def convertStackToMrc(self): stackdata = apStackData.getOnlyStackData(self.params['stackid']) stackfile = os.path.join(stackdata['path']['path'],stackdata['name']) stackbaseroot = os.path.basename(stackfile).split('.')[0] stackroot = os.path.join(stackdata['path']['path'],stackdata['name'][:-4]) apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s.mrc'% (stackroot,stackbaseroot)) self.stackfile = stackbaseroot+'.mrc' apIMAGIC.convertImagicStackToMrcStack(stackroot,self.stackfile)
def convertStackToMrc(self): stackdata = apStackData.getOnlyStackData(self.params["stackid"]) stackfile = os.path.join(stackdata["path"]["path"], stackdata["name"]) stackbaseroot = os.path.basename(stackfile).split(".")[0] stackroot = os.path.join(stackdata["path"]["path"], stackdata["name"][:-4]) apDisplay.printMsg( "converting %s from default IMAGIC stack format to MRC as %s.mrc" % (stackroot, stackbaseroot) ) self.stackfile = stackbaseroot + ".mrc" apIMAGIC.convertImagicStackToMrcStack(stackroot, self.stackfile)
def ImagicStackToMrcStack(self,stackfile): stackroot = stackfile[:-4] stackbaseroot = os.path.basename(stackfile).split('.')[0] apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s.mrc'% (stackroot,stackbaseroot)) apIMAGIC.convertImagicStackToMrcStack(stackroot,stackbaseroot+'.mrc') # clean up non-mrc stack in rundir which may be left from preprocessing such as binning tmpstackdir = os.path.dirname(stackfile) stackext = os.path.basename(stackfile).split('.')[-1] if stackext != 'mrc' and tmpstackdir == self.params['rundir']: os.remove(stackfile) if stackext == 'hed': imgfilepath = stackfile.replace('hed','img') os.remove(imgfilepath)
def ImagicStackToFrealignMrcStack(self,stackfile): stackroot = stackfile[:-4] stackbaseroot = os.path.basename(stackfile).split('.')[0] apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s.mrc'% (stackroot,stackbaseroot)) apIMAGIC.convertImagicStackToMrcStack(stackroot,stackbaseroot+'.mrc') # clean up non-mrc stack in rundir which may be left from preprocessing such as binning tmpstackdir = os.path.dirname(stackfile) stackext = os.path.basename(stackfile).split('.')[-1] if stackext != 'mrc' and tmpstackdir == self.params['rundir']: os.remove(stackfile) if stackext == 'hed': imgfilepath = stackfile.replace('hed','img') os.remove(imgfilepath)
def ImagicStackToMrcStack(self, oldstackfile): ''' Convert IMAGIC Stack into MRC stack with extension .mrcs ''' self.stackErrorCheck(oldstackfile) stackroot = oldstackfile[:-4] mrcstackfile = os.path.join(self.params['rundir'], 'particles.mrcs') apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s'% (stackroot, mrcstackfile)) apIMAGIC.convertImagicStackToMrcStack(stackroot, mrcstackfile) # clean up non-mrc stack in rundir which may be left from preprocessing such as binning if not 'mrc' in oldstackfile and os.path.dirname(oldstackfile) == self.params['rundir']: #apFile.removeStack(oldstackfile) pass
def ImagicStackToMrcStack(self, oldstackfile): ''' Convert IMAGIC Stack into MRC stack with extension .mrcs ''' self.stackErrorCheck(oldstackfile) stackroot = oldstackfile[:-4] mrcstackfile = os.path.join(self.params['rundir'], 'particles.mrcs') apDisplay.printMsg( 'converting %s from default IMAGIC stack format to MRC as %s' % (stackroot, mrcstackfile)) apIMAGIC.convertImagicStackToMrcStack(stackroot, mrcstackfile) # clean up non-mrc stack in rundir which may be left from preprocessing such as binning if not 'mrc' in oldstackfile and os.path.dirname( oldstackfile) == self.params['rundir']: #apFile.removeStack(oldstackfile) pass