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# The Leginon software is Copyright 2004
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# The Scripps Research Institute, La Jolla, CA
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# For terms of the license agreement
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# see http://ami.scripps.edu/software/leginon-license
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#
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# $Source: /ami/sw/cvsroot/pyleginon/calibrationclient.py,v $
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# $Revision: 1.211 $
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# $Name: not supported by cvs2svn $
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# $Date: 2007-05-22 19:21:07 $
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# $Author: pulokas $
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# $State: Exp $
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# $Locker: $
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SAVE_IMAGES = True
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import node, leginondata, event
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import numpy
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import scipy
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import pyami.quietscipy
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import scipy.ndimage
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import math
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from pyami import correlator, peakfinder, arraystats, imagefun, fftfun, numpil, ellipse
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import time
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import sys
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import threading
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import gonmodel
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import tiltcorrector
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import tableau
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import pyami.mrc
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import itertools
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idcounter = itertools.cycle(range(100))
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def saveDebugImage(im, label=None):
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if not SAVE_IMAGES:
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return
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timestamp = time.strftime('%Y%m%d_%H%M%S', time.localtime())
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nextid = idcounter.next()
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if label is None:
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label = ''
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else:
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label = label+'_'
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filename = '%s%s_%s.mrc' % (label, timestamp, nextid)
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allstats = arraystats.all(im)
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print 'Saving %s' % (filename,)
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print '\tstats:\n\t\tmean: %(mean)s\n\t\tstd: %(std)s\n\t\tmin: %(min)s\n\t\tmax: %(max)s' % allstats
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pyami.mrc.write(im, filename)
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class Drifting(Exception):
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pass
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class Abort(Exception):
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pass
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class NoPixelSizeError(Exception):
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pass
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class NoMatrixCalibrationError(Exception):
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def __init__(self, *args, **kwargs):
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if 'state' in kwargs:
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self.state = kwargs['state']
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else:
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self.state = None
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Exception.__init__(self, *args)
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class NoSensitivityError(Exception):
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pass
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class CalibrationClient(object):
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'''
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this is a component of a node that needs to use calibrations
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'''
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mover = False
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def __init__(self, node):
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self.node = node
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try:
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self.instrument = self.node.instrument
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except AttributeError:
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self.instrument = None
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self.correlator = correlator.Correlator()
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self.abortevent = threading.Event()
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self.tiltcorrector = tiltcorrector.TiltCorrector(node)
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self.stagetiltcorrector = tiltcorrector.VirtualStageTilter(node)
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self.rpixelsize = None
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self.powerbinning = 2
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self.debug = False
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def checkAbort(self):
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if self.abortevent.isSet():
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raise Abort()
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def getPixelSize(self, mag, tem=None, ccdcamera=None):
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queryinstance = leginondata.PixelSizeCalibrationData()
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queryinstance['magnification'] = mag
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if tem is None:
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queryinstance['tem'] = self.instrument.getTEMData()
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else:
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queryinstance['tem'] = tem
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if ccdcamera is None:
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queryinstance['ccdcamera'] = self.instrument.getCCDCameraData()
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else:
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queryinstance['ccdcamera'] = ccdcamera
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caldatalist = self.node.research(datainstance=queryinstance, results=1)
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if len(caldatalist) > 0:
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return caldatalist[0]['pixelsize']
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else:
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return None
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def getImagePixelSize(self,imagedata):
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scope = imagedata['scope']['tem']
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ccd = imagedata['camera']['ccdcamera']
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mag = imagedata['scope']['magnification']
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campixelsize = self.getPixelSize(mag,tem=scope, ccdcamera=ccd)
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binning = imagedata['camera']['binning']
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dimension = imagedata['camera']['dimension']
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pixelsize = {'x':campixelsize*binning['x'],'y':campixelsize*binning['y']}
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return pixelsize
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def getImageReciprocalPixelSize(self,imagedata):
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imagepixelsize = self.getImagePixelSize(imagedata)
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dimension = imagedata['camera']['dimension']
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rpixelsize = {'x':1.0/(imagepixelsize['x']*dimension['x']),'y':1.0/(imagepixelsize['y']*dimension['y'])}
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return rpixelsize
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def correctTilt(self, imagedata):
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return self.tiltcorrector.correct_tilt(imagedata)
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def acquireImage(self, scope, settle=0.0, correct_tilt=False, corchannel=0):
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if scope is not None:
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newemdata = leginondata.ScopeEMData(initializer=scope)
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self.instrument.setData(newemdata)
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self.node.startTimer('calclient acquire pause')
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time.sleep(settle)
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self.node.stopTimer('calclient acquire pause')
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imagedata = self.node.acquireCorrectedCameraImageData(corchannel)
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saveDebugImage(imagedata['image'], 'calclient')
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if correct_tilt:
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corrected = self.correctTilt(imagedata)
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if corrected:
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saveDebugImage(imagedata['image'], 'calclient_tiltcorrect')
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newscope = imagedata['scope']
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self.node.setImage(imagedata['image'], 'Image')
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return imagedata
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def measureScopeChange(self, previousimage, nextscope, settle=0.0, correct_tilt=False, correlation_type='phase', lp=None):
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'''
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Acquire an image at nextscope and correlate to previousimage
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'''
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self.checkAbort()
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# make sure previous image is in the correlator
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if self.correlator.getImage(1) is not previousimage['image']:
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self.correlator.insertImage(previousimage['image'])
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## use opposite correction channel
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corchannel = previousimage['correction channel']
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if corchannel:
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corchannel = 0
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else:
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corchannel = 1
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self.checkAbort()
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## acquire neximage
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nextimage = self.acquireImage(nextscope, settle, correct_tilt=correct_tilt, corchannel=corchannel)
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self.correlator.insertImage(nextimage['image'])
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imagearray = nextimage['image']
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if imagearray.max() == 0:
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raise RuntimeError('Bad image intensity range')
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self.checkAbort()
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## correlate
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self.node.startTimer('scope change correlation')
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if correlation_type is None:
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try:
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correlation_type = self.node.settings['correlation type']
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except KeyError:
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correlation_type = 'phase'
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if correlation_type == 'cross':
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cor = self.correlator.crossCorrelate()
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elif correlation_type == 'phase':
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cor = self.correlator.phaseCorrelate()
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else:
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raise RuntimeError('invalid correlation type')
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self.node.stopTimer('scope change correlation')
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if lp is not None:
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cor = scipy.ndimage.gaussian_filter(cor, lp)
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self.displayCorrelation(cor)
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## find peak
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self.node.startTimer('shift peak')
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peak = peakfinder.findSubpixelPeak(cor)
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self.node.stopTimer('shift peak')
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self.node.logger.debug('Peak %s' % (peak,))
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pixelpeak = peak['subpixel peak']
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self.node.startTimer('shift display')
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self.displayPeak(pixelpeak)
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self.node.stopTimer('shift display')
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peakvalue = peak['subpixel peak value']
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shift = correlator.wrap_coord(peak['subpixel peak'], cor.shape)
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self.node.logger.debug('pixel shift (row,col): %s' % (shift,))
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## need unbinned result
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binx = nextimage['camera']['binning']['x']
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biny = nextimage['camera']['binning']['y']
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unbinned = {'row':shift[0] * biny, 'col': shift[1] * binx}
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shiftinfo = {'previous': previousimage, 'next': nextimage, 'pixel shift': unbinned}
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return shiftinfo
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def measureStateDefocus(self, nextscope, settle=0.0):
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'''
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Acquire an image at nextscope and estimate the ctf parameters
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'''
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self.checkAbort()
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## acquire neximage
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nextimage = self.acquireImage(nextscope, settle, correct_tilt=False)
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## get ctf parameters
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self.ht = nextimage['scope']['high tension']
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if not self.rpixelsize:
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self.rpixelsize = self.getImageReciprocalPixelSize(nextimage)
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imagearray = nextimage['image']
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if imagearray.max() == 0:
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raise RuntimeError('Bad image intensity range')
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pow = imagefun.power(imagearray)
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ctfdata = fftfun.fitFirstCTFNode(pow,self.rpixelsize['x'], None, self.ht)
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self.checkAbort()
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if ctfdata is not None:
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self.node.logger.info('defocus: %.3f um, zast: %.3f um' % (ctfdata[0]*1e6,ctfdata[1]*1e6))
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defocusinfo = {'next': nextimage, 'defocus': ctfdata[0]}
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else:
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self.node.logger.warning('ctf estimation failed')
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defocusinfo = {'next': nextimage, 'defocus': None}
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return nextimage, defocusinfo
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def initTableau(self):
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self.tableauimages = []
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self.tableauangles = []
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self.tableaurads = []
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self.tabimage = None
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self.ctfdata = []
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def insertTableau(self, imagedata, angle, rad):
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image = imagedata['image']
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binning = self.powerbinning
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if True:
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pow = imagefun.power(image)
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binned = imagefun.bin(pow, binning)
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s = None
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self.ht = imagedata['scope']['high tension']
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if not self.rpixelsize:
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self.rpixelsize = self.getImageReciprocalPixelSize(imagedata)
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ctfdata = fftfun.fitFirstCTFNode(pow,self.rpixelsize['x'], None, self.ht)
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self.ctfdata.append(ctfdata)
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if ctfdata:
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s = '%d' % int(ctfdata[0]*1e9)
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eparams = ctfdata[4]
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center = numpy.divide(eparams['center'], binning)
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a = eparams['a'] / binning
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b = eparams['b'] / binning
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alpha = eparams['alpha']
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ellipse1 = pyami.ellipse.drawEllipse(binned.shape, 2*numpy.pi/180, center, a, b, alpha)
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ellipse2 = pyami.ellipse.drawEllipse(binned.shape, 5*numpy.pi/180, center, a, b, alpha)
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min = arraystats.min(binned)
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max = arraystats.max(binned)
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numpy.putmask(binned, ellipse1, min)
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numpy.putmask(binned, ellipse2, max)
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#elif self.ace2exe:
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elif False:
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ctfdata = self.estimateCTF(imagedata)
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z0 = (ctfdata['defocus1'] + ctfdata['defocus2']) / 2
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s = '%d' % (int(z0*1e9),)
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if s:
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t = numpil.textArray(s, binning)
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t = min + t * (max-min)
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imagefun.pasteInto(t, binned, (20,20))
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else:
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binned = imagefun.bin(image, binning)
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self.tableauimages.append(binned)
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self.tableauangles.append(angle)
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self.tableaurads.append(rad)
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def renderTableau(self):
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if not self.tableauimages:
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return
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size = self.tableauimages[0].shape[0]
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radinc = numpy.sqrt(2 * size * size)
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tab = tableau.Tableau()
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for i,im in enumerate(self.tableauimages):
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ang = self.tableauangles[i]
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rad = radinc * self.tableaurads[i]
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tab.insertImage(im, angle=ang, radius=rad)
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self.tabimage,self.tabscale = tab.render()
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mean = self.tabimage.mean()
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std = self.tabimage.std()
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newmax = mean + 5 * std
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a = numpy.where(self.tabimage >= newmax, newmax, self.tabimage)
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a = numpy.clip(a, 0, mean*1.5)
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self.tabimage = scipy.ndimage.zoom(a,self.powerbinning/3.0)
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self.displayTableau(self.tabimage)
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def displayImage(self, im):
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try:
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self.node.setImage(im, 'Image')
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except:
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pass
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def displayCorrelation(self, im):
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try:
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self.node.setImage(im, 'Correlation')
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except:
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pass
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def displayTableau(self, im):
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try:
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self.node.setImage(im, 'Tableau')
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except:
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pass
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def displayPeak(self, rowcol=None):
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if rowcol is None:
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targets = []
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else:
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# target display requires x,y order not row,col
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targets = [(rowcol[1], rowcol[0])]
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try:
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self.node.setTargets(targets, 'Peak')
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except:
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pass
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class DoseCalibrationClient(CalibrationClient):
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coulomb = 6.2414e18
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def __init__(self, node):
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CalibrationClient.__init__(self, node)
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self.psizecal = PixelSizeCalibrationClient(node)
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def storeSensitivity(self, ht, sensitivity):
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newdata = leginondata.CameraSensitivityCalibrationData()
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newdata['session'] = self.node.session
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newdata['high tension'] = ht
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newdata['sensitivity'] = sensitivity
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newdata['tem'] = self.instrument.getTEMData()
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newdata['ccdcamera'] = self.instrument.getCCDCameraData()
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self.node.publish(newdata, database=True, dbforce=True)
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def retrieveSensitivity(self, ht, tem, ccdcamera):
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qdata = leginondata.CameraSensitivityCalibrationData()
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qdata['tem'] = tem
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qdata['ccdcamera'] = ccdcamera
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qdata['high tension'] = ht
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results = self.node.research(datainstance=qdata, results=1)
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if results:
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result = results[0]['sensitivity']
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else:
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raise NoSensitivityError('No sensitivity calibration.')
