def _defineParams(self, form):
ProtExtractMovieParticles._defineParams(self, form)
form.addParam('inputCoordinates', PointerParam, pointerClass='SetOfCoordinates',
important=True,
label='Input coordinates')
form.addParam('boxSize', IntParam, default=0,
label='Particle box size', 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 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 from.\n'
' _First_: 1 will be the first frame in the movie.\n'
' _Last_: For any value <= 0, the range will go until '
'the last frame. ')
line.addParam('firstFrame', IntParam, default=1,
label='First')
line.addParam('lastFrame', IntParam, default=0,
label='Last')
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=False,
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). \n ')
form.addParam('backRadius', IntParam, default=-1, condition='doNormalize',
label='Background radius',
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=0, mpi=0)
form.addParallelSection(threads=2, mpi=1)
def _insertAllSteps(self):
#ROB: deal with the case in which sampling rate use for picking and movies
#is different
inputCoords = self.inputCoordinates.get()
#coordinates sampling mic used for picking
samplingCoords = inputCoords.getMicrographs().getSamplingRate()
#coordinates sampling input mic
samplingMic = self.inputMovies.get().getSamplingRate()
self.factor = samplingMic / samplingCoords
#factor = samplingCoords / samplingMic
ProtExtractMovieParticles._insertAllSteps(self)
def _insertAllSteps(self):
#ROB: deal with the case in which sampling rate use for picking and movies
#is different
inputCoords = self.inputCoordinates.get()
#coordinates sampling mic used for picking
samplingCoords = inputCoords.getMicrographs().getSamplingRate()
#coordinates sampling input mic
samplingMic = self.inputMovies.get().getSamplingRate()
self.factor = samplingMic / samplingCoords
#factor = samplingCoords / samplingMic
ProtExtractMovieParticles._insertAllSteps(self)
def __init__(self, **kwargs):
ProtExtractMovieParticles.__init__(self, **kwargs)
self.stepsExecutionMode = STEPS_PARALLEL
def _defineParams(self, form):
ProtExtractMovieParticles._defineParams(self, form)
form.addParam('inputCoordinates',
PointerParam,
pointerClass='SetOfCoordinates',
important=True,
label='Input coordinates')
form.addParam(
'boxSize',
IntParam,
default=0,
label='Particle box size',
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 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 from.\n'
' _First_: 1 will be the first frame in the movie.\n'
' _Last_: For any value <= 0, the range will go until '
'the last frame. ')
line.addParam('firstFrame', IntParam, default=1, label='First')
line.addParam('lastFrame', IntParam, default=0, label='Last')
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=False,
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). \n ')
form.addParam(
'backRadius',
IntParam,
default=-1,
condition='doNormalize',
label='Background radius',
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=0, mpi=0)
form.addParallelSection(threads=2, mpi=1)
def __init__(self, **kwargs):
ProtExtractMovieParticles.__init__(self, **kwargs)
self.stepsExecutionMode = STEPS_SERIAL
self.movieDict = {}
self.ptclDict = {}
def __init__(self, **kwargs):
ProtExtractMovieParticles.__init__(self, **kwargs)
self.stepsExecutionMode = STEPS_PARALLEL