# **************************************************************************
# *
# * Authors: Carlos Oscar S. Sorzano (coss@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
"""
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.mrc"%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.mrc"))
fhCmd.write("open %s\n" % (fnRoot+"_%s.mrc"%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()