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return result
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def dose_from_screen(self, screen_mag, beam_current, beam_diameter):
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## electrons per screen area per second
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beam_area = math.pi * (beam_diameter/2.0)**2
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screen_electrons = beam_current * self.coulomb / beam_area
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## electrons per specimen area per second (dose rate)
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dose_rate = screen_electrons * (screen_mag**2)
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return dose_rate
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def sensitivity(self, dose_rate, camera_mag, camera_pixel_size, exposure_time, counts):
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if camera_mag == 0:
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raise ValueError('invalid camera magnification given')
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camera_dose = float(dose_rate) / float((camera_mag**2))
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self.node.logger.info('Camera dose %.4e' % camera_dose)
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dose_per_pixel = camera_dose * (camera_pixel_size**2)
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electrons_per_pixel = dose_per_pixel * exposure_time
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if electrons_per_pixel == 0:
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raise ValueError('invalid electrons per pixel calculated')
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self.node.logger.info('Calculated electrons/pixel %.4e'
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% electrons_per_pixel)
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counts_per_electron = float(counts) / electrons_per_pixel
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return counts_per_electron
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def sensitivity_from_imagedata(self, imagedata, dose_rate):
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tem = imagedata['scope']['tem']
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ccdcamera = imagedata['camera']['ccdcamera']
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mag = imagedata['scope']['magnification']
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self.node.logger.info('Magnification %.1f' % mag)
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specimen_pixel_size = self.psizecal.retrievePixelSize(tem,
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ccdcamera, mag)
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self.node.logger.info('Specimen pixel size %.4e' % specimen_pixel_size)
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camera_pixel_size = imagedata['camera']['pixel size']['x']
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self.node.logger.info('Camera pixel size %.4e' % camera_pixel_size)
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camera_mag = camera_pixel_size / specimen_pixel_size
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self.node.logger.info('CCD Camera magnification %.1f' % camera_mag)
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exposure_time = imagedata['camera']['exposure time'] / 1000.0
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binning = imagedata['camera']['binning']['x']
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mean_counts = arraystats.mean(imagedata['image']) / (binning**2)
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return self.sensitivity(dose_rate, camera_mag, camera_pixel_size,
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exposure_time, mean_counts)
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def dose_from_imagedata(self, imagedata):
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'''
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imagedata indirectly contains most info needed to calc dose
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'''
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tem = imagedata['scope']['tem']
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if tem is None:
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tem = self.instrument.getTEMData()
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ccdcamera = imagedata['camera']['ccdcamera']
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if ccdcamera is None:
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ccdcamera = self.instrument.getCCDCameraData()
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camera_pixel_size = imagedata['camera']['pixel size']['x']
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ht = imagedata['scope']['high tension']
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binning = imagedata['camera']['binning']['x']
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mag = imagedata['scope']['magnification']
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specimen_pixel_size = self.psizecal.retrievePixelSize(tem, ccdcamera, mag)
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self.node.logger.debug('Specimen pixel size %.4e' % specimen_pixel_size)
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exp_time = imagedata['camera']['exposure time'] / 1000.0
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numdata = imagedata['image']
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sensitivity = self.retrieveSensitivity(ht, tem, ccdcamera)
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self.node.logger.debug('Sensitivity %.2f' % sensitivity)
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mean_counts = arraystats.mean(numdata) / (binning**2)
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self.node.logger.debug('Mean counts %.1f' % mean_counts)
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totaldose = mean_counts / specimen_pixel_size**2 / sensitivity
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return totaldose
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class PixelSizeCalibrationClient(CalibrationClient):
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'''
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basic CalibrationClient for accessing a type of calibration involving
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a matrix at a certain magnification
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'''
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def __init__(self, node):
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CalibrationClient.__init__(self, node)
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def researchPixelSizeData(self, tem, ccdcamera, mag):
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queryinstance = leginondata.PixelSizeCalibrationData()
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queryinstance['magnification'] = mag
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if tem is None:
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queryinstance['tem'] = self.instrument.getTEMData()
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else:
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queryinstance['tem'] = tem
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if ccdcamera is None:
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queryinstance['ccdcamera'] = self.instrument.getCCDCameraData()
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else:
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queryinstance['ccdcamera'] = ccdcamera
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caldatalist = self.node.research(datainstance=queryinstance)
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return caldatalist
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def retrievePixelSize(self, tem, ccdcamera, mag):
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'''
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finds the requested pixel size using magnification
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'''
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caldatalist = self.researchPixelSizeData(tem, ccdcamera, mag)
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if len(caldatalist) < 1:
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raise NoPixelSizeError()
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caldata = caldatalist[0]
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pixelsize = caldata['pixelsize']
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return pixelsize
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def time(self, tem, ccdcamera, mag):
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pdata = self.researchPixelSizeData(tem, ccdcamera, mag)
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if len(pdata) < 1:
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timeinfo = None
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else:
|
|
timeinfo = pdata[0].timestamp
|
|
return timeinfo
|
|
|
|
def retrieveLastPixelSizes(self, tem, camera):
|
|
caldatalist = self.researchPixelSizeData(tem, camera, None)
|
|
last = {}
|
|
for caldata in caldatalist:
|
|
try:
|
|
mag = caldata['magnification']
|
|
except:
|
|
print 'CALDATA', caldata
|
|
raise
|
|
if mag not in last:
|
|
last[mag] = caldata
|
|
return last.values()
|
|
|
|
|
|
class MatrixCalibrationClient(CalibrationClient):
|
|
'''
|
|
basic CalibrationClient for accessing a type of calibration involving
|
|
a matrix at a certain magnification
|
|
'''
|
|
def __init__(self, node):
|
|
CalibrationClient.__init__(self, node)
|
|
|
|
def parameter(self):
|
|
raise NotImplementedError
|
|
|
|
def researchMatrix(self, tem, ccdcamera, caltype, ht, mag):
|
|
queryinstance = leginondata.MatrixCalibrationData()
|
|
queryinstance['tem'] = tem
|
|
queryinstance['ccdcamera'] = ccdcamera
|
|
queryinstance['type'] = caltype
|
|
queryinstance['magnification'] = mag
|
|
queryinstance['high tension'] = ht
|
|
caldatalist = self.node.research(datainstance=queryinstance, results=1)
|
|
if caldatalist:
|
|
caldata = caldatalist[0]
|
|
return caldata
|
|
else:
|
|
excstr = 'no matrix for %s, %s, %s, %seV, %sx' % (tem['name'], ccdcamera['name'], caltype, ht, mag)
|
|
raise NoMatrixCalibrationError(excstr, state=queryinstance)
|
|
|
|
def retrieveMatrix(self, tem, ccdcamera, caltype, ht, mag):
|
|
'''
|
|
finds the requested matrix using magnification and type
|
|
'''
|
|
caldata = self.researchMatrix(tem, ccdcamera, caltype, ht, mag)
|
|
matrix = caldata['matrix'].copy()
|
|
return matrix
|
|
|
|
def time(self, tem, ccdcamera, ht, mag, caltype):
