def _validate(self):
errors = ProtAlignMovies._validate(self)
# Although getFirstItem is not recommended in general, here it is
# used only once, for validation purposes, so performance
# problems not should be appear.
if not self.inputMovies.get() is None:
inputSet = self.inputMovies.get()
movie = inputSet.getFirstItem()
if (not movie.hasAlignment()) and self.useAlignment:
errors.append(
"Your movies have no alignment. Please, set *No* "
"the parameter _Use previous movie alignment to SUM"
" frames?_")
if self.doApplyDoseFilter:
doseFrame = inputSet.getAcquisition().getDosePerFrame()
if doseFrame == 0.0 or doseFrame is None:
errors.append(
'Dose per frame for input movies is 0 or not '
'set. You cannot apply dose filter.')
if self.numberOfThreads > 1 and self.useGpu:
errors.append("GPU and Parallelization can not be used together")
return errors
def _validate(self):
errors = ProtAlignMovies._validate(self)
# Although getFirstItem is not recommended in general, here it is
# used only once, for validation purposes, so performance
# problems not should be appear.
if not self.inputMovies.get() is None:
inputSet = self.inputMovies.get()
movie = inputSet.getFirstItem()
if (not movie.hasAlignment()) and self.useAlignment:
errors.append("Your movies have no alignment. Please, set *No* "
"the parameter _Use previous movie alignment to SUM"
" frames?_")
if self.doApplyDoseFilter:
doseFrame = inputSet.getAcquisition().getDosePerFrame()
if doseFrame == 0.0 or doseFrame is None:
errors.append('Dose per frame for input movies is 0 or not '
'set. You cannot apply dose filter.')
if self.numberOfThreads > 1 and self.useGpu:
errors.append("GPU and Parallelization can not be used together")
return errors
def _validate(self):
if self.autoControlPoints.get():
self._setControlPoints() # make sure we work with proper values
errors = ProtAlignMovies._validate(self)
getXmippHome = self.getClassPackage().Plugin.getHome
if self.doLocalAlignment.get():
cudaBinaryFn = getXmippHome(
'bin', 'xmipp_cuda_movie_alignment_correlation')
if not os.path.isfile(cudaBinaryFn):
errors.append('GPU version not found, make sure that Xmipp is '
'compiled with GPU\n'
'( *CUDA=True* in _scipion.conf_ + '
'_run_: $ *scipion installb xmippSrc* ).')
return errors
elif not self.useGpu.get():
errors.append("GPU is needed to do local alignment.")
return errors
if self.numberOfMpi.get() * self.numberOfThreads.get() > 1:
errors.append(
"Multiple threads and/or mpi is incompatible with"
" useGPU.")
else:
cpuBinaryFn = getXmippHome('bin',
'xmipp_movie_alignment_correlation')
if not os.path.isfile(cpuBinaryFn):
errors.append(
'CPU version not found for some reason, try to GPU=True.')
return errors
if (self.controlPointX < 3):
errors.append("You have to use at least 3 control points in X dim")
return errors # to avoid possible division by zero later
if (self.controlPointY < 3):
errors.append("You have to use at least 3 control points in Y dim")
return errors # to avoid possible division by zero later
if (self.controlPointT < 3):
errors.append("You have to use at least 3 control points in T dim")
return errors # to avoid possible division by zero later
_, _, frames = self.inputMovies.get().getDim()
tPointsRatio = frames / (int(self.controlPointT) - 2)
yPointsRatio = int(self.patchY) / (int(self.controlPointY) - 2)
xPointsRatio = int(self.patchX) / (int(self.controlPointX) - 2)
if (tPointsRatio < 2):
errors.append(
"You need at least 2 measurements per control point, "
"i.e. use movie with more frames or decrease number of control points in T dimension."
)
if (yPointsRatio < 2):
errors.append(
"You need at least 2 measurements per control point, "
"i.e. use more patches in Y dimesion or decrease number of control points."
)
if (xPointsRatio < 2):
errors.append(
"You need at least 2 measurements per control point, "
"i.e. use more patches in X dimesion or decrease number of control points."
)
return errors
def _validate(self):
errors = ProtAlignMovies._validate(self)
# Although getFirstItem is not recommended in general, here it is
# used only once, for validation purposes, so performance
# problems not should be appear.
if not self.inputMovies.get() is None:
inputSet = self.inputMovies.get()
movie = inputSet.getFirstItem()
if (not movie.hasAlignment()) and self.useAlignment:
errors.append("Your movies have no alignment. Please, set *No* "
"the parameter _Use previous movie alignment to SUM"
" frames?_")
if self.doApplyDoseFilter:
doseFrame = inputSet.getAcquisition().getDosePerFrame()
if doseFrame == 0.0 or doseFrame is None:
errors.append('Dose per frame for input movies is 0 or not '
'set. You cannot apply dose filter.')
if self.numberOfThreads > 1 and self.useGpu:
errors.append("GPU and Parallelization can not be used together")
ofCpu = Plugin.getHome("bin", "xmipp_movie_optical_alignment_cpu")
ofGpu = Plugin.getHome("bin", "xmipp_movie_optical_alignment_gpu")
if not (exists(ofGpu) or exists(ofCpu)):
errors.append("It seems that Xmipp Optical Alignment is not installed. "
"OpenCV should be installed in the system to compile it.\n"
"Please, install OpenCV in your system and, then, "
"re-install Xmipp by running 'scipion installb xmippSrc'.")
