Example #1
0
import scisoftpy as dnp

# Jython script for manipulating data sets.
# The variables going into this actor in the workflow are available in the script.
# Expected variable sets available and set when this script is run:
# energy
# I0
# Iref
# It

# Please provide maths of these variables and other available ones in the following lines.
lnI0It = dnp.log(I0 / It)
Example #2
0
def refl(runfiles, pathtofiles, outputpath, scalar, beamheight, footprint, angularfudgefactor, wl, back=()):
        # scalar - scale factor to divide the data by
        # beamheight FWHM in microns
        # footprint in mm
        # angular offset correction in degrees
        #  wavelength in wl
        #  back is an optional variable to subtract a background, set back=1 to do a background subtraction
 
        qq = []
        RR = []
        dR = []
        ii = -1
        for filename in runfiles:
            data = dnp.io.load(pathtofiles + "/" + str(filename) + ".dat")
            ii += 1

            theta = data.alpha
            # work out the q vector
            qqtemp = 4 * dnp.pi * dnp.sin((theta + angularfudgefactor) * dnp.pi /180) / wl
            #qqtemp = data.qdcd
            
            # this section is to allow users to set limits on the q range used from each file
            if not 'qmin' + str(ii) in refl.__dict__:
                qmin = qqtemp.min()
            else:
                print "USER SET",
                qmin = refl.__getattribute__('qmin' + str(ii))
            print 'refl.qmin' + str(ii) + " = " + str(qmin) + " ;",
            if not 'qmax' + str(ii) in refl.__dict__:
                qmax = qqtemp.max()
            else:
                print "USER SET",
                qmax = refl.__getattribute__('qmax' + str(ii))
            print 'refl.qmax' + str(ii) + " = " + str(qmax) + " ;",            
            
            roi1_sum = data.roi1_sum
            roi1_sum = roi1_sum[dnp.where((qqtemp >= qmin) & (qqtemp <= qmax))]
            roi1dr = dnp.sqrt(roi1_sum)
            theta = theta[dnp.where((qqtemp >= qmin) & (qqtemp <= qmax))]
            qqtemp = qqtemp[dnp.where((qqtemp >= qmin) & (qqtemp <= qmax))]
 
            bg_sum = dnp.zeros(len(roi1_sum))
            bg_dr = dnp.zeros(len(roi1dr))
 
            # if background ROI number given as int, convert to a single-item tuple
            if type(back) == int:
                back = (back,)
            
            # subtract any background ROIs from the data
            if len(back) > 0 and back[0] > 0:
                if ii==0:
                    print "Using background from " + str(len(back)) + " ROIs: " + str(back)
                for bg in back:
                    if ('roi' + str(bg) + '_sum' in data.keys()):
                        bg_cur = data[data.keys().index('roi' +str(bg) + '_sum')]
                        dr_cur = dnp.sqrt(bg_cur)
                        (bg_sum, bg_dr) = ep.EPadd(bg_sum, bg_dr, bg_cur, dr_cur)
                (bg_sum, bg_dr) = ep.EPmulk(bg_sum, bg_dr, 1.0/len(back))
            else:
                if ii==0:
                    print "Not subtracting a background"                
            (RRtemp, drtemp) = ep.EPsub(roi1_sum, roi1dr, bg_sum, bg_dr)
 
            # do a footprint correction.
            # assumes that the beam is gaussian in profile, with a FWHM of "beamheight".
            # footprint of sample is measured in mm.
            areamultiplier = 2*(norm.cdf(footprint * dnp.sin((theta + angularfudgefactor) / 180 * dnp.pi) / 2, 0, 1e-3 * beamheight/ (2*dnp.sqrt(2*dnp.log(2)))) - 0.5)
            RRtemp /= areamultiplier
            drtemp /= areamultiplier


            # for the 2nd, 3rd, 4th q ranges have to splice the data on the end of the preexisting data
            if(ii > 0):
                # splice
                (scalingfactor, sferror) = nsplice.getScalingInOverlap(qq, RR, dR, qqtemp, RRtemp, drtemp)
                RRtemp *= scalingfactor
                drtemp *= scalingfactor
                print "Error in scaling factor: %2.3f %%" % (sferror/scalingfactor*100)
            
            # now concatenate the data.
            qq = dnp.concatenate((qq, qqtemp))
            RR = dnp.concatenate((RR, RRtemp))
            dR = dnp.concatenate((dR, drtemp))
        # end of per-file loop

        RR /= scalar
        dR /= scalar
        
        RR = RR[np.argsort(qq)]
        dR = dR[np.argsort(qq)]
        qq = np.sort(qq)
        
        # write out the data.
        np.savetxt(outputpath+"/"+str(runfiles[0])+"_refl.dat",dnp.concatenate((qq,RR,dR)).reshape(3,qq.shape[0]).transpose())
Example #3
0
def rerefl(runfiles):
        global pathtofiles, savedbean, firstfiledata
        qq = []
        RR = []
        dR = []
        ii = -1
        for filename in runfiles:
            roi1sum = []
            roi1dr = []
            bg_sum = []
            bg_dr = []
            data = dnp.io.load(pathtofiles + "/" + str(filename) + ".dat")
            ii += 1
            if ii == 0:
                firstfiledata = data