|
|
try:
|
|
caldata = self.researchMatrix(tem, ccdcamera, caltype, ht, mag)
|
|
except:
|
|
caldata = None
|
|
if caldata is None:
|
|
timestamp = None
|
|
else:
|
|
timestamp = caldata.timestamp
|
|
return timestamp
|
|
|
|
def storeMatrix(self, ht, mag, type, matrix, tem=None, ccdcamera=None):
|
|
'''
|
|
stores a new calibration matrix
|
|
'''
|
|
if tem is None:
|
|
tem = self.instrument.getTEMData()
|
|
if ccdcamera is None:
|
|
ccdcamera = self.instrument.getCCDCameraData()
|
|
newmatrix = numpy.array(matrix, numpy.float64)
|
|
caldata = leginondata.MatrixCalibrationData(session=self.node.session, magnification=mag, type=type, matrix=matrix, tem=tem, ccdcamera=ccdcamera)
|
|
caldata['high tension'] = ht
|
|
self.node.publish(caldata, database=True, dbforce=True)
|
|
|
|
def getMatrixAngles(self, matrix):
|
|
matrix = numpy.linalg.inv(matrix)
|
|
x_shift_row = matrix[0, 0]
|
|
x_shift_col = matrix[1, 0]
|
|
y_shift_row = matrix[0, 1]
|
|
y_shift_col = matrix[1, 1]
|
|
|
|
# calculations invert image coordinates (+y top, -y bottom)
|
|
# angle from the x shift of the parameter
|
|
theta_x = math.atan2(-x_shift_row, x_shift_col)
|
|
# angle from the y shift of the parameter
|
|
theta_y = math.atan2(-y_shift_row, -y_shift_col)
|
|
|
|
return theta_x, theta_y
|
|
|
|
def getAngles(self, *args):
|
|
matrix = self.retrieveMatrix(*args)
|
|
return self.getMatrixAngles(matrix)
|
|
|
|
class BeamTiltCalibrationClient(MatrixCalibrationClient):
|
|
def __init__(self, node):
|
|
MatrixCalibrationClient.__init__(self, node)
|
|
|
|
def getBeamTilt(self):
|
|
try:
|
|
return self.instrument.tem.BeamTilt
|
|
except:
|
|
return None
|
|
|
|
def setBeamTilt(self, bt):
|
|
self.instrument.tem.BeamTilt = bt
|
|
|
|
def storeRotationCenter(self, tem, ht, mag, beamtilt):
|
|
rc = leginondata.RotationCenterData()
|
|
rc['high tension'] = ht
|
|
rc['magnification'] = mag
|
|
rc['beam tilt'] = beamtilt
|
|
rc['tem'] = tem
|
|
rc['session'] = self.node.session
|
|
self.node.publish(rc, database=True, dbforce=True)
|
|
|
|
def retrieveRotationCenter(self, tem, ht, mag):
|
|
rc = leginondata.RotationCenterData()
|
|
rc['tem'] = tem
|
|
rc['high tension'] = ht
|
|
rc['magnification'] = mag
|
|
results = self.node.research(datainstance=rc, results=1)
|
|
if results:
|
|
return results[0]['beam tilt']
|
|
else:
|
|
return None
|
|
|
|
def measureRotationCenter(self, defocus1, defocus2, correlation_type=None, settle=0.5):
|
|
tem = self.instrument.getTEMData()
|
|
cam = self.instrument.getCCDCameraData()
|
|
ht = self.instrument.tem.HighTension
|
|
mag = self.instrument.tem.Magnification
|
|
try:
|
|
fmatrix = self.retrieveMatrix(tem, cam, 'defocus', ht, mag)
|
|
except NoMatrixCalibrationError:
|
|
raise RuntimeError('missing calibration matrix')
|
|
|
|
state1 = leginondata.ScopeEMData()
|
|
state2 = leginondata.ScopeEMData()
|
|
state1['defocus'] = defocus1
|
|
state2['defocus'] = defocus2
|
|
|
|
im1 = self.acquireImage(state1, settle=settle)
|
|
shiftinfo = self.measureScopeChange(im1, state2, settle=settle, correlation_type=correlation_type)
|
|
|
|
shift = shiftinfo['pixel shift']
|
|
d = shift['row'],shift['col']
|
|
bt = self.solveEq10_t(fmatrix, defocus1, defocus2, d)
|
|
return {'x':bt[0], 'y':bt[1]}
|
|
|
|
def measureDefocusStig(self, tilt_value, stig=True, correct_tilt=False, correlation_type=None, settle=0.5, image0=None):
|
|
self.abortevent.clear()
|
|
tem = self.instrument.getTEMData()
|
|
cam = self.instrument.getCCDCameraData()
|
|
ht = self.instrument.tem.HighTension
|
|
mag = self.instrument.tem.Magnification
|
|
try:
|
|
fmatrix = self.retrieveMatrix(tem, cam, 'defocus', ht, mag)
|
|
except NoMatrixCalibrationError:
|
|
raise RuntimeError('missing calibration matrix')
|
|
|
|
## only do stig if stig matrices exist
|
|
amatrix = bmatrix = None
|
|
if stig:
|
|
tiltaxes = ('x','y')
|
|
try:
|
|
amatrix = self.retrieveMatrix(tem, cam, 'stigx', ht, mag)
|
|
bmatrix = self.retrieveMatrix(tem, cam, 'stigy', ht, mag)
|
|
except NoMatrixCalibrationError:
|
|
stig = False
|
|
tiltaxes = ('x',)
|
|
else:
|
|
tiltaxes = ('x',)
|
|
|
|
tiltcenter = self.getBeamTilt()
|
|
|
|
if image0 is None:
|
|
image0 = self.acquireImage(None, settle=settle, correct_tilt=correct_tilt)
|
|
|
|
### need two tilt displacement measurements to get stig
|
|
shifts = []
|
|
tilts = []
|
|
self.checkAbort()
|
|
for tiltaxis in tiltaxes:
|
|
bt2 = dict(tiltcenter)
|
|
bt2[tiltaxis] += tilt_value
|
|
state2 = leginondata.ScopeEMData()
|
|
state2['beam tilt'] = bt2
|
|
try:
|
|
shiftinfo = self.measureScopeChange(image0, state2, settle=settle, correlation_type=correlation_type)
|
|
except Abort:
|
|
break
|
|
|
|
pixshift = shiftinfo['pixel shift']
|
|
|
|
shifts.append( (pixshift['row'], pixshift['col']) )
|
|
if tiltaxis == 'x':
|
|
tilts.append( (tilt_value, 0) )
|
|
else:
|
|
tilts.append( (0, tilt_value) )
|
|
try:
|
|
self.checkAbort()
|
|
except Abort:
|
|
break
|
|
|
|
## return to original beam tilt
|
|
self.instrument.tem.BeamTilt = tiltcenter
|
|
|
|
self.checkAbort()
|
|
|
|
sol = self.solveEq10(fmatrix, amatrix, bmatrix, tilts, shifts)
|
|
return sol
|
|
|
|
def OLDmeasureDefocusStig(self, tilt_value, publish_images=False, drift_threshold=None, stig=True, target=None, correct_tilt=False, correlation_type=None, settle=0.5):
|
|
self.abortevent.clear()
|
|
tem = self.instrument.getTEMData()
|
|
cam = self.instrument.getCCDCameraData()
|
|
ht = self.instrument.tem.HighTension
|
|
mag = self.instrument.tem.Magnification
|
|
try:
|
|
fmatrix = self.retrieveMatrix(tem, cam, 'defocus', ht, mag)
|
|
except NoMatrixCalibrationError:
|
|
raise RuntimeError('missing calibration matrix')
|
|
if stig:
|
|
try:
|
|
amatrix = self.retrieveMatrix(tem, cam, 'stigx', ht, mag)
|
|
bmatrix = self.retrieveMatrix(tem, cam, 'stigy', ht, mag)
|
|
except NoMatrixCalibrationError:
|
|
stig = False
|
|
|
|
tiltcenter = self.getBeamTilt()
|
|
#self.node.logger.info('Tilt center: x = %g, y = %g.' % (tiltcenter['x'], tiltcenter['y']))
|
|
|
|
### need two tilt displacement measurements
|
|
### easiest is one on each tilt axis
|
|
shifts = {}
|
|
tilts = {}
|
|
self.checkAbort()
|
|
nodrift = False
|
|
lastdrift = None
|
|
for tiltaxis in ('x','y'):
|
|
bt1 = dict(tiltcenter)
|
|
bt1[tiltaxis] -= tilt_value
|
|
bt2 = dict(tiltcenter)
|
|
bt2[tiltaxis] += tilt_value
|
|
state1 = leginondata.ScopeEMData()
|
|
state2 = leginondata.ScopeEMData()
|
|
state1['beam tilt'] = bt1
|
|
state2['beam tilt'] = bt2
|
|
## if no drift on 'x' axis, then assume we don't
|
|
## need to check on 'y' axis
|
|
if nodrift:
|
|
drift_threshold = None
|
|
try:
|
|
shiftinfo = self.measureStateShift(state1, state2, publish_images, settle=settle, drift_threshold=drift_threshold, target=target, correct_tilt=correct_tilt, correlation_type=correlation_type)
|
|
except Abort:
|
|
break
|
|
except Drifting:
|
|
## return to original beam tilt
|
|
self.instrument.tem.BeamTilt = tiltcenter
|
|
#self.node.logger.info('Returned to tilt center: x = %g, y = %g.' % (tiltcenter['x'], tiltcenter['y']))
|
|
|
|
raise
|
|
nodrift = True
|
|
if shiftinfo['driftdata'] is not None:
|
|
lastdrift = shiftinfo['driftdata']
|
|
|
|
pixshift = shiftinfo['pixel shift']
|
|
|
|
shifts[tiltaxis] = (pixshift['row'], pixshift['col'])
|
|
if tiltaxis == 'x':
|
|
tilts[tiltaxis] = (2*tilt_value, 0)
|
|
else:
|
|
tilts[tiltaxis] = (0, 2*tilt_value)
|
|
try:
|
|
self.checkAbort()
|
|
except Abort:
|
|
break
|
|
|
|
## return to original beam tilt
|
|
self.instrument.tem.BeamTilt = tiltcenter
|
|
#self.node.logger.info('Returned to tilt center: x = %g, y = %g.' % (tiltcenter['x'], tiltcenter['y']))
|
|
|
|
self.checkAbort()
|
|
|
|
#self.node.logger.info('Tilts %s, shifts %s' % (tilts, shifts))
|
|
|
|
d1 = shifts['x']
|
|
t1 = tilts['x']
|
|
d2 = shifts['y']
|
|
t2 = tilts['y']
|
|
if stig:
|
|
sol = self.solveEq10(fmatrix,amatrix,bmatrix,d1,t1,d2,t2)
|
|
#self.node.logger.info('Defocus: %g, stig.: (%g, %g), min. = %g' % (sol['defocus'], sol['stigx'], sol['stigy'], sol['min']))
|
|
else:
|
|
sol = self.solveEq10_nostig(fmatrix,d1,t1,d2,t2)
|
|
#self.node.logger.info('Defocus: %g, stig.: (not measured), min. = %g' % (sol['defocus'], sol['min']))
|
|
|
|
sol['lastdrift'] = lastdrift
|
|
return sol
|
|
|
|
def solveEq10(self, F, A, B, tilts, shifts):
|
|
'''
|
|
This solves Equation 10 from Koster paper
|
|
F,A,B are the defocus, stigx, and stigy calibration matrices
|
|
(all must be 2x2 numpy arrays)
|
|
d1,d2 are displacements resulting from beam tilts t1,t2
|
|
(all must be 2x1 numpy arrays)
|
|
'''
|
|
|
|
v = numpy.array(shifts, numpy.float64).ravel()
|
|
|
|
matrices = []
|
|
for matrix in (F,A,B):
|
|
if matrix is not None:
|
|
matrices.append(matrix)
|
|
|
|
mt = []
|
|
for tilt in tilts:
|
|
t = numpy.array(tilt)
|
|
t.shape=(2,1)
|
|
mm = []
|
|
for matrix in matrices:
|
|
m = numpy.dot(matrix, t)
|
|
mm.append(m)
|
|
m = numpy.concatenate(mm, 1)
|
|
mt.append(m)
|
|
M = numpy.concatenate(mt, 0)
|
|
|
|
solution = numpy.linalg.lstsq(M, v)
|
|
|
|
result = {'defocus': solution[0][0], 'min': float(solution[1][0])}
|
|
if len(solution[0]) == 3:
|
|
result['stigx'] = solution[0][1]
|
|
result['stigy'] = solution[0][2]
|
|
else:
|
|
result['stigx'] = None
|
|
result['stigy'] = None
|
|
return result
|
|
solveEq10 = classmethod(solveEq10)
|
|
|
|
def solveDefocus(self, F, d, t, tiltaxis):
|
|
if tiltaxis == 'x':
|
|
ft = t * numpy.hypot(*F[:,0])
|
|
else:
|
|
ft = t * numpy.hypot(*F[:,1])
|
|
f = d / ft
|
|
return f
|
|
solveDefocus = classmethod(solveDefocus)
|
|
|
|
def solveEq10_t(self, F, f1, f2, d):
|
|
'''
|
|
This solves t (misalignment) in equation 10 from Koster paper
|
|
given a displacement resulting from a defocus change
|
|
F is defocus calibration matric
|
|
f1, f2 are two defoci used to measure displacement d (row,col)
|
|
'''
|
|
a = (f2-f1) * F
|
|
b = numpy.array(d, numpy.float)
|
|
tiltx,tilty = numpy.linalg.solve(a,b)
|
|
return tiltx,tilty
|
|
|
|
def eq11(self, shifts, parameters, beam_tilt):
|
|
'''
|
|
Equation (11)
|
|
Calculates one column of a beam tilt calibration matrix given
|
|
the following arguments:
|
|
shifts - pixel shift resulting from tilt at parameters
|
|
parameters - value of microscope parameters causing shifts
|
|
beam_tilt - value of the induced beam tilt
|
|
'''
|
|
shift = numpy.zeros((2,), numpy.float)
|
|
shift[0] = shifts[1]['row'] - shifts[0]['row']
|
|
shift[1] = shifts[1]['col'] - shifts[0]['col']
|
|
|
|
try:
|
|
return shift/(2*(parameters[1] - parameters[0])*beam_tilt)
|
|
except ZeroDivisionError:
|
|
raise ValueError('invalid measurement, scale is zero')
|
|
|
|
def measureDisplacements(self, tilt_axis, tilt_value, states, **kwargs):
|
|
'''
|
|
This measures the displacements that go into eq. (11)
|
|
Each call of this function acquires four images
|
|
and returns two shift displacements.
