def _loadInput(self):
partsFile = self.inputParticles.get().getFileName()
inPartsSet = SetOfParticles(filename=partsFile)
inPartsSet.loadAllProperties()
if self.check == None:
writeSetOfParticles(inPartsSet,
self.fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation')
else:
writeSetOfParticles(inPartsSet,
self.fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation',
where='creation>"' + str(self.check) + '"')
writeSetOfParticles(inPartsSet,
self.fnInputOldMd,
alignType=em.ALIGN_NONE,
orderBy='creation',
where='creation<"' + str(self.check) + '"')
for p in inPartsSet.iterItems(orderBy='creation', direction='DESC'):
self.check = p.getObjCreation()
break
streamClosed = inPartsSet.isStreamClosed()
inputSize = inPartsSet.getSize()
inPartsSet.close()
return inputSize, streamClosed
class XmippProtEliminateEmptyParticles(XmippProtEliminateEmptyBase):
""" Takes a set of particles and using statistical methods
(variance of variances of sub-parts of input image) eliminates those samples,
where there is no object/particle (only noise is presented there).
Threshold parameter can be used for fine-tuning the algorithm for type of data.
"""
_label = 'eliminate empty particles'
def __init__(self, **args):
XmippProtEliminateEmptyBase.__init__(self, **args)
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label=Message.LABEL_INPUT)
# - - - F O R P A R T I C L E S - - -
form.addParam('inputParticles',
param.PointerParam,
important=True,
label="Input particles",
pointerClass='SetOfParticles',
help='Select the input particles to be classified.')
form.addParam('threshold',
param.FloatParam,
default=1.1,
label='Threshold used in elimination:',
help='Higher threshold => more particles will be '
'eliminated. Set to -1 for no elimination, even so '
'the "xmipp_scoreEmptiness" value will be attached to '
'every paricle for a posterior inspection.')
self.addAdvancedParams(form)
# --------------------------- INSERT steps functions ----------------------
def _checkNewInput(self):
# Check if there are new particles to process from the input set
partsFile = self.inputParticles.get().getFileName()
self.lastCheck = getattr(self, 'lastCheck', datetime.now())
mTime = datetime.fromtimestamp(os.path.getmtime(partsFile))
# If the input movies.sqlite have not changed since our last check,
# it does not make sense to check for new input data
if self.lastCheck > mTime:
return None
self.lastCheck = datetime.now()
outputStep = self._getFirstJoinStep()
fDeps = self._insertNewPartsSteps()
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
def eliminationStep(self, fnInputMd):
self.inputImages = self.inputParticles.get()
partsFile = self.inputImages.getFileName()
self.partsSet = SetOfParticles(filename=partsFile)
self.partsSet.loadAllProperties()
self.streamClosed = self.partsSet.isStreamClosed()
if self.check == None:
writeSetOfParticles(self.partsSet,
fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation')
else:
writeSetOfParticles(self.partsSet,
fnInputMd,
alignType=em.ALIGN_NONE,
orderBy='creation',
where='creation>"' + str(self.check) + '"')
for p in self.partsSet.iterItems(orderBy='creation', direction='DESC'):
self.check = p.getObjCreation()
break
self.partsSet.close()
self.lenPartsSet = len(self.partsSet)
print("os.path.exists(fnInputMd)): %s" % os.path.exists(fnInputMd))
args = "-i %s -o %s -e %s -t %f" % (
fnInputMd, self.fnOutputMd, self.fnElimMd, self.threshold.get())
if self.addFeatures:
args += " --addFeatures"
if self.useDenoising:
args += " --useDenoising -d %f" % self.denoising.get()
self.runJob("xmipp_image_eliminate_empty_particles", args)
cleanPath(fnInputMd)
def createOutputs(self):
streamMode = Set.STREAM_CLOSED if getattr(self, 'finished', False) \
else Set.STREAM_OPEN
def updateOutputs(mdFn, suffix):
newData = os.path.exists(mdFn)
lastToClose = getattr(self, 'finished', False) and \
hasattr(self, '%sParticles'%suffix)
if newData or lastToClose:
outSet = self._loadOutputSet(em.SetOfParticles,
'%sParticles.sqlite' % suffix)
if newData:
partsSet = self._createSetOfParticles("AUX")
readSetOfParticles(mdFn, partsSet)
outSet.copyItems(partsSet,
updateItemCallback=self._updateParticle,
itemDataIterator=md.iterRows(
mdFn, sortByLabel=md.MDL_ITEM_ID))
self.outputSize = self.outputSize + len(partsSet)
self._updateOutputSet('%sParticles' % suffix, outSet,
streamMode)
cleanPath(mdFn)
updateOutputs(self.fnOutMdTmp, 'output')
updateOutputs(self.fnElimMdTmp, 'eliminated')
def getInput(self):
return self.inputParticles.get()
