def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('alignFrameRange', IntParam,
default=-1,
label='Number frames per movie ',
help='How many frames per monie. -1 -> all frames ')
form.addParam('doApplyDoseFilter', BooleanParam, default=True,
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames '
'before summing them')
form.addParam('exposurePerFrame', FloatParam,
label='Exposure per frame (e/A^2)',
help='Exposure per frame, in electrons per square '
'Angstrom')
#group = form.addGroup('Expert Options')
form.addParam('Bfactor', FloatParam,
default=1500.,
label='B-factor (A^2)',
help='B-factor to apply to images (A^2)',
expertLevel=LEVEL_ADVANCED)
form.addParam('doRestoreNoisePower', BooleanParam,
default=True,
label='Restore Noise Power? ',
help='Restore Noise Power? ',
expertLevel=LEVEL_ADVANCED)
form.addParam('doVerboseOutput', BooleanParam,
default=False,
label='Verbose Output?',
help='Verbose Output?',
expertLevel=LEVEL_ADVANCED)
form.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('alignFrameRange', IntParam,
default=-1,
label='Number frames per movie ',
help='How many frames per monie. -1 -> all frames ')
form.addParam('doApplyDoseFilter', BooleanParam, default=True,
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames before summing them')
form.addParam('exposurePerFrame', FloatParam,
label='Exposure per frame (e/A^2)',
help='Exposure per frame, in electrons per square Angstrom')
#group = form.addGroup('Expert Options')
form.addParam('minShiftInitSearch', FloatParam,
default=2.,
label='Min. Shift Initial search (A)',
help='Initial search will be limited to between the inner and outer radii',
expertLevel=LEVEL_ADVANCED)
form.addParam('OutRadShiftLimit', FloatParam,
default=200.,
label='Outer radius shift limit (A)',
help='The maximum shift of each alignment step will be limited to this value',
expertLevel=LEVEL_ADVANCED)
form.addParam('Bfactor', FloatParam,
default=1500.,
label='B-factor (A^2)',
help='B-factor to apply to images (A^2)',
expertLevel=LEVEL_ADVANCED)
form.addParam('HWVertFourMask', IntParam,
default=1,
label='Half-width vertical Fourier mask',
help='The vertical line mask will be twice this size. The central cross mask helps reduce problems by line artefacts from the detector',
expertLevel=LEVEL_ADVANCED)
form.addParam('HWHoriFourMask', IntParam,
default=1,
label='Half-width horizontal Fourier mask',
help='The horizontal line mask will be twice this size. The central cross mask helps reduce problems by line artefacts from the detector',
expertLevel=LEVEL_ADVANCED)
form.addParam('terminationShiftThreshold', FloatParam,
default=0.1,
label='Termination shift threshold',
help='Alignment will stop at this number, even if the threshold shift is not reached',
expertLevel=LEVEL_ADVANCED)
form.addParam('maximumNumberIterations', IntParam,
default=10,
label='Maximum number of iterations',
help='Maximum number of iterations',
expertLevel=LEVEL_ADVANCED)
form.addParam('doRestoreNoisePower', BooleanParam,
default=True,
label='Restore Noise Power? ',
help='Restore Noise Power? ',
expertLevel=LEVEL_ADVANCED)
form.addParam('doVerboseOutput', BooleanParam,
default=False,
label='Verbose Output?',
help='Verbose Output?',
expertLevel=LEVEL_ADVANCED)
form.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
group = form.addGroup('Frame range')
line1 = group.addLine('Used in alignment',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0*.' )
line1.addParam('alignFrame0', IntParam, default=0, label='First')
line1.addParam('alignFrameN', IntParam, default=0, label='Last',
help='If *0*, use maximum value')
line2 = group.addLine('Used in final sum',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0*.' )
line2.addParam('sumFrame0', IntParam, default=0, label='First')
line2.addParam('sumFrameN', IntParam, default=0, label='Last',
help='If *0*, use maximum value')
form.addParam('gpuId', StringParam, default='0',
expertLevel=LEVEL_ADVANCED,
label='GPU id',
help='GPU device ID')
form.addParam('extraParams', StringParam, default='',
expertLevel=LEVEL_ADVANCED,
label='Additional parameters',
help="""
-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.
-ssc 0 1: Save aligned stack. 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.
