def _defineParams(self, form):
ProtParticlePickingAuto._defineParams(self, form)
form.addParam('boxSize',
IntParam,
default=100,
allowsPointers=True,
label='Box Size',
help='Box size in pixels')
line = form.addLine('Picker range',
help='CCF threshold range for automatic picking')
line.addParam('lowerThreshold', FloatParam, default='1', label='Lower')
line.addParam('higherThreshold',
FloatParam,
default='30',
label='Higher')
form.addParam('gaussWidth',
FloatParam,
default='1',
label='Gauss Width',
help='Width of the Gaussian kernel used')
form.addParam('useVarImg',
BooleanParam,
default=False,
expertLevel=LEVEL_ADVANCED,
label='Use variance image?')
form.addParam('doInvert',
BooleanParam,
default=True,
expertLevel=LEVEL_ADVANCED,
label='Invert contrast?',
help='Picker expects particles to be white.')
form.addParallelSection(threads=1, mpi=0)
def _defineParams(self, form):
ProtParticlePickingAuto._defineParams(self, form)
form.addParam('diameter',
params.IntParam,
default=100,
label='Diameter of particle')
form.addParam('invert',
params.BooleanParam,
default=False,
label='Invert',
help="Invert image before picking, DoG normally picks "
"white particles.")
form.addParam('threshold',
params.FloatParam,
default=0.5,
label='Threshold',
help="Threshold in standard deviations above the mean, "
"e.g. --thresh=0.7")
form.addParam('extraParams',
params.StringParam,
expertLevel=params.LEVEL_ADVANCED,
label='Additional parameters',
help='Additional parameters for dogpicker: \n '
'--numberSizes, --sizeRange, --threshold,...')
def _defineParams(self, form):
ProtParticlePickingAuto._defineParams(self, form)
form.addParam('boxSize',
IntParam,
default=128,
label='Box size (px)',
help="Box size in pixels.")
form.addParam('particleSize',
IntParam,
default=100,
label='Particle size (px)',
help="Longest axis of particle in pixels (diameter, "
"not radius).")
form.addParam(
'boxerMode',
EnumParam,
choices=['local search', 'by ref', 'gauss', 'neural net'],
label="Autopicker mode:",
default=AUTO_LOCAL,
display=EnumParam.DISPLAY_COMBO,
help="Choose autopicker mode:\n\n"
" _local search_ - Reference based search by "
"downsampling and 2-D alignment to references.\n"
" _by ref_ - simple reference-based "
"cross-correlation picker with exhaustive "
"rotational search.\n"
" _gauss_ - Gaussian sparx picker.\n"
" _neural net_ - convolutional neural network "
"boxer.")
form.addParam('threshold',
FloatParam,
default='5.0',
label='Threshold')
form.addSection('References')
form.addParam('goodRefs',
PointerParam,
pointerClass='SetOfAverages',
important=True,
label="Good references",
help="Good particle references.")
form.addParam('badRefs',
PointerParam,
pointerClass='SetOfAverages',
allowsNull=True,
label="Bad references",
help="Bad particle references like ice contamination "
"or large aggregation.")
form.addParam('bgRefs',
PointerParam,
pointerClass='SetOfAverages',
allowsNull=True,
label="Background references",
help="Pure noise regions in micrograph.")
form.addParallelSection(threads=1, mpi=0)
def _defineParams(self, form):
ProtParticlePickingAuto._defineParams(self, form)
form.addParam('boxSize', IntParam, default=100,
label='Box Size', help='Box size in pixels')
line = form.addLine('Picker range',
help='CCF threshold range for automatic picking')
line.addParam('lowerThreshold', FloatParam, default='1',
label='Lower')
line.addParam('higherThreshold', FloatParam, default='30',
label='Higher')
form.addParam('gaussWidth', FloatParam, default='1',
label='Gauss Width',
help='Width of the Gaussian kernel used')
def _createSetOfCoordinates(self, micSet, suffix=''):
""" Override this method to set the box size. """
coordSet = ProtParticlePickingAuto._createSetOfCoordinates(self, micSet,
suffix=suffix)
coordSet.setBoxSize(self.getBoxSize())
return coordSet
def _createSetOfCoordinates(self, micSet, suffix=''):
""" Override this method to set the box size. """
coordSet = ProtParticlePickingAuto._createSetOfCoordinates(
self, micSet, suffix=suffix)
coordSet.setBoxSize(self.getBoxSize())
return coordSet
def _defineParams(self, form):
ProtParticlePickingAuto._defineParams(self, form)
form.addParam('radius', params.IntParam,
label='Radius of particle (px)')
form.addParam('height', params.FloatParam, default=0.5,
label="Min. height",
help='The minimum height of the virus peak compared to '
'the average peak.')
form.addParam('squareWidth', params.FloatParam, default=1.5,
label="Square width",
help='Minimum distance between two viruses is:\n'
'2 * SQUARE_WIDTH_PARAM * RADIUS.')