|
|
'''
|
|
|
|
# try/finally to be sure we return to original beam tilt
|
|
try:
|
|
# set up to measure states
|
|
beam_tilt = self.instrument.tem.BeamTilt
|
|
beam_tilts = (dict(beam_tilt), dict(beam_tilt))
|
|
beam_tilts[0][tilt_axis] += tilt_value
|
|
beam_tilts[1][tilt_axis] -= tilt_value
|
|
|
|
pixel_shifts = []
|
|
m = 'Beam tilt measurement (%d of '
|
|
m += str(len(states))
|
|
m += '): (%g, %g) pixels'
|
|
for i, state in enumerate(states):
|
|
args = []
|
|
s0 = leginondata.ScopeEMData(initializer=state)
|
|
s0['beam tilt'] = beam_tilts[0]
|
|
s1 = leginondata.ScopeEMData(initializer=state)
|
|
s1['beam tilt'] = beam_tilts[1]
|
|
im0 = self.acquireImage(s0, **kwargs)
|
|
result = self.measureScopeChange(im0, s1, **kwargs)
|
|
pixel_shift = result['pixel shift']
|
|
pixel_shifts.append(pixel_shift)
|
|
|
|
args = (i + 1, pixel_shift['col'], pixel_shift['row'])
|
|
self.node.logger.info(m % args)
|
|
finally:
|
|
# return to original beam tilt
|
|
self.instrument.tem.BeamTilt = beam_tilt
|
|
|
|
return tuple(pixel_shifts)
|
|
|
|
def measureDefocusDifference(self, tiltvector, settle):
|
|
'''
|
|
Measure defocus difference between tilting plus tiltvector
|
|
compared to minus tiltvector
|
|
'''
|
|
btorig = self.getBeamTilt()
|
|
bt0 = btorig['x'], btorig['y']
|
|
#im0 = self.acquireImage(None, settle=settle)
|
|
d_diff = None
|
|
try:
|
|
d = []
|
|
for tsign in (1,-1):
|
|
delta = numpy.multiply(tsign, tiltvector)
|
|
bt = numpy.add(bt0, delta)
|
|
state1 = leginondata.ScopeEMData()
|
|
state1['beam tilt'] = {'x': bt[0], 'y': bt[1]}
|
|
im1, defocusinfo = self.measureStateDefocus(state1, settle=settle)
|
|
defocusshift = defocusinfo['defocus']
|
|
self.measured_defocii.append(defocusshift)
|
|
d.append(defocusshift)
|
|
angle = math.atan2(tiltvector[1],tiltvector[0]) * tsign
|
|
if angle == 0.0 and tsign == -1:
|
|
angle = math.pi
|
|
self.insertTableau(im1, angle, 1/math.sqrt(2))
|
|
tlength = math.hypot(tiltvector[0],tiltvector[1])
|
|
d_diff = numpy.multiply((d[1]-d[0])/tlength, tiltvector)
|
|
self.renderTableau()
|
|
finally:
|
|
self.setBeamTilt(btorig)
|
|
return d_diff
|
|
|
|
def getMeasured_Defocii(self):
|
|
return self.measured_defocii
|
|
|
|
def measureMatrixC(self, m, t, settle):
|
|
'''
|
|
determine matrix C, the beam-tilt coma matrix
|
|
m = misalignment value, t = tilt value
|
|
'''
|
|
self.rpixelsize = None
|
|
self.ht = None
|
|
self.initTableau()
|
|
# original beam tilt
|
|
btorig = self.getBeamTilt()
|
|
bt0 = btorig['x'], btorig['y']
|
|
diffs = {}
|
|
self.measured_defocii = []
|
|
try:
|
|
for axisn, axisname in ((0,'x'),(1,'y')):
|
|
diffs[axisname] = {}
|
|
for msign in (1,-1):
|
|
## misalign beam tilt
|
|
mis_delta = [0,0]
|
|
mis_delta[axisn] = msign * m
|
|
mis_bt = numpy.add(bt0, mis_delta)
|
|
mis_bt = {'x': mis_bt[0], 'y': mis_bt[1]}
|
|
self.setBeamTilt(mis_bt)
|
|
tvect = [0, 0]
|
|
tvect[axisn] = t
|
|
diff = self.measureDefocusDifference(tvect, settle)
|
|
if diff is None or not self.confirmDefocusInRange():
|
|
raise
|
|
diffs[axisname][msign] = diff
|
|
finally:
|
|
## return to original beam tilt
|
|
self.setBeamTilt(btorig)
|
|
|
|
matrix = numpy.zeros((2,2), numpy.float32)
|
|
if m!=0:
|
|
matrix[:,0] = numpy.divide(numpy.subtract(diffs['x'][-1], diffs['x'][1]), 2 * m * t)
|
|
matrix[:,1] = numpy.divide(numpy.subtract(diffs['y'][-1], diffs['y'][1]), 2 * m * t)
|
|
return matrix
|
|
|
|
def confirmDefocusInRange(self):
|
|
if len(self.measured_defocii) < 1:
|
|
return False
|
|
defocusarray = numpy.array(self.measured_defocii)
|
|
defocusmean = defocusarray.mean()
|
|
aimed_defocus = self.instrument.tem.Defocus
|
|
if (((abs(aimed_defocus)+1e-6)*3) < defocusmean) or (abs((aimed_defocus+1e-6)*0.2)) > defocusmean:
|
|
self.node.logger.warning('Estimated defocus out of range at %e' % defocusmean)
|
|
return False
|
|
return True
|
|
|
|
def calculateImageShiftComaMatrix(self,tdata,xydata):
|
|
''' Fit the beam tilt vector induced by image shift
|
|
to a straight line on individual axis.
|
|
Strickly speaking we should use orthogonal distance regression.'''