""")
group2 = form.addGroup('Crop and binning')
line = group2.addLine('Crop offsets (px)')
line.addParam('cropOffsetX', IntParam, default=0, label='X')
line.addParam('cropOffsetY', IntParam, default=0, label='Y')
line = group2.addLine('Crop dimensions (px)',
help='How many pixels to crop from offset\n'
'If equal to 0, use maximum size.')
line.addParam('cropDimX', IntParam, default=0, label='X')
line.addParam('cropDimY', IntParam, default=0, label='Y')
group2.addParam('binFactor', IntParam, default=1,
label='Binning factor',
help='1x or 2x. Bin stack before processing.')
form.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('useEst', params.BooleanParam, default=False,
label='Use previous estimation?',
help='Use previously calculated parameters of '
'magnification anisotropy.')
form.addParam('inputEst', params.PointerParam,
pointerClass='ProtMagDistEst', condition='useEst',
label='Input protocol',
help='Select previously executed estimation protocol.')
form.addParam('scaleMaj', params.FloatParam, default=1.0,
condition='not useEst',
label='Major scale factor',
help='Major scale factor.')
form.addParam('scaleMin', params.FloatParam, default=1.0,
condition='not useEst',
label='Minor scale factor',
help='Minor scale factor.')
form.addParam('angDist', params.FloatParam, default=0.0,
condition='not useEst',
label='Distortion angle (deg)',
help='Distortion angle, in degrees.')
form.addParam('newPix', params.FloatParam,
condition='not useEst',
label='New pixel size (A)',
help='Assign a new corrected pixel size, in Angstrom.')
form.addParam('doGain', params.BooleanParam, default=False,
expertLevel=params.LEVEL_ADVANCED,
label='Do gain correction before undistorting?',
help='If Yes, gain reference that you provided during '
'movies import will be chosen.')
form.addParam('doResample', params.BooleanParam, default=False,
expertLevel=params.LEVEL_ADVANCED,
label='Resample images?',
help='Resample images after distortion correction and gain'
' correction, by cropping their Fourier transforms')
line = form.addLine('New dimensions (px)',
expertLevel=params.LEVEL_ADVANCED,
condition='doResample')
line.addParam('newX', params.IntParam, default=2048,
label='X',
expertLevel=params.LEVEL_ADVANCED,
condition='doResample')
line.addParam('newY', params.IntParam, default=2048,
label='Y',
expertLevel=params.LEVEL_ADVANCED,
condition='doResample')
form.addParallelSection(threads=2, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam(
"alignFrameRange",
IntParam,
default=-1,
label="Number frames per movie ",
help="How many frames per monie. -1 -> all frames ",
)
form.addParam(
"doApplyDoseFilter",
BooleanParam,
default=True,
label="Apply Dose filter",
help="Apply a dose-dependent filter to frames before summing them",
)
form.addParam(
"exposurePerFrame",
FloatParam,
label="Exposure per frame (e/A^2)",
help="Exposure per frame, in electrons per square Angstrom",
)
# group = form.addGroup('Expert Options')
form.addParam(
"Bfactor",
FloatParam,
default=1500.0,
label="B-factor (A^2)",
help="B-factor to apply to images (A^2)",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"doRestoreNoisePower",
BooleanParam,
default=True,
label="Restore Noise Power? ",
help="Restore Noise Power? ",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"doVerboseOutput",
BooleanParam,
default=False,
label="Verbose Output?",
help="Verbose Output?",
expertLevel=LEVEL_ADVANCED,
)
form.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('alignFrameRange',
IntParam,
default=-1,
label='Number frames per movie ',
help='How many frames per monie. -1 -> all frames ')
form.addParam('doApplyDoseFilter',
BooleanParam,
default=True,
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames '
'before summing them')
form.addParam('exposurePerFrame',
FloatParam,
label='Exposure per frame (e/A^2)',
help='Exposure per frame, in electrons per square '
'Angstrom')
#group = form.addGroup('Expert Options')
form.addParam('Bfactor',
FloatParam,
default=1500.,
label='B-factor (A^2)',
help='B-factor to apply to images (A^2)',
expertLevel=LEVEL_ADVANCED)
form.addParam('doRestoreNoisePower',
