Esempio n. 1
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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
Esempio n. 2
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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
Esempio n. 3
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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
Esempio n. 7
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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
Esempio n. 9
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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