def _preprocessOutputMicrograph(self, mic, movie):
if self.doComputePSD:
mic.psdCorr = em.Image(location=self._getPsdCorr(movie))
mic.psdJpeg = em.Image(location=self._getPsdJpeg(movie))
mic.plotGlobal = em.Image(location=self._getPlotGlobal(movie))
if self._doComputeMicThumbnail():
mic.thumbnail = em.Image(location=self._getOutputMicThumbnail(movie))
def _setPlotInfo(self, movie, mic):
mic.plotGlobal = em.Image(location=self._getPlotGlobal(movie))
if self.doComputePSD:
mic.psdCorr = em.Image(location=self._getPsdCorr(movie))
if self._doComputeMicThumbnail():
mic.thumbnail = em.Image(
location=self._getOutputMicThumbnail(movie))
def _postprocessImageRow(self, img, imgRow):
self.imgCount += 1
img.spectraPlot = em.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(xmipp.MDL_REF) # get class number
classItem.spectraPlot = em.Image()
classItem.spectraPlot.setFileName(self._createSpectraPlot('class',
self.classArray,
ref))
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 = em.Image()
obj.plotCart.setFileName(self._getPlotCart(movie))
if self.doComputePSD:
obj.psdCorr = em.Image()
obj.psdCorr.setFileName(self._getPsdCorr(movie))
meanX, meanY = self._loadMeanShifts(movie)
obj._xmipp_ShiftX = pwobj.CsvList()
obj._xmipp_ShiftX.set(meanX)
obj._xmipp_ShiftY = pwobj.CsvList()
obj._xmipp_ShiftY.set(meanY)
def createOutputStep(self):
inputMovies = self.inputMovies.get()
micSet = self._createSetOfMicrographs()
micSet.copyInfo(inputMovies)
# Also create a Set of Movies with the alignment parameters
if self.doSaveMovie:
movieSet = self._createSetOfMovies()
movieSet.copyInfo(inputMovies)
movieSet.cropOffsetX = Integer(self.cropOffsetX)
movieSet.cropOffsetY = Integer(self.cropOffsetY)
movieSet.cropDimX = Integer(self.cropDimX)
movieSet.cropDimY = Integer(self.cropDimY)
movieSet.sumFrame0 = Integer(self.sumFrame0)
movieSet.sumFrameN = Integer(self.sumFrameN)
alMethod = self.alignMethod.get()
for movie in self.inputMovies.get():
micName = self._getNameExt(movie.getFileName(), '_aligned', 'mrc')
metadataName = self._getNameExt(movie.getFileName(), '_aligned',
'xmd')
plotCartName = self._getNameExt(movie.getFileName(), '_plot_cart',
'png')
psdCorrName = self._getNameExt(movie.getFileName(),
'_aligned_corrected', 'psd')
# Parse the alignment parameters and store the log files
alignedMovie = movie.clone()
if self.run:
alignedMovie.setFileName(
self._getExtraPath(
self._getNameExt(movie.getFileName(), '_aligned',
'mrcs')))
####>>>This is wrong. Save an xmipp metadata
alignedMovie.alignMetaData = String(
self._getExtraPath(metadataName))
alignedMovie.plotCart = self._getExtraPath(plotCartName)
alignedMovie.psdCorr = self._getExtraPath(psdCorrName)
'''if (alMethod == AL_OPTICAL or
alMethod == AL_DOSEFGPUOPTICAL or
alMethod == AL_CROSSCORRELATIONOPTICAL):
movieCreatePlot(alignedMovie, True)'''
if self.doSaveMovie:
movieSet.append(alignedMovie)
mic = em.Micrograph()
# All micrograph are copied to the 'extra' folder after each step
mic.setFileName(self._getExtraPath(micName))
# The micName of a micrograph MUST be the same as the original movie
# mic.setMicName(micName)
mic.setMicName(movie.getMicName())
if (alMethod == AL_OPTICAL or alMethod == AL_DOSEFGPUOPTICAL
or alMethod == AL_CROSSCORRELATIONOPTICAL):
mic.alignMetaData = String(self._getExtraPath(metadataName))
mic.plotCart = self._getExtraPath(plotCartName)
movieCreatePlot(mic, True)
mic.plotCart = em.Image()
mic.plotCart.setFileName(self._getExtraPath(plotCartName))
#if alMethod != AL_DOSEFGPU and alMethod != AL_CROSSCORRELATION:
mic.psdCorr = em.Image()
mic.psdCorr.setFileName(self._getExtraPath(psdCorrName))
micSet.append(mic)
# TODO: Methods for dosefgpu should be transferred to here
"""
if alMethod == AL_DOSEFGPU:
# Parse the alignment parameters and store the log files
alignedMovie = movie.clone()
logFile = self._getExtraPath(self._getLogFile(movie.getObjId()))
import pyworkflow.em.packages.dosefgpu as dosefgpu
alignment = dosefgpu.parseMovieAlignment(logFile)
alignedMovie.setAlignment(alignment)
movieSet.append(alignedMovie)
"""
self._defineOutputs(outputMicrographs=micSet)
self._defineSourceRelation(self.inputMovies, micSet)
if self.doSaveMovie:
self._defineOutputs(outputMovies=movieSet)
"""
