def _defineAlignmentParams(self, form):
ProtAlignMovies._defineAlignmentParams(self, form)
form.addParam('splineOrder',
params.EnumParam,
condition="doSaveAveMic or doSaveMovie",
default=self.INTERP_CUBIC,
choices=['linear', 'cubic'],
expertLevel=cons.LEVEL_ADVANCED,
label='Interpolation',
help="linear (faster but lower quality), "
"cubic (slower but more accurate).")
form.addParam('maxFreq',
params.FloatParam,
default=4,
label='Filter at (A)',
help="For the calculation of the shifts with Xmipp, "
"micrographs are filtered (and downsized "
"accordingly) to this resolution. Then shifts are "
"calculated, and they are applied to the original "
"frames without any filtering and downsampling.")
form.addParam('doComputePSD',
params.BooleanParam,
default=True,
label="Compute PSD (before/after)?",
help="If Yes, the protocol will compute for each movie "
"the PSD of the average micrograph (without CC "
"alignement) and after that, to compare each PSDs")
form.addParam('maxShift',
params.IntParam,
default=30,
expertLevel=cons.LEVEL_ADVANCED,
label="Maximum shift (pixels)",
help='Maximum allowed distance (in pixels) that each '
'frame can be shifted with respect to the next.')
form.addParam('outsideMode',
params.EnumParam,
choices=['Wrapping', 'Average', 'Value'],
default=self.OUTSIDE_WRAP,
expertLevel=cons.LEVEL_ADVANCED,
label="How to fill borders",
help='How to fill the borders when shifting the frames')
form.addParam('outsideValue',
params.FloatParam,
default=0.0,
expertLevel=cons.LEVEL_ADVANCED,
condition="outsideMode==2",
label='Fill value',
help="Fixed value for filling borders")
form.addParallelSection(threads=1, mpi=1)
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 _defineAlignmentParams(self, form):
ProtAlignMovies._defineAlignmentParams(self, form)
form.addParam('splineOrder', params.EnumParam, condition="doSaveAveMic or doSaveMovie",
default=self.INTERP_CUBIC, choices=['linear', 'cubic'],
expertLevel=cons.LEVEL_ADVANCED,
label='Interpolation',
help="linear (faster but lower quality), "
"cubic (slower but more accurate).")
form.addParam('maxFreq', params.FloatParam, default=4,
label='Filter at (A)',
help="For the calculation of the shifts with Xmipp, "
"micrographs are filtered (and downsized "
"accordingly) to this resolution. Then shifts are "
"calculated, and they are applied to the original "
"frames without any filtering and downsampling.")
form.addParam('doComputePSD', params.BooleanParam, default=True,
label="Compute PSD (before/after)?",
help="If Yes, the protocol will compute for each movie "
"the PSD of the average micrograph (without CC "
"alignement) and after that, to compare each PSDs")
form.addParam('maxShift', params.IntParam, default=30,
expertLevel=cons.LEVEL_ADVANCED,
label="Maximum shift (pixels)",
help='Maximum allowed distance (in pixels) that each '
'frame can be shifted with respect to the next.')
form.addParam('outsideMode', params.EnumParam,
choices=['Wrapping','Average','Value'],
default=self.OUTSIDE_WRAP,
expertLevel=cons.LEVEL_ADVANCED,
label="How to fill borders",
help='How to fill the borders when shifting the frames')
form.addParam('outsideValue', params.FloatParam, default=0.0,
expertLevel=cons.LEVEL_ADVANCED,
condition="outsideMode==2",
label='Fill value',
help="Fixed value for filling borders")
form.addParallelSection(threads=1, mpi=1)
def _createOutputMovie(self, movie):
""" Overwrite this function to store the Relion's specific
Motion model coefficients.
