source: trunk/GSASIIimage.py @ 1185

# -*- coding: utf-8 -*-
#GSASII image calculations: ellipse fitting & image integration        
########### SVN repository information ###################
# $Date: 2014-01-08 21:26:10 +0000 (Wed, 08 Jan 2014) $
# $Author: vondreele $
# $Revision: 1185 $
# $URL: trunk/GSASIIimage.py $
# $Id: GSASIIimage.py 1185 2014-01-08 21:26:10Z vondreele $
########### SVN repository information ###################
'''
*GSASIIimage: Image calc module*
================================

Ellipse fitting & image integration

'''

import math
import time
import numpy as np
import numpy.linalg as nl
import numpy.ma as ma
import polymask as pm
from scipy.optimize import leastsq
import copy
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 1185 $")
import GSASIIplot as G2plt
import GSASIIlattice as G2lat
import GSASIIpwd as G2pwd
import fellipse as fel

# trig functions in degrees
sind = lambda x: math.sin(x*math.pi/180.)
asind = lambda x: 180.*math.asin(x)/math.pi
tand = lambda x: math.tan(x*math.pi/180.)
atand = lambda x: 180.*math.atan(x)/math.pi
atan2d = lambda y,x: 180.*math.atan2(y,x)/math.pi
cosd = lambda x: math.cos(x*math.pi/180.)
acosd = lambda x: 180.*math.acos(x)/math.pi
rdsq2d = lambda x,p: round(1.0/math.sqrt(x),p)
#numpy versions
npsind = lambda x: np.sin(x*np.pi/180.)
npasind = lambda x: 180.*np.arcsin(x)/np.pi
npcosd = lambda x: np.cos(x*np.pi/180.)
npacosd = lambda x: 180.*np.arccos(x)/np.pi
nptand = lambda x: np.tan(x*np.pi/180.)
npatand = lambda x: 180.*np.arctan(x)/np.pi
npatan2d = lambda y,x: 180.*np.arctan2(y,x)/np.pi
    
def pointInPolygon(pXY,xy):
    'Needs a doc string'
    #pXY - assumed closed 1st & last points are duplicates
    Inside = False
    N = len(pXY)
    p1x,p1y = pXY[0]
    for i in range(N+1):
        p2x,p2y = pXY[i%N]
        if (max(p1y,p2y) >= xy[1] > min(p1y,p2y)) and (xy[0] <= max(p1x,p2x)):
            if p1y != p2y:
                xinters = (xy[1]-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
            if p1x == p2x or xy[0] <= xinters:
                Inside = not Inside
        p1x,p1y = p2x,p2y
    return Inside
    
def peneCorr(tth,dep,tilt=0.,azm=0.):
    'Needs a doc string'
    return dep*(1.-npcosd(abs(tilt*npsind(azm))-tth*npcosd(azm)))
#    return dep*(1.-npcosd(tth))         #best one
#    return dep*npsind(tth)             #not as good as 1-cos2Q
        
def makeMat(Angle,Axis):
    '''Make rotation matrix from Angle and Axis

    :param float Angle: in degrees
    :param int Axis: 0 for rotation about x, 1 for about y, etc.
    '''
    cs = cosd(Angle)
    ss = sind(Angle)
    M = np.array(([1.,0.,0.],[0.,cs,-ss],[0.,ss,cs]),dtype=np.float32)
    return np.roll(np.roll(M,Axis,axis=0),Axis,axis=1)
                    
def FitEllipse(xy):
    
    def ellipse_center(p):
        ''' gives ellipse center coordinates
        '''
        b,c,d,f,g,a = p[1]/2, p[2], p[3]/2, p[4]/2, p[5], p[0]
        num = b*b-a*c
        x0=(c*d-b*f)/num
        y0=(a*f-b*d)/num
        return np.array([x0,y0])
    
    def ellipse_angle_of_rotation( p ):
        ''' gives rotation of ellipse major axis from x-axis
        range will be -90 to 90 deg
        '''
        b,c,d,f,g,a = p[1]/2, p[2], p[3]/2, p[4]/2, p[5], p[0]
        return 0.5*npatand(2*b/(a-c))
    
    def ellipse_axis_length( p ):
        ''' gives ellipse radii in [minor,major] order
        '''
        b,c,d,f,g,a = p[1]/2, p[2], p[3]/2, p[4]/2, p[5], p[0]
        up = 2*(a*f*f+c*d*d+g*b*b-2*b*d*f-a*c*g)
        down1=(b*b-a*c)*( (c-a)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a))
        down2=(b*b-a*c)*( (a-c)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a))
        res1=np.sqrt(up/down1)
        res2=np.sqrt(up/down2)
        return np.array([ res2,res1])
    
    xy = np.array(xy)
    x = np.asarray(xy.T[0])[:,np.newaxis]
    y = np.asarray(xy.T[1])[:,np.newaxis]
    D =  np.hstack((x*x, x*y, y*y, x, y, np.ones_like(x)))
    S = np.dot(D.T,D)
    C = np.zeros([6,6])
    C[0,2] = C[2,0] = 2; C[1,1] = -1
    E, V =  nl.eig(np.dot(nl.inv(S), C))
    n = np.argmax(np.abs(E))
    a = V[:,n]
    cent = ellipse_center(a)
    phi = ellipse_angle_of_rotation(a)
    radii = ellipse_axis_length(a)
    phi += 90.
    if radii[0] > radii[1]:
        radii = [radii[1],radii[0]]
        phi -= 90.
    return cent,phi,radii

def FitDetector(rings,varyList,parmDict,Print=True):
    'Needs a doc string'
        
