def _processMovie(self, movie):
movieFolder = self._getOutputMovieFolder(movie)
x, y, n = movie.getDim()
s0, sN = self._getFrameRange(n, 'sum')
inputMd = os.path.join(movieFolder, 'input_movie.xmd')
writeMovieMd(movie, inputMd, s0, sN,
useAlignment=(movie.hasAlignment() and self.useAlignment))
outputMicFn = self._getExtraPath(self._getOutputMicName(movie))
if self.cropRegion == CROP_ALIGNMENT and movie.hasAlignment():
roi = movie.getAlignment().getRoi()
elif self.cropRegion == CROP_NEW:
roi = [self.cropOffsetX.get(), self.cropOffsetY.get(),
self.cropDimX.get(), self.cropDimY.get()]
else:
roi = None
self.averageMovie(movie, inputMd, outputMicFn, self.binFactor.get(),
roi, self.inputMovies.get().getDark(),
self.inputMovies.get().getGain(),
splineOrder=self.INTERP_MAP[self.splineOrder.get()])
self._storeSummary(movie)
def _processMovie(self, movie):
movieFolder = self._getOutputMovieFolder(movie)
x, y, n = movie.getDim()
s0, sN = self._getFrameRange(n, 'sum')
inputMd = os.path.join(movieFolder, 'input_movie.xmd')
writeMovieMd(movie,
inputMd,
s0,
sN,
useAlignment=(movie.hasAlignment() and self.useAlignment))
outputMicFn = self._getExtraPath(self._getOutputMicName(movie))
if self.cropRegion == CROP_ALIGNMENT and movie.hasAlignment():
roi = movie.getAlignment().getRoi()
elif self.cropRegion == CROP_NEW:
roi = [
self.cropOffsetX.get(),
self.cropOffsetY.get(),
self.cropDimX.get(),
self.cropDimY.get()
]
else:
roi = None
gainFn = self.inputMovies.get().getGain()
ext = pwutils.getExt(
self.inputMovies.get().getFirstItem().getFileName()).lower()
if self.inputMovies.get().getGain() and ext in ['.tif', '.tiff']:
self.flipY = True
inGainFn = self.inputMovies.get().getGain()
gainFn = xmutils.flipYImage(inGainFn, outDir=self._getExtraPath())
self.averageMovie(
movie,
inputMd,
outputMicFn,
self.binFactor.get(),
roi,
self.inputMovies.get().getDark(),
gainFn,
splineOrder=self.INTERP_MAP[self.splineOrder.get()],
outxmd="\"\"") # we're not interested in the metadata
self._storeSummary(movie)
def _processMovie(self, movie):
inputMovies = self.inputMovies.get()
if self.doApplyDoseFilter:
outMicFn = self._getExtraPath(self._getOutputMicWtName(movie))
else:
outMicFn = self._getExtraPath(self._getOutputMicName(movie))
outMovieFn = self._getExtraPath(self._getOutputMovieName(movie))
aveMic = self._getFnInMovieFolder(movie, "uncorrected_mic.mrc")
dark = inputMovies.getDark()
gain = inputMovies.getGain()
# Get the number of frames and the range
# to be used for alignment and sum
x, y, n = movie.getDim()
a0, aN = self._getFrameRange(n, 'align')
gpuId = self.gpuList.get()
inputMd = self._getFnInMovieFolder(movie, 'input_movie.xmd')
writeMovieMd(movie, inputMd, a0, aN, useAlignment=self.useAlignment)
args = '-i %s ' % inputMd
args += '-o "%s" ' % self._getOutputShifts(movie)
args += ' --frameRange %d %d ' % (0, aN - a0)
if dark:
args += '--dark %s ' % dark
if gain:
args += '--gain %s ' % gain
winSize = self.winSize.get()
doSaveMovie = self.doSaveMovie.get()
groupSize = self.groupSize.get()
args += ' --winSize %(winSize)d --groupSize %(groupSize)d ' % locals()
if self.useGpu:
program = 'xmipp_movie_optical_alignment_gpu'
args += '--gpu %s ' % gpuId
else:
program = 'xmipp_movie_optical_alignment_cpu'
# We should save the movie either if the user selected it (default)
# or if the PSD is going to be computed
if self.doSaveAveMic or self.doComputePSD:
