Source code for xmipp3.protocols.protocol_shift_volume

# -*- coding: utf-8 -*-
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# * Authors:     Estrella Fernandez Gimenez (
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# *  BCU, Centro Nacional de Biotecnologia, CSIC
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from pyworkflow.protocol.params import PointerParam, FloatParam, BooleanParam, IntParam
import pyworkflow.object as pwobj
from pwem.protocols import EMProtocol
from pwem.objects import Volume

[docs]class XmippProtShiftVolume(EMProtocol): """ This protocol shifts a volume according to the input shifts""" _label = 'shift volume' # --------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputVol', PointerParam, pointerClass='Volume', label="Volume", help='Volume to shift') form.addParam('shiftBool', BooleanParam, label='Use the same shifts as for the particles?', default='True', help='Use output shifts of protocol "shift particles" which should be executed previously') form.addParam('inputProtocol', PointerParam, pointerClass='XmippProtShiftParticles', allowsNull=True, label="Shift particles protocol", condition='shiftBool') COND = 'not shiftBool' form.addParam('x', FloatParam, label="x", condition=COND, allowsNull=True) form.addParam('y', FloatParam, label="y", condition=COND, allowsNull=True) form.addParam('z', FloatParam, label="z", condition=COND, allowsNull=True) form.addParam('boxSizeBool', BooleanParam, label='Use original box size for the shifted volume?', default='True', help='Use input volume box size for the shifted volume.') form.addParam('boxSize', IntParam, label='Final box size', condition='not boxSizeBool', help='Box size of the shifted volume.') # --------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('shiftStep') self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions --------------------------------------------
[docs] def shiftStep(self): fnVol = self.inputVol.get().getFileName() if not self.boxSizeBool: box = self.boxSize.get() self.runJob('xmipp_transform_window', '-i "%s" -o "%s" --size %d %d %d' % (fnVol, self._getExtraPath("resized_volume.mrc"), box, box, box)) fnVol = self._getExtraPath("resized_volume.mrc") if self.shiftBool: shiftprot = self.inputProtocol.get() self.shiftx = shiftprot.shiftX.get() self.shifty = shiftprot.shiftY.get() self.shiftz = shiftprot.shiftZ.get() else: self.shiftx = self.x.get() self.shifty = self.y.get() self.shiftz = self.z.get() program = "xmipp_transform_geometry" args = '-i %s -o %s --shift %f %f %f --dont_wrap' % \ (fnVol, self._getExtraPath("shift_volume.mrc"), self.shiftx, self.shifty, self.shiftz) self.runJob(program, args)
[docs] def createOutputStep(self): out_vol = Volume() in_vol = self.inputVol.get() out_vol.setSamplingRate(in_vol.getSamplingRate()) out_vol.setFileName(self._getExtraPath("shift_volume.mrc")) self._defineOutputs(outputVolume=out_vol) self._defineOutputs(shiftX=pwobj.Float(self.shiftx), shiftY=pwobj.Float(self.shifty), shiftZ=pwobj.Float(self.shiftz)) self._defineSourceRelation(in_vol, out_vol)
# --------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] if not hasattr(self, 'outputVolume'): summary.append("Output volume not ready yet.") else: if self.shiftBool: summary.append("Volume shift as particles in %s" % self.inputProtocol.get()) else: summary.append("User defined shift") return summary