    def CalibPrint(ValSig):
        print 'Image Parameters:'
        ptlbls = 'names :'
        ptstr =  'values:'
        sigstr = 'esds  :'
        for name,fmt,value,sig in ValSig:
            ptlbls += "%s" % (name.rjust(12))
            if name == 'phi':
                ptstr += fmt % (value%360.)
            else:
                ptstr += fmt % (value)
            if sig:
                sigstr += fmt % (sig)
            else:
                sigstr += 12*' '
        print ptlbls
        print ptstr
        print sigstr        
        
    def ellipseCalcD(B,xyd,varyList,parmDict):
        x,y,dsp = xyd
        wave = parmDict['wave']
        if 'dep' in varyList:
            dist,x0,y0,tilt,chi,dep = B[:6]
        else:
            dist,x0,y0,tilt,chi = B[:5]
            dep = parmDict['dep']
        if 'wave' in varyList:
            wave = B[-1]
        phi = chi-90.               #get rotation of major axis from tilt axis
        tth = 2.0*npasind(wave/(2.*dsp))
        phi0 = npatan2d(y-y0,x-x0)
        dxy = peneCorr(tth,dep,tilt,phi0)
        ttth = nptand(tth)
        stth = npsind(tth)
        cosb = npcosd(tilt)
        tanb = nptand(tilt)        
        tbm = nptand((tth-tilt)/2.)
        tbp = nptand((tth+tilt)/2.)
        sinb = npsind(tilt)
        d = dist+dxy
        fplus = d*tanb*stth/(cosb+stth)
        fminus = d*tanb*stth/(cosb-stth)
        vplus = d*(tanb+(1+tbm)/(1-tbm))*stth/(cosb+stth)
        vminus = d*(tanb+(1-tbp)/(1+tbp))*stth/(cosb-stth)
        R0 = np.sqrt((vplus+vminus)**2-(fplus+fminus)**2)/2.      #+minor axis
        R1 = (vplus+vminus)/2.                                    #major axis
        zdis = (fplus-fminus)/2.
        Robs = np.sqrt((x-x0)**2+(y-y0)**2)
        rsqplus = R0**2+R1**2
        rsqminus = R0**2-R1**2
        R = rsqminus*npcosd(2.*phi0-2.*phi)+rsqplus
        Q = np.sqrt(2.)*R0*R1*np.sqrt(R-2.*zdis**2*npsind(phi0-phi)**2)
        P = 2.*R0**2*zdis*npcosd(phi0-phi)
        Rcalc = (P+Q)/R
        M = Robs-Rcalc
        return M
        
    names = ['dist','det-X','det-Y','tilt','phi','dep','wave']
    fmt = ['%12.3f','%12.3f','%12.3f','%12.3f','%12.3f','%12.3f','%12.5f']
    p0 = [parmDict[key] for key in varyList]
    result = leastsq(ellipseCalcD,p0,args=(rings.T,varyList,parmDict),full_output=True,ftol=1.e-8)
    chisq = np.sum(result[2]['fvec']**2)
    parmDict.update(zip(varyList,result[0]))
    vals = list(result[0])
    sig = list(np.sqrt(chisq*np.diag(result[1])))
    sigList = np.zeros(7)
    for i,name in enumerate(names):
        if name in varyList:
            sigList[i] = sig[varyList.index(name)]
    ValSig = zip(names,fmt,vals,sig)
    if Print:
        CalibPrint(ValSig)
    return chisq
                    
def ImageLocalMax(image,w,Xpix,Ypix):
    'Needs a doc string'
    w2 = w*2
    sizey,sizex = image.shape
    xpix = int(Xpix)            #get reference corner of pixel chosen
    ypix = int(Ypix)
    if (w < xpix < sizex-w) and (w < ypix < sizey-w) and image[ypix,xpix]:
        Z = image[ypix-w:ypix+w,xpix-w:xpix+w]
        Zmax = np.argmax(Z)
        Zmin = np.argmin(Z)
        xpix += Zmax%w2-w
        ypix += Zmax/w2-w
        return xpix,ypix,np.ravel(Z)[Zmax],max(0.0001,np.ravel(Z)[Zmin])   #avoid neg/zero minimum
    else:
        return 0,0,0,0      
    
def makeRing(dsp,ellipse,pix,reject,scalex,scaley,image):
    'Needs a doc string'
    def ellipseC():
        'compute estimate of ellipse circumference'
        if radii[0] < 0:        #hyperbola
            theta = npacosd(1./np.sqrt(1.+(radii[0]/radii[1])**2))
            print theta
            return 0
        apb = radii[1]+radii[0]
        amb = radii[1]-radii[0]
        return np.pi*apb*(1+3*(amb/apb)**2/(10+np.sqrt(4-3*(amb/apb)**2)))
        
    cent,phi,radii = ellipse
    cphi = cosd(phi-90.)        #convert to major axis rotation
    sphi = sind(phi-90.)
    ring = []
    C = int(ellipseC())         #ring circumference
    for i in range(0,C,1):      #step around ring in 1mm increments
        a = 360.*i/C
        x = radii[1]*cosd(a)        #major axis
        y = radii[0]*sind(a)
        X = (cphi*x-sphi*y+cent[0])*scalex      #convert mm to pixels
        Y = (sphi*x+cphi*y+cent[1])*scaley
        X,Y,I,J = ImageLocalMax(image,pix,X,Y)
        if I and J and I/J > reject:
            X += .5                             #set to center of pixel
            Y += .5
            X /= scalex                         #convert back to mm
            Y /= scaley
            if [X,Y,dsp] not in ring:           #no duplicates!
                ring.append([X,Y,dsp])
    if len(ring) < 10:
        ring = []
    return ring
    
def GetEllipse2(tth,dxy,dist,cent,tilt,phi):
    '''uses Dandelin spheres to find ellipse or hyperbola parameters from detector geometry
    on output
    radii[0] (b-minor axis) set < 0. for hyperbola
    
