol.getHostConfig()
# Create the steps executor
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
# Finally run the protocol
self.protocol.runJob(program, args, env=Plugin.getEnviron(),
cwd=None)
def test_basicObjectOutput(self):
"""Test the list with several Complex"""
fn = self.getOutputPath("protocol.sqlite")
mapper = SqliteMapper(fn, globals())
prot = ProtOutputTest(mapper=mapper,
n=2,
workingDir=self.getOutputPath(''))
# Add and old style output, not in the outputs dictionary
prot.output1 = EMObject()
self.assertFalse(prot._useOutputList.get(),
"useOutputList wrongly initialized")
outputs = [output for output in prot.iterOutputAttributes()]
self.assertTrue(1, len(outputs))
prot._stepsExecutor = StepExecutor(hostConfig=None)
prot.run()
self.assertEqual(prot._steps[0].getStatus(), STATUS_FINISHED)
# Check there is an output
self.assertOutput(prot)
outputs = [output for output in prot.iterOutputAttributes()]
# We are intentionally ignoring a protocol with output (EMObject)
# That has been continued, We do not find a real case now.
self.assertEqual(1,
len(outputs),
msg="Integer output not registered properly.")
outputs = [output for output in prot.iterOutputAttributes(Integer)]
# Test passing a filter
self.assertEqual(1,
len(outputs),
msg="Integer not matched when filtering outputs.")
# Test with non existing class
outputs = [output for output in prot.iterOutputAttributes(DataSet)]
# Test passing a class
self.assertEqual(0,
len(outputs),
msg="Filter by class in iterOutputAttributes does "
"not work.")
self.assertTrue(prot._useOutputList.get(),
"useOutputList not activated")
def test_StepExecutor(self):
"""Test the list with several Complex"""
fn = self.getOutputPath("protocol.sqlite")
mapper = SqliteMapper(fn, globals())
prot = MyProtocol(mapper=mapper,
n=2,
workingDir=self.getOutputPath(''))
prot._stepsExecutor = StepExecutor(hostConfig=None)
prot.run()
self.assertEqual(prot._steps[0].getStatus(), STATUS_FINISHED)
mapper2 = SqliteMapper(fn, globals())
prot2 = mapper2.selectById(prot.getObjId())
self.assertEqual(prot.endTime.get(), prot2.endTime.get())
def _extraWork():
program = Plugin.getProgram('').split()[:-1] # remove cryodrgn command
fn = self.protocol._getFileName('output_notebook',
epoch=self._epoch)
program.append('jupyter notebook %s' % os.path.basename(fn))
if os.path.exists(fn):
fnDir = os.path.dirname(fn)
hostConfig = self.protocol.getHostConfig()
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
self.protocol.runJob(" ".join(program), '',
env=Plugin.getEnviron(),
cwd=fnDir)
else:
self.showError('Jupyter notebook not found! Have you run analysis?')
def _showEmanPlot(self, paramName=None):
program = eman2.Plugin.getProgram('e2tiltvalidate.py')
args = "--path=TiltValidate_01 --radcut=%0.2f --gui --planethres=%0.2f" % (
self.radcut.get(), self.planethres.get())
if self.colozaxis:
args += " --colorzaxis"
hostConfig = self.protocol.getHostConfig()
# Create the steps executor
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
# Finally run the protocol
self.protocol.runJob(program,
args,
cwd=self.protocol._getExtraPath(),
numberOfMpi=1,
numberOfThreads=1)
return []