def _setPlotInfo(self, movie, mic):
mic.plotGlobal = Image(location=self._getPlotGlobal(movie))
if self.doComputePSD:
mic.psdCorr = Image(location=self._getPsdCorr(movie))
mic.psdJpeg = Image(location=self._getPsdJpeg(movie))
if self.doComputeMicThumbnail:
mic.thumbnail = Image(location=self._getOutputMicThumbnail(movie))
def _setPlotInfo(self, movie, mic):
mic.plotGlobal = Image(location=self._getPlotGlobal(movie))
if self.doComputePSD:
mic.psdCorr = Image(location=self._getPsdCorr(movie))
if self._doComputeMicThumbnail():
mic.thumbnail = Image(location=self._getOutputMicThumbnail(movie))
if self.doApplyDoseFilter:
total, early, late = self.calcFrameMotion(movie)
mic._rlnAccumMotionTotal = Float(total)
mic._rlnAccumMotionEarly = Float(early)
mic._rlnAccumMotionLate = Float(late)
def testWriteValidate(self):
img = Image()
for counter in range(self.nframes.get(), 0, -1):
img.read("%d@%s" %
(counter, os.path.join(self._getExtraPath(), "kk.mrcs")))
mean, dev, min, max = img.computeStats()
if (min == max) and (min == counter) and (dev == 0):
print("frame %d ok" % counter)
else:
print("frame %d no OK mean dev, min max" % counter, mean, dev,
min, max)
break
def _postprocessImageRow(self, img, imgRow):
self.imgCount += 1
img.spectraPlot = Image()
img.spectraPlot.setFileName(self._createSpectraPlot('image',
self.imgArray,
self.imgCount,
img.getObjId()))
def _preprocessClass(self, classItem, classRow):
KendersomBaseClassify._preprocessClass(self, classItem, classRow)
ref = classRow.getValue(emlib.MDL_REF) # get class number
classItem.spectraPlot = Image()
classItem.spectraPlot.setFileName(self._createSpectraPlot('class',
self.classArray,
ref))
def _preprocessOutputMicrograph(self, mic, movie):
self._setPlotInfo(movie, mic)
self._setMotionValues(movie, mic)
if self._savePsSum():
outPs = self._getExtraPath(self._getOutputMicPsName(movie))
mic._powerSpectra = Image(location=outPs)
mic._powerSpectra.setSamplingRate(self._calcPSSampling())
def updateGainsOutput(self, movie, imgSet, imageFile):
movieId = movie.getObjId()
imgOut = Image()
imgOut.setObjId(movieId)
imgOut.setSamplingRate(movie.getSamplingRate())
imgOut.setFileName(imageFile)
imgSet.setSamplingRate(movie.getSamplingRate())
imgSet.append(imgOut)
return imgSet
def _setAlignmentInfo(self, movie, obj):
""" Set alignment info such as plot and psd filename, and
the cumulative shifts values.
Params:
movie: Pass the reference movie
obj: should pass either the created micrograph or movie
"""
obj.plotCart = Image()
obj.plotCart.setFileName(self._getPlotCart(movie))
if self.doComputePSD:
obj.psdCorr = Image()
obj.psdCorr.setFileName(self._getPsdCorr(movie))
meanX, meanY = self._loadMeanShifts(movie)
obj._xmipp_OFMeanX = pwobj.CsvList()
obj._xmipp_OFMeanX.set(meanX)
obj._xmipp_OFMeanY = pwobj.CsvList()
obj._xmipp_OFMeanY.set(meanY)
def _updateClass(self, item):
classId = item.getObjId()
classRow = findRow(self.mdClasses, emlib.MDL_REF2, classId)
representative = item.getRepresentative()
representative.setTransform(rowToAlignment(classRow, ALIGN_PROJ))
representative.setLocation(
xmippToLocation(classRow.getValue(emlib.MDL_IMAGE)))
setXmippAttributes(representative, classRow, emlib.MDL_ANGLE_ROT)
setXmippAttributes(representative, classRow, emlib.MDL_ANGLE_TILT)
setXmippAttributes(representative, classRow, emlib.MDL_CLASS_COUNT)
self.averageSet.append(representative)
reprojection = Image()
reprojection.setLocation(
xmippToLocation(classRow.getValue(emlib.MDL_IMAGE1)))
item.reprojection = reprojection
def __setXmippImage(label):
attr = '_xmipp_' + emlib.label2Str(label)
if not hasattr(particle, attr):
img = Image()
setattr(particle, attr, img)
img.setSamplingRate(particle.getSamplingRate())
else:
img = getattr(particle, attr)
img.setLocation(xmippToLocation(row.getValue(label)))
def _preprocessOutputMicrograph(self, mic, movie):
mic.plotGlobal = Image(location=self._getPlotGlobal(movie))
if self.doComputePSD:
mic.psdCorr = Image(location=self._getPsdCorr(movie))
if self._doComputeMicThumbnail():
mic.thumbnail = Image(location=self._getOutputMicThumbnail(movie))
def createReferenceStep(self):
img = Image()
img.setDataType(DT_FLOAT)
img.resize(self.xDim.get(), self.yDim.get())
img.initConstant(1.)
img.write(self._getExtraPath("reference.mrc"))
img.write('%d@%s' % (self.nframes, self._getExtraPath('kk.mrcs')))