    '''
    radii = [0,0]
    ttth = tand(tth)
    stth = sind(tth)
    ctth = cosd(tth)
    cosb = cosd(tilt)
    tanb = tand(tilt)
    tbm = tand((tth-tilt)/2.)
    tbp = tand((tth+tilt)/2.)
    sinb = sind(tilt)
    d = dist+dxy
    if tth+abs(tilt) < 90.:      #ellipse
        fplus = d*tanb*stth/(cosb+stth)
        fminus = d*tanb*stth/(cosb-stth)
        vplus = d*(tanb+(1+tbm)/(1-tbm))*stth/(cosb+stth)
        vminus = d*(tanb+(1-tbp)/(1+tbp))*stth/(cosb-stth)
        radii[0] = np.sqrt((vplus+vminus)**2-(fplus+fminus)**2)/2.      #+minor axis
        radii[1] = (vplus+vminus)/2.                                    #major axis
        zdis = (fplus-fminus)/2.
    else:   #hyperbola!
        f = d*abs(tanb)*stth/(cosb+stth)
        v = d*(abs(tanb)+tand(tth-abs(tilt)))
        delt = d*stth*(1.+stth*cosb)/(abs(sinb)*cosb*(stth+cosb))
        eps = (v-f)/(delt-v)
        radii[0] = -eps*(delt-f)/np.sqrt(eps**2-1.)                     #-minor axis
        radii[1] = eps*(delt-f)/(eps**2-1.)                             #major axis
        if tilt > 0:
            zdis = f+radii[1]*eps
        else:
            zdis = -f
#NB: zdis is || to major axis & phi is rotation of minor axis
#thus shift from beam to ellipse center is [Z*sin(phi),-Z*cos(phi)]
    elcent = [cent[0]+zdis*sind(phi),cent[1]-zdis*cosd(phi)]
    return elcent,phi,radii
    
def GetEllipse(dsp,data):
    '''uses Dandelin spheres to find ellipse or hyperbola parameters from detector geometry
    as given in image controls dictionary (data) and a d-spacing (dsp)
    '''
    cent = data['center']
    tilt = data['tilt']
    phi = data['rotation']
    dep = data['DetDepth']
    tth = 2.0*asind(data['wavelength']/(2.*dsp))
    dxy = peneCorr(tth,dep,tilt)
    dist = data['distance']
    return GetEllipse2(tth,dxy,dist,cent,tilt,phi)
        
def GetDetectorXY(dsp,azm,data):
    'Needs a doc string'
    
    elcent,phi,radii = GetEllipse(dsp,data)
    phi = data['rotation']-90.          #to give rotation of major axis
    tilt = data['tilt']
    dist = data['distance']
    cent = data['center']
    tth = 2.0*asind(data['wavelength']/(2.*dsp))
    ttth = tand(tth)
    stth = sind(tth)
    ctth = cosd(tth)
    cosb = cosd(tilt)
    if radii[0] > 0.:
        sinb = sind(tilt)
        tanb = tand(tilt)
        fplus = dist*tanb*stth/(cosb+stth)
        fminus = dist*tanb*stth/(cosb-stth)
        zdis = (fplus-fminus)/2.
        rsqplus = radii[0]**2+radii[1]**2
        rsqminus = radii[0]**2-radii[1]**2
        R = rsqminus*cosd(2.*azm-2.*phi)+rsqplus
        Q = np.sqrt(2.)*radii[0]*radii[1]*np.sqrt(R-2.*zdis**2*sind(azm-phi)**2)
        P = 2.*radii[0]**2*zdis*cosd(azm-phi)
        radius = (P+Q)/R
        xy = np.array([radius*cosd(azm),radius*sind(azm)])
        xy += cent
    else:   #hyperbola - both branches (one is way off screen!)
        sinb = abs(sind(tilt))
        tanb = abs(tand(tilt))
        f = dist*tanb*stth/(cosb+stth)
        v = dist*(tanb+tand(tth-abs(tilt)))
        delt = dist*stth*(1+stth*cosb)/(sinb*cosb*(stth+cosb))
        ecc = (v-f)/(delt-v)
        R = radii[1]*(ecc**2-1)/(1-ecc*cosd(azm))
        if tilt > 0.:
            offset = 2.*radii[1]*ecc+f      #select other branch
            xy = [-R*cosd(azm)-offset,R*sind(azm)]
        else:
            offset = -f
            xy = [-R*cosd(azm)-offset,-R*sind(azm)]
        xy = -np.array([xy[0]*cosd(phi)+xy[1]*sind(phi),xy[0]*sind(phi)-xy[1]*cosd(phi)])
        xy += cent
    return xy
    
def GetDetXYfromThAzm(Th,Azm,data):
    'Needs a doc string'
    dsp = data['wavelength']/(2.0*npsind(Th))    
    return GetDetectorXY(dsp,azm,data)
                    
def GetTthAzmDsp(x,y,data):
    'Needs a doc string - checked OK for ellipses & hyperbola'
    wave = data['wavelength']
    cent = data['center']
    tilt = data['tilt']
    dist = data['distance']/cosd(tilt)
    x0 = data['distance']*tand(tilt)
    phi = data['rotation']
    dep = data['DetDepth']
    LRazim = data['LRazimuth']
    azmthoff = data['azmthOff']
    dx = np.array(x-cent[0],dtype=np.float32)
    dy = np.array(y-cent[1],dtype=np.float32)
    D = ((dx-x0)**2+dy**2+data['distance']**2)      #sample to pixel distance
    X = np.array(([dx,dy,np.zeros_like(dx)]),dtype=np.float32).T
    X = np.dot(X,makeMat(phi,2))
    Z = np.dot(X,makeMat(tilt,0)).T[2]
    tth = npatand(np.sqrt(dx**2+dy**2-Z**2)/(dist-Z))
    dxy = peneCorr(tth,dep,tilt,npatan2d(dy,dx))
    DX = dist-Z+dxy
    DY = np.sqrt(dx**2+dy**2-Z**2)
    tth = npatan2d(DY,DX) 
    dsp = wave/(2.*npsind(tth/2.))
    azm = (npatan2d(dy,dx)+azmthoff+720.)%360.
    G = D/data['distance']**2       #for geometric correction = 1/cos(2theta)^2 if tilt=0.
    return np.array([tth,azm,G,dsp])
    
