def _fillVolSetFromIter(self, volSet, rLev=None, it=None):
it = self._lastIter() if it is None else it
rLev = self._rLev if rLev is None else rLev
volSet.setSamplingRate(self._getInputParticles().getSamplingRate())
modelFn = self._getFileName('model', ruNum=rLev, iter=it)
print('modelFn: ', modelFn)
modelStar = md.MetaData('model_classes@' + modelFn)
idList = []
volFnList = []
clsDistList = []
accRotList = []
accTransList = []
resoList = []
for row in md.iterRows(modelStar):
accurracyRot = row.getValue('rlnAccuracyRotations')
if accurracyRot <= 90:
fn = row.getValue('rlnReferenceImage')
print('Volume: ', fn)
fnMrc = fn + ":mrc"
itemId = self._getClassId(fn)
classDistrib = row.getValue('rlnClassDistribution')
accurracyTras = row.getValue('rlnAccuracyTranslations')
resol = row.getValue('rlnEstimatedResolution')
idList.append(itemId)
volFnList.append(fnMrc)
clsDistList.append(classDistrib)
accRotList.append(accurracyRot)
accTransList.append(accurracyTras)
resoList.append(resol)
std = self.std if hasattr(self, 'std') else None
score = self._estimateScore(accRotList, clsDistList, None, std)
threshold = 1 / float(self.numOfVols.get())
print("score: ", score)
for i, s in enumerate(score):
vol = Volume()
self._invertScaleVol(volFnList[i])
vol.setFileName(self._getOutputVolFn(volFnList[i]))
vol.setObjId(idList[i])
if s <= threshold:
vol._objEnabled = False
vol._cmScore = pwObj.Float(s)
vol._rlnClassDistribution = Float(clsDistList[i])
vol._rlnAccuracyRotations = Float(accRotList[i])
vol._rlnAccuracyTranslations = Float(accTransList[i])
vol._rlnEstimatedResolution = Float(resoList[i])
volSet.append(vol)
def _fillVolSetFromIter(self, volSet, it):
volSet.setSamplingRate(self._getInputParticles().getSamplingRate())
modelStar = md.MetaData('model_classes@' +
self._getFileName('model', iter=it))
for row in md.iterRows(modelStar):
fn = row.getValue('rlnReferenceImage')
fnMrc = fn + ":mrc"
itemId = self._getClassId(fn)
classDistrib = row.getValue('rlnClassDistribution')
accurracyRot = row.getValue('rlnAccuracyRotations')
accurracyTras = row.getValue('rlnAccuracyTranslations')
resol = row.getValue('rlnEstimatedResolution')
if classDistrib > 0:
vol = Volume()
self._invertScaleVol(fnMrc)
vol.setFileName(self._getOutputVolFn(fnMrc))
vol.setObjId(itemId)
vol._rlnClassDistribution = Float(classDistrib)
vol._rlnAccuracyRotations = Float(accurracyRot)
vol._rlnAccuracyTranslations = Float(accurracyTras)
vol._rlnEstimatedResolution = Float(resol)
volSet.append(vol)
def convertInputStep(self, classesFn):
inputSet = self.inputSet.get()
if isinstance(inputSet, SetOfClasses2D):
writeSetOfClasses2D(inputSet, classesFn, writeParticles=False)
else:
writeSetOfParticles(inputSet, classesFn)
# To re-sample input images
fnDir = self._getExtraPath()
fnNewParticles = join(fnDir, "input_classes.stk")
TsOrig = self.inputSet.get().getSamplingRate()
TsRefVol = -1
if self.thereisRefVolume:
TsRefVol = self.refVolume.get().getSamplingRate()
if self.useMaxRes:
self.TsCurrent = max([TsOrig, self.maxResolution.get(), TsRefVol])
self.TsCurrent = self.TsCurrent / 3
Xdim = self.inputSet.get().getDimensions()[0]
self.newXdim = int(round(Xdim * TsOrig / self.TsCurrent))
if self.newXdim < 40:
self.newXdim = int(40)
self.TsCurrent = float(TsOrig) * (float(Xdim) /
float(self.newXdim))
if self.newXdim != Xdim:
self.runJob("xmipp_image_resize",
"-i %s -o %s --fourier %d" %
(self.imgsFn, fnNewParticles, self.newXdim),
numberOfMpi=self.numberOfMpi.get() *
self.numberOfThreads.get())
else:
self.runJob("xmipp_image_convert",
"-i %s -o %s "
"--save_metadata_stack %s" %
(self.imgsFn, fnNewParticles,
join(fnDir, "input_classes.xmd")),
numberOfMpi=1)
# To resample the refVolume if exists with the newXdim calculated
# previously
if self.thereisRefVolume:
fnFilVol = self._getExtraPath('filteredVolume.vol')
self.runJob("xmipp_image_convert",
"-i %s -o %s -t vol" %
(self.refVolume.get().getFileName(), fnFilVol),
numberOfMpi=1)
# TsVol = self.refVolume.get().getSamplingRate()
if self.useMaxRes:
if self.newXdim != Xdim:
self.runJob('xmipp_image_resize',
"-i %s --fourier %d" %
(fnFilVol, self.newXdim),
numberOfMpi=1)
self.runJob('xmipp_transform_window',
"-i %s --size %d" % (fnFilVol, self.newXdim),
numberOfMpi=1)
args = "-i %s --fourier low_pass %f --sampling %f " % (
fnFilVol, self.maxResolution.get(), self.TsCurrent)
self.runJob("xmipp_transform_filter", args, numberOfMpi=1)
if not self.useMaxRes:
inputVolume = self.refVolume.get()
else:
inputVolume = Volume(fnFilVol)
inputVolume.setSamplingRate(self.TsCurrent)
inputVolume.setObjId(self.refVolume.get().getObjId())
fnVolumes = self._getExtraPath('input_volumes.xmd')
row = metadata.Row()
volumeToRow(inputVolume, row, alignType=ALIGN_NONE)
md = emlib.MetaData()
row.writeToMd(md, md.addObject())
md.write(fnVolumes)