"""
m = ProtAlignMovies._createOutputMovie(self, movie)
# Load local motion values only if the patches are more than one
if self.patchX.get() * self.patchY.get() > 1:
table = md.Table(fileName=self._getMovieExtraFn(movie, '.star'),
tableName='local_motion_model')
coeffs = [row.rlnMotionModelCoeff for row in table]
m._rlnMotionModelCoeff = pwobj.String(json.dumps(coeffs))
return m
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 _createOutputMovie(self, movie):
alignedMovie = ProtAlignMovies._createOutputMovie(self, movie)
self._setAlignmentInfo(movie, alignedMovie)
return alignedMovie
def _createOutputMovie(self, movie):
alignedMovie = ProtAlignMovies._createOutputMovie(self, movie)
self._setAlignmentInfo(movie, alignedMovie)
return alignedMovie
def _defineAlignmentParams(self, form):
ProtAlignMovies._defineAlignmentParams(self, form)
form.addSection("Aditional Parameters")
# GROUP GPU PARAMETERS
#group = form.addGroup('GPU')
form.addHidden(
params.USE_GPU,
params.BooleanParam,
default=False,
label="Use GPU (vs CPU)",
help="Set to true if you want the GPU implementation of "
"Optical Flow")
form.addHidden(
params.GPU_LIST,
params.StringParam,
default=0,
expertLevel=params.LEVEL_ADVANCED,
label="Choose GPU core",
help="GPU may have several cores. Set it to zero if you "
"do not know what we are talking about. First core "
"index is 0, second 1 and so on.")
group = form.addGroup('OF Parameters')
group.addParam('winSize',
params.IntParam,
default=150,
expertLevel=params.LEVEL_ADVANCED,
label="Window size",
help="Window size (shifts are assumed to be constant "
"within this window).")
group.addParam('groupSize',
params.IntParam,
default=1,
expertLevel=params.LEVEL_ADVANCED,
label="Group Size",
help="The number of frames in each group at the "
"last step")
group.addParam(
'useAlignment',
params.BooleanParam,
default=True,
label="Use previous movie alignment to SUM frames?",
help="Input movies could have alignment information from"
"a previous protocol. If you select *Yes*, the "
"previous alignment will be taken into account.")
group.addParam('doComputePSD',
params.BooleanParam,
default=True,
label="Compute PSD (before/after)?",
help="If Yes, the protocol will compute for each movie "
"the PSD of the average micrograph (without OF "
"alignement) and after that, to compare each PSDs")
group.addParam(
'memory',
params.BooleanParam,
default=False,
label="Keep images in RAM ?",
help="If True, the protocol will increase the demand of "
"RAM, decreasing disc access")
group = form.addGroup('Dose Compensation')
group.addParam('doApplyDoseFilter',
params.BooleanParam,
default=False,
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames before '
'summing them. Pre-exposure and dose per frame '
'should be specified during movies import.')
group.addParam('doSaveUnweightedMic',
params.BooleanParam,
default=True,
condition='doSaveAveMic and doApplyDoseFilter',
label="Save unweighted micrographs?",
help="Yes by default, if you have selected to apply a "
"dose-dependent filter to the frames")
group.addParam('applyDosePreAlign',
params.BooleanParam,
default=False,
condition='doApplyDoseFilter',
label="Apply Dose filter before alignment?",
help="if *True*, you apply dose filter before perform "
"the alignment; else will apply after alignment.")
form.addParallelSection(threads=8, mpi=1)
def _defineAlignmentParams(self, form):
ProtAlignMovies._defineAlignmentParams(self, form)
form.addParam('splineOrder',
params.EnumParam,
condition="doSaveAveMic or doSaveMovie",
default=self.INTERP_CUBIC,
choices=['linear', 'cubic'],
expertLevel=cons.LEVEL_ADVANCED,
label='Interpolation',
help="linear (faster but lower quality), "
"cubic (slower but more accurate).")
form.addHidden(
params.USE_GPU,
params.BooleanParam,
default=True,
label="Use GPU for execution",
help="This protocol has both CPU and GPU implementation.\
Select the one you want to use.")
