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')
