Source code for xmipp3.protocols.protocol_normalize_strain

# **************************************************************************
# *
# * Authors:     Carlos Oscar S. Sorzano (coss@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# *  e-mail address 'scipion@cnb.csic.es'
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"""
This sub-package contains the XmippProtNormalizeStrain protocol
"""

import os

from pyworkflow import VERSION_1_1
from pwem.protocols import ProtAnalysis3D
from pyworkflow.protocol.params import MultiPointerParam

from pwem import emlib


[docs]class XmippProtNormalizeStrain(ProtAnalysis3D): """ Normalize the local strain and rotations amongst several runs """ _label = 'normalize strain' _lastUpdateVersion = VERSION_1_1 def __init__(self, **args): ProtAnalysis3D.__init__(self, **args) def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputRuns', MultiPointerParam, pointerClass='XmippProtVolumeStrain', label="input strain calculations", help='Select the runs of strain calculations to be normalized') #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('normalize',"localrot") self._insertFunctionStep('normalize',"strain")
[docs] def normalize(self,what): # Get overall minimum and maximum V=emlib.Image() minAll=1e38 maxAll=-1e38 for prot in self.inputRuns: protId=prot.get().getObjId() protDir=prot.get()._getPath('') fnVol=os.path.join(protDir,"extra","result_%s.vol"%what) V.read(fnVol) _, _, minVal, maxVal = V.computeStats() minAll = min(minAll,minVal) maxAll = max(maxAll,maxVal) # Write the Chimera file for prot in self.inputRuns: protId=prot.get().getObjId() protDir=prot.get()._getPath('') fnRoot=os.path.relpath(os.path.join(protDir,"extra","result"),self._getPath('')) scriptFile = self._getPath('%d_result_%s_chimera.cxc'%(protId,what)) fhCmd = open(scriptFile, 'w') fhCmd.write("open %s\n" % (fnRoot+"_final.vol")) fhCmd.write("open %s\n" % (fnRoot+"_%s.vol"%what)) fhCmd.write("vol #1 hide\n") fhCmd.write("scolor #0 volume #1 cmap rainbow cmapRange %f,%f reverseColors True\n"%(minAll,maxAll)) fhCmd.close()