form.addHidden(params.GPU_LIST,
params.StringParam,
default='0',
expertLevel=cons.LEVEL_ADVANCED,
label="Choose GPU IDs",
help="Add a list of GPU devices that can be used")
form.addParam('maxFreq',
params.FloatParam,
default=4,
label='Filter at (A)',
help="For the calculation of the shifts with Xmipp, "
"micrographs are filtered (and downsized "
"accordingly) to this resolution. Then shifts are "
"calculated, and they are applied to the original "
"frames without any filtering and downsampling.")
form.addParam('doComputePSD',
params.BooleanParam,
default=True,
label="Compute PSD (before/after)?",
help="If Yes, the protocol will compute for each movie "
"the PSD of the average micrograph (without CC "
"alignement) and after that, to compare each PSDs")
form.addParam('maxShift',
params.IntParam,
default=30,
expertLevel=cons.LEVEL_ADVANCED,
label="Maximum shift (pixels)",
help='Maximum allowed distance (in pixels) that each '
'frame can be shifted with respect to the next.')
form.addParam('outsideMode',
params.EnumParam,
choices=['Wrapping', 'Average', 'Value'],
default=self.OUTSIDE_WRAP,
expertLevel=cons.LEVEL_ADVANCED,
label="How to fill borders",
help='How to fill the borders when shifting the frames')
#Local alignment params
group = form.addGroup('Local alignment')
group.addParam(
'doLocalAlignment',
params.BooleanParam,
default=True,
label="Compute local alignment?",
help=
"If Yes, the protocol will try to determine local shifts, similarly to MotionCor2."
)
group.addParam(
'autoControlPoints',
params.BooleanParam,
default=True,
label="Auto control points",
expertLevel=cons.LEVEL_ADVANCED,
condition='doLocalAlignment',
help=
"If on, protocol will automatically determine necessary number of control points."
)
line = group.addLine('Number of control points',
expertLevel=cons.LEVEL_ADVANCED,
help='Number of control points use for BSpline.',
condition='not autoControlPoints')
line.addParam('controlPointX', params.IntParam, default=6, label='X')
line.addParam('controlPointY', params.IntParam, default=6, label='Y')
line.addParam('controlPointT', params.IntParam, default=5, label='t')
line = group.addLine(
'Number of patches',
expertLevel=cons.LEVEL_ADVANCED,
help=
'Number of patches to be used. Depending on the size of the movie, they may \
overlap.',
condition='doLocalAlignment')
line.addParam('patchX', params.IntParam, default=10, label='X')
line.addParam('patchY', params.IntParam, default=10, label='Y')
group.addParam(
'groupNFrames',
params.IntParam,
default=3,
expertLevel=cons.LEVEL_ADVANCED,
label='Group N frames',
help=
'Group every specified number of frames by adding them together. \
The alignment is then performed on the summed frames.',
condition='doLocalAlignment')
form.addParam('outsideValue',
params.FloatParam,
default=0.0,
expertLevel=cons.LEVEL_ADVANCED,
condition="outsideMode==2",
label='Fill value',
help="Fixed value for filling borders")
form.addParallelSection(threads=1, mpi=1)
def _defineAlignmentParams(self, form):
form.addParam('gpuMsg', params.LabelParam, default=True,
label='WARNING! You need to have installed CUDA'
' libraries and a Nvidia GPU')
form.addHidden(params.GPU_LIST, params.StringParam, default='0',
expertLevel=cons.LEVEL_ADVANCED,
label="Choose GPU IDs",
help="GPU may have several cores. Set it to zero"
" if you do not know what we are talking about."
" First core index is 0, second 1 and so on."
" Motioncor2 can use multiple GPUs - in that case"
" set to i.e. *0 1 2*.")