BooleanParam,
default=True,
label='Restore Noise Power? ',
help='Restore Noise Power? ',
expertLevel=LEVEL_ADVANCED)
form.addParam('doVerboseOutput',
BooleanParam,
default=False,
label='Verbose Output?',
help='Verbose Output?',
expertLevel=LEVEL_ADVANCED)
form.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam(
"alignMethod",
EnumParam,
choices=[
"optical flow",
"dosefgpu",
"dosefgpu + optical flow",
"average",
"croscorrelation",
"croscorrelation + optical flow",
],
label="Alignment method",
default=AL_OPTICAL,
display=EnumParam.DISPLAY_COMBO,
help="Method to use for movie alignment. "
"dosefgpu requires a GPU. Croscorrelation "
"and dosefgpu with default parameters are equivalent. "
"Croscorrelation is a CPU implementation of dosefgpu "
"with limited functionality (only aligns whole frames)",
)
# GROUP COMMON PARAMETERS
group = form.addGroup("Common parameters")
line = group.addLine(
"Used in alignment",
help="First and last frames used in alignment.\n" "The first frame in the stack is *0*.",
)
line.addParam("alignFrame0", IntParam, default=0, label="First")
line.addParam("alignFrameN", IntParam, default=0, label="Last", help="If *0*, use maximum value")
# GROUP GPU PARAMETERS
group = form.addGroup(
"GPU",
condition="alignMethod==%d or (alignMethod==%d and expertLevel==%d)"
" or (alignMethod==%d and expertLevel==%d)"
% (AL_OPTICAL, AL_DOSEFGPUOPTICAL, LEVEL_ADVANCED, AL_DOSEFGPU, LEVEL_ADVANCED),
)
group.addParam(
"doGPU",
BooleanParam,
default=False,
label="Use GPU (vs CPU)",
condition="alignMethod==%d or alignMethod==%d" % (AL_OPTICAL, AL_DOSEFGPUOPTICAL),
help="Set to true if you want the GPU implementation of Optical Flow",
)
group.addParam(
"GPUCore",
IntParam,
default=0,
expertLevel=LEVEL_ADVANCED,
label="Choose GPU core",
condition="doGPU or alignMethod==%d or alignMethod==%d " % (AL_DOSEFGPU, AL_DOSEFGPUOPTICAL),
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 OPTICAL FLOW PARAMETERS
group = form.addGroup(
"Optical Flow parameters",
expertLevel=LEVEL_ADVANCED,
condition="alignMethod==%d or alignMethod==%d " % (AL_OPTICAL, AL_DOSEFGPUOPTICAL),
)
group.addParam(
"winSize",
IntParam,
default=150,
label="Window size",
expertLevel=LEVEL_ADVANCED,
help="Window size (shifts are assumed to be constant within this window).",
)
# ---------------------------------- DosefGPU Params--------------------------------
# GROUP DOSEFGPU PARAMETERS
group = form.addGroup(
"DosefGPU/Croscorrelation parameters",
condition="alignMethod==%d "
"or alignMethod==%d"
"or alignMethod==%d"
"or alignMethod==%d" % (AL_DOSEFGPU, AL_DOSEFGPUOPTICAL, AL_CROSSCORRELATION, AL_CROSSCORRELATIONOPTICAL),
)
line = group.addLine(
"Used in final sum",
help="First and last frames used in alignment.\n" "The first frame in the stack is *0*.",
)
line.addParam("sumFrame0", IntParam, default=0, label="First")
line.addParam("sumFrameN", IntParam, default=0, label="Last", help="If *0*, use maximum value")
line = group.addLine("Crop offsets (px)")
line.addParam("cropOffsetX", IntParam, default=0, label="X")
line.addParam("cropOffsetY", IntParam, default=0, label="Y")
line = group.addLine(
"Crop dimensions (px)", help="How many pixels to crop from offset\n" "If equal to 0, use maximum size."
)
line.addParam("cropDimX", IntParam, default=0, label="X")
line.addParam("cropDimY", IntParam, default=0, label="Y")
group.addParam(
"binFactor",
IntParam,
default=1,
condition="alignMethod==%d " "or alignMethod==%d" % (AL_DOSEFGPU, AL_DOSEFGPUOPTICAL),
label="Binning factor",
help="1x or 2x. Bin stack before processing.",
)
group.addParam(
"filterFactor",
FloatParam,
default=4,
condition="alignMethod==%d " "or alignMethod==%d" % (AL_CROSSCORRELATION, AL_CROSSCORRELATIONOPTICAL),
label="Filter at (A)",
help="1x or 2x. Bin stack before processing.",
)
group.addParam(
"extraParams",
StringParam,
default="",
expertLevel=LEVEL_ADVANCED,
label="Additional parameters",
help="""
-bft 150 BFactor in pix^2.
-pbx 96 Box dimension for searching CC peak.
-fod 2 Number of frame offset for frame comparision.
-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.
