Source code for xmipp3.protocols.protocol_volume_consensus

# -*- coding: utf-8 -*-
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# *
# * Authors:  Estrella Fernandez Gimenez (me.fernandez@cnb.csic.es)
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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from pyworkflow.protocol.params import MultiPointerParam
from pwem.objects import Volume, Transform
from pwem.protocols import ProtInitialVolume


[docs]class XmippProtVolConsensus(ProtInitialVolume): """ This protocol performs a fusion of all the input volumes, which should be preprocessed with protocol 'volume substraction' saving volume 2, in order to be as similar as possible before the fusion. The output of this protocol is the consensus volume and another volume which indicates the maximun difference between input volumes in each voxel.""" _label = 'volume consensus' # --------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('vols', MultiPointerParam, pointerClass='Volume', label="Volumes", help='Select the volumes for the consensus.') # --------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('fusionStep') self._insertFunctionStep('createOutputStep') self._insertFunctionStep("createChimeraScript") # --------------------------- STEPS functions ---------------------------------------------------
[docs] def fusionStep(self): inputVols = self._getExtraPath("input_volumes.txt") fhInputVols = open(inputVols, 'w') for i, vol in enumerate(self.vols): fileName = vol.get().getFileName() if fileName.endswith(':mrc'): fileName = fileName[:-4] fhInputVols.write(fileName + '\n') fhInputVols.close() outVolFn = self._getExtraPath("consensus_volume.mrc") args = " -i %s -o %s" % (inputVols, outVolFn) self.runJob("xmipp_volume_consensus", args)
[docs] def createOutputStep(self): outVol = Volume() outVol.setSamplingRate(self.vols[0].get().getSamplingRate()) outVol.setFileName(self._getExtraPath("consensus_volume.mrc")) outVol2 = Volume() outVol2.setSamplingRate(self.vols[0].get().getSamplingRate()) outVol2.setFileName(self._getExtraPath("consensus_volume_diff.mrc")) self._defineOutputs(outputVolume=outVol) self._defineOutputs(outputVolumeDiff=outVol2)
[docs] def createChimeraScript(self): fnRoot = "extra/" scriptFile = self._getPath('result') + '_fusion_chimera.cxc' fhCmd = open(scriptFile, 'w') fhCmd.write("open %s\n" % (fnRoot+"consensus_volume.mrc")) fhCmd.write("open %s\n" % (fnRoot+"consensus_volume_diff.mrc")) fhCmd.write("vol #2 hide\n") fhCmd.write("color sample #1 map #2 palette rainbow\n") fhCmd.close()
# --------------------------- INFO functions -------------------------------------------- def _summary(self): summary = [] if not hasattr(self, 'outputVolume'): summary.append("Output volume not ready yet.") else: for i, vol in enumerate(self.vols): summary.append("Volume %d: %s" % (i+1, vol.get().getFileName())) return summary def _methods(self): methods = [] if not hasattr(self, 'outputVolume'): methods.append("Output volume not ready yet.") else: methods.append("We compute a consensus volume from %d input volumes at %f A/px" % (self.vols.getSize(), self.vols[0].get().getSamplingRate())) return methods