ProtAlignMovies._defineAlignmentParams(self, form)
form.addParam('doComputePSD', params.BooleanParam, default=False,
expertLevel=cons.LEVEL_ADVANCED,
label="Compute PSD (before/after)?",
help="If Yes, the protocol will compute for each movie "
"the average PSD before and after alignment, "
"for comparison")
form.addParam('doComputeMicThumbnail', params.BooleanParam,
expertLevel=cons.LEVEL_ADVANCED,
default=False,
label='Compute micrograph thumbnail?',
help='When using this option, we will compute a '
'micrograph thumbnail and keep it with the '
'micrograph object for visualization purposes. ')
form.addParam('computeAllFramesAvg', params.BooleanParam,
expertLevel=cons.LEVEL_ADVANCED,
default=False,
label='Compute all frames average?',
help='Computing all the frames average could provide a '
'sanity check about the microscope and the camera.')
form.addParam('extraParams', params.StringParam, default='',
expertLevel=cons.LEVEL_ADVANCED,
label='Additional parameters',
help="""Extra parameters for motioncorr (NOT motioncor2)\n
-bft 150 BFactor in pix^2.
-pbx 96 Box dimension for searching CC peak.
-fod 2 Number of frame offset for frame comparison.
-nps 0 Radius of noise peak.
-sub 0 1: Save as sub-area corrected sum. 0: Not.
-srs 0 1: Save uncorrected sum. 0: Not.
-scc 0 1: Save CC Map. 0: Not.
-slg 1 1: Save Log. 0: Not.
-atm 1 1: Align to middle frame. 0: Not.
-dsp 1 1: Save quick results. 0: Not.
-fsc 0 1: Calculate and log FSC. 0: Not.
""")
form.addParam('extraProtocolParams', params.StringParam, default='',
expertLevel=cons.LEVEL_ADVANCED,
label='Additional protocol parameters',
help="Here you can provide some extra parameters for the "
"protocol, not the underlying motioncor program."
"You can provide many options separated by space. "
"\n*Options:* \n"
"--use_worker_thread \n"
" Use an extra thread to compute"
" PSD and thumbnail. This will allow a more effective"
" use of the GPU card, but requires an extra CPU. ")
form.addSection(label="Motioncor2")
form.addParam('useMotioncor2', params.BooleanParam, default=True,
label='Use motioncor2',
help='Use new *motioncor2* program with local '
'patch-based motion correction and dose weighting.')
form.addParam('doApplyDoseFilter', params.BooleanParam, default=True,
condition='useMotioncor2',
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames before '
'summing them. Pre-exposure and dose per frame '
'should be specified during movies import.')
line = form.addLine('Number of patches', condition='useMotioncor2',
help='Number of patches to be used for patch based '
'alignment. Set to *0 0* to do only global motion '
'correction. \n')
line.addParam('patchX', params.IntParam, default=5, label='X')
line.addParam('patchY', params.IntParam, default=5, label='Y')
if self.versionGE('1.0.1'): # Patch overlap was introduced in 1.0.1
form.addParam('patchOverlap', params.IntParam, default=0,
condition='useMotioncor2',
label='Patches Overlap (%)',
help='In versions > 1.0.1 it is possible to specify'
'the overlapping between patches. '
'\nFor example, overlap=20 means that '
'each patch will have a 20% overlapping \n'
'with its neighboring patches in each dimension.')
form.addParam('group', params.IntParam, default='1',
label='Group N frames', condition='useMotioncor2',
help='Group every specified number of frames by adding '
'them together. The alignment is then performed on '
'the summed frames. By default, no grouping is '
'performed.')
form.addParam('tol', params.FloatParam, default='0.5',
label='Tolerance (px)', condition='useMotioncor2',
help='Tolerance for iterative alignment, default *0.5px*.')
if self._supportsMagCorrection():
group = form.addGroup('Magnification correction')
group.addParam('doMagCor', params.BooleanParam, default=False,
label='Correct anisotropic magnification?',
condition='useMotioncor2',
help='Correct anisotropic magnification by '
'stretching image along the major axis, '
'the axis where the lower magnification is '
'detected.')