-ssc 0 1: Save aligned stack. 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.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
self._defineAlignmentParams(form)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('inputCoordinates',
PointerParam,
pointerClass='SetOfCoordinates',
important=True,
label='Input coordinates')
form.addParam('boxSize',
IntParam,
default=0,
label='Particle box size (px)',
validators=[Positive],
help='In pixels. The box size is the size of the boxed '
'particles, actual particles may be smaller than '
'this.')
form.addParam('applyAlignment',
BooleanParam,
default=False,
label='Apply movie alignments to extract?',
help='If the input movies contains frames alignment, '
'you decide whether to use that information '
'for extracting the particles taking into account '
'the shifts between frames.')
line = form.addLine(
'Frames range',
help='Specify the frames range to extract particles. '
'The first frame is 1. If you set 0 in the '
'last frame, it means that you will use until the '
'last frame of the movie. If you apply the '
'previous alignment of the movies, you only can use '
'a frame range equal or less as used to alignment.')
line.addParam('frame0', IntParam, label='First')
line.addParam('frameN', IntParam, label='Last')
# TODO: implement this and extraction from movies, not frames
#form.addParam('avgFrames', IntParam, default=1,
# label='Average every so many frames', validators=[Positive],
# help='Average over this number of individual movie frames. '
# 'For Relion movie refinement it is recommended to '
# 'adjust this value to have a dose of at least '
# 'approximately 1 e/A^2 in the averaged frames, '
# 'so use a value higher than 1 if you have a '
# 'dose of less than 0.5-1 e/A^2 in each '
# 'individual movie frame.')
form.addParam(
'doBorders',
BooleanParam,
default=True,
label='Fill pixels outside borders',
help='Xmipp by default create blank particles whose boxes fall '
'outside of the micrograph borders. Set this '
'option to True if you want those pixels outside '
'the borders to be filled with the closest pixel '
'value available')
form.addSection(label='Preprocess')
form.addParam('doRemoveDust',
BooleanParam,
default=True,
important=True,
label='Dust removal (Recommended)',
help='Sets pixels with unusually large values to random '
'values from a Gaussian with zero-mean and '
'unity-standard deviation.')
form.addParam('thresholdDust',
FloatParam,
default=3.5,
condition='doRemoveDust',
expertLevel=LEVEL_ADVANCED,
label='Threshold for dust removal',
help='Pixels with a signal higher or lower than this '
'value times the standard deviation of the image '
'will be affected. For cryo, 3.5 is a good value. '
'For high-contrast negative stain, the signal '
'itself may be affected so that a higher value may '
'be preferable.')
form.addParam('doInvert',
BooleanParam,
default=None,
label='Invert contrast',
help='Invert the contrast if your particles are black '
'over a white background.')
form.addParam('doNormalize',
BooleanParam,
default=True,
label='Normalize (Recommended)',
help='It subtract a ramp in the gray values and '
'normalizes so that in the background there is 0 '
'mean and standard deviation 1.')
form.addParam('normType',
EnumParam,
choices=['OldXmipp', 'NewXmipp', 'Ramp'],
default=2,
condition='doNormalize',
expertLevel=LEVEL_ADVANCED,
display=EnumParam.DISPLAY_COMBO,
label='Normalization type',
help='OldXmipp (mean(Image)=0, stddev(Image)=1). \n'
'NewXmipp (mean(background)=0, '
'stddev(background)=1)\n'
'Ramp (subtract background+NewXmipp).')
form.addParam('backRadius',
IntParam,
default=-1,
condition='doNormalize',
label='Background radius (px)',
help='Pixels outside this circle are assumed to be '
'noise and their stddev is set to 1. Radius for '
'background circle definition (in pix.). If this '
'value is 0, then half the box size is used.',
expertLevel=LEVEL_ADVANCED)
form.addParallelSection(threads=3, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('alignMethod', EnumParam, choices=['optical flow'
, 'dosefgpu'
, 'dosefgpu + optical flow'
, 'average'
, 'croscorrelation'
, 'croscorrelation + optical flow'
],
label="Alignment method", default=AL_OPTICAL,
display=EnumParam.DISPLAY_COMBO,
help='Method to use for movie alignment. '
'dosefgpu requires a GPU. Croscorrelation '
'and dosefgpu with default parameters are equivalent. '
'Croscorrelation is a CPU implementation of dosefgpu '
'with limited functionality (only aligns whole frames)'
)
# GROUP COMMON PARAMETERS
group = form.addGroup('Common parameters')
line = group.addLine('Used in alignment',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0*.' )
line.addParam('alignFrame0', IntParam, default=0, label='First')
line.addParam('alignFrameN', IntParam, default=0, label='Last',
help='If *0*, use maximum value')
# GROUP GPU PARAMETERS
group = form.addGroup('GPU',condition="alignMethod==%d or (alignMethod==%d and expertLevel==%d)"
" or (alignMethod==%d and expertLevel==%d)"
% (AL_OPTICAL, AL_DOSEFGPUOPTICAL, LEVEL_ADVANCED, AL_DOSEFGPU, LEVEL_ADVANCED))
group.addParam('doGPU', BooleanParam, default=False,
label="Use GPU (vs CPU)",
condition="alignMethod==%d or alignMethod==%d" % (AL_OPTICAL, AL_DOSEFGPUOPTICAL),
help="Set to true if you want the GPU implementation of Optical Flow")
group.addParam('GPUCore', IntParam, default=0, expertLevel=LEVEL_ADVANCED,
label="Choose GPU core",
condition="doGPU or alignMethod==%d or alignMethod==%d " % (AL_DOSEFGPU, AL_DOSEFGPUOPTICAL),
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 OPTICAL FLOW PARAMETERS
group = form.addGroup('Optical Flow parameters', expertLevel=LEVEL_ADVANCED, condition="alignMethod==%d or alignMethod==%d or alignMethod==%d " % (AL_OPTICAL, AL_DOSEFGPUOPTICAL, AL_CROSSCORRELATIONOPTICAL))
group.addParam('winSize', IntParam, default=150,
label="Window size", expertLevel=LEVEL_ADVANCED,
help="Window size (shifts are assumed to be constant within this window).")
