Source code for xmipp3.protocols.protocol_volume_local_adjust

# -*- coding: utf-8 -*-
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# * Authors:  Estrella Fernandez Gimenez (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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from pyworkflow.protocol.params import PointerParam, BooleanParam, IntParam

from pwem.convert import headers
from pwem.objects import Volume, Transform
from pwem.protocols import EMProtocol

[docs]class XmippProtLocalVolAdj(EMProtocol): """Protocol to adjust locally volume intensity to a reference volume. Occupancy volume is saved in protocol folder. Based on""" _label = 'volume local adjustment' _possibleOutputs = Volume # --------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('vol1', PointerParam, pointerClass='Volume', label="Reference volume", help='Specify a volume to be used as reference volume.') form.addParam('vol2', PointerParam, pointerClass='Volume', label="Input volume", help='Specify a volume which will be adjusted to the reference volume.') form.addParam('mask', PointerParam, pointerClass='VolumeMask', label="Mask for reference volume", help='Specify a mask to define region of interest (which is signal in white (1s) and background in ' 'black (0s))') form.addParam('neighborhood', IntParam, label="Neighborhood (A)", default=5, help='Side length (in Angstroms) of a square which will define the region of adjustment') form.addParam('subtract', BooleanParam, label="Perform subtraction?", default=False, help='Perform subtraction of reference volume minus input volume in real space') # --------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('adjustStep') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions --------------------------------------------
[docs] def adjustStep(self): vol1 = self.vol1.get().clone() fnVol1 = vol1.getFileName() vol2 = self.vol2.get().getFileName() if fnVol1.endswith('.mrc'): fnVol1 += ':mrc' if vol2.endswith('.mrc'): vol2 += ':mrc' program = "xmipp_local_volume_adjust" args = '--i1 %s --i2 %s -o %s --mask %s --neighborhood %d --sampling %s --save %s' % \ (fnVol1, vol2, self._getExtraPath("output_volume.mrc"), self.mask.get().getFileName(), self.neighborhood.get(), vol1.getSamplingRate(), self._getExtraPath()) if self.subtract.get(): args += ' --sub' self.runJob(program, args)
[docs] def createOutputStep(self): vol1 = self.vol1.get() volume = Volume() volume.setSamplingRate(vol1.getSamplingRate()) if vol1.getFileName().endswith('mrc'): origin = Transform() ccp4header = headers.Ccp4Header(vol1.getFileName(), readHeader=True) shifts = ccp4header.getOrigin() origin.setShiftsTuple(shifts) volume.setOrigin(origin) volume.setFileName(self._getExtraPath("output_volume.mrc")) filename = volume.getFileName() if filename.endswith('.mrc') or filename.endswith('.map'): volume.setFileName(filename + ':mrc') self._defineOutputs(outputVolume=volume)
# --------------------------- INFO functions -------------------------------------------- def _summary(self): neighborhood = self.neighborhood.get() vol1 = self.vol1.get() summary = ["Volume 1: %s\nVolume 2: %s\nInput mask 1: %s\n\nNeighborhood: %d Å (%d px)" % (vol1.getFileName(), self.vol2.get().getFileName(), self.mask.get().getFileName(), neighborhood, round(neighborhood/vol1.getSamplingRate()))] if self.subtract.get(): summary.append("\nSubtraction performed") return summary def _methods(self): methods = [] if not hasattr(self, 'outputVolume'): methods.append("Output volume not ready yet.") else: methods.append("Volume %s adjusted to volume %s" % (self.vol2.get().getFileName(), self.vol1.get().getFileName())) return methods def _validate(self): errors = [] if self.vol1.get().getSamplingRate() != self.vol2.get().getSamplingRate(): errors.append('Input volumes should have same pixel size') if self.vol1.get().getSamplingRate() != self.mask.get().getSamplingRate(): errors.append('\nInput mask and volumes should have same pixel size') return errors