def show(self, form, *params):
# This are the greetings:
greetings = [
String("Hello world"),
String("Hola mundo"),
String("Bonjour le monde"),
String("Hallo Welt"),
String("Kon'nichiwa sekai"),
String("Nǐ hǎo, shìjiè"),
String("Ciao mondo"),
String("Hallo Wereld"),
String("Privet, mir")
]
# Get a data provider from the greetings to be used in the tree (dialog)
provider = ListTreeProviderString(greetings)
# Show the dialog
dlg = dialog.ListDialog(form.root, "Greetings from the world",
provider, "Select one of the greetings)")
# Set the chosen value back to the form
form.setVar('message', dlg.values[0].get())
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
# The following attribute is only for testing
self.importFolder = String(args.get('importFolder', None))
class XmippProtParticlePickingPairs(ProtParticlePicking, XmippProtocol):
"""Xmipp protocol to pick particles in a set of micrographs
either manually or using supervised picking support """
_label = 'tilt pairs particle picking'
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
# The following attribute is only for testing
self.importFolder = String(args.get('importFolder', None))
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputMicrographsTiltedPair', PointerParam, label="Micrographs tilt pair",
pointerClass='MicrographsTiltPair',
help='Select the MicrographsTiltPair ')
form.addParam('memory', FloatParam, default=2,
label='Memory to use (In Gb)', expertLevel=2)
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
"""The Particle Picking proccess is realized for a pair of set of micrographs"""
self.micsFn = self._getPath('input_micrographs.xmd')
# Convert input into xmipp Metadata format
self._insertFunctionStep('convertInputStep')
# Launch Particle Picking GUI
if not self.importFolder.hasValue():
self._insertFunctionStep('launchParticlePickGUIStep', interactive=True)
else: # This is only used for test purposes
self._insertFunctionStep('_importFromFolderStep')
#--------------------------- STEPS functions ----------------------------------------------------
def convertInputStep(self):
# Get the converted input micrographs in Xmipp format
writeSetOfMicrographsPairs(self.inputMicrographsTiltedPair.get().getUntilted(),
self.inputMicrographsTiltedPair.get().getTilted(),
self.micsFn)
def launchParticlePickGUIStep(self):
extraDir = self._getExtraPath()
process = launchTiltPairPickerGUI(self.memory.get(), self.micsFn, extraDir, 'manual', self)
process.wait()
print 'launch ended'
def _importFromFolderStep(self):
""" This function will copy Xmipp .pos files for
simulating a particle picking run...this is only
for testing purposes.
"""
for f in getFiles(self.importFolder.get()):
copyFile(f, self._getExtraPath())
extradir = self._getExtraPath()
inputset = self.inputMicrographsTiltedPair.get()
uSet = inputset.getUntilted()
tSet = inputset.getTilted()
# Create Untilted and Tilted SetOfCoordinates
uCoordSet = self._createSetOfCoordinates(uSet, suffix='Untilted')
readSetOfCoordinates(extradir, uSet, uCoordSet)
uCoordSet.write()
tCoordSet = self._createSetOfCoordinates(tSet, suffix='Tilted')
readSetOfCoordinates(extradir, tSet, tCoordSet)
tCoordSet.write()
# Read Angles from faked input micrographs
micsFn = self._getExtraPath('input_micrographs.xmd')
setAngles = self._createSetOfAngles()
readAnglesFromMicrographs(micsFn, setAngles)
setAngles.write()
# Create CoordinatesTiltPair object
outputset = CoordinatesTiltPair(filename=self._getPath('coordinates_pairs.sqlite'))
outputset.setTilted(tCoordSet)
outputset.setUntilted(uCoordSet)
outputset.setAngles(setAngles)
outputset.setMicsPair(inputset)
outputset.setObjComment(self.getSummary(outputset))
for coordU, coordT in izip(uCoordSet, tCoordSet):
outputset.append(TiltPair(coordU, coordT))
self._defineOutputs(outputCoordinatesTiltPair=outputset)
self._defineSourceRelation(inputset, outputset)
#--------------------------- INFO functions --------------------------------------------
def _citations(self):
return []
#--------------------------- UTILS functions -------------------------------------------
def __str__(self):
""" String representation of a Particle Picking Tilt run """
if not hasattr(self, 'outputCoordinatesTiltPair'):
msg = "No particles picked yet."
