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 onVariables(self):
if pluginDict is not None:
msg = ""
pluginsVars = pluginDict.values()[0].getPluginClass().getVars()
for var in pluginsVars:
msg = msg + var + ': ' + pluginsVars[var] + '\n'
pwgui.showInfo("Plugin variables", msg, tk.Frame())
def _onVarChanged(self, *args):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
self.computeFit()
self.plotResults()
else:
dialog.showInfo("Warning","Please select some sample(s) to plot.",self)
def _onVarChanged(self, *args):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
self.computeFit()
self.plotResults()
else:
dialog.showInfo("Warning","Please select some sample(s) to plot.",self)
def checkFileIntegrityGUI(fn, parent):
ok = verifyMD5(fn)
if ok:
showInfo("File integrity", "File is OK", parent)
else:
showError(
"File integrity",
"File seems to have been modified since its creation. Not OK",
parent)
def _showHelp(self, event=None):
showInfo(
'CTFTomoSeries viewer help',
'This viewer calculates the standard deviation with respect '
'to the mean of the defocusU and defocusV values. If the '
'values of the images are not in the 20% range from the average '
'they are marked as *Failed* and therefore the CTFTomoSerie is '
'marked as *Failed* as well.\n\n'
'On the other hand, the viewer allows you to create two '
'subsets of CTFTomoSeries which are classified as good '
'and bad respectively.\n\n'
'Note: The series that are checked are the ones that '
'represent the bad CTFTomoSeries', self.parent)
def _onSampleChanged(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
# When the sample is changed we need to re-compute (with log or not)
# the x, y values
self.sample = self.experiment.samples[sampleKeys[0]]
self.xValues, self.yValues = self.sample.getXYValues(self.varNameX,
self.varNameY)
self.newXValues, self.newYValues = self.computePlotValues(self.xValues[0],
self.yValues[0])
self._updateModel()
self.computeFit()
self.plotResults()
else:
dialog.showInfo("Warning","Please select some sample(s) to plot.",self)
def show(self, form, *params):
try:
acquisitionInfo = form.protocol.loadAcquisitionInfo()
if isinstance(acquisitionInfo, dict):
# If acquisitionInfo is None means something is wrong.
# Now, let's try to show a meaningful error message.
self._setAcquisition(form, acquisitionInfo)
else:
# If not dict, it should be an error message
dialog.showError("Input error", acquisitionInfo, form.root)
except FileNotFoundError as e:
dialog.showInfo(
"File not found",
"Metadata file with acquisition not found.\n\n %s" % e,
form.root)
def _onSampleChanged(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
# When the sample is changed we need to re-compute (with log or not)
# the x, y values
self.sample = self.experiment.samples[sampleKeys[0]]
self.xValues, self.yValues = self.sample.getXYValues(self.varNameX,
self.varNameY)
self.newXValues, self.newYValues = self.computePlotValues(self.xValues[0],
self.yValues[0])
self._updateModel()
self.computeFit()
self.plotResults()
else:
dialog.showInfo("Warning","Please select some sample(s) to plot.",self)
def checkFileIntegrityGUI(fn,parent):
ok = verifyMD5(fn)
if ok:
showInfo("File integrity", "File is OK", parent)
else:
showError("File integrity","File seems to have been modified since its creation. Not OK", parent)