|
|
ordered_axes = ['x','y']
|
|
matrix = numpy.zeros((2,2))
|
|
coma0 = {'x':0.0,'y':0.0}
|
|
for index1, axis1 in enumerate(ordered_axes):
|
|
data = xydata[axis1]
|
|
for axis2 in data.keys():
|
|
(slope,t_intercept) = scipy.polyfit(numpy.array(tdata[axis1]),numpy.array(xydata[axis1][axis2]),1)
|
|
index2 = ordered_axes.index(axis2)
|
|
matrix[index1,index2] = slope
|
|
coma0[axis2] += t_intercept
|
|
coma0[axis2] /= len(ordered_axes)
|
|
return matrix, coma0
|
|
|
|
def measureComaFree(self, tilt_value, settle):
|
|
tem = self.instrument.getTEMData()
|
|
cam = self.instrument.getCCDCameraData()
|
|
ht = self.instrument.tem.HighTension
|
|
mag = self.instrument.tem.Magnification
|
|
self.rpixelsize = None
|
|
self.ht = ht
|
|
self.initTableau()
|
|
try:
|
|
par = 'beam-tilt coma'
|
|
cmatrix = self.retrieveMatrix(tem, cam, 'beam-tilt coma', ht, mag)
|
|
except NoMatrixCalibrationError:
|
|
raise RuntimeError('missing %s calibration matrix' % par)
|
|
dc = [0,0]
|
|
for axisn, axisname in ((0,'x'),(1,'y')):
|
|
tvect = [0, 0]
|
|
tvect[axisn] = tilt_value
|
|
dc[axisn] = self.measureDefocusDifference(tvect, settle)
|
|
dc = numpy.array(dc) / tilt_value
|
|
cftilt = numpy.linalg.solve(cmatrix, dc)
|
|
if not self.confirmDefocusInRange():
|
|
cftilt[(0,0)] = 0
|
|
cftilt[(1,1)] = 0
|
|
return cftilt
|
|
|
|
def repeatMeasureComaFree(self, tilt_value, settle, repeat=1):
|
|
'''repeat measuremnet to increase precision'''
|
|
tilts = {'x':[],'y':[]}
|
|
self.measured_defocii = []
|
|
self.node.logger.debug("===================")
|
|
for i in range(0,repeat):
|
|
try:
|
|
cftilt = self.measureComaFree(tilt_value, settle)
|
|
except Exception, e:
|
|
cftilt = None
|
|
raise
|
|
if cftilt is None:
|
|
comatilt = {'x':None, 'y':None}
|
|
else:
|
|
tilts['x'].append(cftilt[(0,0)])
|
|
tilts['y'].append(cftilt[(1,1)])
|
|
comatilt = {'x':cftilt[(0,0)],'y':cftilt[(1,1)]}
|
|
self.node.logger.debug(" %5.2f, %5.2f" % (cftilt[(0,0)]*1000,cftilt[(1,1)]*1000))
|
|
if len(tilts['x']):
|
|
xarray = numpy.array(tilts['x'])
|
|
yarray = numpy.array(tilts['y'])
|
|
self.node.logger.debug("--------------------")
|
|
self.node.logger.debug("m %5.2f, %5.2f" %(xarray.mean()*1000,yarray.mean()*1000))
|
|
self.node.logger.debug("std %5.2f, %5.2f" %(xarray.std()*1000,yarray.std()*1000))
|
|
return xarray,yarray
|
|
|
|
def transformImageShiftToBeamTilt(self, imageshift, tem, cam, ht, zerobeamtilt, mag):
|
|
newbeamtilt = {}
|
|
par = 'image-shift coma'
|
|
try:
|
|
# not to query specific mag for now
|
|
matrix = self.retrieveMatrix(tem, cam, 'image-shift coma', ht, None)
|
|
except NoMatrixCalibrationError:
|
|
raise RuntimeError('missing %s calibration matrix' % par)
|
|
self.node.logger.debug("Image Shift ( %5.2f, %5.2f)" % (imageshift['x']*1e6,imageshift['y']*1e6))
|
|
shiftvect = numpy.array((imageshift['x'], imageshift['y']))
|
|
change = numpy.dot(matrix, shiftvect)
|
|
newbeamtilt['x'] = zerobeamtilt['x'] + change[0]
|
|
newbeamtilt['y'] = zerobeamtilt['y'] + change[1]
|
|
self.node.logger.debug("Beam Tilt Correction ( %5.2f, %5.2f)" % (change[0]*1e3,change[1]*1e3))
|
|
self.node.logger.debug("Beam Tilt ( %5.2f, %5.2f)" % (newbeamtilt['x']*1e3,newbeamtilt['y']*1e3))
|
|
return newbeamtilt
|
|
|
|
def correctImageShiftComa(self):
|
|
tem = self.instrument.getTEMData()
|
|
cam = self.instrument.getCCDCameraData()
|
|
ht = self.instrument.tem.HighTension
|
|
mag = self.instrument.tem.Magnification
|
|
shift = self.instrument.tem.ImageShift
|
|
scopestate = leginondata.ScopeEMData(tem=tem,magnification=mag)
|
|
camerastate = leginondata.ScopeEMData(ccdcamera=cam)
|
|
tilt0 = self.instrument.tem.BeamTilt
|
|
scopestate['high tension'] = ht
|
|
scopestate['image shift'] = shift0
|
|
scopestate['beam tilt'] = tilt0
|
|
beamtilt = scopestate['beam tilt']
|
|
beamtilt = transformImageShiftToBeamTilt(shift, tem, cam, ht, beamtilt, mag)
|
|
self.setBeamTilt(beamtilt)
|
|
|
|
class SimpleMatrixCalibrationClient(MatrixCalibrationClient):
|
|
mover = True
|
|
def __init__(self, node):
|
|
MatrixCalibrationClient.__init__(self, node)
|
|
|
|
def parameter(self):
|
|
'''
|
|
returns a scope key for the calibrated parameter
|
|
'''
|
|
raise NotImplementedError()
|
|
|
|
def measurementToMatrix(self, measurement):
|
|
'''
|
|
convert a mesurement in pixels/[TEM parameter] to a matrix
|
|
in [TEM parameter]/pixel
|
|
'''
|
|
xrow = measurement['x']['row']
|
|
xcol = measurement['x']['col']
|
|
yrow = measurement['y']['row']
|
|
ycol = measurement['y']['col']
|
|
matrix = numpy.array([[xrow,yrow],[xcol,ycol]],numpy.float)
|
|
matrix = numpy.linalg.inv(matrix)
|
|
return matrix
|
|
|
|
def transform(self, pixelshift, scope, camera):
|
|
'''
|
|
Calculate a new scope state from the given pixelshift
|
|
The input scope and camera state should refer to the image
|
|
from which the pixelshift originates
|
|
'''
|
|
mag = scope['magnification']
|
|
ht = scope['high tension']
|
|
binx = camera['binning']['x']
|
|
biny = camera['binning']['y']
|
|
par = self.parameter()
|
|
tem = scope['tem']
|
|
ccdcamera = camera['ccdcamera']
|
|
matrix = self.retrieveMatrix(tem, ccdcamera, par, ht, mag)
|
|
|
|
pixrow = pixelshift['row'] * biny
|
|
pixcol = pixelshift['col'] * binx
|
|
pixvect = numpy.array((pixrow, pixcol))
|
|
|
|
change = numpy.dot(matrix, pixvect)
|
|
changex = change[0]
|
|
changey = change[1]
|
|
|
|
### take into account effect of alpha tilt on Y stage pos
|
|
if par == 'stage position':
|
|
if 'a' in scope[par] and scope[par]['a'] is not None:
|
|
alpha = scope[par]['a']
|
|
changey = changey / numpy.cos(alpha)
|
|
|
|
new = leginondata.ScopeEMData(initializer=scope)
|
|
## make a copy of this since it will be modified
|
|
new[par] = dict(scope[par])
|
|
new[par]['x'] += changex
|
|
new[par]['y'] += changey
|
|
return new
|
|
|
|
def itransform(self, position, scope, camera):
|
|
parameter = self.parameter()
|
|
args = (
|
|
scope['tem'],
|
|
camera['ccdcamera'],
|
|
parameter,
|
|
scope['high tension'],
|
|
scope['magnification'],
|
|
)
|
|
matrix = self.retrieveMatrix(*args)
|
|
inverse_matrix = numpy.linalg.inv(matrix)
|
|
|
|
shift = dict(position)
|
|
shift['x'] -= scope[parameter]['x']
|
|
shift['y'] -= scope[parameter]['y']
|
|
|
|
# take into account effect of stage alpha tilt on y stage position
|
|
if parameter == 'stage position':
|
|
if 'a' in scope[parameter] and scope[parameter]['a'] is not None:
|
|
alpha = scope[parameter]['a']
|
|
shift['y'] = shift['y']*numpy.cos(alpha)
|
|
|
|
shift_vector = numpy.array((shift['x'], shift['y']))
|
|
pixel = numpy.dot(inverse_matrix, shift_vector)
|
|
|
|
pixel_shift = {
|
|
'row': pixel[0]/camera['binning']['y'],
|
|
'col': pixel[1]/camera['binning']['x'],
|
|
}
|
|
|
|
return pixel_shift
|
|
|
|
class ImageShiftCalibrationClient(SimpleMatrixCalibrationClient):
|
|
def __init__(self, node):
|
|
SimpleMatrixCalibrationClient.__init__(self, node)
|
|
|
|
def parameter(self):
|
|
return 'image shift'
|
|
|
|
def pixelToPixel(self, tem, ccdcamera, ht, mag1, mag2, p1):
|
|
'''
|
|
Using stage position as a global coordinate system, we can
|
|
do pixel to pixel transforms between mags.
|
|
This function will calculate a pixel vector at mag2, given
|
|
a pixel vector at mag1.
|
|
'''
|
|
par = self.parameter()
|
|
matrix1 = self.retrieveMatrix(tem, ccdcamera, par, ht, mag1)
|
|
matrix2 = self.retrieveMatrix(tem, ccdcamera, par, ht, mag2)
|
|
matrix2inv = numpy.linalg.inv(matrix2)
|
|
p1 = numpy.array(p1)
|
|
stagepos = numpy.dot(matrix1, p1)
|
|
p2 = numpy.dot(matrix2inv, stagepos)
|
|
return p2
|
|
|
|
class BeamShiftCalibrationClient(SimpleMatrixCalibrationClient):
|
|
mover = False
|
|
def __init__(self, node):
|
|
SimpleMatrixCalibrationClient.__init__(self, node)
|
|
|
|
def parameter(self):
|
|
return 'beam shift'
|
|
|
|
class ImageBeamShiftCalibrationClient(ImageShiftCalibrationClient):
|
|
def __init__(self, node):
|
|
ImageShiftCalibrationClient.__init__(self, node)
|
|
self.beamcal = BeamShiftCalibrationClient(node)
|
|
|
|
def transform(self, pixelshift, scope, camera):
|
|
scope2 = ImageShiftCalibrationClient.transform(self, pixelshift, scope, camera)
|
|
## do beam shift in oposite direction
|
|
opposite = {'row': -pixelshift['row'], 'col': -pixelshift['col']}
|
|
scope3 = self.beamcal.transform(opposite, scope2, camera)
|
|
return scope3
|
|
|
|
class StageCalibrationClient(SimpleMatrixCalibrationClient):
|
|
def __init__(self, node):
|
|
SimpleMatrixCalibrationClient.__init__(self, node)
|
|
|
|
def parameter(self):
|
|
return 'stage position'
|
|
|
|
def pixelToPixel(self, tem, ccdcamera, ht, mag1, mag2, p1):
|
|
'''
|
|
Using stage position as a global coordinate system, we can
|
|
do pixel to pixel transforms between mags.
|
|
This function will calculate a pixel vector at mag2, given
|
|
a pixel vector at mag1.
|
|
'''
|
|
par = self.parameter()
|
|
matrix1 = self.retrieveMatrix(tem, ccdcamera, par, ht, mag1)
|
|
matrix2 = self.retrieveMatrix(tem, ccdcamera, par, ht, mag2)
|
|
matrix2inv = numpy.linalg.inv(matrix2)
|
|
p1 = numpy.array(p1)
|
|
stagepos = numpy.dot(matrix1, p1)
|
|
p2 = numpy.dot(matrix2inv, stagepos)
|
|
return p2
|
|
|
|
class StageTiltCalibrationClient(StageCalibrationClient):
|
|
def __init__(self, node):
|
|
StageCalibrationClient.__init__(self, node)
|
|
|
|
def measureZ(self, tilt_value, correlation_type=None):
|
|
'''
|
|
This is currently hard coded based on our Tecnai, but should be calibrated
|
|
for every scope.