group.addParam('groupSize', IntParam, default=1,
label="Group Size", expertLevel=LEVEL_ADVANCED,
help="In cases with low SNR, the average of a number of frames can be used in alignment")
group.addParam('doSaveMovie', BooleanParam, default=False,
label="Save movie", expertLevel=LEVEL_ADVANCED,
help="Save Aligned movie")
#---------------------------------- DosefGPU Params--------------------------------
# GROUP DOSEFGPU PARAMETERS
group = form.addGroup('DosefGPU/Croscorrelation parameters',condition="alignMethod==%d "
"or alignMethod==%d"
"or alignMethod==%d"
"or alignMethod==%d" %
(AL_DOSEFGPU,\
AL_DOSEFGPUOPTICAL,\
AL_CROSSCORRELATION,\
AL_CROSSCORRELATIONOPTICAL)
)
line = group.addLine('Used in final sum',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0*.' )
line.addParam('sumFrame0', IntParam, default=0, label='First')
line.addParam('sumFrameN', IntParam, default=0, label='Last',
help='If *0*, use maximum value')
line = group.addLine('Crop offsets (px)')
line.addParam('cropOffsetX', IntParam, default=0, label='X')
line.addParam('cropOffsetY', IntParam, default=0, label='Y')
line = group.addLine('Crop dimensions (px)',
help='How many pixels to crop from offset\n'
'If equal to 0, use maximum size.')
line.addParam('cropDimX', IntParam, default=0, label='X')
line.addParam('cropDimY', IntParam, default=0, label='Y')
group.addParam('binFactor', IntParam, default=1,condition="alignMethod==%d "
"or alignMethod==%d" %
(AL_DOSEFGPU,\
AL_DOSEFGPUOPTICAL\
),
label='Binning factor',
help='1x or 2x. Bin stack before processing.')
group.addParam('filterFactor', FloatParam, default=4,condition="alignMethod==%d "
"or alignMethod==%d" %
(AL_CROSSCORRELATION,\
AL_CROSSCORRELATIONOPTICAL\
),
label='Filter at (A)',
help='Maximum frequency for a low pass filter')
group.addParam('extraParams', StringParam, default='',
expertLevel=LEVEL_ADVANCED,
label='Additional parameters',
help="""
-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.
-ssc 0 1: Save aligned stack. 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.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('inputCoordinates', PointerParam,
pointerClass='SetOfCoordinates',
important=True,
label='Input coordinates')
form.addParam('boxSize', IntParam, default=0,
label='Particle box size (px)', validators=[Positive],
help='In pixels. The box size is the size of the boxed '
'particles, actual particles may be smaller than '
'this.')
form.addParam('applyAlignment', BooleanParam, default=False,
label='Apply movie alignments to extract?',
help='If the input movies contains frames alignment, '
'you decide whether to use that information '
'for extracting the particles taking into account '
'the shifts between frames.')
line = form.addLine('Frames range',
help='Specify the frames range to extract particles. '
'The first frame is 1. If you set 0 in the '
'last frame, it means that you will use until the '
'last frame of the movie. If you apply the '
'previous alignment of the movies, you only can use '
'a frame range equal or less as used to alignment.')