def GetTth(x,y,data):
    'Give 2-theta value for detector x,y position; calibration info in data'
    return GetTthAzmDsp(x,y,data)[0]
    
def GetTthAzm(x,y,data):
    'Give 2-theta, azimuth values for detector x,y position; calibration info in data'
    return GetTthAzmDsp(x,y,data)[0:2]
    
def GetTthAzmD(x,y,data):
    '''Give 2-theta, azimuth & d-spacing values for detector x,y position;
     calibration info in data
    '''
    return GetTthAzmDsp(x,y,data)[0:3]

def GetDsp(x,y,data):
    'Give d-spacing value for detector x,y position; calibration info in data'
    return GetTthAzmDsp(x,y,data)[3]
       
def GetAzm(x,y,data):
    'Give azimuth value for detector x,y position; calibration info in data'
    return GetTthAzmDsp(x,y,data)[1]
       
def ImageCompress(image,scale):
    'Needs a doc string'
    if scale == 1:
        return image
    else:
        return image[::scale,::scale]
        
def checkEllipse(Zsum,distSum,xSum,ySum,dist,x,y):
    'Needs a doc string'
    avg = np.array([distSum/Zsum,xSum/Zsum,ySum/Zsum])
    curr = np.array([dist,x,y])
    return abs(avg-curr)/avg < .02

def EdgeFinder(image,data):
    '''this makes list of all x,y where I>edgeMin suitable for an ellipse search?
    Not currently used but might be useful in future?
    '''
    import numpy.ma as ma
    Nx,Ny = data['size']
    pixelSize = data['pixelSize']
    edgemin = data['edgemin']
    scalex = pixelSize[0]/1000.
    scaley = pixelSize[1]/1000.    
    tay,tax = np.mgrid[0:Nx,0:Ny]
    tax = np.asfarray(tax*scalex,dtype=np.float32)
    tay = np.asfarray(tay*scaley,dtype=np.float32)
    tam = ma.getmask(ma.masked_less(image.flatten(),edgemin))
    tax = ma.compressed(ma.array(tax.flatten(),mask=tam))
    tay = ma.compressed(ma.array(tay.flatten(),mask=tam))
    return zip(tax,tay)
    
def MakeFrameMask(data,frame):
    pixelSize = data['pixelSize']
    scalex = pixelSize[0]/1000.
    scaley = pixelSize[1]/1000.
    blkSize = 512
    Nx,Ny = data['size']
    nXBlks = (Nx-1)/blkSize+1
    nYBlks = (Ny-1)/blkSize+1
    tam = ma.make_mask_none(data['size'])
    for iBlk in range(nXBlks):
        iBeg = iBlk*blkSize
        iFin = min(iBeg+blkSize,Nx)
        for jBlk in range(nYBlks):
            jBeg = jBlk*blkSize
            jFin = min(jBeg+blkSize,Ny)                
            nI = iFin-iBeg
            nJ = jFin-jBeg
            tax,tay = np.mgrid[iBeg+0.5:iFin+.5,jBeg+.5:jFin+.5]         #bin centers not corners
            tax = np.asfarray(tax*scalex,dtype=np.float32)
            tay = np.asfarray(tay*scaley,dtype=np.float32)
            tamp = ma.make_mask_none((1024*1024))
            tamp = ma.make_mask(pm.polymask(nI*nJ,tax.flatten(),
                tay.flatten(),len(frame),frame,tamp)[:nI*nJ])-True  #switch to exclude around frame
            if tamp.shape:
                tamp = np.reshape(tamp[:nI*nJ],(nI,nJ))
                tam[iBeg:iFin,jBeg:jFin] = ma.mask_or(tamp[0:nI,0:nJ],tam[iBeg:iFin,jBeg:jFin])
            else:
                tam[iBeg:iFin,jBeg:jFin] = True
    return tam.T
    