form.addParam('ringWidth', params.FloatParam, default=1.2,
label="Ring width",
help='Width of the ring in ring filter is: \n'
'RING_WIDTH_PARAM * RADIUS - RADIUS.')
form.addParam('dist', params.FloatParam, default=0.1,
label="Distance",
help='Distance which the peak can move in x or y '
'direction during center refinement is: \n'
'DIST_PARAM * RADIUS.')
form.addParam('reduction', params.IntParam, default=0,
label="Reduction",
help='REDUCTION_PARAM * REDUCTION_PARAM pixels are '
'averaged before filtering. The value has to be '
'integer. Special value 0 means that the program '
'determines the parameter.')
form.addParam('doRefine', params.BooleanParam, default=True,
label="Refine particle centers?",
help='')
form.addParam('doSectorTest', params.BooleanParam, default=True,
label="Perform sector test?",
help='')
form.addParam('doHeightTest', params.BooleanParam, default=True,
label="Perform height test?",
help='')
form.addParam('doDistanceTest', params.BooleanParam, default=True,
label="Perform peak pair distance test?",
help='')
def _defineParams(self, form):
ProtParticlePickingAuto._defineParams(self, form)
form.addParam('diameter', params.IntParam, default=100,
label='Diameter of particle')
form.addParam('invert', params.BooleanParam, default=False,
label='Invert',
help = "Invert image before picking, DoG normally picks "
"white particles.")
form.addParam('threshold', params.FloatParam, default=0.5,
label='Threshold',
help = "Threshold in standard deviations above the mean, "
"e.g. --thresh=0.7")
form.addParam('extraParams', params.StringParam,
expertLevel=params.LEVEL_ADVANCED,
label='Additional parameters',
help='Additional parameters for dogpicker: \n '
'--numberSizes, --sizeRange, --threshold,...')
def _insertAllSteps(self):
self.inputStreaming = self.getInputMicrographs().isStreamOpen()
if self.inputStreaming and not self.isRunOptimize():
# If the input is in streaming, follow the base class policy
# about inserting new steps and discovery new input/output
ProtParticlePickingAuto._insertAllSteps(self)
self.createOutputStep = self._doNothing
else:
# If not in streaming, then we will just insert a single step to
# pick all micrographs at once since it is much faster
self._insertInitialSteps()
self._insertFunctionStep('_pickMicrographsFromStar',
self._getPath('input_micrographs.star'),
*self._getPickArgs())
self._insertFunctionStep('createOutputStep')
# Disable streaming functions:
self._insertFinalSteps = self._doNothing
self._stepsCheck = self._doNothing
def _insertAllSteps(self):
self.inputStreaming = self.getInputMicrographs().isStreamOpen()
if self.inputStreaming and not self.isRunOptimize():
# If the input is in streaming, follow the base class policy
# about inserting new steps and discovery new input/output
ProtParticlePickingAuto._insertAllSteps(self)
self.createOutputStep = self._doNothing
else:
# If not in streaming, then we will just insert a single step to
# pick all micrographs at once since it is much faster
self._insertInitialSteps()
self._insertFunctionStep('_pickMicrographsFromStar',
self._getPath('input_micrographs.star'),
*self._getPickArgs())
self._insertFunctionStep('createOutputStep')
# Disable streaming functions:
self._insertFinalSteps = self._doNothing
self._stepsCheck = self._doNothing
def _defineParams(self, form):
ProtParticlePickingAuto._defineParams(self, form)
form.addParam('boxSize',
IntParam,
default=100,
label='Box Size',
help='Box size in pixels')
line = form.addLine('Picker range',
help='CCF threshold range for automatic picking')
line.addParam('lowerThreshold', FloatParam, default='1', label='Lower')
line.addParam('higherThreshold',
FloatParam,
default='30',
label='Higher')
form.addParam('gaussWidth',
FloatParam,
default='1',
label='Gauss Width',
help='Width of the Gaussian kernel used')
def __init__(self, **args):
ProtParticlePickingAuto.__init__(self, **args)
def __init__(self, **kwargs):
ProtParticlePickingAuto.__init__(self, **kwargs)
self.extraParams = ('pixel_input=1:pixel_output=1:invert_contrast'
'=True:use_variance=True')
def __init__(self, **kwargs):
ProtParticlePickingAuto.__init__(self, **kwargs)
self.extraParams = ('pixel_input=1:pixel_output=1:invert_contrast'
'=True:use_variance=True')
def getFiles(self):
return (self.inputMicrographs.get().getFiles() |
ProtParticlePickingAuto.getFiles(self))
def __init__(self, **kwargs):
ProtParticlePickingAuto.__init__(self, **kwargs)
self.stepsExecutionMode = STEPS_PARALLEL
def __init__(self, **kwargs):
ProtParticlePickingAuto.__init__(self, **kwargs)
def getFiles(self):
return (self.inputMicrographs.get().getFiles()
| ProtParticlePickingAuto.getFiles(self))
def __init__(self, **kwargs):
ProtParticlePickingAuto.__init__(self, **kwargs)
self.extraParams = 'pixel_input=1:pixel_output=1'