def insertAlignIteration(alignrundata, protomodata, params, refinedict,
refimagedata):
# protmoalign refinement cycle parameters
refineparamsq = appiondata.ApProtomoRefinementParamsData()
refineparamsq['protomo'] = protomodata
refineparamsq['cycle'] = params['cycle']
refineparamsq['alismp'] = refinedict['alismp']
refineparamsq['alibox'] = {
'x': refinedict['alibox_x'],
'y': refinedict['alibox_y']
}
refineparamsq['cormod'] = refinedict['cormod']
refineparamsq['imgref'] = refinedict['imgref']
refineparamsq['reference'] = refimagedata
refineparamsdata = apTomo.publish(refineparamsq)
# good cycle used for reset tlt params
if params['goodcycle'] is None:
goodrefineparamsdata = None
else:
goodq = appiondata.ApProtomoRefinementParamsData(
protomo=protomodata, cycle=params['goodcycle'])
results = goodq.query(results=1)
if results:
goodrefineparamsdata = results[0]
else:
goodrefineparamsdata = None
# protomoaligner parameters
alignerdata = apTomo.insertAlignerParams(alignrundata, params, protomodata,
refineparamsdata,
goodrefineparamsdata,
refimagedata)
return alignerdata
def insertModel2(alignerdata, geometrydict):
# general protomo2 model data
q = appiondata.ApProtomoModelData()
q['aligner'] = alignerdata
q['psi'] = geometrydict['psi']
q['theta'] = geometrydict['theta']
q['phi'] = geometrydict['phi']
q['azimuth'] = geometrydict['azimuth']
modeldata = apTomo.publish(q)
return modeldata
def insertModel(alignerdata, results):
# general protmo parameters
q = appiondata.ApProtomoModelData()
q['aligner'] = alignerdata
q['psi'] = results[-2]['psi']
q['theta'] = results[-2]['theta']
q['phi'] = results[-2]['phi']
q['azimuth'] = results[-2]['azimuth']
modeldata = apTomo.publish(q)
return modeldata
def insertModel2(alignerdata, geometrydict): # general protomo2 model data q = appiondata.ApProtomoModelData() q['aligner'] = alignerdata q['psi'] = geometrydict['psi'] q['theta'] = geometrydict['theta'] q['phi'] = geometrydict['phi'] q['azimuth'] = geometrydict['azimuth'] modeldata = apTomo.publish(q) return modeldata
def insertModel(alignerdata, results): # general protmo parameters q = appiondata.ApProtomoModelData() q['aligner'] = alignerdata q['psi'] = results[-2]['psi'] q['theta'] = results[-2]['theta'] q['phi'] = results[-2]['phi'] q['azimuth'] = results[-2]['azimuth'] modeldata = apTomo.publish(q) return modeldata
def insertTiltAlignment(alignerdata,imagedata,number,result,center=None):
if not center:
imgshape = imagedata['image'].shape
center = {'x':imgshape[1]/2,'y':imgshape[0]/2}
q = appiondata.ApProtomoAlignmentData()
q['aligner'] = alignerdata
q['image'] = imagedata
q['number'] = number
q['rotation'] = result['rotation']
q['shift'] = {'x':result['x'] - center['x'], 'y':result['y'] - center['y']}
aligndata = apTomo.publish(q)
return aligndata
def insertTiltAlignment(alignerdata, imagedata, number, result, center=None):
if not center:
imgshape = imagedata['image'].shape
center = {'x': imgshape[1] / 2, 'y': imgshape[0] / 2}
q = appiondata.ApProtomoAlignmentData()
q['aligner'] = alignerdata
q['image'] = imagedata
q['number'] = number
q['rotation'] = result['rotation']
q['shift'] = {
'x': result['x'] - center['x'],
'y': result['y'] - center['y']
}
aligndata = apTomo.publish(q)
return aligndata
def insertAlignIteration(alignrundata, protomodata, params, refinedict,refimagedata):
# protmoalign refinement cycle parameters
refineparamsq = appiondata.ApProtomoRefinementParamsData()
refineparamsq['protomo'] = protomodata
refineparamsq['cycle'] = params['cycle']
refineparamsq['alismp'] = refinedict['alismp']
refineparamsq['alibox'] = {'x':refinedict['alibox_x'],'y':refinedict['alibox_y']}
refineparamsq['cormod'] = refinedict['cormod']
refineparamsq['imgref'] = refinedict['imgref']
refineparamsq['reference'] = refimagedata
refineparamsdata = apTomo.publish(refineparamsq)
# good cycle used for reset tlt params
if params['goodcycle'] is None:
goodrefineparamsdata = None
else:
goodq = appiondata.ApProtomoRefinementParamsData(protomo=protomodata,cycle=params['goodcycle'])
results = goodq.query(results=1)
if results:
goodrefineparamsdata = results[0]
else:
goodrefineparamsdata = None
# protomoaligner parameters
alignerdata = apTomo.insertAlignerParams(alignrundata,params,protomodata,refineparamsdata,goodrefineparamsdata,refimagedata)
return alignerdata
def insertProtomoParams(seriesname):
# general protmo parameters
protomoq = appiondata.ApProtomoParamsData()
protomoq['series_name'] = seriesname
protomodata = apTomo.publish(protomoq)
return protomodata
def insertProtomoParams(seriesname): # general protmo parameters protomoq = appiondata.ApProtomoParamsData() protomoq['series_name'] = seriesname protomodata = apTomo.publish(protomoq) return protomodata