def ImageRecalibrate(self,data,masks):
    'Needs a doc string'
    import ImageCalibrants as calFile
    print 'Image recalibration:'
    time0 = time.time()
    pixelSize = data['pixelSize']
    scalex = 1000./pixelSize[0]
    scaley = 1000./pixelSize[1]
    pixLimit = data['pixLimit']
    cutoff = data['cutoff']
    data['rings'] = []
    data['ellipses'] = []
    if not data['calibrant']:
        print 'no calibration material selected'
        return True    
    skip = data['calibskip']
    dmin = data['calibdmin']
    Bravais,Cells = calFile.Calibrants[data['calibrant']][:2]
    HKL = []
    for bravais,cell in zip(Bravais,Cells):
        A = G2lat.cell2A(cell)
        hkl = G2lat.GenHBravais(dmin,bravais,A)
        HKL += hkl
    HKL = G2lat.sortHKLd(HKL,True,False)
    varyList = ['dist','det-X','det-Y','tilt','phi']
    parmDict = {'dist':data['distance'],'det-X':data['center'][0],'det-Y':data['center'][1],
        'tilt':data['tilt'],'phi':data['rotation'],'wave':data['wavelength'],'dep':data['DetDepth']}
    Found = False
    wave = data['wavelength']
    frame = masks['Frames']
    tam = ma.make_mask_none(self.ImageZ.shape)
    if frame:
        tam = ma.mask_or(tam,MakeFrameMask(data,frame))
    for iH,H in enumerate(HKL): 
        dsp = H[3]
        tth = 2.0*asind(wave/(2.*dsp))
        if tth+abs(data['tilt']) > 90.:
            print 'next line is a hyperbola - search stopped'
            break
        ellipse = GetEllipse(dsp,data)
        Ring = makeRing(dsp,ellipse,pixLimit,cutoff,scalex,scaley,ma.array(self.ImageZ,mask=tam))
        if Ring:
            if iH >= skip:
                data['rings'].append(np.array(Ring))
            data['ellipses'].append(copy.deepcopy(ellipse+('r',)))
            Found = True
        elif not Found:         #skipping inner rings, keep looking until ring found 
            continue
        else:                   #no more rings beyond edge of detector
            break
    rings = np.concatenate((data['rings']),axis=0)
    if data['DetDepthRef']:
        varyList.append('dep')
    FitDetector(rings,varyList,parmDict)
    data['distance'] = parmDict['dist']
    data['center'] = [parmDict['det-X'],parmDict['det-Y']]
    data['rotation'] = np.mod(parmDict['phi'],360.0)
    data['tilt'] = parmDict['tilt']
    data['DetDepth'] = parmDict['dep']
    N = len(data['ellipses'])
    data['ellipses'] = []           #clear away individual ellipse fits
    for H in HKL[:N]:
        ellipse = GetEllipse(H[3],data)
        data['ellipses'].append(copy.deepcopy(ellipse+('b',)))
    
    print 'calibration time = ',time.time()-time0
    G2plt.PlotImage(self,newImage=True)        
    return True
            
def ImageCalibrate(self,data):
    'Needs a doc string'
    import copy
    import ImageCalibrants as calFile
    print 'Image calibration:'
    time0 = time.time()
    ring = data['ring']
    pixelSize = data['pixelSize']
    scalex = 1000./pixelSize[0]
    scaley = 1000./pixelSize[1]
    pixLimit = data['pixLimit']
    cutoff = data['cutoff']
    if len(ring) < 5:
        print 'not enough inner ring points for ellipse'
        return False
        
    #fit start points on inner ring
    data['ellipses'] = []
    data['rings'] = []
    outE = FitEllipse(ring)
    fmt  = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f'
    fmt2 = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f, chi^2: %.3f, N: %d'
    if outE:
        print fmt%('start ellipse: ',outE[0][0],outE[0][1],outE[1],outE[2][0],outE[2][1])
        ellipse = outE
    else:
        return False
        
    #setup 360 points on that ring for "good" fit
    data['ellipses'].append(ellipse[:]+('g',))
    Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ)
    if Ring:
        ellipse = FitEllipse(Ring)
        Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ)    #do again
        ellipse = FitEllipse(Ring)
    else:
        print '1st ring not sufficiently complete to proceed'
        return False
    print fmt2%('inner ring:    ',ellipse[0][0],ellipse[0][1],ellipse[1],ellipse[2][0],ellipse[2][1],0.,len(Ring))     #cent,phi,radii
    data['ellipses'].append(ellipse[:]+('r',))
    data['rings'].append(np.array(Ring))
    G2plt.PlotImage(self,newImage=True)
    
#setup for calibration
    data['rings'] = []
    if not data['calibrant']:
        print 'no calibration material selected'
        return True
    