line.addParam('frame0', IntParam, label='First')
line.addParam('frameN', IntParam, label='Last')
# TODO: implement this and extraction from movies, not frames
#form.addParam('avgFrames', IntParam, default=1,
# label='Average every so many frames', validators=[Positive],
# help='Average over this number of individual movie frames. '
# 'For Relion movie refinement it is recommended to '
# 'adjust this value to have a dose of at least '
# 'approximately 1 e/A^2 in the averaged frames, '
# 'so use a value higher than 1 if you have a '
# 'dose of less than 0.5-1 e/A^2 in each '
# 'individual movie frame.')
form.addParam('doBorders', BooleanParam, default=True,
label='Fill pixels outside borders',
help='Xmipp by default create blank particles whose boxes fall '
'outside of the micrograph borders. Set this '
'option to True if you want those pixels outside '
'the borders to be filled with the closest pixel '
'value available')
form.addSection(label='Preprocess')
form.addParam('doRemoveDust', BooleanParam, default=True,
important=True,
label='Dust removal (Recommended)',
help='Sets pixels with unusually large values to random '
'values from a Gaussian with zero-mean and '
'unity-standard deviation.')
form.addParam('thresholdDust', FloatParam, default=3.5,
condition='doRemoveDust', expertLevel=LEVEL_ADVANCED,
label='Threshold for dust removal',
help='Pixels with a signal higher or lower than this '
'value times the standard deviation of the image '
'will be affected. For cryo, 3.5 is a good value. '
'For high-contrast negative stain, the signal '
'itself may be affected so that a higher value may '
'be preferable.')
form.addParam('doInvert', BooleanParam, default=None,
label='Invert contrast',
help='Invert the contrast if your particles are black '
'over a white background.')
form.addParam('doNormalize', BooleanParam, default=True,
label='Normalize (Recommended)',
help='It subtract a ramp in the gray values and '
'normalizes so that in the background there is 0 '
'mean and standard deviation 1.')
form.addParam('normType', EnumParam,
choices=['OldXmipp', 'NewXmipp', 'Ramp'], default=2,
condition='doNormalize', expertLevel=LEVEL_ADVANCED,
display=EnumParam.DISPLAY_COMBO,
label='Normalization type',
help='OldXmipp (mean(Image)=0, stddev(Image)=1). \n'
'NewXmipp (mean(background)=0, '
'stddev(background)=1)\n'
'Ramp (subtract background+NewXmipp).')
form.addParam('backRadius', IntParam, default=-1,
condition='doNormalize',
label='Background radius (px)',
help='Pixels outside this circle are assumed to be '
'noise and their stddev is set to 1. Radius for '
'background circle definition (in pix.). If this '
'value is 0, then half the box size is used.',
expertLevel=LEVEL_ADVANCED)
form.addParallelSection(threads=3, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
group = form.addGroup('Frame range')
line1 = group.addLine('Used in alignment',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0*.')
line1.addParam('alignFrame0', IntParam, default=0, label='First')
line1.addParam('alignFrameN',
IntParam,
default=0,
label='Last',
help='If *0*, use maximum value')
line2 = group.addLine('Used in final sum',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0*.')
line2.addParam('sumFrame0', IntParam, default=0, label='First')
line2.addParam('sumFrameN',
IntParam,
default=0,
label='Last',
help='If *0*, use maximum value')
form.addParam('gpuId',
StringParam,
default='0',
expertLevel=LEVEL_ADVANCED,
label='GPU id',
help='GPU device ID')
form.addParam('extraParams',
StringParam,
default='',
expertLevel=LEVEL_ADVANCED,
label='Additional parameters',
help="""
-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.
-ssc 0 1: Save aligned stack. 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.
""")
group2 = form.addGroup('Crop and binning')
line = group2.addLine('Crop offsets (px)')
line.addParam('cropOffsetX', IntParam, default=0, label='X')
line.addParam('cropOffsetY', IntParam, default=0, label='Y')
line = group2.addLine('Crop dimensions (px)',
help='How many pixels to crop from offset\n'
'If equal to 0, use maximum size.')
line.addParam('cropDimX', IntParam, default=0, label='X')
line.addParam('cropDimY', IntParam, default=0, label='Y')
group2.addParam('binFactor',
IntParam,
default=1,
label='Binning factor',
help='1x or 2x. Bin stack before processing.')
form.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam(
'alignMethod',
EnumParam,
choices=[
'optical flow', 'dosefgpu', 'dosefgpu + optical flow',
'average', 'croscorrelation', 'croscorrelation + optical flow'
],
label="Alignment method",
default=AL_OPTICAL,
display=EnumParam.DISPLAY_COMBO,
help='Method to use for movie alignment:\n'
'1. dosefgpu performs in-plane drift correction and requires a GPU.\n'
'2. Croscorrelation is a CPU implementation of dosefgpu '
'with limited functionality (only aligns whole frames). With default parameters '
'it is equivalent to dosefgpu.\n'
'3. Optical flow works best for correction of local beam-induced motion.\n'
'4. Average will simply sum the frames together.')