group.addParam('useEst', params.BooleanParam, default=True,
label='Use previous estimation?',
condition='useMotioncor2 and doMagCor',
help='Use previously calculated parameters of '
'magnification anisotropy (from magnification '
'distortion estimation protocol).')
group.addParam('inputEst', params.PointerParam,
pointerClass='ProtMagDistEst',
condition='useEst and useMotioncor2 and doMagCor',
label='Input protocol',
help='Select previously executed estimation protocol.')
group.addParam('scaleMaj', params.FloatParam, default=1.0,
condition='not useEst and useMotioncor2 and doMagCor',
label='Major scale factor',
help='Major scale factor.')
group.addParam('scaleMin', params.FloatParam, default=1.0,
condition='not useEst and useMotioncor2 and doMagCor',
label='Minor scale factor',
help='Minor scale factor.')
group.addParam('angDist', params.FloatParam, default=0.0,
condition='not useEst and useMotioncor2 and doMagCor',
label='Distortion angle (deg)',
help='Distortion angle, in degrees.')
else:
form.addParam('motioncor2Version', params.LabelParam,
condition='useMotioncor2',
label='Scipion supports some versions of motioncor2 '
'that can do magnification correction, '
'but they do not seems to be installed. Check '
'available versions with: \n'
'scipion install --help.\n'
'Also, make sure MOTIONCOR2_CUDA_LIB or '
'CUDA_LIB point to cuda-8.0/lib path')
if self.isSemVersion():
form.addParam('defectFile', params.FileParam, allowsNull=True,
expertLevel=cons.LEVEL_ADVANCED,
condition='useMotioncor2',
label='Camera defects file',
help='Defect file that stores entries of defects on camera.\n'
'Each entry corresponds to a rectangular region in image. '
'The pixels in such a region are replaced by '
'neighboring good pixel values. Each entry contains '
'4 integers x, y, w, h representing the x, y '
'coordinates, width, and height, respectively.')
form.addParam('extraParams2', params.StringParam, default='',
expertLevel=cons.LEVEL_ADVANCED,
condition='useMotioncor2',
label='Additional parameters',
help="""Extra parameters for motioncor2\n
-Bft 100 BFactor for alignment, in px^2.
-Iter 5 Maximum iterations for iterative alignment.
-MaskCent 0 0 Center of subarea that will be used for alignment,
default *0 0* corresponding to the frame center.
-MaskSize 1.0 1.0 The size of subarea that will be used for alignment,
default *1.0 1.0* corresponding full size.
-Align 1 Generate aligned sum (1) or simple sum (0).
-FmRef -1 Specify which frame to be the reference to which
all other frames are aligned, by default (-1) the
the central frame is chosen. The central frame is
at N/2 based upon zero indexing where N is the
number of frames that will be summed, i.e., not
including the frames thrown away.
-RotGain 0 Rotate gain reference counter-clockwise: 0 - no rotation,
1 - 90 degrees, 2 - 180 degrees, 3 - 270 degrees.
-FlipGain 0 Flip gain reference after gain rotation: 0 - no flipping,
1 - flip upside down, 2 - flip left right.
-Tilt 0 0 Tilt angle range for a dose fractionated tomographic
tilt series, e.g. *-60 60*
Since version *1.1.0*:
-GpuMemUsage 0.5 Specify how much GPU memory is used to buffer movie frames.
It is recommended when running side by side processes in
the same card. By default is 50% (i. e 0.5)
-InFmMotion 1 Takes into account of motion-induced blurring of
each frame. It has shown resolution improvement
in some test cases. By default this option is off.
-Bft 500 150 Since version 1.1.0 this option can take two arguments.
First one is used in global-motion measurement and the
second one is for local-motion. (default 500 150).