|
|
For a positive stage tilt on Tecnai:
|
|
If Z is too positive, Y moves negative
|
|
If Z is too negative, Y moves positive
|
|
'''
|
|
orig_a = self.instrument.tem.StagePosition['a']
|
|
|
|
state1 = leginondata.ScopeEMData()
|
|
state2 = leginondata.ScopeEMData()
|
|
state1['stage position'] = {'a':-tilt_value}
|
|
state2['stage position'] = {'a':tilt_value}
|
|
## alpha backlash correction
|
|
self.instrument.tem.StagePosition = state1['stage position']
|
|
self.instrument.tem.StagePosition = state2['stage position']
|
|
## do tilt and measure image shift
|
|
im1 = self.acquireImage(state1)
|
|
shiftinfo = self.measureScopeChange(im1, state2, correlation_type=correlation_type)
|
|
self.instrument.tem.StagePosition = {'a':orig_a}
|
|
|
|
state1 = shiftinfo['previous']['scope']
|
|
state2 = shiftinfo['next']['scope']
|
|
pixelshift = shiftinfo['pixel shift']
|
|
#psize = self.getPixelSize(state1['magnification'])
|
|
#dist = psize * math.hypot(pixelshift['row'], pixelshift['col'])
|
|
|
|
# fake the current state for the transform with alpha = 0
|
|
scope = leginondata.ScopeEMData(initializer=state1)
|
|
scope['stage position']['a'] = 0.0
|
|
cam = leginondata.CameraEMData()
|
|
# measureScopeChange already unbinned it, so fake cam bin = 1
|
|
cam['binning'] = {'x':1,'y':1}
|
|
cam['ccdcamera'] = self.instrument.getCCDCameraData()
|
|
# get the virtual x,y movement
|
|
newscope = self.transform(pixelshift, scope, cam)
|
|
# y component is all we care about to get Z
|
|
y = newscope['stage position']['y'] - scope['stage position']['y']
|
|
z = y / 2.0 / math.sin(tilt_value)
|
|
return z
|
|
|
|
def measureTiltAxisLocation(self, tilt_value=0.26, numtilts=1, tilttwice=False,
|
|
update=False, snrcut=10.0, correlation_type='phase', medfilt=False):
|
|
"""
|
|
measure position on image of tilt axis
|
|
tilt_value is in radians
|
|
"""
|
|
|
|
### BEGIN TILTING
|
|
|
|
# need to do something with this data
|
|
pixelshiftree = []
|
|
for i in range(numtilts):
|
|
#get first image
|
|
imagedata0, ps = self._getPeakFromTiltStates(tilt0imagedata=None,
|
|
tilt1=-tilt_value, medfilt=medfilt, snrcut=snrcut, correlation_type=correlation_type)
|
|
if ps['snr'] > snrcut:
|
|
pixelshiftree.append(ps)
|
|
|
|
if tilttwice is True:
|
|
#get second image
|
|
imagedata0, ps = self._getPeakFromTiltStates(tilt0imagedata=imagedata0,
|
|
tilt1=tilt_value, medfilt=medfilt, snrcut=snrcut)
|
|
if ps['snr'] > snrcut:
|
|
pixelshiftree.append(ps)
|
|
|
|
### END TILTING; BEGIN ASSESSMENT
|
|
|
|
if len(pixelshiftree) < 1:
|
|
#wasn't a good enough fit
|
|
self.node.logger.error("image correction failed, snr below cutoff")
|
|
return imagedata0, pixelshift
|
|
else:
|
|
self.node.logger.info("averaging %s measurements for final value" % (len(pixelshiftree)))
|
|
|
|
snrtotal = 0.0
|
|
rowtotal = 0.0
|
|
coltotal = 0.0
|
|
for ps in pixelshiftree:
|
|
snrtotal += ps['snr']
|
|
rowtotal += ps['row']*ps['snr']
|
|
coltotal += ps['col']*ps['snr']
|
|
self.node.logger.info("measured pixel shift: %s, %s" % (ps['row'], ps['col']))
|
|
|
|
pixelshift = {
|
|
'row':rowtotal/snrtotal,
|
|
'col':coltotal/snrtotal,
|
|
'snr':snrtotal/float(len(pixelshiftree))
|
|
}
|
|
self.node.logger.info("final pixel shift: %s, %s" % (pixelshift['row'], pixelshift['col']))
|
|
|
|
### END ASSESSMENT; BEGIN CORRECTION
|
|
|
|
## convert pixel shift into stage movement
|
|
newscope = self.transform(pixelshift, imagedata0['scope'], imagedata0['camera'])
|
|
## only want the y offset (distance from tilt axis)
|
|
deltay = newscope['stage position']['y'] - imagedata0['scope']['stage position']['y']
|
|
## scale correlation shift to the axis offset
|
|
scale = 1.0 / numpy.tan(tilt_value/2.0) / numpy.tan(tilt_value)
|
|
deltay *= scale
|
|
|
|
tem = self.instrument.getTEMData()
|
|
ccdcamera = self.instrument.getCCDCameraData()
|
|
|
|
axisoffset = leginondata.StageTiltAxisOffsetData(offset=deltay,tem=tem,ccdcamera=ccdcamera)
|
|
|
|
if update:
|
|
q = leginondata.StageTiltAxisOffsetData(tem=tem,ccdcamera=ccdcamera)
|
|
offsets = self.node.research(q, results=1)
|
|
if offsets:
|
|
axisoffset['offset'] += offsets[0]['offset']
|
|
|
|
self.node.publish(axisoffset, database=True, dbforce=True)
|
|
|
|
self.node.logger.info('stage delta y: %s' % (deltay,))
|
|
|
|
shift = {'x':0, 'y':deltay}
|
|
position = dict(imagedata0['scope']['stage position'])
|
|
position['x'] += shift['x']
|
|
position['y'] += shift['y']
|
|
pixelshift = self.itransform(position, imagedata0['scope'], imagedata0['camera'])
|
|
self.node.logger.info('pixelshift for delta y: %s' % (pixelshift,))
|
|
|
|
pixelshift = {'row':pixelshift['row'], 'col':pixelshift['col']}
|
|
self.node.logger.info('pixelshift from axis: %s' % (pixelshift,))
|
|
|
|
return imagedata0, pixelshift
|
|
|
|
|
|
def measureTiltAxisLocation2(self, tilt_value=0.0696, tilttwice=False,
|
|
update=False, correlation_type='phase', beam_tilt=0.01):
|
|
"""
|
|
measure position on image of tilt axis
|
|
tilt_value is in radians
|
|
"""
|
|
|
|
### BEGIN TILTING
|
|
|
|
# need to do something with this data
|
|
defshifts = []
|
|
#get first image
|
|
imagedata0, defshift = self._getDefocDiffFromTiltStates(tilt0imagedata=None,
|
|
tilt1=-tilt_value, correlation_type=correlation_type, beam_tilt_value=beam_tilt)
|
|
if defshift is not None and abs(defshift) < 1e-5:
|
|
defshifts.append(-defshift)
|
|
|
|
if tilttwice is True:
|
|
#get second image
|
|
imagedata0, defshift = self._getDefocDiffFromTiltStates(tilt0imagedata=imagedata0,
|
|
tilt1=tilt_value, correlation_type=correlation_type, beam_tilt_value=beam_tilt)
|
|
if defshift is not None and abs(defshift) < 1e-5:
|
|
defshifts.append(defshift)
|
|
print defshifts
|
|
### END TILTING; BEGIN ASSESSMENT
|
|
|
|
if len(defshifts) < 1:
|
|
#no good defocus measurement
|
|
self.node.logger.error("bad defocus measurements")
|
|
return imagedata0, None
|
|
else:
|
|
self.node.logger.info("averaging %s measurements for final value" % (len(defshifts)))
|
|
|
|
deltaz = sum(defshifts)/len(defshifts)
|
|
self.node.logger.info("final defocus shift: %.2f um" % (deltaz/1e-6))
|
|
|
|
### END ASSESSMENT; BEGIN CORRECTION
|
|
|
|
## only want the y offset (distance from tilt axis)
|
|
deltay = deltaz/math.sin(tilt_value)
|
|
## scale correlation shift to the axis offset
|
|
|
|
tem = self.instrument.getTEMData()
|
|
ccdcamera = self.instrument.getCCDCameraData()
|
|
|
|
axisoffset = leginondata.StageTiltAxisOffsetData(offset=deltay,tem=tem,ccdcamera=ccdcamera)
|
|
|
|
if update:
|
|
q = leginondata.StageTiltAxisOffsetData(tem=tem,ccdcamera=ccdcamera)
|
|
offsets = self.node.research(q, results=1)
|
|
if offsets:
|
|
axisoffset['offset'] += offsets[0]['offset']
|
|
|
|
self.node.publish(axisoffset, database=True, dbforce=True)
|
|
|
|
self.node.logger.info('stage delta y: %s' % (deltay,))
|
|
|
|
shift = {'x':0, 'y':deltay}
|
|
position = dict(imagedata0['scope']['stage position'])
|
|
position['x'] += shift['x']
|
|
position['y'] += shift['y']
|
|
pixelshift = self.itransform(position, imagedata0['scope'], imagedata0['camera'])
|
|
self.node.logger.info('pixelshift for delta y: %s' % (pixelshift,))
|
|
|
|
pixelshift = {'row':pixelshift['row'], 'col':pixelshift['col']}
|
|
self.node.logger.info('pixel shift from axis: %s' % (pixelshift,))
|
|
|
|
return imagedata0, pixelshift
|
|
|
|
def _getPeakFromTiltStates(self, tilt0imagedata=None, tilt1=0.26, medfilt=True, snrcut=10.0, correlation_type='phase'):
|
|
orig_a = self.instrument.tem.StagePosition['a']
|
|
state0 = leginondata.ScopeEMData()
|
|
state1 = leginondata.ScopeEMData()
|
|
state0['stage position'] = {'a':0.0}
|
|
state1['stage position'] = {'a':tilt1}
|
|
tilt1deg = round(-tilt1*180.0/math.pi,4)
|
|
|
|
if tilt0imagedata is None:
|
|
self.node.logger.info('acquiring tilt=0 degrees')
|
|
self.instrument.setData(state0)
|
|
time.sleep(0.5)
|
|
imagedata0 = self.node.acquireCorrectedCameraImageData()
|
|
im0 = imagedata0['image']
|
|
self.displayImage(im0)
|
|
else:
|
|
imagedata0 = tilt0imagedata
|
|
im0 = imagedata0['image']
|
|
self.displayImage(im0)
|
|
|
|
self.node.logger.info('acquiring tilt=%s degrees' % (tilt1deg))
|
|
self.instrument.setData(state1)
|
|
time.sleep(0.5)
|
|
imagedata1 = self.node.acquireCorrectedCameraImageData()
|
|
self.stagetiltcorrector.undo_tilt(imagedata1)
|
|
im1 = imagedata1['image']
|
|
self.displayImage(im1)
|
|
|
|
### RETURN SCOPE TO ORIGINAL STATE
|
|
self.instrument.tem.StagePosition = {'a':orig_a}