# GROUP COMMON PARAMETERS
group = form.addGroup('Common parameters')
line = group.addLine('Used in alignment',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0* '
'If the last frame is *0*, use maximum value')
line.addParam('alignFrame0', IntParam, default=0, label='First')
line.addParam('alignFrameN', IntParam, default=0, label='Last')
# GROUP GPU PARAMETERS
group = form.addGroup(
'GPU',
condition="alignMethod==%d or (alignMethod==%d and expertLevel==%d)"
" or (alignMethod==%d and expertLevel==%d)" %
(AL_OPTICAL, AL_DOSEFGPUOPTICAL, LEVEL_ADVANCED, AL_DOSEFGPU,
LEVEL_ADVANCED))
group.addParam(
'doGPU',
BooleanParam,
default=False,
label="Use GPU (vs CPU)",
condition="alignMethod==%d or alignMethod==%d" %
(AL_OPTICAL, AL_DOSEFGPUOPTICAL),
help=
"Set to true if you want the GPU implementation of Optical Flow")
group.addParam(
'GPUCore',
IntParam,
default=0,
expertLevel=LEVEL_ADVANCED,
label="Choose GPU core",
condition="doGPU or alignMethod==%d or alignMethod==%d " %
(AL_DOSEFGPU, AL_DOSEFGPUOPTICAL),
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 OPTICAL FLOW PARAMETERS
group = form.addGroup(
'Optical Flow parameters',
expertLevel=LEVEL_ADVANCED,
condition="alignMethod==%d or alignMethod==%d or alignMethod==%d "
% (AL_OPTICAL, AL_DOSEFGPUOPTICAL, AL_CROSSCORRELATIONOPTICAL))
group.addParam(
'winSize',
IntParam,
default=150,
label="Window size",
expertLevel=LEVEL_ADVANCED,
help=
"Window size (shifts are assumed to be constant within this window)."
)
group.addParam(
'groupSize',
IntParam,
default=1,
label="Group Size",
expertLevel=LEVEL_ADVANCED,
help=
"In cases with low SNR, the average of a number of frames can be used in alignment"
)
group.addParam('doSaveMovie',
BooleanParam,
default=False,
label="Save movie",
expertLevel=LEVEL_ADVANCED,
help="Save Aligned movie")
#---------------------------------- DosefGPU Params--------------------------------
# GROUP DOSEFGPU PARAMETERS
group = form.addGroup('DosefGPU/Croscorrelation parameters',condition="alignMethod==%d "
"or alignMethod==%d"
"or alignMethod==%d"
"or alignMethod==%d" %
(AL_DOSEFGPU,\
AL_DOSEFGPUOPTICAL,\
AL_CROSSCORRELATION,\
AL_CROSSCORRELATIONOPTICAL)
)
line = group.addLine('Used in final sum',
help='First and last frames used in alignment.\n'
'The first frame in the stack is *0*.')
line.addParam('sumFrame0', IntParam, default=0, label='First')
line.addParam('sumFrameN',
IntParam,
default=0,
label='Last',
help='If *0*, use maximum value')
line = group.addLine('Crop offsets (px)')
line.addParam('cropOffsetX', IntParam, default=0, label='X')
line.addParam('cropOffsetY', IntParam, default=0, label='Y')
line = group.addLine('Crop dimensions (px)',
help='How many pixels to crop from offset\n'
'If equal to 0, use maximum size.')
line.addParam('cropDimX', IntParam, default=0, label='X')
line.addParam('cropDimY', IntParam, default=0, label='Y')
group.addParam('binFactor', IntParam, default=1,condition="alignMethod==%d "
"or alignMethod==%d" %
(AL_DOSEFGPU,\
AL_DOSEFGPUOPTICAL\
),
label='Binning factor',
help='1x or 2x. Bin stack before processing.')
group.addParam('filterFactor', FloatParam, default=4,condition="alignMethod==%d "
"or alignMethod==%d" %
(AL_CROSSCORRELATION,\
AL_CROSSCORRELATIONOPTICAL\
),
label='Filter at (A)',
help='Maximum frequency for a low pass filter')
group.addParam('extraParams',
StringParam,
default='',
expertLevel=LEVEL_ADVANCED,
label='Additional parameters',
help="""
-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.
