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('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('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='')