def _loadInputCoords(self, micDict):
""" Load coordinates from the input streaming.
"""
coordsFn = self.getCoords().getFileName()
self.debug("Loading input db: %s" % coordsFn)
coordSet = SetOfCoordinates(filename=coordsFn)
# FIXME: Temporary to avoid loadAllPropertiesFail
coordSet._xmippMd = String()
coordSet.loadAllProperties()
for micKey, mic in micDict.iteritems():
micId = mic.getObjId()
coordList = []
self.debug("Loading coords for mic: %s (%s)" % (micId, micKey))
for coord in coordSet.iterItems(where='_micId=%s' % micId):
# TODO: Check performance penalty of using this clone
coordList.append(coord.clone())
self.debug(" Coords found: %s" % len(coordList))
if coordList:
self.coordDict[micId] = coordList
else:
del micDict[micKey]
self.coordsClosed = coordSet.isStreamClosed()
coordSet.close()
self.debug("Coords are closed? %s" % self.coordsClosed)
self.debug("Closed db.")
return micDict
def _loadInputCoords(self, micDict):
""" Load coordinates from the input streaming.
"""
coordsFn = self.getCoords().getFileName()
self.debug("Loading input db: %s" % coordsFn)
coordSet = SetOfCoordinates(filename=coordsFn)
# FIXME: Temporary to avoid loadAllPropertiesFail
coordSet._xmippMd = String()
coordSet.loadAllProperties()
for micKey, mic in micDict.iteritems():
micId = mic.getObjId()
coordList = []
self.debug("Loading coords for mic: %s (%s)" % (micId, micKey))
for coord in coordSet.iterItems(where='_micId=%s' % micId):
# TODO: Check performance penalty of using this clone
coordList.append(coord.clone())
self.debug(" Coords found: %s" % len(coordList))
if coordList:
self.coordDict[micId] = coordList
else:
del micDict[micKey]
self.coordsClosed = coordSet.isStreamClosed()
coordSet.close()
self.debug("Coords are closed? %s" % self.coordsClosed)
self.debug("Closed db.")
return micDict
def _checkNewInput(self):
newMics = []
for idx, coordSet in enumerate(self.inputCoordinates):
coorSet = SetOfCoordinates(filename=coordSet.get().getFileName())
coorSet._xmippMd = String()
coorSet.loadAllProperties()
self.streamClosed = coorSet.isStreamClosed()
coorSet.close()
if self.check[idx] == "":
newMics.append(
[c.clone() for c in coordSet.get().getMicrographs()])
else:
newMics.append([
c.clone()
for c in coordSet.get().getMicrographs().iterItems(
orderBy='creation',
where='creation>"' + str(self.check[idx]) + '"')
])
if len(newMics[idx]) < 1:
continue
else:
for p in coordSet.get().getMicrographs().iterItems(
orderBy='creation', direction='DESC'):
self.check[idx] = p.getObjCreation()
break
newMics[:] = [item for item in newMics if len(item) > 0]
if len(newMics) > 0:
fDeps = self.insertNewCoorsSteps(min(newMics, key=len))
self.inputMics = self.inputMics + len(min(newMics, key=len))
outputStep = self._getFirstJoinStep()
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
def _loadInputCoords(self, micDict):
""" Load coordinates from the input streaming.
"""
# TODO: this takes for ever if you are NOT
# doing streaming and have several thousands of mics
# so I add a counter to keep the user entertained
import sys
a = datetime.now()
counter = 1
coordsFn = self.getCoords().getFileName()
self.debug("Loading input db: %s" % coordsFn)
coordSet = SetOfCoordinates(filename=coordsFn)
# FIXME: Temporary to avoid loadAllPropertiesFail
coordSet._xmippMd = String()
coordSet.loadAllProperties()
# TODO: horrible code. Rewrite using
# for coord in coordSet.iterItems(orderBy='_micId',
# direction='ASC'):
# micId = coord.getMicId()
# if micId != lastMicId:
# lastMicId = micId
# ...
# ...
for micKey, mic in micDict.iteritems():
if counter % 50 == 0:
b = datetime.now()
print(b - a, 'reading coordinates for mic number',
"%06d" % counter)
sys.stdout.flush() # force buffer to print
counter += 1
micId = mic.getObjId()
coordList = []
self.debug("Loading coords for mic: %s (%s)" % (micId, micKey))
for coord in coordSet.iterItems(where='_micId=%s' % micId):
# TODO: Check performance penalty of using this clone
coordList.append(coord.clone())
self.debug("Coords found: %s" % len(coordList))
if coordList:
self.coordDict[micId] = coordList
else:
del micDict[micKey]
self.coordsClosed = coordSet.isStreamClosed()
coordSet.close()
self.debug("Coords are closed? %s" % self.coordsClosed)
self.debug("Closed db.")
return micDict