else:
if self.useGpu and not exists(ofGpu):
errors.append("It seems that Xmipp Optical Alignment has not been "
"compiled with CUDA.\nPlease, try with *GPU=No*.\n"
"Error: '%s' not found." % ofGpu)
if not self.useGpu and not exists(ofCpu):
errors.append("It seems that Xmipp Optical Alignment has been "
"compiled with CUDA.\nPlease, try with *GPU=Yes*.\n"
"Error: '%s' not found." % ofCpu)
return errors
def _validate(self):
# Check base validation before the specific ones for Motioncorr
errors = ProtAlignMovies._validate(self)
program = MOTIONCOR2_PATH if self.useMotioncor2 else MOTIONCORR_PATH
if not os.path.exists(program):
errors.append('Missing %s' % program)
# Check CUDA paths
cudaLib = getCudaLib(useMC2=self.useMotioncor2)
cudaConst = (MOTIONCOR2_CUDA_LIB
if self.useMotioncor2 else MOTIONCORR_CUDA_LIB)
if cudaLib is None:
errors.append("Do not know where to find CUDA lib path. "
" %s or %s variables have None value or are not"
" present in scipion configuration." %
(cudaConst, CUDA_LIB))
elif not pwutils.existsVariablePaths(cudaLib):
errors.append("Either %s or %s variables points to a non existing "
"path (%s). Please, check scipion configuration." %
(cudaConst, CUDA_LIB, cudaLib))
gpu = self.GPUIDs.get()
if not self.useMotioncor2:
bin = self.binFactor.get()
if not (bin == 1.0 or bin == 2.0):
errors.append("Binning factor can only be 1 or 2")
if len(gpu) > 1:
errors.append("Old motioncorr2.1 does not support multiple "
"GPUs, use motioncor2.")
else:
if not self.doSaveAveMic:
errors.append(
'Option not supported. Please select Yes for '
'Save aligned micrograph. '
'Optionally you could add -Align 0 to additional '
'parameters so that protocol '
'produces simple movie sum.')
if self.doSaveMovie and not self._isOutStackSupport:
errors.append('Saving aligned movies is not supported by '
'this version of motioncor2. '
'By default, the protocol will produce '
'outputMovies equivalent to the input '
'however containing alignment information.')
if not self.useAlignToSum:
errors.append('Frame range for ALIGN and SUM must be '
'equivalent in case of motioncor2. \n Please, '
'set *YES* _Use ALIGN frames range to SUM?_ '
'flag or use motioncorr')
if self.doApplyDoseFilter and self.inputMovies.get():
inputMovies = self.inputMovies.get()
doseFrame = inputMovies.getAcquisition().getDosePerFrame()
if doseFrame == 0.0 or doseFrame is None:
errors.append(
'Dose per frame for input movies is 0 or not '
'set. You cannot apply dose filter.')
return errors
def _validate(self):
# Check base validation before the specific ones for Motioncorr
errors = ProtAlignMovies._validate(self)
program = MOTIONCOR2_PATH if self.useMotioncor2 else MOTIONCORR_PATH
if not os.path.exists(program):
errors.append('Missing %s' % program)
# Check CUDA paths
cudaLib = getCudaLib(useMC2=self.useMotioncor2)
cudaConst = (MOTIONCOR2_CUDA_LIB if self.useMotioncor2 else
MOTIONCORR_CUDA_LIB)
if cudaLib is None:
errors.append("Do not know where to find CUDA lib path. "
" %s or %s variables have None value or are not"
" present in scipion configuration."
% (cudaConst, CUDA_LIB))
elif not pwutils.existsVariablePaths(cudaLib):
errors.append("Either %s or %s variables points to a non existing "
"path (%s). Please, check scipion configuration."
% (cudaConst, CUDA_LIB, cudaLib))
gpu = self.gpuList.get()
if not self.useMotioncor2:
bin = self.binFactor.get()
if not (bin == 1.0 or bin == 2.0):
errors.append("Binning factor can only be 1 or 2")
if len(gpu) > 1:
errors.append("Old motioncorr2.1 does not support multiple "
"GPUs, use motioncor2.")
else:
if not self.doSaveAveMic:
errors.append('Option not supported. Please select Yes for '
'Save aligned micrograph. '
'Optionally you could add -Align 0 to additional '
'parameters so that protocol '
'produces simple movie sum.')
if self.doSaveMovie and not self._isOutStackSupport:
errors.append('Saving aligned movies is not supported by '
'this version of motioncor2. '
'By default, the protocol will produce '
'outputMovies equivalent to the input '
'however containing alignment information.')
if not self.useAlignToSum:
errors.append('Frame range for ALIGN and SUM must be '
'equivalent in case of motioncor2. \n Please, '
'set *YES* _Use ALIGN frames range to SUM?_ '
'flag or use motioncorr')
if self.doApplyDoseFilter and self.inputMovies.get():
inputMovies = self.inputMovies.get()
doseFrame = inputMovies.getAcquisition().getDosePerFrame()
if doseFrame == 0.0 or doseFrame is None:
errors.append('Dose per frame for input movies is 0 or not '
'set. You cannot apply dose filter.')
return errors
def _validate(self):
# Check base validation before the specific ones for Motioncorr
errors = ProtAlignMovies._validate(self)
return errors