def _defineParams(self, form):
ProtParticlePicking._defineParams(self, form)
form.addParam('useNewBoxer',
BooleanParam,
default=True,
label='Use new e2boxer?',
help='Requires EMAN version 2.21 or newer')
form.addParam('boxSize',
IntParam,
default=-1,
condition='useNewBoxer',
label='Box size (px)',
help="Box size in pixels.")
form.addParam('particleSize',
IntParam,
default=-1,
condition='useNewBoxer',
label='Particle size (px)',
help="Longest axis of particle in pixels (diameter, "
"not radius).")
form.addParam('invertY',
BooleanParam,
default=False,
label='Invert Y coordinates',
help='In some cases, using dm3 or tiff Y coordinates '
'must be flipped. Check output and activate this'
' if needed.')
form.addParallelSection(threads=1, mpi=0)
def _defineParams(self, form):
ProtParticlePicking._defineParams(self, form)
form.addParam('diameter',
IntParam,
default=100,
label='Diameter of particle')
form.addParam('invert',
BooleanParam,
default=False,
label='Invert',
help="Invert image before picking, "
"DoG normally picks white particles.")
form.addParam('threshold',
FloatParam,
default=0.5,
label='Threshold',
help="Threshold in standard "
"deviations above the mean, "
"e.g. --thresh=0.7")
form.addParam(
'extraParams',
StringParam,
expertLevel=LEVEL_ADVANCED,
label='Additional parameters',
help='Additional parameters for dogpicker: \n --numberSizes, '
'--sizeRange, --threshold,...')
def _defineParams(self, form):
ProtParticlePicking._defineParams(self, form)
form.addParam('invertY',
BooleanParam,
default=False,
label='Invert Y coordinates',
help='In some cases, using dm3 or tiff Y coordinates '
'must be flipped. Check output and activate this'
' if needed.')
def _defineParams(self, form):
ProtParticlePicking._defineParams(self, form)
form.addParam('boxSize', IntParam, default=100,
label='Box Size')
line = form.addLine('Picker range',
help='')
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')
def _defineParams(self, form):
ProtParticlePicking._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 _defineParams(self, form):
ProtParticlePicking._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 _defineParams(self, form):
ProtParticlePicking._defineParams(self, form)
form.addParam('diameter', IntParam, default=100,
label='Diameter of particle')
form.addParam('invert', BooleanParam, default=False,
label='Invert', help = "Invert image before picking, DoG normally picks white particles.")
form.addParam('threshold', FloatParam, default=0.5,
label='Threshold', help = "Threshold in standard deviations above the mean, e.g. --thresh=0.7")
# form.addParam('numberSizes', IntParam, expertLevel=LEVEL_ADVANCED,
# label='Number of sizes', help = "Number of different sizes to try.")
# form.addParam('sizeRange', IntParam, expertLevel=LEVEL_ADVANCED,
# label='Size range', help = "Size range in pixels about diam to search.")
# form.addParam('maxThreshold', FloatParam, expertLevel=LEVEL_ADVANCED,
# label='Max threshold', help = "Threshold in standard deviations above the mean, e.g. --thresh=0.7")
# form.addParam('maxArea', FloatParam, expertLevel=LEVEL_ADVANCED,
# label='Max area', help = "When thresholded the peak must be less than maxarea*pi*r^2.")
# form.addParam('maxPeaks', FloatParam, expertLevel=LEVEL_ADVANCED,
# label='Max peaks', help = "Maximum number of allowed peaks.")
form.addParam('extraParams', StringParam, expertLevel=LEVEL_ADVANCED,
label='Additional parameters',
help='Additional parameters for dogpicker: \n --numberSizes, --sizeRange, --threshold,...')
def _defineParams(self, form):
ProtParticlePicking._defineParams(self, form)
form.addParam('diameter', IntParam, default=100,
label='Diameter of particle')
form.addParam('invert', BooleanParam, default=False,
label='Invert', help = "Invert image before picking, DoG normally picks white particles.")
form.addParam('threshold', FloatParam, default=0.5,
label='Threshold', help = "Threshold in standard deviations above the mean, e.g. --thresh=0.7")
# form.addParam('numberSizes', IntParam, expertLevel=LEVEL_ADVANCED,
# label='Number of sizes', help = "Number of different sizes to try.")
# form.addParam('sizeRange', IntParam, expertLevel=LEVEL_ADVANCED,
# label='Size range', help = "Size range in pixels about diam to search.")
# form.addParam('maxThreshold', FloatParam, expertLevel=LEVEL_ADVANCED,
# label='Max threshold', help = "Threshold in standard deviations above the mean, e.g. --thresh=0.7")
# form.addParam('maxArea', FloatParam, expertLevel=LEVEL_ADVANCED,
# label='Max area', help = "When thresholded the peak must be less than maxarea*pi*r^2.")
# form.addParam('maxPeaks', FloatParam, expertLevel=LEVEL_ADVANCED,
# label='Max peaks', help = "Maximum number of allowed peaks.")
form.addParam('extraParams', StringParam, expertLevel=LEVEL_ADVANCED,
label='Additional parameters',
help='Additional parameters for dogpicker: \n --numberSizes, --sizeRange, --threshold,...')
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
ProtParticles.__init__(self, **args)
self.allowMpi = False
self.allowThreads = False
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
def getFiles(self):
filePaths = self.inputMicrographs.get().getFiles() | ProtParticlePicking.getFiles(self)
return filePaths
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
# The following attribute is only for testing
self.importFolder = String(args.get('importFolder', None))
def getFiles(self):
filePaths = self.inputMicrographs.get().getFiles() | ProtParticlePicking.getFiles(self)
return filePaths
def _runSteps(self, startIndex):
# Redefine run to change to workingDir path
# Change to protocol working directory
self._enterWorkingDir()
ProtParticlePicking._runSteps(self, startIndex)
def getFiles(self):
return self.inputMicrographs.get().getFiles() | ProtParticlePicking.getFiles(self)
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
# The following attribute is only for testing
self.importFolder = String(args.get('importFolder', None))
def _defineParams(self, form):
ProtParticlePicking._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 getFiles(self):
return self.inputMicrographs.get().getFiles() | ProtParticlePicking.getFiles(self)
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
self.extraParams = 'pixel_input=1:pixel_output=1:invert_contrast=True:use_variance=True'
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
self.extraParams = 'pixel_input=1:pixel_output=1:invert_contrast=True:use_variance=True'
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
self.stepsExecutionMode = params.STEPS_SERIAL
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
ProtParticles.__init__(self, **args)
self.allowMpi = False
self.allowThreads = False
def __init__(self, **args):
ProtParticlePicking.__init__(self, **args)
self.stepsExecutionMode = STEPS_SERIAL
