def convertGlobalTransformProtomoToImod(protomoprefix,imodprefix, center=(1024,1024)): # axes are in order of x,y,z protomotltfile = protomoprefix+"-fitted.tlt" imodtltfile = imodprefix+".xf" fout = open(imodtltfile,'w') specimen_euler, tiltaz, tilts, origins, rotations = readProtomoTltFile(protomotltfile) imodaffines = convertProtomoToImod(specimen_euler, tiltaz, origins, rotations,center) apImod.writeTransformFile('', imodprefix,imodaffines,'xf')
def createTransformFile(self): # Get alignment from database specimen_euler, tiltaz, origins, rotations = apTomo.getAlignmentFromDB(self.alignerdata,self.imgcenter) centertuple = (self.imgcenter['x'],self.imgcenter['y']) imodaffines = apProTomo.convertProtomoToImod(specimen_euler, tiltaz, origins, rotations,centertuple) processdir = self.params['rundir'] apImod.writeTransformFile(processdir, self.seriesname,imodaffines,ext='xf') imodlocalaffines = apTomo.convertGlobalToLocalAffines(imodaffines) apImod.writeTransformFile(processdir, self.seriesname,imodlocalaffines,ext='prexf')
def convertGlobalTransformProtomoToImod(protomoprefix, imodprefix, center=(1024, 1024)): # axes are in order of x,y,z protomotltfile = protomoprefix + "-fitted.tlt" imodtltfile = imodprefix + ".xf" fout = open(imodtltfile, 'w') specimen_euler, tiltaz, tilts, origins, rotations = readProtomoTltFile( protomotltfile) imodaffines = convertProtomoToImod(specimen_euler, tiltaz, origins, rotations, center) apImod.writeTransformFile('', imodprefix, imodaffines, 'xf')
def createTransformFile(self): # Get alignment from database specimen_euler, tiltaz, origins, rotations = apTomo.getAlignmentFromDB( self.alignerdata, self.imgcenter) centertuple = (self.imgcenter['x'], self.imgcenter['y']) imodaffines = apProTomo.convertProtomoToImod(specimen_euler, tiltaz, origins, rotations, centertuple) processdir = self.params['rundir'] apImod.writeTransformFile(processdir, self.seriesname, imodaffines, ext='xf') imodlocalaffines = apTomo.convertGlobalToLocalAffines(imodaffines) apImod.writeTransformFile(processdir, self.seriesname, imodlocalaffines, ext='prexf')