else:
picked = self.outputCoordinatesTiltPair.getTilted().getSize()
msg = "Number of particles picked: %d (from %d micrographs)" % (picked, self.inputMicrographsTiltedPair.get().getTilted().getSize())
return msg
def getMethods(self, output):#output is not used but to overwrite getMethods it is used
msg = ""
configfile = join(self._getExtraPath(), 'config.xmd')
existsConfig = exists(configfile)
if existsConfig:
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
particleSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, configobj)
manualParticlesSize = md.getValue(xmipp.MDL_PICKING_MANUALPARTICLES_SIZE, configobj)
msg = 'User picked %d particles with a particle size of %d.' % (manualParticlesSize, particleSize)
return msg
def _summary(self):
if self.getOutputsSize() > 0:
return ProtParticlePicking._summary(self)
else:
return [self.getSummary(None)]
def _methods(self):
if self.getOutputsSize() > 0:
return ProtParticlePicking._methods(self)
else:
return [self.getMethods(None)]
def getInputMicrographs(self):
return self.inputMicrographsTiltedPair.get().getTilted()
def getCoords(self):
count = self.getOutputsSize()
suffix = str(count) if count > 1 else ''
outputName = 'outputCoordinatesTiltPair' + suffix
return getattr(self, outputName)
def getSummary(self, coordsSet):
summary = []
configfile = join(self._getExtraPath(), 'config.xmd')
if exists(configfile):
md = xmipp.MetaData('properties@' + configfile)
configobj = md.firstObject()
activemic = md.getValue(xmipp.MDL_MICROGRAPH, configobj)
manualParticlesSize = md.getValue(xmipp.MDL_PICKING_MANUALPARTICLES_SIZE, configobj)
particleSize = md.getValue(xmipp.MDL_PICKING_PARTICLE_SIZE, configobj)
summary.append("Particles picked: %d"%manualParticlesSize)
summary.append("Particle size: %d"%particleSize)
summary.append("Last micrograph: " + activemic)
return "\n".join(summary)
def registerCoords(self, args):
from pyworkflow.em.packages.xmipp3 import readSetOfCoordinates, readAnglesFromMicrographs
extradir = self._getExtraPath()
count = self.getOutputsSize()
suffix = str(count + 1) if count > 0 else ''
inputset = self.inputMicrographsTiltedPair.get()
uSet = inputset.getUntilted()
tSet = inputset.getTilted()
outputName = 'outputCoordinatesTiltPair' + suffix
uSuffix = 'Untilted' + suffix
tSuffix = 'Tilted' + suffix
# Create Untilted and Tilted SetOfCoordinates
uCoordSet = self._createSetOfCoordinates(uSet, suffix=uSuffix)
readSetOfCoordinates(extradir, uSet, uCoordSet)
uCoordSet.write()
tCoordSet = self._createSetOfCoordinates(tSet, suffix=tSuffix)
readSetOfCoordinates(extradir, tSet, tCoordSet)
tCoordSet.write()
# Read Angles from input micrographs
micsFn = self._getPath('input_micrographs.xmd')
setAngles = self._createSetOfAngles(suffix=suffix)
readAnglesFromMicrographs(micsFn, setAngles)
setAngles.write()
# Create CoordinatesTiltPair object
outputset = CoordinatesTiltPair(filename=self._getPath('coordinates_pairs%s.sqlite' % suffix))
outputset.setTilted(tCoordSet)
outputset.setUntilted(uCoordSet)
outputset.setAngles(setAngles)
outputset.setMicsPair(inputset)
for coordU, coordT in izip(uCoordSet, tCoordSet):
outputset.append(TiltPair(coordU, coordT))
summary = self.getSummary(outputset)
outputset.setObjComment(summary)
outputs = {outputName: outputset}
self._defineOutputs(**outputs)
self._defineSourceRelation(inputset, outputset)
self._store()