    skip = data['calibskip']
    dmin = data['calibdmin']
#generate reflection set
    Bravais,Cells = calFile.Calibrants[data['calibrant']][:2]
    HKL = []
    for bravais,cell in zip(Bravais,Cells):
        A = G2lat.cell2A(cell)
        hkl = G2lat.GenHBravais(dmin,bravais,A)[skip:]
        HKL += hkl
    HKL = G2lat.sortHKLd(HKL,True,False)
    wave = data['wavelength']
#set up 1st ring
    elcent,phi,radii = ellipse              #from fit of 1st ring
    dsp = HKL[0][3]
    tth = 2.0*asind(wave/(2.*dsp))
    Ring0 = makeRing(dsp,ellipse,3,cutoff,scalex,scaley,self.ImageZ)
    ttth = nptand(tth)
    stth = npsind(tth)
    ctth = npcosd(tth)
#1st estimate of tilt; assume ellipse - don't know sign though
    tilt = npasind(np.sqrt(max(0.,1.-(radii[0]/radii[1])**2))*ctth)
    if not tilt:
        print 'WARNING - selected ring was fitted as a circle'
        print ' - if detector was tilted we suggest you skip this ring - WARNING'
#1st estimate of dist: sample to detector normal to plane
    data['distance'] = dist = radii[0]**2/(ttth*radii[1])
#ellipse to cone axis (x-ray beam); 2 choices depending on sign of tilt
    zdisp = radii[1]*ttth*tand(tilt)
    zdism = radii[1]*ttth*tand(-tilt)
#cone axis position; 2 choices. Which is right?     
#NB: zdisp is || to major axis & phi is rotation of minor axis
#thus shift from beam to ellipse center is [Z*sin(phi),-Z*cos(phi)]
    centp = [elcent[0]+zdisp*sind(phi),elcent[1]-zdisp*cosd(phi)]
    centm = [elcent[0]+zdism*sind(phi),elcent[1]-zdism*cosd(phi)]
#check get same ellipse parms either way
#now do next ring; estimate either way & do a FitDetector each way; best fit is correct one
    dsp = HKL[1][3]
    tth = 2.0*asind(wave/(2.*dsp))
    ellipsep = GetEllipse2(tth,0.,dist,centp,tilt,phi)
    print fmt%('plus ellipse :',ellipsep[0][0],ellipsep[0][1],ellipsep[1],ellipsep[2][0],ellipsep[2][1])
    Ringp = makeRing(dsp,ellipsep,3,cutoff,scalex,scaley,self.ImageZ)
    parmDict = {'dist':dist,'det-X':centp[0],'det-Y':centp[1],
        'tilt':tilt,'phi':phi,'wave':wave,'dep':0.0}
    varyList = ['dist','det-X','det-Y','tilt','phi']
    if len(Ringp) > 10:
        chip = FitDetector(np.array(Ring0+Ringp),varyList,parmDict,True)
        tiltp = parmDict['tilt']
        phip = parmDict['phi']
        centp = [parmDict['det-X'],parmDict['det-Y']]
    else:
        chip = 1e6
    ellipsem = GetEllipse2(tth,0.,dist,centm,-tilt,phi)
    print fmt%('minus ellipse:',ellipsem[0][0],ellipsem[0][1],ellipsem[1],ellipsem[2][0],ellipsem[2][1])
    Ringm = makeRing(dsp,ellipsem,3,cutoff,scalex,scaley,self.ImageZ)
    if len(Ringm) > 10:
        parmDict['tilt'] *= -1
        chim = FitDetector(np.array(Ring0+Ringm),varyList,parmDict,True)
        tiltm = parmDict['tilt']
        phim = parmDict['phi']
        centm = [parmDict['det-X'],parmDict['det-Y']]
    else:
        chim = 1e6
    if chip < chim:
        data['tilt'] = tiltp
        data['center'] = centp
        data['rotation'] = phip
    else:
        data['tilt'] = tiltm
        data['center'] = centm
        data['rotation'] = phim
    data['ellipses'].append(ellipsep[:]+('b',))
    data['rings'].append(np.array(Ringp))
    data['ellipses'].append(ellipsem[:]+('r',))
    data['rings'].append(np.array(Ringm))
    G2plt.PlotImage(self,newImage=True)
    parmDict = {'dist':data['distance'],'det-X':data['center'][0],'det-Y':data['center'][1],
        'tilt':data['tilt'],'phi':data['rotation'],'wave':data['wavelength'],'dep':data['DetDepth']}
    varyList = ['dist','det-X','det-Y','tilt','phi']
    if data['DetDepthRef']:
        varyList.append('dep')
    data['rings'] = []
    data['ellipses'] = []
    for i,H in enumerate(HKL):
        dsp = H[3]
        tth = 2.0*asind(wave/(2.*dsp))
        if tth+abs(data['tilt']) > 90.:
            print 'next line is a hyperbola - search stopped'
            break
        print 'HKLD:',H[:4],'2-theta: %.4f'%(tth)
        elcent,phi,radii = ellipse = GetEllipse(dsp,data)
        data['ellipses'].append(copy.deepcopy(ellipse+('g',)))
        print fmt%('predicted ellipse:',elcent[0],elcent[1],phi,radii[0],radii[1])
        Ring = makeRing(dsp,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ)
        if Ring:
            data['rings'].append(np.array(Ring))
            rings = np.concatenate((data['rings']),axis=0)
            if i:
                chisq = FitDetector(rings,varyList,parmDict,False)
                data['distance'] = parmDict['dist']
                data['center'] = [parmDict['det-X'],parmDict['det-Y']]
                data['rotation'] = parmDict['phi']
                data['tilt'] = parmDict['tilt']
                data['DetDepth'] = parmDict['dep']
                elcent,phi,radii = ellipse = GetEllipse(dsp,data)
                print fmt2%('fitted ellipse:   ',elcent[0],elcent[1],phi,radii[0],radii[1],chisq,len(rings))
            data['ellipses'].append(copy.deepcopy(ellipse+('r',)))
#            G2plt.PlotImage(self,newImage=True)
        else:
            print 'insufficient number of points in this ellipse to fit'
            break
    G2plt.PlotImage(self,newImage=True)
    fullSize = len(self.ImageZ)/scalex
    if 2*radii[1] < .9*fullSize:
        print 'Are all usable rings (>25% visible) used? Try reducing Min ring I/Ib'
    N = len(data['ellipses'])
    if N > 2:
        FitDetector(rings,varyList,parmDict)
        data['distance'] = parmDict['dist']
        data['center'] = [parmDict['det-X'],parmDict['det-Y']]
        data['rotation'] = parmDict['phi']
        data['tilt'] = parmDict['tilt']
        data['DetDepth'] = parmDict['dep']
    for H in HKL[:N]:
        ellipse = GetEllipse(H[3],data)
        data['ellipses'].append(copy.deepcopy(ellipse+('b',)))
    print 'calibration time = ',time.time()-time0
    G2plt.PlotImage(self,newImage=True)        
    return True
    
def Make2ThetaAzimuthMap(data,masks,iLim,jLim):
    'Needs a doc string'
    #transforms 2D image from x,y space to 2-theta,azimuth space based on detector orientation
    pixelSize = data['pixelSize']
    scalex = pixelSize[0]/1000.
    scaley = pixelSize[1]/1000.
    