""")
form.addParam('doSaveUnweightedMic', params.BooleanParam, default=True,
condition='doSaveAveMic and useMotioncor2 and doApplyDoseFilter',
label="Save unweighted micrographs?",
help="Yes by default, if you have selected to apply a "
"dose-dependent filter to the frames")
# Since only runs on GPU, do not allow neither threads nor mpi
form.addParallelSection(threads=1, mpi=1)
def __init__(self, **args):
ProtAlignMovies.__init__(self, **args)
self.stepsExecutionMode = STEPS_PARALLEL
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 _defineAlignmentParams(self, form):
ProtAlignMovies._defineAlignmentParams(self, form)
form.addSection("Aditional Parameters")
# GROUP GPU PARAMETERS
#group = form.addGroup('GPU')
form.addHidden(params.USE_GPU, params.BooleanParam, default=False,
label="Use GPU (vs CPU)",
help="Set to true if you want the GPU implementation of "
"Optical Flow")
form.addHidden(params.GPU_LIST, params.StringParam, default=0,
expertLevel=params.LEVEL_ADVANCED,
label="Choose GPU core",
help="GPU may have several cores. Set it to zero if you "
"do not know what we are talking about. First core "
"index is 0, second 1 and so on.")
group = form.addGroup('OF Parameters')
group.addParam('winSize', params.IntParam, default=150,
expertLevel=params.LEVEL_ADVANCED,
label="Window size",
help="Window size (shifts are assumed to be constant "
"within this window).")
group.addParam('groupSize', params.IntParam, default=1,
expertLevel=params.LEVEL_ADVANCED,
label="Group Size",
help="The number of frames in each group at the "
"last step")
group.addParam('useAlignment', params.BooleanParam, default=True,
label="Use previous movie alignment to SUM frames?",
help="Input movies could have alignment information from"
"a previous protocol. If you select *Yes*, the "
"previous alignment will be taken into account.")
group.addParam('doComputePSD', params.BooleanParam, default=True,
label="Compute PSD (before/after)?",
help="If Yes, the protocol will compute for each movie "
"the PSD of the average micrograph (without OF "
"alignement) and after that, to compare each PSDs")
group.addParam('memory', params.BooleanParam, default=False,
label="Keep images in RAM ?",
help="If True, the protocol will increase the demand of "
"RAM, decreasing disc access")
group = form.addGroup('Dose Compensation')
group.addParam('doApplyDoseFilter', params.BooleanParam, default=False,
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames before '
'summing them. Pre-exposure and dose per frame '
'should be specified during movies import.')
group.addParam('doSaveUnweightedMic', params.BooleanParam, default=True,
condition='doSaveAveMic and doApplyDoseFilter',
label="Save unweighted micrographs?",
help="Yes by default, if you have selected to apply a "
"dose-dependent filter to the frames")
group.addParam('applyDosePreAlign', params.BooleanParam, default=False,
condition='doApplyDoseFilter',
label="Apply Dose filter before alignment?",
help="if *True*, you apply dose filter before perform "
"the alignment; else will apply after alignment.")
form.addParallelSection(threads=8, mpi=1)
def __init__(self, **args):
ProtAlignMovies.__init__(self, **args)
self.stepsExecutionMode = STEPS_PARALLEL
def _validate(self):
# Check base validation before the specific ones for Motioncorr
errors = ProtAlignMovies._validate(self)
return errors
def _convertInputStep(self):
self.info("Relion version:")
self.runJob("which", "relion_run_motioncorr", numberOfMpi=1)
ProtAlignMovies._convertInputStep(self)
def _defineAlignmentParams(self, form):
form.addParam('gpuMsg',
params.LabelParam,
default=True,
label='WARNING! You need to have installed CUDA'
' libraries and a Nvidia GPU')
form.addParam('GPUIDs',
params.StringParam,
default='0',
expertLevel=cons.LEVEL_ADVANCED,
label="Choose GPU IDs",
help="GPU may have several cores. Set it to zero"
" if you do not know what we are talking about."