|
|
|
|
self.node.logger.info('correlating images for tilt %s' % (tilt1deg))
|
|
self.correlator.setImage(0, im0)
|
|
self.correlator.setImage(1, im1)
|
|
if correlation_type is 'phase':
|
|
pc = self.correlator.phaseCorrelate()
|
|
if medfilt is True:
|
|
pc = scipy.ndimage.median_filter(pc, size=3)
|
|
else:
|
|
pc = self.correlator.crossCorrelate()
|
|
self.displayCorrelation(pc)
|
|
|
|
peak01 = peakfinder.findSubpixelPeak(pc)
|
|
snr = 1.0
|
|
if 'snr' in peak01:
|
|
snr = peak01['snr']
|
|
if snr < snrcut:
|
|
#wasn't a good enough fit
|
|
self.node.logger.warning("beam tilt axis measurement failed, snr below cutoff; "+
|
|
"continuing for rest of images")
|
|
|
|
## translate peak into image shift coordinates
|
|
peak01a = peak01['subpixel peak']
|
|
shift01 = correlator.wrap_coord(peak01a, pc.shape)
|
|
self.displayPeak(peak01a)
|
|
if tilt1 > 0:
|
|
pixelshift = {'row':-1.0*shift01[0], 'col':-1.0*shift01[1], 'snr':snr }
|
|
else:
|
|
pixelshift = {'row':shift01[0], 'col':shift01[1], 'snr':snr }
|
|
|
|
self.node.logger.info("measured pixel shift: %s, %s" % (pixelshift['row'], pixelshift['col']))
|
|
self.node.logger.info("signal-to-noise ratio: %s" % (round(snr,2),))
|
|
|
|
return imagedata0, pixelshift
|
|
|
|
def _getDefocDiffFromTiltStates(self, tilt0imagedata=None, tilt1=0.26, correlation_type='phase',beam_tilt_value=0.01):
|
|
orig_a = self.instrument.tem.StagePosition['a']
|
|
state0 = leginondata.ScopeEMData()
|
|
state1 = leginondata.ScopeEMData()
|
|
state0['stage position'] = {'a':0.0}
|
|
state1['stage position'] = {'a':tilt1}
|
|
tilt1deg = round(-tilt1*180.0/math.pi,4)
|
|
|
|
if tilt0imagedata is None:
|
|
self.node.logger.info('acquiring tilt=0 degrees')
|
|
self.instrument.setData(state0)
|
|
time.sleep(0.5)
|
|
imagedata0 = self.node.acquireCorrectedCameraImageData()
|
|
im0 = imagedata0['image']
|
|
self.displayImage(im0)
|
|
else:
|
|
imagedata0 = tilt0imagedata
|
|
im0 = imagedata0['image']
|
|
self.displayImage(im0)
|
|
try:
|
|
defresult = self.node.btcalclient.measureDefocusStig(beam_tilt_value, False, False, correlation_type, 0.5, imagedata0)
|
|
except RuntimeError, e:
|
|
self.node.logger.error('Measurement failed: %s' % e)
|
|
return imagedata0, None
|
|
def0 = defresult['defocus']
|
|
print defresult
|
|
minres = defresult['min']
|
|
self.node.logger.info('acquiring tilt=%s degrees' % (tilt1deg))
|
|
self.instrument.setData(state1)
|
|
time.sleep(0.5)
|
|
imagedata1 = self.node.acquireCorrectedCameraImageData()
|
|
self.stagetiltcorrector.undo_tilt(imagedata1)
|
|
im1 = imagedata1['image']
|
|
self.displayImage(im1)
|
|
defresult = self.node.btcalclient.measureDefocusStig(beam_tilt_value, False, False, correlation_type, 0.5, imagedata1)
|
|
def1 = defresult['defocus']
|
|
print defresult
|
|
minres = min((minres,defresult['min']))
|
|
if minres > 5000000:
|
|
self.node.logger.error('Measurement not reliable: residual= %.0f' % minres)
|
|
return imagedata0, None
|
|
|
|
### RETURN SCOPE TO ORIGINAL STATE
|
|
self.instrument.tem.StagePosition = {'a':orig_a}
|
|
|
|
## calculate defocus difference
|
|
defocusdiff = def1 - def0
|
|
self.node.logger.info("measured defocus difference is %.2f um" % (defocusdiff*1e6))
|
|
|
|
return imagedata0, defocusdiff
|
|
|
|
class ModeledStageCalibrationClient(MatrixCalibrationClient):
|
|
mover = True
|
|
def __init__(self, node):
|
|
CalibrationClient.__init__(self, node)
|
|
|
|
def parameter(self):
|
|
return 'stage position'
|
|
|
|
def pixelToPixel(self, tem, ccdcamera, ht, mag1, mag2, p1):
|
|
'''
|
|
Using stage position as a global coordinate system, we can
|
|
do pixel to pixel transforms between mags.
|
|
This function will calculate a pixel vector at mag2, given
|
|
a pixel vector at mag1.
|
|
'''
|
|
|
|
scope = leginondata.ScopeEMData()
|
|
scope['tem'] = tem
|
|
scope['high tension'] = ht
|
|
scope['stage position'] = {'x':0.0, 'y':0.0}
|
|
camera = leginondata.CameraEMData()
|
|
camera['ccdcamera'] = ccdcamera
|
|
camera['binning'] = {'x':1,'y':1}
|
|
|
|
scope['magnification'] = mag1
|
|
pixelshift = {'row':p1[0], 'col':p1[1]}
|
|
newscope = self.transform(pixelshift, scope, camera)
|
|
|
|
scope['magnification'] = mag2
|
|
position = newscope['stage position']
|
|
pix = self.itransform(position, scope, camera)
|
|
|
|
return pix['row'],pix['col']
|
|
|
|
def storeMagCalibration(self, tem, cam, label, ht, mag, axis, angle, mean):
|
|
caldata = leginondata.StageModelMagCalibrationData()
|
|
caldata['session'] = self.node.session
|
|
caldata['tem'] = tem
|
|
caldata['ccdcamera'] = cam
|
|
caldata['label'] = label
|
|
caldata['high tension'] = ht
|
|
caldata['magnification'] = mag
|
|
caldata['axis'] = axis
|
|
caldata['angle'] = angle
|
|
caldata['mean'] = mean
|
|
self.node.publish(caldata, database=True, dbforce=True)
|
|
|
|
def researchMagCalibration(self, tem, cam, ht, mag, axis):
|
|
qinst = leginondata.StageModelMagCalibrationData(magnification=mag, axis=axis)
|
|
qinst['high tension'] = ht
|
|
if tem is None:
|
|
qinst['tem'] = self.instrument.getTEMData()
|
|
else:
|
|
qinst['tem'] = tem
|
|
if cam is None:
|
|
qinst['ccdcamera'] = self.instrument.getCCDCameraData()
|
|
else:
|
|
qinst['ccdcamera'] = cam
|
|
|
|
caldatalist = self.node.research(datainstance=qinst, results=1)
|
|
if len(caldatalist) > 0:
|
|
caldata = caldatalist[0]
|
|
else:
|
|
caldata = None
|
|
return caldata
|
|
|
|
def retrieveMagCalibration(self, tem, cam, ht, mag, axis):
|
|
caldata = self.researchMagCalibration(tem, cam, ht, mag, axis)
|
|
if caldata is None:
|
|
raise RuntimeError('no model mag calibration in axis %s'% axis)
|
|
else:
|
|
caldata2 = dict(caldata)
|
|
return caldata2
|
|
|
|
def timeMagCalibration(self, tem, cam, ht, mag, axis):
|
|
caldata = self.researchMagCalibration(tem, cam, ht, mag, axis)
|
|
if caldata is None:
|
|
timeinfo = None
|
|
else:
|
|
timeinfo = caldata.timestamp
|
|
return timeinfo
|
|
|
|
def getMatrixFromStageModelMag(self, tem, cam, ht, mag):
|
|
try:
|
|
caldatax = self.retrieveMagCalibration(tem, cam, ht, mag, 'x')
|
|
caldatay = self.retrieveMagCalibration(tem, cam, ht, mag, 'y')
|
|
except Exception, e:
|
|
matrix = None
|
|
self.node.logger.warning('Cannot get matrix from stage model: %s' % e)
|
|
return matrix
|
|
|
|
means = [caldatax['mean'],caldatay['mean']]
|
|
angles = [caldatax['angle'],caldatay['angle']]
|
|
matrix = numpy.ones((2,2), numpy.float64)
|
|
matrix[0, 0]=means[0]*math.sin(angles[0])
|
|
matrix[1, 0]=-means[0]*math.cos(angles[0])
|
|
matrix[0, 1]=-means[1]*math.sin(angles[1])
|
|
matrix[1, 1]=means[1]*math.cos(angles[1])
|
|
|
|
return matrix
|
|
|
|
def storeModelCalibration(self, tem, cam, label, axis, period, a, b):
|
|
caldata = leginondata.StageModelCalibrationData()
|
|
caldata['tem'] = tem
|
|
caldata['ccdcamera'] = cam
|
|
caldata['session'] = self.node.session
|
|
caldata['tem'] = self.instrument.getTEMData()
|
|
caldata['ccdcamera'] = self.instrument.getCCDCameraData()
|
|
caldata['label'] = label
|
|
caldata['axis'] = axis
|
|
caldata['period'] = period
|
|
## force it to be 2 dimensional so sqldict likes it
|
|
a.shape = (1,len(a))
|
|
b.shape = (1,len(b))
|
|
caldata['a'] = a
|
|
caldata['b'] = b
|
|
|
|
self.node.publish(caldata, database=True, dbforce=True)
|
|
|
|
def researchModelCalibration(self, tem, ccdcamera, axis):
|
|
qinst = leginondata.StageModelCalibrationData(axis=axis)
|
|
if tem is None:
|
|
qinst['tem'] = self.instrument.getTEMData()
|
|
else:
|
|
qinst['tem'] = tem
|
|
if ccdcamera is None:
|
|
qinst['ccdcamera'] = self.instrument.getCCDCameraData()
|
|
else:
|
|
qinst['ccdcamera'] = ccdcamera
|
|
caldatalist = self.node.research(datainstance=qinst, results=1)
|
|
if len(caldatalist) > 0:
|
|
caldata = caldatalist[0]
|
|
else:
|
|
caldata = None
|
|
return caldata
|
|
|
|
def retrieveModelCalibration(self, tem, ccd, axis):
|
|
caldata = self.researchModelCalibration(tem, ccd, axis)
|
|
if caldata is None:
|
|
raise RuntimeError('no model calibration in axis %s'% axis)
|
|
else:
|
|
## return it to rank 0 array
|
|
caldata2 = {}
|
|
caldata2['axis'] = caldata['axis']
|
|
caldata2['period'] = caldata['period']
|
|
caldata2['a'] = numpy.ravel(caldata['a']).copy()
|
|
caldata2['b'] = numpy.ravel(caldata['b']).copy()
|
|
return caldata2
|
|
|
|
def timeModelCalibration(self, tem, cam, axis):
|
|
caldata = self.researchModelCalibration(tem, cam, axis)
|
|
if caldata is None:
|
|
timeinfo = None
|
|
else:
|
|