    tay,tax = np.mgrid[iLim[0]+0.5:iLim[1]+.5,jLim[0]+.5:jLim[1]+.5]         #bin centers not corners
    tax = np.asfarray(tax*scalex,dtype=np.float32)
    tay = np.asfarray(tay*scaley,dtype=np.float32)
    nI = iLim[1]-iLim[0]
    nJ = jLim[1]-jLim[0]
    #make position masks here
    frame = masks['Frames']
    tam = ma.make_mask_none((nI,nJ))
    if frame:
        tamp = ma.make_mask_none((1024*1024))
        tamp = ma.make_mask(pm.polymask(nI*nJ,tax.flatten(),
            tay.flatten(),len(frame),frame,tamp)[:nI*nJ])-True  #switch to exclude around frame
        tam = ma.mask_or(tam.flatten(),tamp)
    polygons = masks['Polygons']
    for polygon in polygons:
        if polygon:
            tamp = ma.make_mask_none((1024*1024))
            tamp = ma.make_mask(pm.polymask(nI*nJ,tax.flatten(),
                tay.flatten(),len(polygon),polygon,tamp)[:nI*nJ])
            tam = ma.mask_or(tam.flatten(),tamp)
    if tam.shape: tam = np.reshape(tam,(nI,nJ))
    spots = masks['Points']
    for X,Y,diam in spots:
        tamp = ma.getmask(ma.masked_less((tax-X)**2+(tay-Y)**2,(diam/2.)**2))
        tam = ma.mask_or(tam,tamp)
    TA = np.array(GetTthAzmD(tax,tay,data))     #includes geom. corr. as dist**2/d0**2
    TA[1] = np.where(TA[1]<0,TA[1]+360,TA[1])
    return np.array(TA),tam           #2-theta, azimuth & geom. corr. arrays & position mask

def Fill2ThetaAzimuthMap(masks,TA,tam,image):
    'Needs a doc string'
    Zlim = masks['Thresholds'][1]
    rings = masks['Rings']
    arcs = masks['Arcs']
    TA = np.dstack((ma.getdata(TA[1]),ma.getdata(TA[0]),ma.getdata(TA[2])))    #azimuth, 2-theta, dist
    tax,tay,tad = np.dsplit(TA,3)    #azimuth, 2-theta, dist**2/d0**2
    for tth,thick in rings:
        tam = ma.mask_or(tam.flatten(),ma.getmask(ma.masked_inside(tay.flatten(),max(0.01,tth-thick/2.),tth+thick/2.)))
    for tth,azm,thick in arcs:
        tamt = ma.getmask(ma.masked_inside(tay.flatten(),max(0.01,tth-thick/2.),tth+thick/2.))
        tama = ma.getmask(ma.masked_inside(tax.flatten(),azm[0],azm[1]))
        tam = ma.mask_or(tam.flatten(),tamt*tama)
    taz = ma.masked_outside(image.flatten(),int(Zlim[0]),Zlim[1])
    tabs = np.ones_like(taz)
    tam = ma.mask_or(tam.flatten(),ma.getmask(taz))
    tax = ma.compressed(ma.array(tax.flatten(),mask=tam))
    tay = ma.compressed(ma.array(tay.flatten(),mask=tam))
    taz = ma.compressed(ma.array(taz.flatten(),mask=tam))
    tad = ma.compressed(ma.array(tad.flatten(),mask=tam))
    tabs = ma.compressed(ma.array(tabs.flatten(),mask=tam))
    return tax,tay,taz,tad,tabs
    
def ImageIntegrate(image,data,masks,blkSize=128,dlg=None):
    'Needs a doc string'
    import histogram2d as h2d
    print 'Begin image integration'
    LUtth = data['IOtth']
    LRazm = np.array(data['LRazimuth'],dtype=np.float64)
    numAzms = data['outAzimuths']
    numChans = data['outChannels']
    Dtth = (LUtth[1]-LUtth[0])/numChans
    Dazm = (LRazm[1]-LRazm[0])/numAzms
    if data['centerAzm']:
        LRazm += Dazm/2.
    NST = np.zeros(shape=(numAzms,numChans),order='F',dtype=np.float32)
    H0 = np.zeros(shape=(numAzms,numChans),order='F',dtype=np.float32)
    imageN = len(image)
    Nx,Ny = data['size']
    nXBlks = (Nx-1)/blkSize+1
    nYBlks = (Ny-1)/blkSize+1
    Nup = nXBlks*nYBlks*3+3
    t0 = time.time()
    Nup = 0
    if dlg:
        dlg.Update(Nup)
    for iBlk in range(nYBlks):
        iBeg = iBlk*blkSize
        iFin = min(iBeg+blkSize,Ny)
        for jBlk in range(nXBlks):
            jBeg = jBlk*blkSize
            jFin = min(jBeg+blkSize,Nx)                
            TA,tam = Make2ThetaAzimuthMap(data,masks,(iBeg,iFin),(jBeg,jFin))           #2-theta & azimuth arrays & create position mask
            
            Nup += 1
            if dlg:
                dlg.Update(Nup)
            Block = image[iBeg:iFin,jBeg:jFin]
            tax,tay,taz,tad,tabs = Fill2ThetaAzimuthMap(masks,TA,tam,Block)    #and apply masks
            Nup += 1
            if dlg:
                dlg.Update(Nup)
            tax = np.where(tax > LRazm[1],tax-360.,tax)                 #put azm inside limits if possible
            tax = np.where(tax < LRazm[0],tax+360.,tax)
            if data['SampleAbs'][1]:
                muR = data['SampleAbs'][0]*(1.+npsind(tax)**2/2.)/(npcosd(tay))
                tabs = G2pwd.Absorb(data['SampleShape'],muR,tay)
            if any([tax.shape[0],tay.shape[0],taz.shape[0]]):
                NST,H0 = h2d.histogram2d(len(tax),tax,tay,taz*tad*tabs,numAzms,numChans,LRazm,LUtth,Dazm,Dtth,NST,H0)
            Nup += 1
            if dlg:
                dlg.Update(Nup)
    NST = np.array(NST)
    H0 = np.divide(H0,NST)
    H0 = np.nan_to_num(H0)
    del NST
    if Dtth:
        H2 = np.array([tth for tth in np.linspace(LUtth[0],LUtth[1],numChans+1)])
    else:
        H2 = np.array(LUtth)
    if Dazm:        
        H1 = np.array([azm for azm in np.linspace(LRazm[0],LRazm[1],numAzms+1)])
    else:
        H1 = LRazm
    H0 /= npcosd(H2[:-1])**2
    if data['Oblique'][1]:
        H0 /= G2pwd.Oblique(data['Oblique'][0],H2[:-1])
    if 'SASD' in data['type'] and data['PolaVal'][1]:
        H0 /= np.array([G2pwd.Polarization(data['PolaVal'][0],H2[:-1],Azm=azm)[0] for azm in H1[:-1]+np.diff(H1)/2.])
    Nup += 1
    if dlg:
        dlg.Update(Nup)
    t1 = time.time()
    print 'Integration complete'
    print "Elapsed time:","%8.3f"%(t1-t0), "s"
    return H0,H1,H2
    
