Source code for bsoft.protocols.protocol_bfilter

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (
# *
# * SciLifeLab, Stockholm University
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# * This program is free software; you can redistribute it and/or modify
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# * (at your option) any later version.
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# * This program is distributed in the hope that it will be useful,
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# * along with this program; if not, write to the Free Software
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import pyworkflow.utils as pwutils
import pyworkflow.protocol.params as params
from pwem.protocols import ProtFilterParticles

import bsoft
from bsoft.constants import (FILTER_MEDIAN, FILTER_PEAK,


-invert	            Invert density in the image.
-rescale -0.1,5.2	Rescale data to average and standard deviation after filtering.
-minmax -0.5,1.2	Rescale data to minimum and maximum.
-average 7,5,3	    Averaging/smoothing filter: kernel size.
-gaussian 11,2.6	Gaussian smoothing filter: kernel size and sigma.
-median 3	        Median filter: kernel edge size.
-peak 5	            Peak filter: kernel edge size.
-gradient	        Gradient filter (3x3x3).
-laplacian	        Laplacian filter (3x3x3).
-LoG 2.5	        Laplacian-of-Gaussian filter.
-DoG 1.5,3.1	    Difference-of-Gaussians filter.
-denoise 2,0.4	    Denoising filter: distance and density difference sigmas.
-rollingball 5,4.3	Rolling ball filter: radius and density scaling (default scaling=1).
-variance 11,1	    Calculate a local variance image using the given size kernel,
                    with a flag to indicate standard deviation rather than variance.
-extremes his	    Filter image extremes: his=histogram-based, mg=for micrograph.
-replacemaxima 1.5	Replace maxima above the given threshold with surrounding average.
-bandpass 25.3,200,0.02	Bandpass filter: resolution limits (angstrom) and band edge width (1/angstrom).
-amplitude 8.3	    Amplitude filter: setting all amplitudes below the threshold to zero.
-phasesonly	        Set all amplitudes to one.
-Bfactor 44,25.3	B-factor application: B-factor (A^2), high resolution limit (A,optional)
                    Multiplied in reciprocal space by exp(-B-factor/4 * s^2).

-verbose 1	        Verbosity of output.
-datatype u	        Force writing of a new data type.
-sampling 1.5,1.5,1.5	Sampling (A/pixel; default from input file; a single value can be given).
-wrap	            Turn wrapping on (default off, use with -denoise option).

[docs]class BsoftProtBfilter(ProtFilterParticles): """ Wrapper around bfilter program of BSOFT. """ _label = 'bfilter' def __init__(self, **kwargs): ProtFilterParticles.__init__(self, **kwargs) # --------------------------- DEFINE param functions ------------------------ def _defineProcessParams(self, form): form.addParam('filterType', params.EnumParam, choices=['median', 'peak', 'gradient', 'laplacian', 'denoise'], label="Filter type", default=0, help="Select what type of filter do you want to apply.") form.addParam('kernelEdgeSize', params.IntParam, default=3, label='Kernel edge size', condition='filterType==%d or filterType==%d' % ( FILTER_MEDIAN, FILTER_PEAK)) line = form.addLine('Denoise', condition='filterType==%d' % FILTER_DENOISE, help="Denoising filter: distance and density difference sigmas.") line.addParam('denoiseDistance', params.IntParam, default=2, label='distance') line.addParam('denoiseDensity', params.FloatParam, default=0.4, label='density') form.addParam('wrap', params.BooleanParam, default=False, condition='filterType==%d' % FILTER_DENOISE, label='Wrap?', help="Turn wrapping on ") # -denoise 2,0.4 Denoising filter: distance and density difference sigmas. # line = form.addLine('Frequency', # condition='filterType > %d and filterType != %d' % (FILTER_SPACE_REAL,FILTER_FERMI), # help='Range to apply the filter. Expected values between 0 and 0.5.') # line.addParam('lowFreq', DigFreqParam, condition='filterMode==%d' % FILTER_HIGHPASS, default=0.1, # label='Lowest') # line.addParam('highFreq', DigFreqParam, condition='filterMode==%d' % FILTER_LOWPASS, # default=0.2, label='Highest') # # form.addParam('temperature', FloatParam, default=0.3, # label='Temperature T:', # condition='filterType == %d' % FILTER_FERMI, # help='Enter a temperature parameter T The filter falls off roughly within \n' # 'this reciprocal distance (in terms of frequency units).') # --------------------------- INSERT steps functions ----------------------- def _insertAllSteps(self): # Insert processing steps self._insertFunctionStep('convertInputStep', self.inputParticles.get().strId()) self._insertFunctionStep('filterStep', self.getFilterArgs()) self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions ------------------------------
[docs] def convertInputStep(self, strId): # we need to put all images into a single stack # to ease the call of bsoft programs self.inputParticles.get().writeStack(self._getPath('particles.spi:stk'))
[docs] def getFilterArgs(self): """ Build the bfilter command line base on selected params. Exclude only the input and output files""" filterText = self.getEnumText('filterType') filterType = self.filterType.get() # by default use always the filter type as first argument args = '-%s' % filterText if filterType in [FILTER_MEDIAN, FILTER_PEAK]: args += ' %d' % self.kernelEdgeSize elif filterType == FILTER_DENOISE: args += ' %d,%0.3f' % (self.denoiseDistance, self.denoiseDensity) return args
[docs] def runFilter(self, inputStk, outputStk): """ Util function used by wizard. """ self.setStepsExecutor() # set default execution args = self.getFilterArgs() self.runJob(bsoft.Plugin.getProgram('bfilter'), args + ' %s %s' % (inputStk, outputStk), env=bsoft.Plugin.getEnviron())
[docs] def filterStep(self, args): """ Apply the selected filter to particles. Create the set of particles. """ particlesStk = self._getPath('particles.spi') tmpStk = particlesStk.replace('.spi', '_tmp.spi') self.runJob(bsoft.Plugin.getProgram('bfilter'), args + ' %s %s' % (particlesStk, tmpStk), env=bsoft.Plugin.getEnviron()) pwutils.moveFile(tmpStk, particlesStk.replace('.spi', '.stk')) # just we prefer stk as stack of spider images pwutils.cleanPath(particlesStk)
[docs] def createOutputStep(self): particlesStk = self._getPath('particles.stk') inputSet = self.inputParticles.get() outputSet = self._createSetOfParticles() outputSet.copyInfo(inputSet) for i, img in enumerate(inputSet): img.setLocation(i + 1, particlesStk) outputSet.append(img) self._defineOutputs(outputParticles=outputSet) self._defineTransformRelation(inputSet, outputSet)
# --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] return errors def _summary(self): summary = [] return summary def _methods(self): methods = [] return methods