args += '--oavg "%s" ' % outMicFn
if self.doComputePSD:
args += '--oavgInitial %s ' % aveMic
if doSaveMovie:
args += '--outMovie %s ' % outMovieFn
roi = [
self.cropOffsetX.get(),
self.cropOffsetY.get(),
self.cropDimX.get(),
self.cropDimY.get()
]
args += '--cropULCorner %d %d ' % (roi[0], roi[1])
args += '--cropDRCorner %d %d ' % (roi[0] + roi[2] - 1,
roi[1] + roi[3] - 1)
if self.memory:
args += ' --inmemory'
toDelete = []
if self.doApplyDoseFilter:
pxSize = movie.getSamplingRate()
vol = movie.getAcquisition().getVoltage()
preExp, dose = self._getCorrectedDose(inputMovies)
args += ' --doseCorrection %f %f %f %f' % (dose, pxSize, vol,
preExp)
if self.applyDosePreAlign:
args += ' pre'
else:
args += ' post'
if self.doSaveUnweightedMic:
outUnwtMicFn = self._getExtraPath(
self._getOutputMicName(movie))
outUnwtMovieFn = self._getExtraPath(
self._getOutputMovieUnWtName(movie))
args += ' --oUnc %s %s' % (outUnwtMicFn, outUnwtMovieFn)
toDelete.append(outUnwtMovieFn)
try:
self.runJob(program, args)
if self.doSaveAveMic:
if not exists(outMicFn):
raise Exception("Micrograph %s not produced after "
"running %s " % (outMicFn, program))
if self.doSaveMovie:
if not exists(outMovieFn):
raise Exception("Movie %s not produced after running %s " %
(outMovieFn, program))
if self.doComputePSD:
self.computePSDImages(movie,
aveMic,
outMicFn,
outputFnCorrected=outMicFn + 'psd.png')
# If the micrograph was only saved for computing the PSD
# we can remove it
if not self.doSaveAveMic:
pwutils.cleanPath(outMicFn)
for fn in toDelete:
pwutils.cleanPath(fn)
self._saveAlignmentPlots(movie)
except Exception as e:
print("ERROR: %s failed for movie %s.\n Exception: %s" %
(program, movie.getFileName(), e))
def _processMovie(self, movie):
movieFolder = self._getOutputMovieFolder(movie)
x, y, n = movie.getDim()
a0, aN = self._getFrameRange(n, 'align')
s0, sN = self._getFrameRange(n, 'sum')
inputMd = os.path.join(movieFolder, 'input_movie.xmd')
writeMovieMd(movie, inputMd, a0, aN, useAlignment=False)
args = '-i "%s" ' % inputMd
args += '-o "%s" ' % self._getShiftsFile(movie)
args += '--sampling %f ' % movie.getSamplingRate()
args += '--max_freq %f ' % self.maxFreq
args += '--Bspline %d ' % self.INTERP_MAP[self.splineOrder.get()]
if self.binFactor > 1:
args += '--bin %f ' % self.binFactor
# Assume that if you provide one cropDim, you provide all
offsetX = self.cropOffsetX.get()
offsetY = self.cropOffsetY.get()
cropDimX = self.cropDimX.get()
cropDimY = self.cropDimY.get()
args += '--cropULCorner %d %d ' % (offsetX, offsetY)
if cropDimX <= 0:
dimX = x - 1
else:
dimX = offsetX + cropDimX - 1
if cropDimY <= 0:
dimY = y - 1
else:
dimY = offsetY + cropDimY - 1
args += '--cropDRCorner %d %d ' % (dimX, dimY)
if self.outsideMode == self.OUTSIDE_WRAP:
args += "--outside wrap"
elif self.outsideMode == self.OUTSIDE_AVG:
args += "--outside avg"
elif self.outsideMode == self.OUTSIDE_AVG:
args += "--outside value %f" % self.outsideValue
args += ' --frameRange %d %d ' % (0, aN - a0)
args += ' --frameRangeSum %d %d ' % (s0 - a0, sN - a0)
args += ' --max_shift %d ' % self.maxShift
if self.doSaveAveMic or self.doComputePSD:
fnAvg = self._getExtraPath(self._getOutputMicName(movie))
args += ' --oavg "%s"' % fnAvg
if self.doComputePSD:
fnInitial = os.path.join(movieFolder, "initialMic.mrc")
args += ' --oavgInitial %s' % fnInitial
if self.doSaveMovie:
args += ' --oaligned %s' % self._getExtraPath(