-ssc 0 1: Save aligned stack. 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.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam(
"alignFrameRange",
IntParam,
default=-1,
label="Number frames per movie ",
help="How many frames per monie. -1 -> all frames ",
)
form.addParam(
"doApplyDoseFilter",
BooleanParam,
default=True,
label="Apply Dose filter",
help="Apply a dose-dependent filter to frames before summing them",
)
form.addParam(
"exposurePerFrame",
FloatParam,
label="Exposure per frame (e/A^2)",
help="Exposure per frame, in electrons per square Angstrom",
)
# group = form.addGroup('Expert Options')
form.addParam(
"minShiftInitSearch",
FloatParam,
default=2.0,
label="Min. Shift Initial search (A)",
help="Initial search will be limited to between the inner and outer radii",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"OutRadShiftLimit",
FloatParam,
default=200.0,
label="Outer radius shift limit (A)",
help="The maximum shift of each alignment step will be limited to this value",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"Bfactor",
FloatParam,
default=1500.0,
label="B-factor (A^2)",
help="B-factor to apply to images (A^2)",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"HWVertFourMask",
IntParam,
default=1,
label="Half-width vertical Fourier mask",
help="The vertical line mask will be twice this size. The central cross mask helps reduce problems by line artefacts from the detector",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"HWHoriFourMask",
IntParam,
default=1,
label="Half-width horizontal Fourier mask",
help="The horizontal line mask will be twice this size. The central cross mask helps reduce problems by line artefacts from the detector",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"terminationShiftThreshold",
FloatParam,
default=0.1,
label="Termination shift threshold",
help="Alignment will stop at this number, even if the threshold shift is not reached",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"maximumNumberIterations",
IntParam,
default=10,
label="Maximum number of iterations",
help="Maximum number of iterations",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"doRestoreNoisePower",
BooleanParam,
default=True,
label="Restore Noise Power? ",
help="Restore Noise Power? ",
expertLevel=LEVEL_ADVANCED,
)
form.addParam(
"doVerboseOutput",
BooleanParam,
default=False,
label="Verbose Output?",
help="Verbose Output?",
expertLevel=LEVEL_ADVANCED,
)
form.addParallelSection(threads=1, mpi=1)
def _defineParams(self, form):
ProtProcessMovies._defineParams(self, form)
form.addParam('alignFrameRange',
IntParam,
default=-1,
label='Number frames per movie ',
help='How many frames per monie. -1 -> all frames ')
form.addParam('doApplyDoseFilter',
BooleanParam,
default=True,
label='Apply Dose filter',
help='Apply a dose-dependent filter to frames before '
'summing them')
form.addParam('exposurePerFrame',
FloatParam,
label='Exposure per frame (e/A^2)',
help='Exposure per frame, in electrons per square '
'Angstrom')
#group = form.addGroup('Expert Options')
form.addParam('minShiftInitSearch',
FloatParam,
default=2.,
label='Min. Shift Initial search (A)',
help='Initial search will be limited to between the '
'inner and outer radii',
expertLevel=LEVEL_ADVANCED)
form.addParam('OutRadShiftLimit',
FloatParam,
default=200.,
label='Outer radius shift limit (A)',
help='The maximum shift of each alignment step will be '
'limited to this value',
expertLevel=LEVEL_ADVANCED)
form.addParam('Bfactor',
FloatParam,
default=1500.,
label='B-factor (A^2)',
help='B-factor to apply to images (A^2)',
expertLevel=LEVEL_ADVANCED)
form.addParam('HWVertFourMask',
IntParam,
default=1,
label='Half-width vertical Fourier mask',
help='The vertical line mask will be twice this size. '
'The central cross mask helps reduce problems by '
'line artefacts from the detector',
expertLevel=LEVEL_ADVANCED)
form.addParam('HWHoriFourMask',
IntParam,
default=1,
label='Half-width horizontal Fourier mask',
help='The horizontal line mask will be twice this size. '
'The central cross mask helps reduce problems by '
'line artefacts from the detector',
expertLevel=LEVEL_ADVANCED)
form.addParam('terminationShiftThreshold',
FloatParam,
default=0.1,
label='Termination shift threshold',
help='Alignment will stop at this number, even if the '
'threshold shift is not reached',
expertLevel=LEVEL_ADVANCED)
form.addParam('maximumNumberIterations',
IntParam,
default=10,
label='Maximum number of iterations',
help='Maximum number of iterations',
expertLevel=LEVEL_ADVANCED)
form.addParam('doRestoreNoisePower',
BooleanParam,
default=True,
label='Restore Noise Power? ',
help='Restore Noise Power? ',
expertLevel=LEVEL_ADVANCED)
form.addParam('doVerboseOutput',
BooleanParam,
default=False,
label='Verbose Output?',
help='Verbose Output?',
expertLevel=LEVEL_ADVANCED)
form.addParallelSection(threads=1, mpi=1)