" First core index is 0, second 1 and so on."
" Motioncor2 can use multiple GPUs - in that case"
" set to i.e. *0 1 2*.")
ProtAlignMovies._defineAlignmentParams(self, form)
form.addParam('doComputePSD',
params.BooleanParam,
default=False,
expertLevel=cons.LEVEL_ADVANCED,
label="Compute PSD (before/after)?",
help="If Yes, the protocol will compute for each movie "
"the average PSD before and after alignment, "
"for comparison")
form.addParam('doComputeMicThumbnail',
params.BooleanParam,
expertLevel=cons.LEVEL_ADVANCED,
default=False,
label='Compute micrograph thumbnail?',
help='When using this option, we will compute a '
'micrograph thumbnail and keep it with the '
'micrograph object for visualization purposes. ')
form.addParam('computeAllFramesAvg',
params.BooleanParam,
expertLevel=cons.LEVEL_ADVANCED,
default=False,
label='Compute all frames average?',
help='Computing all the frames average could provide a '
'sanity check about the microscope and the camera.')
form.addParam(
'extraParams',
params.StringParam,
default='',
expertLevel=cons.LEVEL_ADVANCED,
label='Additional parameters',
help="""Extra parameters for motioncorr (NOT motioncor2)\n
-bft 150 BFactor in pix^2.
-pbx 96 Box dimension for searching CC peak.
-fod 2 Number of frame offset for frame comparison.
-nps 0 Radius of noise peak.
-sub 0 1: Save as sub-area corrected sum. 0: Not.
-srs 0 1: Save uncorrected sum. 0: Not.
-scc 0 1: Save CC Map. 0: Not.
-slg 1 1: Save Log. 0: Not.
-atm 1 1: Align to middle frame. 0: Not.
-dsp 1 1: Save quick results. 0: Not.
-fsc 0 1: Calculate and log FSC. 0: Not.
""")
form.addSection(label="Motioncor2")
form.addParam('useMotioncor2',
params.BooleanParam,
default=True,
label='Use motioncor2',
help='Use new *motioncor2* program with local '
'patch-based motion correction and dose weighting.')
form.addParam('doApplyDoseFilter',
params.BooleanParam,
default=True,
condition='useMotioncor2',
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames before '
'summing them. Pre-exposure and dose per frame '
'should be specified during movies import.')
line = form.addLine(
'Number of patches',
condition='useMotioncor2',
help='Number of patches to be used for patch based '
'alignment. Set to *0 0* to do only global motion '
'correction. \n')
line.addParam('patchX', params.IntParam, default=5, label='X')
line.addParam('patchY', params.IntParam, default=5, label='Y')
if self.versionGE('1.0.1'): # Patch overlap was introduced in 1.0.1
form.addParam('patchOverlap',
params.IntParam,
default=0,
condition='useMotioncor2',
label='Patches Overlap (%)',
help='In versions > 1.0.1 it is possible to specify'
'the overlapping between patches. '
'\nFor example, overlap=20 means that '
'each patch will have a 20% overlapping \n'
'with its neighboring patches in each dimension.')
form.addParam('group',
params.IntParam,
default='1',
label='Group N frames',
condition='useMotioncor2',
help='Group every specified number of frames by adding '
'them together. The alignment is then performed on '
'the summed frames. By default, no grouping is '
'performed.')
form.addParam(
'tol',
params.FloatParam,
default='0.5',
label='Tolerance (px)',
condition='useMotioncor2',
help='Tolerance for iterative alignment, default *0.5px*.')
if self._supportsMagCorrection():
group = form.addGroup('Magnification correction')
group.addParam('doMagCor',
params.BooleanParam,
default=False,
label='Correct anisotropic magnification?',
condition='useMotioncor2',
help='Correct anisotropic magnification by '
'stretching image along the major axis, '
'the axis where the lower magnification is '
'detected.')