            # define theta
            theta = data.alpha
            # define q
            qqtemp = 4 * dnp.pi * dnp.sin((theta + angularfudgefactor) * dnp.pi /180) / wl
            #qqtemp = data.qdcd
            
            qmin = qqtemp.min()
            qmax = qqtemp.max()

            # plot first image of first file
            if ii == 0:
                global image
                image = dnp.io.load(replace_path(data['file'][imgdisp]), warn=False)
                dnp.plot.image(image[0], name='Plot 1', resetaxes=False)

            # find ROIs from saved bean
            try:
                rois = dnp.plot.getrois(savedbean)
                norois = len(rois)
            # if we don't have any ROIs yet, ask the user to draw some
            except(KeyError, TypeError, NameError):
                if ii==0:
                    print "\nPlease define some regions of interest then type getrois()"
                    print "You must type getrois() after adding/changing any regions due to a bug in DAWN."
                norois = 0                
            
            # this section to be restored when ROIs are working again
            ## find ROIs from plot window
            #bean = dnp.plot.getbean('Plot 1')
            #try:
            #    rois = dnp.plot.getrois(bean)
            #    norois = len(rois)
            ## if we don't have any ROIs yet, ask the user to draw some
            #except(KeyError, TypeError):
            #    if ii==0:
            #        print "Please define some regions of interest"
            #    norois = 0
            
            if norois > 0:
                if ii == 0:
                    print str(norois) + " ROIs defined, " + str(norois-1) + " will be used for the background"
 
                for imgfile in data['file']:
                    imgdata = dnp.io.load(replace_path(imgfile), warn=False)
                    dnp.plot.image(imgdata[0], name="Plot 1", resetaxes=False)
                    image = imgdata[0].transpose() # Pilatus images load with axes transposed for some reason
                    bg_pt = 0
                    bgdr_pt = 0
                    for j in range(0,norois):
                        roi = image[int(rois[j].spt[0]):int(rois[j].spt[0]+rois[j].len[0]), int(rois[j].spt[1]):int(rois[j].spt[1]+rois[j].len[1])]
                        roisum_pt = dnp.float(roi.sum())
                        if j == 0:
                            roi1sum.append(roisum_pt)
                            roi1dr.append(dnp.sqrt(roisum_pt))
                        else:
                            (bg_pt, bgdr_pt) = ep.EPadd(bg_pt, bgdr_pt, roisum_pt, dnp.sqrt(roisum_pt))
                    bg_sum.append(bg_pt)
                    bg_dr.append(bgdr_pt)

                # convert lists to arrays
                (roi1sum, roi1dr, bg_sum, bg_dr) = (dnp.array(roi1sum), dnp.array(roi1dr), dnp.array(bg_sum), dnp.array(bg_dr))
                
                # normalise background
                if norois > 1:
                    bgsize = 0
                    for k in range(1, norois):
                        bgsize += rois[k].len[0]*rois[k].len[1]
                    (bg_sum, bg_dr) = ep.EPmulk(bg_sum, bg_dr, rois[0].len[0]*rois[0].len[1]/bgsize)

                # subtract background
                (RRtemp, drtemp) = ep.EPsub(roi1sum, roi1dr, bg_sum, bg_dr)

                # do a footprint correction.
                # assumes that the beam is gaussian in profile, with a FWHM of "beamheight".
                # footprint of sample is measured in mm.
                areamultiplier = 2*(norm.cdf(dnp.float(footprint) * dnp.sin((theta + dnp.float(angularfudgefactor)) / 180 * dnp.pi) / 2, 0, 1e-3 * dnp.float(beamheight)/ (2*dnp.sqrt(2*dnp.log(2)))) - 0.5)
                RRtemp /= areamultiplier
                drtemp /= areamultiplier


                # for the 2nd, 3rd, 4th q ranges have to splice the data on the end of the preexisting data
                if(ii > 0):
                    (scalingfactor, sferror) = nsplice.getScalingInOverlap(qq, RR, dR, qqtemp, RRtemp, drtemp)
                    RRtemp *= scalingfactor
                    drtemp *= scalingfactor
            
                # now concatenate the data.
                qq = dnp.concatenate((qq, qqtemp))
                RR = dnp.concatenate((RR, RRtemp))
                dR = dnp.concatenate((dR, drtemp))
        # end of per-file loop
        if norois > 0:
            RR /= dnp.float(scalar)
            dR /= dnp.float(scalar)
        
            RR = RR[np.argsort(qq)]
            dR = dR[np.argsort(qq)]
            qq = np.sort(qq)
       
            # write out the data.
            np.savetxt(outputpath+"/"+str(runfiles[0])+"_rerefl_bkg1.dat",dnp.concatenate((qq,RR,dR)).reshape(3,qq.shape[0]).transpose(), fmt="%.10f %.10e %.10e")
            print "Output saved to " + outputpath+"/"+str(runfiles[0])+"_rerefl_bkg1.dat"