timeinfo = caldata.timestamp
|
|
return timeinfo
|
|
|
|
def getLabeledData(self, tem, cam, label, mag, axis):
|
|
qdata = leginondata.StageMeasurementData()
|
|
qdata['tem'] = tem
|
|
qdata['ccdcamera'] = cam
|
|
qdata['label'] = label
|
|
qdata['magnification'] = mag
|
|
qdata['axis'] = axis
|
|
measurements = self.node.research(datainstance=qdata)
|
|
if not measurements:
|
|
raise RuntimeError('no measurements')
|
|
self.node.logger.info('len(measurements) %d' % len(measurements))
|
|
ht = measurements[0]['high tension']
|
|
datapoints = []
|
|
for measurement in measurements:
|
|
if measurement['high tension'] != ht:
|
|
raise RuntimeError('inconsistent high tension in measurements')
|
|
datapoint = []
|
|
datapoint.append(measurement['x'])
|
|
datapoint.append(measurement['y'])
|
|
datapoint.append(measurement['delta'])
|
|
datapoint.append(measurement['imagex'])
|
|
datapoint.append(measurement['imagey'])
|
|
datapoints.append(datapoint)
|
|
return {'datapoints':datapoints, 'ht': ht}
|
|
|
|
def fit(self, tem, cam, label, mag, axis, terms):
|
|
if tem is None:
|
|
tem = self.node.instrument.getTEMData()
|
|
if cam is None:
|
|
cam = self.node.instrument.getCCDCameraData()
|
|
# get data from DB
|
|
info = self.getLabeledData(tem, cam, label, mag, axis)
|
|
datapoints = info['datapoints']
|
|
ht = info['ht']
|
|
dat = gonmodel.GonData()
|
|
dat.import_data(mag, axis, datapoints)
|
|
|
|
## fit a model to the data
|
|
mod = gonmodel.GonModel()
|
|
mod.fit_data(dat, terms)
|
|
|
|
### mag info
|
|
axis = dat.axis
|
|
mag = dat.mag
|
|
angle = dat.angle
|
|
# using data mean, could use model mean
|
|
mean = dat.avg
|
|
#mean = mod.a0
|
|
self.node.logger.info('model mean: %5.3e meter/pixel, angle: %6.3f radian' % (mean,angle))
|
|
|
|
### model info
|
|
period = mod.period
|
|
a = mod.a
|
|
b = mod.b
|
|
if terms > 0:
|
|
self.node.logger.info('model period: %6.1f micrometer' % (period*1e6,))
|
|
|
|
self.storeMagCalibration(tem, cam, label, ht, mag, axis, angle, mean)
|
|
self.storeModelCalibration(tem, cam, label, axis, period, a, b)
|
|
|
|
matrix = self.getMatrixFromStageModelMag(tem, cam, ht, mag)
|
|
if matrix is not None:
|
|
self.storeMatrix(ht, mag, 'stage position', matrix, tem, cam)
|
|
|
|
def fitMagOnly(self, tem, cam, label, mag, axis):
|
|
if tem is None:
|
|
tem = self.node.instrument.getTEMData()
|
|
if cam is None:
|
|
cam = self.node.instrument.getCCDCameraData()
|
|
# get data from DB
|
|
info = self.getLabeledData(tem, cam, label, mag, axis)
|
|
datapoints = info['datapoints']
|
|
ht = info['ht']
|
|
dat = gonmodel.GonData()
|
|
dat.import_data(mag, axis, datapoints)
|
|
|
|
## fit a model to existing model
|
|
modeldata = self.retrieveModelCalibration(tem, cam, axis)
|
|
mod = gonmodel.GonModel()
|
|
mod.fromDict(modeldata)
|
|
|
|
mean = mod.fitInto(dat)
|
|
|
|
### mag info
|
|
axis = dat.axis
|
|
mag = dat.mag
|
|
angle = dat.angle
|
|
self.node.logger.info('model mean: %5.3e, angle: %6.3e ' % (mean,angle))
|
|
|
|
self.storeMagCalibration(tem, cam, label, ht, mag, axis, angle, mean)
|
|
|
|
matrix = self.getMatrixFromStageModelMag(tem, cam, ht, mag)
|
|
if matrix is not None:
|
|
self.storeMatrix(ht, mag, 'stage position', matrix, tem, cam)
|
|
|
|
def itransform(self, position, scope, camera):
|
|
curstage = scope['stage position']
|
|
|
|
tem = scope['tem']
|
|
ccd = camera['ccdcamera']
|
|
binx = camera['binning']['x']
|
|
biny = camera['binning']['y']
|
|
|
|
xmodcal = self.retrieveModelCalibration(tem, ccd, 'x')
|
|
ymodcal = self.retrieveModelCalibration(tem, ccd, 'y')
|
|
self.node.logger.debug('x model a %s' % xmodcal['a'])
|
|
self.node.logger.debug('x model b %s' % xmodcal['b'])
|
|
self.node.logger.debug('y model a shape %s' % ymodcal['a'].shape)
|
|
self.node.logger.debug('y model b shape %s' % ymodcal['b'].shape)
|
|
xmod = gonmodel.GonModel()
|
|
xmod.fromDict(xmodcal)
|
|
ymod = gonmodel.GonModel()
|
|
ymod.fromDict(ymodcal)
|
|
|
|
xmagcal = self.retrieveMagCalibration(tem, ccd, scope['high tension'], scope['magnification'], 'x')
|
|
ymagcal = self.retrieveMagCalibration(tem, ccd, scope['high tension'], scope['magnification'], 'y')
|
|
self.node.logger.debug('x mag cal %s' % (xmagcal,))
|
|
self.node.logger.debug('y mag cal %s' % (ymagcal,))
|
|
|
|
newx = position['x']
|
|
newy = position['y']
|
|
pix = self.tixpix(xmod, ymod, xmagcal, ymagcal, curstage['x'], curstage['y'], newx, newy)
|
|
pixelshift = {'row': pix[0]/biny, 'col': pix[1]/binx}
|
|
return pixelshift
|
|
|
|
def transform(self, pixelshift, scope, camera):
|
|
curstage = scope['stage position']
|
|
|
|
binx = camera['binning']['x']
|
|
biny = camera['binning']['y']
|
|
pixrow = pixelshift['row'] * biny
|
|
pixcol = pixelshift['col'] * binx
|
|
tem = scope['tem']
|
|
ccd = camera['ccdcamera']
|
|
|
|
## do modifications to newstage here
|
|
xmodcal = self.retrieveModelCalibration(tem, ccd, 'x')
|
|
ymodcal = self.retrieveModelCalibration(tem, ccd, 'y')
|
|
self.node.logger.debug('x model a %s' % xmodcal['a'])
|
|
self.node.logger.debug('x model b %s' % xmodcal['b'])
|
|
self.node.logger.debug('y model a shape %s' % ymodcal['a'].shape)
|
|
self.node.logger.debug('y model b shape %s' % ymodcal['b'].shape)
|
|
xmod = gonmodel.GonModel()
|
|
xmod.fromDict(xmodcal)
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ymod = gonmodel.GonModel()
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|
ymod.fromDict(ymodcal)
|
|
|
|
xmagcal = self.retrieveMagCalibration(tem, ccd, scope['high tension'], scope['magnification'], 'x')
|
|
ymagcal = self.retrieveMagCalibration(tem, ccd, scope['high tension'], scope['magnification'], 'y')
|
|
self.node.logger.debug('x mag cal %s' % (xmagcal,))
|
|
self.node.logger.debug('y mag cal %s' % (ymagcal,))
|
|
|
|
|
|
delta = self.pixtix(xmod, ymod, xmagcal, ymagcal, curstage['x'], curstage['y'], pixcol, pixrow)
|
|
|
|
### take into account effect of alpha tilt on Y stage pos
|
|
if 'a' in curstage and curstage['a'] is not None:
|
|
alpha = curstage['a']
|
|
delta['y'] = delta['y'] / numpy.cos(alpha)
|
|
|
|
newscope = leginondata.ScopeEMData(initializer=scope)
|
|
newscope['stage position'] = dict(scope['stage position'])
|
|
newscope['stage position']['x'] += delta['x']
|
|
newscope['stage position']['y'] += delta['y']
|
|
return newscope
|
|
|
|
def pixtix(self, xmod, ymod, xmagcal, ymagcal, gonx, gony, pixx, pixy):
|
|
modavgx = xmagcal['mean']
|
|
modavgy = ymagcal['mean']
|
|
anglex = xmagcal['angle']
|
|
angley = ymagcal['angle']
|
|
|
|
gonx1 = xmod.rotate(anglex, pixx, pixy)
|
|
gony1 = ymod.rotate(angley, pixx, pixy)
|
|
|
|
gonx1 = gonx1 * modavgx
|
|
gony1 = gony1 * modavgy
|
|
|
|
gonx1 = xmod.predict(gonx,gonx1)
|
|
gony1 = ymod.predict(gony,gony1)
|
|
|
|
return {'x':gonx1, 'y':gony1}
|
|
|
|
def tixpix(self, xmod, ymod, xmagcal, ymagcal, gonx0, gony0, gonx1, gony1):
|
|
## integrate
|
|
gonx = xmod.integrate(gonx0,gonx1)
|
|
gony = ymod.integrate(gony0,gony1)
|
|
|
|
## rotate/scale
|
|
modavgx = xmagcal['mean']
|
|
modavgy = ymagcal['mean']
|
|
anglex = xmagcal['angle']
|
|
angley = ymagcal['angle']
|
|
|
|
gonx = gonx / modavgx
|
|
gony = gony / modavgy
|
|
|
|
m = numpy.array(((numpy.cos(anglex),numpy.sin(anglex)),(numpy.cos(angley),numpy.sin(angley))), numpy.float32)
|
|
minv = numpy.linalg.inv(m)
|
|
ix,iy = numpy.dot(minv, (gonx,gony))
|
|
|
|
return iy,ix
|
|
|
|
class EucentricFocusClient(CalibrationClient):
|
|
def __init__(self, node):
|
|
CalibrationClient.__init__(self, node)
|
|
|
|
def researchEucentricFocus(self, ht, mag, tem=None, ccdcamera=None):
|
|
query = leginondata.EucentricFocusData()
|
|
if tem is None:
|
|
query['tem'] = self.instrument.getTEMData()
|
|
else:
|
|
query['tem'] = tem
|
|
if ccdcamera is None:
|
|
query['ccdcamera'] = self.instrument.getCCDCameraData()
|
|
else:
|
|
query['ccdcamera'] = ccdcamera
|
|
query['high tension'] = ht
|
|
query['magnification'] = mag
|
|
datalist = self.node.research(datainstance=query, results=1)
|
|
if datalist:
|
|
eucfoc = datalist[0]
|
|
else:
|
|
eucfoc = None
|
|
return eucfoc
|
|
|
|
def publishEucentricFocus(self, ht, mag, ef):
|
|
newdata = leginondata.EucentricFocusData()
|
|
newdata['session'] = self.node.session
|
|
newdata['tem'] = self.instrument.getTEMData()
|
|
newdata['ccdcamera'] = self.instrument.getCCDCameraData()
|
|
newdata['high tension'] = ht
|
|
newdata['magnification'] = mag
|
|
newdata['focus'] = ef
|
|
self.node.publish(newdata, database=True, dbforce=True)
|