def MakeStrStaRing(ring,Image,Controls):
    ellipse = GetEllipse(ring['Dset'],Controls)
    pixSize = Controls['pixelSize']
    scalex = 1000./pixSize[0]
    scaley = 1000./pixSize[1]
    Ring = np.array(makeRing(ring['Dset'],ellipse,ring['pixLimit'],ring['cutoff'],scalex,scaley,Image)).T   #returns x,y,dsp for each point in ring
    if len(Ring):
        ring['ImxyObs'] = copy.copy(Ring[:2])
        TA = GetTthAzm(Ring[0],Ring[1],Controls)       #convert x,y to tth,azm
        TA[0] = Controls['wavelength']/(2.*npsind(TA[0]/2.))      #convert 2th to d
        ring['ImtaObs'] = TA
        ring['ImtaCalc'] = np.zeros_like(ring['ImtaObs'])
        Ring[0] = TA[0]
        Ring[1] = TA[1]
        return Ring,ring
    else:
        return [],[]    #bad ring; no points found
    
def FitStrSta(Image,StrSta,Controls):
    'Needs a doc string'
    
    StaControls = copy.deepcopy(Controls)
    phi = StrSta['Sample phi']
    wave = Controls['wavelength']
    StaControls['distance'] += StrSta['Sample z']*cosd(phi)

    for ring in StrSta['d-zero']:       #get observed x,y,d points for the d-zeros
        dset = ring['Dset']
        Ring,R = MakeStrStaRing(ring,Image,StaControls)
        if len(Ring):
            ring.update(R)
            p0 = ring['Emat']
            ring['Emat'] = FitStrain(Ring,p0,dset,wave,phi)
    CalcStrSta(StrSta,Controls)
    
def CalcStrSta(StrSta,Controls):

    wave = Controls['wavelength']
    phi = StrSta['Sample phi']
    E = StrSta['strain']
    for ring in StrSta['d-zero']:
        Eij = ring['Emat']
        E = [[Eij[0],Eij[1],0],[Eij[1],Eij[2],0],[0,0,0]]
        th,azm = ring['ImtaObs']
        th0 = np.ones_like(azm)*npasind(wave/(2.*ring['Dset']))
        V = 1.+np.sum(np.sum(E*calcFij(90.,phi,azm,th0).T/1.e6,axis=2),axis=1)
        ring['ImtaCalc'] = np.array([V*ring['Dset'],azm])

def calcFij(omg,phi,azm,th):
    '''Does something...

    Uses parameters as defined by Bob He & Kingsley Smith, Adv. in X-Ray Anal. 41, 501 (1997)

    :param omg: his omega = sample omega rotation; 0 when incident beam || sample surface, 
        90 when perp. to sample surface
    :param phi: his phi = sample phi rotation; usually = 0, axis rotates with omg.
    :param azm: his chi = azimuth around incident beam
    :param th:  his theta = theta
    '''
    a = npsind(th)*npcosd(omg)+npsind(azm)*npcosd(th)*npsind(omg)
    b = -npcosd(azm)*npcosd(th)
    c = npsind(th)*npsind(omg)-npsind(azm)*npcosd(th)*npcosd(omg)
    d = a*npcosd(phi)-b*npsind(phi)
    e = a*npsind(phi)+b*npcosd(phi)
    Fij = np.array([
        [d**2,d*e,c*d],
        [d*e,e**2,c*e],
        [c*d,c*e,c**2]])
    return -Fij*nptand(th)

def FitStrain(rings,p0,dset,wave,phi):
    'Needs a doc string'
    def StrainPrint(ValSig,dset):
        print 'Strain tensor for Dset: %.6f'%(dset)
        ptlbls = 'names :'
        ptstr =  'values:'
        sigstr = 'esds  :'
        for name,fmt,value,sig in ValSig:
            ptlbls += "%s" % (name.rjust(12))
            ptstr += fmt % (value)
            if sig:
                sigstr += fmt % (sig)
            else:
                sigstr += 12*' '
        print ptlbls
        print ptstr
        print sigstr
        
    def strainCalc(p,xyd,dset,wave,phi):
        E = np.array([[p[0],p[1],0],[p[1],p[2],0],[0,0,0]])
        dspo,azm,dsp = xyd
        th = npasind(wave/(2.0*dspo))
        V = 1.+np.sum(np.sum(E*calcFij(90.,phi,azm,th).T/1.e6,axis=2),axis=1)
        dspc = dset*V
        return dspo**2-dspc**2
        
    names = ['e11','e12','e22']
    fmt = ['%12.2f','%12.2f','%12.2f']
    result = leastsq(strainCalc,p0,args=(rings,dset,wave,phi),full_output=True)
    vals = list(result[0])
    chisq = np.sum(result[2]['fvec']**2)
    sig = list(np.sqrt(chisq*np.diag(result[1])))
    ValSig = zip(names,fmt,vals,sig)
    StrainPrint(ValSig,dset)
    return vals