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Merge pull request #1 from ando-lab/dev-spm
Dev spm
2 parents 9e92dcd + 77f1d8f commit 191f367

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‎+geom/@Profile/Profile.m

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classdef Profile
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%PROFILE a collection of methods for spot profile calculations
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% <Detailed explanation goes here>
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methods(Static)
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function [idx,hkl_refl] = hkl2idx(h,k,l)
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% assign each pixel an index to its nearest reflection
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h = round(h);
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k = round(k);
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l = round(l);
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[hkl_refl,~,ic] = unique([h(:),k(:),l(:)],'rows');
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idx = reshape(ic,size(h));
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end
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function [e1,e2,e3] = s2e(s_refl,Source)
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% calculate local coordinate system for each reflection
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s0 = Source.wavevector;
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e1 = zeros(size(s_refl));
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e2 = zeros(size(s_refl));
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e3 = zeros(size(s_refl));
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for j=1:size(s_refl,1)
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k1 = s0 + s_refl(j,:);
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e1(j,:) = quickcross(k1,s0);
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e1(j,:) = e1(j,:)/sqrt(quickdot(e1(j,:),e1(j,:)));
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e2(j,:) = quickcross(k1,e1(j,:));
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e2(j,:) = e2(j,:)/sqrt(quickdot(e2(j,:),e2(j,:)));
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e3(j,:) = (k1 + s0);
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e3(j,:) = e3(j,:)/sqrt(quickdot(e3(j,:),e3(j,:)));
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end
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end
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function [phixy1,phixy2] = s2phi(s_refl,Source,Spindle,Detector)
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% I changed how this works on 3/25/2019. It used to return:
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% [phi, x, y] for whichever solution had the lowest value of
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% |phi|.
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s0 = Source.wavevector;
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m2 = Spindle.rotationAxis;
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f = Detector.f;
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ed = Detector.ed;
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[phixy1, phixy2] = calc_reflection_center(s0, m2, f, ed, s_refl);
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% [c1,c2] = calc_reflection_center(s0, m2, f, ed, s_refl);
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% all_phi = [c1(:,1),c2(:,1)];
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% [~,ix] = min(abs(all_phi),[],2);
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%
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% c = c1;
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% for j=1:size(all_phi,1)
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% if ix(j)==2
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% c(j,:) = c2(j,:);
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% end
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% end
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%
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% x = c(:,2);
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% y = c(:,3);
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% phi = c(:,1);
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end
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function [eps1,eps2] = s2eps(sx,sy,sz,idx,s,e1,e2,Source,Detector)
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nrefl = size(s,1);
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s0 = Source.wavevector;
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ed = Detector.ed;
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d1 = ed(:,1)';
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d2 = ed(:,2)';
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d3 = ed(:,3)';
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krefl = s + repmat(s0,nrefl,1);
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krefl_mag = sqrt(sum(krefl.*krefl,2));
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d1_dot_e1 = sum(repmat(d1,nrefl,1).*e1,2);
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d1_dot_e2 = sum(repmat(d1,nrefl,1).*e2,2);
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d2_dot_e1 = sum(repmat(d2,nrefl,1).*e1,2);
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d2_dot_e2 = sum(repmat(d2,nrefl,1).*e2,2);
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d3_dot_e1 = sum(repmat(d3,nrefl,1).*e1,2);
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d3_dot_e2 = sum(repmat(d3,nrefl,1).*e2,2);
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sx_refl = s(:,1);
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sy_refl = s(:,2);
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sz_refl = s(:,3);
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eps1 = (180/pi)*((sx - sx_refl(idx)).*d1_dot_e1(idx) + ...
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(sy - sy_refl(idx)).*d2_dot_e1(idx) + ...
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(sz - sz_refl(idx)).*d3_dot_e1(idx))./krefl_mag(idx);
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eps2 =(180/pi)* ((sx - sx_refl(idx)).*d1_dot_e2(idx) + ...
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(sy - sy_refl(idx)).*d2_dot_e2(idx) + ...
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(sz - sz_refl(idx)).*d3_dot_e2(idx))./krefl_mag(idx);
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end
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function Rj = partiality(phi,e1,sigmaM,Spindle,frame)
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% added frame argument on March 25, 2019
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m2 = Spindle.rotationAxis;
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dPhi = Spindle.oscillationRange;
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phiMid = Spindle.frame2phi(frame);
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phi1 = phiMid - dPhi/2;
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phi2 = phiMid + dPhi/2; % before, assumed phimid = 0
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%disp([phi1,phi2])
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Rj = calc_partiality(phi,e1,phi1,phi2,sigmaM,m2);
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end
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end
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end
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function c = quickdot(a,b)
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c = a(1)*b(1) + a(2)*b(2) + a(3)*b(3);
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end
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function c = quickcross(a,b)
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c = zeros(1,3);
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c(1) = a(2)*b(3) - a(3)*b(2);
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c(2) = a(3)*b(1) - a(1)*b(3);
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c(3) = a(1)*b(2) - a(2)*b(1);
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end
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‎+geom/@Profile/private/calc_partiality.m