group.addParam('useEst',
params.BooleanParam,
default=True,
label='Use previous estimation?',
condition='useMotioncor2 and doMagCor',
help='Use previously calculated parameters of '
'magnification anisotropy (from magnification '
'distortion estimation protocol).')
group.addParam(
'inputEst',
params.PointerParam,
pointerClass='ProtMagDistEst',
condition='useEst and useMotioncor2 and doMagCor',
label='Input protocol',
help='Select previously executed estimation protocol.')
group.addParam(
'scaleMaj',
params.FloatParam,
default=1.0,
condition='not useEst and useMotioncor2 and doMagCor',
label='Major scale factor',
help='Major scale factor.')
group.addParam(
'scaleMin',
params.FloatParam,
default=1.0,
condition='not useEst and useMotioncor2 and doMagCor',
label='Minor scale factor',
help='Minor scale factor.')
group.addParam(
'angDist',
params.FloatParam,
default=0.0,
condition='not useEst and useMotioncor2 and doMagCor',
label='Distortion angle (deg)',
help='Distortion angle, in degrees.')
else:
form.addParam('motioncor2Version',
params.LabelParam,
condition='useMotioncor2',
label='Scipion supports some versions of motioncor2 '
'that can do magnification correction, '
'but they do not seems to be installed. Check '
'available versions with: \n'
'scipion install --help.\n'
'Also, make sure MOTIONCOR2_CUDA_LIB or '
'CUDA_LIB point to cuda-8.0/lib path')
if self.isSemVersion():
form.addParam(
'defectFile',
params.FileParam,
allowsNull=True,
expertLevel=cons.LEVEL_ADVANCED,
condition='useMotioncor2',
label='Camera defects file',
help='Defect file that stores entries of defects on camera.\n'
'Each entry corresponds to a rectangular region in image. '
'The pixels in such a region are replaced by '
'neighboring good pixel values. Each entry contains '
'4 integers x, y, w, h representing the x, y '
'coordinates, width, and height, respectively.')
form.addParam('extraParams2',
params.StringParam,
default='',
expertLevel=cons.LEVEL_ADVANCED,
condition='useMotioncor2',
label='Additional parameters',
help="""Extra parameters for motioncor2\n
-Bft 100 BFactor for alignment, in px^2.
-Iter 5 Maximum iterations for iterative alignment.
-MaskCent 0 0 Center of subarea that will be used for alignment,
default *0 0* corresponding to the frame center.
-MaskSize 1.0 1.0 The size of subarea that will be used for alignment,
default *1.0 1.0* corresponding full size.
-Align 1 Generate aligned sum (1) or simple sum (0).
-FmRef -1 Specify which frame to be the reference to which
all other frames are aligned, by default (-1) the
the central frame is chosen. The central frame is
at N/2 based upon zero indexing where N is the
number of frames that will be summed, i.e., not
including the frames thrown away.
-RotGain 0 Rotate gain reference counter-clockwise: 0 - no rotation,
1 - 90 degrees, 2 - 180 degrees, 3 - 270 degrees.
-FlipGain 0 Flip gain reference after gain rotation: 0 - no flipping,
1 - flip upside down, 2 - flip left right.
-Tilt 0 0 Tilt angle range for a dose fractionated tomographic
tilt series, e.g. *-60 60*
""")
form.addParam(
'doSaveUnweightedMic',
params.BooleanParam,
default=True,
condition='doSaveAveMic and useMotioncor2 and doApplyDoseFilter',
label="Save unweighted micrographs?",
help="Yes by default, if you have selected to apply a "
"dose-dependent filter to the frames")
# Since only runs on GPU, do not allow neither threads nor mpi
form.addParallelSection(threads=1, mpi=1)
def __init__(self, **kwargs):
ProtAlignMovies.__init__(self, **kwargs)
self.stepsExecutionMode = STEPS_SERIAL