Source code for relion.protocols.protocol_autopick_log

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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# *  All comments concerning this program package may be sent to the
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from os.path import relpath

import pyworkflow.protocol.params as params
from pyworkflow.protocol import STEPS_SERIAL
from pwem.protocols import ProtParticlePickingAuto

from .protocol_autopick import ProtRelionAutopickBase


[docs]class ProtRelionAutopickLoG(ProtRelionAutopickBase): """ This Relion protocol uses 'relion_autopick' program for the Laplacian of Gaussian (LoG) option. """ _label = 'auto-picking LoG' def __init__(self, **kwargs): ProtParticlePickingAuto.__init__(self, **kwargs) self.stepsExecutionMode = STEPS_SERIAL # -------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputMicrographs', params.PointerParam, pointerClass='SetOfMicrographs', label='Input micrographs', important=True, help='Select the input micrographs. ' 'If using the *Optimize* mode, just a subset of ' 'micrographs are used to compute the FOM maps. ' 'If in *Compute* mode, all micrographs will be ' 'auto-picked.') form.addParam('boxSize', params.IntParam, label='Box size (px)', help="Box size in pixels.") group = form.addGroup('Laplacian of Gaussian') line = group.addLine('Diameter for LoG filter (A)', help="Min and Max of LoG filter") line.addParam('minDiameter', params.IntParam, default=200, label='Min') line.addParam('maxDiameter', params.IntParam, default=250, label='Max') group.addParam('areParticlesWhite', params.BooleanParam, default=False, label='Are the particles white?', help='Set this option to No if the particles are black, ' 'and to Yes if the particles are white.') group.addParam('maxResolution', params.FloatParam, default=20, label='Maximum resolution to consider (A)', help='The Laplacian-of-Gaussian filter will be applied ' 'to downscaled micrographs with the corresponding ' 'size. Give a negative value to skip downscaling.') group.addParam('threshold', params.FloatParam, default=0, label='Adjust default threshold (stddev)', help='Use this to pick more (negative number -> lower ' 'threshold) or less (positive number -> higher ' 'threshold) particles compared to the default ' 'setting.') group.addParam('threshold2', params.FloatParam, default=999, label='Upper threshold (stddev)', help='Use this to discard picks with LoG thresholds ' 'that are this many standard deviations above ' 'the average, e.g. to avoid high contrast ' 'contamination like ice and ethane droplets. ' 'Good values depend on the contrast of ' 'micrographs and need to be interactively ' 'explored; for low contrast micrographs, ' 'values of ~ 1.5 may be reasonable, but the ' 'same value will be too low for high-contrast ' 'micrographs.') form.addParam('extraParams', params.StringParam, default='', label='Additional arguments:', help='In this box command-line arguments may be provided ' 'that are not generated by the GUI. This may be ' 'useful for testing developmental options and/or ' 'expert use of the program. \n' 'The command "relion_autopick" will print a list ' 'of possible options.') self._defineStreamingParams(form) form.addParallelSection(threads=0, mpi=4) # -------------------------- STEPS functions ------------------------------
[docs] def getAutopickParams(self): """ Return the autopicking parameters except for the interactive ones. """ params = ' --pickname autopick --odir "./" --LoG --shrink 0' params += ' --lowpass %0.3f' % self.maxResolution # Add extra params is any params += ' %s' % self.extraParams return params
def _getPickArgs(self): """ This method is used by base class to provide the arguments to new inserted steps. """ args = [ self.getAutopickParams(), self.minDiameter.get(), self.maxDiameter.get(), self.threshold.get(), self.threshold2.get() ] return args def _pickMicrographsFromStar(self, micStarFile, cwd, params, minDiameter, maxDiameter, threshold, threshold2): """ Launch the 'relion_autopick' for micrographs in the inputStarFile. If the input set of complete, the star file will contain all the micrographs. If working in streaming, it will be only one micrograph. """ params += ' --i %s' % relpath(micStarFile, cwd) params += ' --LoG_diam_min %0.3f' % minDiameter params += ' --LoG_diam_max %0.3f' % maxDiameter params += ' --LoG_adjust_threshold %0.3f' % threshold params += ' --LoG_upper_threshold %0.3f' % threshold2 program = self._getProgram('relion_autopick') self.runJob(program, params, cwd=cwd) # -------------------------- INFO functions -------------------------------- def _validate(self): errors = [] return errors def _summary(self): summary = [] return summary # -------------------------- UTILS functions -------------------------------
[docs] def getBoxSize(self): """ Return a reasonable box-size in pixels. """ return self.boxSize.get()