self._getOutputMovieName(movie))
if self.inputMovies.get().getDark():
args += ' --dark ' + self.inputMovies.get().getDark()
if self.inputMovies.get().getGain():
args += ' --gain ' + self.inputMovies.get().getGain()
if self.autoControlPoints.get():
self._setControlPoints()
if self.useGpu.get():
args += ' --device %(GPU)s'
if self.doLocalAlignment.get():
args += ' --processLocalShifts '
args += ' --storage ' + self._getExtraPath("fftBenchmark.txt")
args += ' --controlPoints %d %d %d' % (
self.controlPointX, self.controlPointY, self.controlPointT)
args += ' --patches %d %d' % (self.patchX, self.patchY)
args += ' --locCorrDownscale 4 4'
args += ' --patchesAvg %d' % self.groupNFrames
self.runJob('xmipp_cuda_movie_alignment_correlation',
args,
numberOfMpi=1)
else:
self.runJob('xmipp_movie_alignment_correlation',
args,
numberOfMpi=1)
if self.doComputePSD:
self.computePSDs(movie, fnInitial, fnAvg)
# If the micrograph was only saved for computing the PSD
# we can remove it
pwutils.cleanPath(fnInitial)
if not self.doSaveAveMic:
pwutils.cleanPath(fnAvg)
self._saveAlignmentPlots(movie)
def tryProcessMovie(self, movie):
movieFolder = self._getOutputMovieFolder(movie)
x, y, n = movie.getDim()
a0, aN = self._getFrameRange(n, 'align')
s0, sN = self._getFrameRange(n, 'sum')
inputMd = os.path.join(movieFolder, 'input_movie.xmd')
writeMovieMd(movie, inputMd, a0, aN, useAlignment=False)
args = '-i "%s" ' % inputMd
args += ' -o "%s"' % self._getShiftsFile(movie)
args += ' --sampling %f' % movie.getSamplingRate()
args += ' --maxResForCorrelation %f' % self.maxResForCorrelation
args += ' --Bspline %d' % self.INTERP_MAP[self.splineOrder.get()]
if self.binFactor > 1:
args += ' --bin %f' % self.binFactor
args += self.getCropCornerArg(x, y)
args += self.getOutsideModeArg()
args += ' --frameRange %d %d' % (0, aN - a0)
args += ' --frameRangeSum %d %d' % (s0 - a0, sN - a0)
args += ' --max_shift %d' % self.maxShift
if self.doSaveAveMic or self.doComputePSD:
fnAvg = self._getExtraPath(self._getOutputMicName(movie))
args += ' --oavg "%s"' % fnAvg
if self.doComputePSD:
fnInitial = os.path.join(movieFolder, "initialMic.mrc")
args += ' --oavgInitial "%s"' % fnInitial
if self.doSaveMovie:
args += ' --oaligned "%s"' % self._getExtraPath(
self._getOutputMovieName(movie))
if self.inputMovies.get().getDark():
args += ' --dark "%s"' % self.inputMovies.get().getDark()
if self.inputMovies.get().getGain():
ext = pwutils.getExt(
self.inputMovies.get().getFirstItem().getFileName()).lower()
if ext in ['.tif', '.tiff']:
self.flipY = True
inGainFn = self.inputMovies.get().getGain()
gainFn = xmutils.flipYImage(inGainFn,
outDir=self._getExtraPath())
else:
gainFn = self.inputMovies.get().getGain()
if self.gainRot.get() != 0 or self.gainFlip.get() != 0:
gainFn = self.transformGain(gainFn)
args += ' --gain "%s"' % gainFn
if self.autoControlPoints.get():
self._setControlPoints()
if self.minLocalRes.get():
args += ' --minLocalRes %f' % self.minLocalRes
if self.useGpu.get():
args += self.getGPUArgs()
self.runJob('xmipp_cuda_movie_alignment_correlation',
args,
numberOfMpi=1)
else:
self.runJob('xmipp_movie_alignment_correlation',
args,
numberOfMpi=1)
if self.doComputePSD:
self.computePSDImages(movie, fnInitial, fnAvg)
# If the micrograph was only saved for computing the PSD
# we can remove it
pwutils.cleanPath(fnInitial)
if not self.doSaveAveMic:
pwutils.cleanPath(fnAvg)
self._saveAlignmentPlots(movie)