ConvertNewCTFModelOldCTF

#!/usr/bin/env xmipp_python
"""/***************************************************************************
 *
 * Authors:     Roberto Marabini          (roberto@cnb.csic.es)
*                    Josue Gomez
 *
 * 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 'xmipp@cnb.csic.es'
 ***************************************************************************/
"""
#!/usr/bin/env xmipp_python

import os
from protlib_xmipp import XmippScript, RowMetaData
from xmipp import *

#old=_old
#for i in */xmipp_ctf.ctfparam
#do
#  echo $i
#  ./toOldCTF.py -i $i -o $i$old
#done

class ScriptImportCtfparam(XmippScript):
    def __init__(self):
        XmippScript.__init__(self)
        
    def defineParams(self):
        self.addUsageLine('Import a ctfparam file from Xmipp3.0 version')
        self.addUsageLine('The new style ctfparam file is converted to a old')
        self.addUsageLine('ctfparam file')
        ## params
        self.addParamsLine(' -i <xmd>                      : micrographs.xmd')
#         self.addParamsLine(' -o <old_ctfparam>          : Old Xmipp2.4 CTF definition file (.ctfparam)')
        ## examples
#         self.addExampleLine('   xmipp_import_ctfparam -i new.ctfparam -o old.ctfparam')
      
    def run(self):
        micsMd = self.getParam('-i')
#         oldCtf = self.getParam('-o')
    
        CTF_BASIC_LABELS = [
                            MDL_CTF_DEFOCUSU,
                            MDL_CTF_DEFOCUSV,
                            MDL_CTF_DEFOCUS_ANGLE,
                            MDL_CTF_SAMPLING_RATE,
                            MDL_CTF_VOLTAGE,
                            MDL_CTF_CS,
                            MDL_CTF_Q0,
                            MDL_CTF_K]
        oldLabelsName = [
             'defocusU', 
             'defocusV', 
             'azimuthal_angle',
                     'sampling_rate', 
                     'voltage', 
                         'spherical_aberration', 
             'Q0', 
             'K']  
        conversionDict = dict(zip(CTF_BASIC_LABELS, oldLabelsName))
        mdMics = MetaData(micsMd)
        for objId in mdMics:
            
            newCtf = mdMics.getValue(MDL_CTF_MODEL, objId)
            micFn = os.path.basename(mdMics.getValue(MDL_MICROGRAPH, objId)).split('.')[0]
            
            md = MetaData(newCtf)
            oldCtfDir = os.path.join('Preprocessing_down1', micFn)
            os.makedirs(oldCtfDir)
            oldCtf = os.path.join(oldCtfDir, 'down1_' + micFn + '_Periodogramavg.ctfparam')
        
            f = open(oldCtf,'w')
            for label in CTF_BASIC_LABELS:
                value = md.getValue(label,1L)
                if(label==MDL_CTF_DEFOCUSU):
                     value = -value
                elif(label==MDL_CTF_DEFOCUSV):
                     value = -value
                elif(label==MDL_CTF_Q0):
                     value = -value
                elif(label==MDL_CTF_K):
                     value = 1.
                elif(label==MDL_CTF_SAMPLING_RATE):
                     value=value
                elif(label==MDL_CTF_VOLTAGE):
                     value= int(value)
                #print conversionDict[label]+'='+str(value)
                f.write(conversionDict[label]+'= '+str(value)+'\n')
            f.close()
    
if __name__ == '__main__':
    ScriptImportCtfparam().tryRun()

-- Main.RobertoMarabini - 2014-08-01