def registerCoords(self, coordsDir):
count = self.getOutputsSize()
suffix = str(count + 1) if count > 0 else ""
outputName = "outputCoordinates" + suffix
from pyworkflow.em.packages.xmipp3 import readSetOfCoordinates
inputset = self.getInputMicrographs()
outputset = self._createSetOfCoordinates(
inputset, suffix=suffix
) # micrographs are the input set if protocol is not finished
readSetOfCoordinates(coordsDir, outputset.getMicrographs(), outputset)
summary = self.getSummary(outputset)
outputset.setObjComment(summary)
outputs = {outputName: outputset}
self._defineOutputs(**outputs)
self._defineSourceRelation(self.inputMicrographs, outputset)
self._store()
def registerCoords(self, coordsDir):
""" This methods is usually inherited from all Pickers
and it is used from the Java picking GUI to register
a new SetOfCoordinates when the user click on +Particles button.
"""
suffix = self.__getOutputSuffix()
outputName = self.OUTPUT_PREFIX + suffix
from pyworkflow.em.packages.xmipp3 import readSetOfCoordinates
inputset = self.getInputMicrographs()
outputset = self._createSetOfCoordinates(inputset, suffix=suffix)#micrographs are the input set if protocol is not finished
readSetOfCoordinates(coordsDir, outputset.getMicrographs(), outputset)
summary = self.getSummary(outputset)
outputset.setObjComment(summary)
outputs = {outputName: outputset}
self._defineOutputs(**outputs)
self._defineSourceRelation(self.inputMicrographs, outputset)
self._store()
def registerCoords(self, coordsDir):
""" This methods is usually inherited from all Pickers
and it is used from the Java picking GUI to register
a new SetOfCoordinates when the user click on +Particles button.
"""
suffix = self.__getOutputSuffix()
outputName = self.OUTPUT_PREFIX + suffix
from pyworkflow.em.packages.xmipp3 import readSetOfCoordinates
inputset = self.getInputMicrographs()
# micrographs are the input set if protocol is not finished
outputset = self._createSetOfCoordinates(inputset, suffix=suffix)
readSetOfCoordinates(coordsDir, outputset.getMicrographs(), outputset)
summary = self.getSummary(outputset)
outputset.setObjComment(summary)
outputs = {outputName: outputset}
self._defineOutputs(**outputs)
self._defineSourceRelation(self.inputMicrographs, outputset)
self._store()
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()
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)
def registerCoords(self, coordsDir):
""" This method is usually inherited by all Pickers
and it is used from the Java picking GUI to register
a new SetOfCoordinates when the user click on +Particles button.
"""
suffix = self.__getOutputSuffix()
outputName = self.OUTPUT_PREFIX + suffix
from pyworkflow.em.packages.xmipp3 import readSetOfCoordinates
inputset = self.getInputMicrographs()
# micrographs are the input set if protocol is not finished
outputset = self._createSetOfCoordinates(inputset, suffix=suffix)
readSetOfCoordinates(coordsDir, outputset.getMicrographs(), outputset)
summary = self.getSummary(outputset)
outputset.setObjComment(summary)
outputs = {outputName: outputset}
self._defineOutputs(**outputs)
# Using a pointer to define the relations is more robust to scheduling
# and id changes between the protocol run.db and the main project
# database. The pointer defined below points to the outputset object
self._defineSourceRelation(self.getInputMicrographsPointer(),
Pointer(value=self, extended=outputName))
self._store()
def registerCoords(self, coordsDir):
""" This method is usually inherited by all Pickers
and it is used from the Java picking GUI to register
a new SetOfCoordinates when the user click on +Particles button.
"""
suffix = self.__getOutputSuffix()
outputName = self.OUTPUT_PREFIX + suffix
from pyworkflow.em.packages.xmipp3 import readSetOfCoordinates
inputset = self.getInputMicrographs()
# micrographs are the input set if protocol is not finished
outputset = self._createSetOfCoordinates(inputset, suffix=suffix)
readSetOfCoordinates(coordsDir, outputset.getMicrographs(), outputset)
summary = self.getSummary(outputset)
outputset.setObjComment(summary)
outputs = {outputName: outputset}
self._defineOutputs(**outputs)
# Using a pointer to define the relations is more robust to scheduling
# and id changes between the protocol run.db and the main project
# database. The pointer defined below points to the outputset object
self._defineSourceRelation(self.getInputMicrographsPointer(),
Pointer(value=self, extended=outputName))
self._store()