            # plot the resulting
            dnp.plot.line(qq,dnp.log10(RR),name='Plot 2')
import scisoftpy as dnp

# Jython script for manipulating data sets.
# The variables going into this actor in the workflow are available in the script.
# Expected variable sets available and set when this script is run:
# energy
# I0
# Iref
# It

# Please provide maths of these variables and other available ones in the following lines.
lnI0It = dnp.log(I0/It)
Example #5
0
def refl(runfiles,
         pathtofiles,
         outputpath,
         scalar,
         beamheight,
         footprint,
         angularfudgefactor,
         wl,
         back=()):
    # scalar - scale factor to divide the data by
    # beamheight FWHM in microns
    # footprint in mm
    # angular offset correction in degrees
    #  wavelength in wl
    #  back is an optional variable to subtract a background, set back=1 to do a background subtraction

    qq = []
    RR = []
    dR = []
    ii = -1
    for filename in runfiles:
        data = dnp.io.load(pathtofiles + "/" + str(filename) + ".dat")
        ii += 1

        theta = data.alpha
        # work out the q vector
        qqtemp = 4 * dnp.pi * dnp.sin(
            (theta + angularfudgefactor) * dnp.pi / 180) / wl
        #qqtemp = data.qdcd

        # this section is to allow users to set limits on the q range used from each file
        if not 'qmin' + str(ii) in refl.__dict__:
            qmin = qqtemp.min()
        else:
            print "USER SET",
            qmin = refl.__getattribute__('qmin' + str(ii))
        print 'refl.qmin' + str(ii) + " = " + str(qmin) + " ;",
        if not 'qmax' + str(ii) in refl.__dict__:
            qmax = qqtemp.max()
        else:
            print "USER SET",
            qmax = refl.__getattribute__('qmax' + str(ii))
        print 'refl.qmax' + str(ii) + " = " + str(qmax) + " ;",

        roi1_sum = data.roi1_sum
        roi1_sum = roi1_sum[dnp.where((qqtemp >= qmin) & (qqtemp <= qmax))]
        roi1dr = dnp.sqrt(roi1_sum)
        theta = theta[dnp.where((qqtemp >= qmin) & (qqtemp <= qmax))]
        qqtemp = qqtemp[dnp.where((qqtemp >= qmin) & (qqtemp <= qmax))]

        bg_sum = dnp.zeros(len(roi1_sum))
        bg_dr = dnp.zeros(len(roi1dr))

        # if background ROI number given as int, convert to a single-item tuple
        if type(back) == int:
            back = (back, )

        # subtract any background ROIs from the data
        if len(back) > 0 and back[0] > 0:
            if ii == 0:
                print "Using background from " + str(
                    len(back)) + " ROIs: " + str(back)
            for bg in back:
                if ('roi' + str(bg) + '_sum' in data.keys()):
                    bg_cur = data[data.keys().index('roi' + str(bg) + '_sum')]
                    dr_cur = dnp.sqrt(bg_cur)
                    (bg_sum, bg_dr) = ep.EPadd(bg_sum, bg_dr, bg_cur, dr_cur)
            (bg_sum, bg_dr) = ep.EPmulk(bg_sum, bg_dr, 1.0 / len(back))
        else:
            if ii == 0:
                print "Not subtracting a background"
        (RRtemp, drtemp) = ep.EPsub(roi1_sum, roi1dr, bg_sum, bg_dr)

        # do a footprint correction.
        # assumes that the beam is gaussian in profile, with a FWHM of "beamheight".
        # footprint of sample is measured in mm.
        areamultiplier = 2 * (norm.cdf(
            footprint * dnp.sin(
                (theta + angularfudgefactor) / 180 * dnp.pi) / 2, 0,
            1e-3 * beamheight / (2 * dnp.sqrt(2 * dnp.log(2)))) - 0.5)
        RRtemp /= areamultiplier
        drtemp /= areamultiplier

        # for the 2nd, 3rd, 4th q ranges have to splice the data on the end of the preexisting data
        if (ii > 0):
            # splice
            (scalingfactor,
             sferror) = nsplice.getScalingInOverlap(qq, RR, dR, qqtemp, RRtemp,
                                                    drtemp)
            RRtemp *= scalingfactor
            drtemp *= scalingfactor
            print "Error in scaling factor: %2.3f %%" % (sferror /
                                                         scalingfactor * 100)

        # now concatenate the data.
        qq = dnp.concatenate((qq, qqtemp))
        RR = dnp.concatenate((RR, RRtemp))
        dR = dnp.concatenate((dR, drtemp))
    # end of per-file loop

    RR /= scalar
    dR /= scalar

    RR = RR[np.argsort(qq)]
    dR = dR[np.argsort(qq)]
    qq = np.sort(qq)

    # write out the data.
    np.savetxt(
        outputpath + "/" + str(runfiles[0]) + "_refl.dat",
        dnp.concatenate((qq, RR, dR)).reshape(3, qq.shape[0]).transpose())