def _checkNewOutput(self):
if getattr(self, 'finished', False):
return
self.finished = self.streamClosed and self.checkedMics == self.processedMics
streamMode = Set.STREAM_CLOSED if self.finished else Set.STREAM_OPEN
newFiles = getFiles(self._getTmpPath())
if newFiles or self.finished: # when finished to close the output set
outSet = self._loadOutputSet(SetOfCoordinates,
'coordinates.sqlite')
for fnTmp in newFiles:
coords = np.loadtxt(fnTmp)
moveFile(fnTmp, self._getExtraPath())
if coords.size == 2: # special case with only one coordinate
coords = [coords]
for coord in coords:
newCoord = Coordinate()
micrographs = self.getMainInput().getMicrographs()
newCoord.setMicrograph(micrographs[self.getMicId(fnTmp)])
newCoord.setPosition(coord[0], coord[1])
outSet.append(newCoord)
firstTime = not self.hasAttribute(self.outputName)
self._updateOutputSet(self.outputName, outSet, streamMode)
if firstTime:
self.defineRelations(outSet)
outSet.close()
if self.finished: # Unlock createOutputStep if finished all jobs
outputStep = self._getFirstJoinStep()
if outputStep and outputStep.isWaiting():
outputStep.setStatus(STATUS_NEW)
def _checkNewInput(self):
# If continue from an stopped run, don't repeat what is done
if not self.checkedMics:
for fn in getFiles(self._getExtraPath()):
fn = removeBaseExt(fn)
if fn.startswith(self.FN_PREFIX):
self.checkedMics.update([self.getMicId(fn)])
self.processedMics.update([self.getMicId(fn)])
readyMics, self.streamClosed = getReadyMics(
self.inputCoordinates.get())
newMicsIds = readyMics.difference(self.checkedMics)
if newMicsIds:
self.checkedMics.update(newMicsIds)
inMics = self.getMainInput().getMicrographs()
newMics = [inMics[micId].clone() for micId in newMicsIds]
fDeps = self.insertNewCoorsSteps(newMics)
outputStep = self._getFirstJoinStep()
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
def _importFromFolderStep(self):
""" This function will copy Xmipp .pos files for
simulating a particle picking run...this is only
for testing purposes.
"""
extraDir = self._getExtraPath()
for f in pwutils.getFiles(self.importFolder.get()):
pwutils.copyFile(f, extraDir)
self.registerCoords(extraDir, readFromExtra=True)
def _importFromFolderStep(self):
""" This function will copy Xmipp .pos files for
simulating a particle picking run...this is only
for testing purposes.
"""
extraDir = self._getExtraPath()
for f in pwutils.getFiles(self.importFolder.get()):
pwutils.copyFile(f, extraDir)
self.registerCoords(extraDir, readFromExtra=True)
def _checkNewInput(self):
# If continue from an stopped run, don't repeat what is done
if not self.checkedMics:
for fn in getFiles(self._getExtraPath()):
fn = removeBaseExt(fn)
if fn.startswith(self.FN_PREFIX):
self.checkedMics.update([self.getMicId(fn)])
self.processedMics.update([self.getMicId(fn)])
streamClosed = []
readyMics = None
allMics = set()
for coordSet in self.inputCoordinates:
currentPickMics, isSetClosed = getReadyMics(coordSet.get())
streamClosed.append(isSetClosed)
if not readyMics: # first time
readyMics = currentPickMics
else: # available mics are those ready for all pickers
readyMics.intersection_update(currentPickMics)
allMics = allMics.union(currentPickMics)
self.streamClosed = all(streamClosed)
if self.streamClosed:
# for non streaming do all and in the last iteration of streaming do the rest
newMicIds = allMics.difference(self.checkedMics)
else: # for streaming processing, only go for the ready mics in all pickers
newMicIds = readyMics.difference(self.checkedMics)
if newMicIds:
self.checkedMics.update(newMicIds)
inMics = self.getMainInput().getMicrographs()
newMics = [inMics[micId].clone() for micId in newMicIds]
fDeps = self.insertNewCoorsSteps(newMics)
outputStep = self._getFirstJoinStep()
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()