Source code for xmipp3.protocols.protocol_create_gallery

# **************************************************************************
# *
# * Authors:     Carlos Oscar S. Sorzano (coss@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * This program is free software; you can redistribute it and/or modify
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# * GNU General Public License for more details.
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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
# *  e-mail address 'scipion@cnb.csic.es'
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from pwem.emlib.image import ImageHandler
from pyworkflow import VERSION_1_1
from pyworkflow.protocol import PointerParam, StringParam, FloatParam
from pyworkflow.protocol.constants import LEVEL_ADVANCED

from pwem.protocols import ProtAnalysis3D


from pwem.emlib import MetaData, MDL_ANGLE_ROT, MDL_ANGLE_TILT
from xmipp3.convert import readSetOfParticles


[docs]class XmippProtCreateGallery(ProtAnalysis3D): """ Create a gallery of projections from a volume. This gallery of projections may help to understand the images observed in the microscope. """ _label = 'create gallery' _version = VERSION_1_1 #--------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='General parameters') form.addParam('inputVolume', PointerParam, pointerClass="Volume", label='Input volume') form.addParam('symmetryGroup', StringParam, default="c1", label='Symmetry group', help='See' 'http://xmipp.cnb.uam.es/twiki/bin/view/Xmipp/Symmetry ' 'for a description of the symmetry groups format. ' 'If no symmetry is present, give c1') rot = form.addLine('Rotational angle', help='Minimum, maximum and step values for ' 'rotational angle range, all in degrees.') rot.addParam('rot0', FloatParam, default=0, label='Min') rot.addParam('rotF', FloatParam, default=360, label='Max') rot.addParam('rotStep', FloatParam, default=5, label='Step') tilt = form.addLine('Tilt angle', help='In degrees. tilt=0 is a top view, ' 'while tilt=90 is a side view"') tilt.addParam('tilt0', FloatParam, default=0, label='Min') tilt.addParam('tiltF', FloatParam, default=180, label='Max') tilt.addParam('tiltStep', FloatParam, default=5, label='Step') form.addParam('maxFreq',FloatParam, default=0.25, expertLevel=LEVEL_ADVANCED, label='Maximum frequency', help="Normalized to 0.5") form.addParam('shiftSigma',FloatParam, default=0.0, expertLevel=LEVEL_ADVANCED, label='Shift sigma', help="In pixels") #--------------------------- INSERT steps functions ------------------------ def _insertAllSteps(self): self._insertFunctionStep('copyInput') self._insertFunctionStep('createGallery') self._insertFunctionStep('createOutput') #--------------------------- STEPS functions -------------------------------
[docs] def copyInput(self): ImageHandler().convert(self.inputVolume.get(), self._getTmpPath("volume.vol"))
[docs] def createGallery(self): xdim = self.inputVolume.get().getXDim() rotN = round((self.rotF.get()-self.rot0.get())/self.rotStep.get()) tiltN = round((self.tiltF.get()-self.tilt0.get())/self.tiltStep.get()) paramContent ="""# XMIPP_STAR_1 * data_block1 _dimensions2D '%d %d' _projRotRange '%f %f %d' _projRotRandomness even _projTiltRange '%f %f %d' _projTiltRandomness even _projPsiRange '0 0 1' _projPsiRandomness even _noiseCoord '%f 0' """ % (xdim, xdim, self.rot0, self.rotF,rotN, self.tilt0, self.tiltF, tiltN, self.shiftSigma) fhParam = open(self._getExtraPath("projectionParameters.xmd"), 'w') fhParam.write(paramContent) fhParam.close() self.runJob("xmipp_phantom_project", "-i %s -o %s --params %s --method fourier 2 %f --sym %s" % (self._getTmpPath("volume.vol"), self._getPath("images.stk"), self._getExtraPath("projectionParameters.xmd"), self.maxFreq, self.symmetryGroup))
[docs] def createOutput(self): imgSetOut = self._createSetOfAverages() imgSetOut.setSamplingRate(self.inputVolume.get().getSamplingRate()) imgSetOut.setAlignmentProj() readSetOfParticles(self._getPath("images.xmd"), imgSetOut) self._defineOutputs(outputReprojections=imgSetOut) self._defineSourceRelation(self.inputVolume, imgSetOut)
#--------------------------- INFO functions -------------------------------- def _summary(self): messages = [] messages.append("Rot.angle from %0.2f to %0.2f in steps of %0.2f" % (self.rot0, self.rotF, self.rotStep)) messages.append("Tilt.angle from %0.2f to %0.2f in steps of %0.2f" % (self.tilt0, self.tiltF, self.tiltStep)) return messages