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function R = calc_partiality(phi,e1,phi1,phi2,sigmaM,m2)
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% Feb 16, 2017: modified to use m2 as input rather than xds_parm
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%m2 = xds_parm.rotation_axis;
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nrefl = size(phi,1);
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% xi = m2 dot e1
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xi = sum(repmat(m2,nrefl,1).*e1,2);
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a = abs(xi)/(sqrt(2)*sigmaM);
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R = 0.5 * (erf(a.*(phi2-phi)) - erf(a.*(phi1-phi)));
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end

‎+geom/@Profile/private/calc_reflection_center.m

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function [c1,c2] = calc_reflection_center(s0, m2, f, ed, p0star)
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%
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% columns of c1, c2: phi,x,y,p1,p2,p3
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%
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% where p1,p2,p3 are the reciprocal space coordinates once rotated into the
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% diffraction condition
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%
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% xparm = structure containing xds parameters
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%
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% p0star = some arbitrary point of interest in reciprocal space of the
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% unrotated crystal (inverse angstrom)
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%
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% c1 = [phi,x,y]; <- first set of solutions
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% c2 = [phi,x,y]; <- second set of solutions
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%
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% partly vectorized on May 18, 2015
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% (several operations could be more succinctly written as matrix
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% multiplications)
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%
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% removed x0, and y0 (x and y are now relative to detector origin)
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%
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% moved to scatterbrain project: Feb 17, 2017
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%
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% removed xparm. now s0, m2, f, ed are passed as arguments
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%s0 = xparm.incident_wavevector;
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%m2 = xparm.rotation_axis;
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m1 = cross(m2,s0); m1 = m1/sqrt(dot(m1,m1));
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m3 = cross(m1,m2);
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%f = xparm.detector.f;
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%d1 = xparm.detector.ed(:,1)';
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%d2 = xparm.detector.ed(:,2)';
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%d3 = xparm.detector.ed(:,3)';
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d1 = ed(:,1)';
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d2 = ed(:,2)';
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d3 = ed(:,3)';
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p0star_dot_p0star = ...
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p0star(:,1).*p0star(:,1) + ...
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p0star(:,2).*p0star(:,2) + ...
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p0star(:,3).*p0star(:,3);
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p0star_dot_m2 = ...
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p0star(:,1)*m2(1) + ...
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p0star(:,2)*m2(2) + ...
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p0star(:,3)*m2(3);
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p0star_dot_m1 = ...
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p0star(:,1)*m1(1) + ...
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p0star(:,2)*m1(2) + ...
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p0star(:,3)*m1(3);
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p0star_dot_m3 = ...
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p0star(:,1)*m3(1) + ...
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p0star(:,2)*m3(2) + ...
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p0star(:,3)*m3(3);
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rho_squared = p0star_dot_p0star - p0star_dot_m2.*p0star_dot_m2;
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%rho = sqrt(rho_squared); % distance to rot. axis
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pstar_dot_m3 = (-0.5*p0star_dot_p0star - p0star_dot_m2*dot(s0,m2))/dot(s0,m3);
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pstar_dot_m2 = p0star_dot_m2;
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% check not in blind region
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isoutside = rho_squared < (pstar_dot_m3.*pstar_dot_m3) | ...
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p0star_dot_p0star > 4*dot(s0,s0);
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pstar_dot_m1 = sqrt(rho_squared - pstar_dot_m3.*pstar_dot_m3);
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pstar_dot_m1(isoutside) = NaN;
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cos_phi = (pstar_dot_m1.*p0star_dot_m1 + ...
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pstar_dot_m3.*p0star_dot_m3)./rho_squared;
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sin_phi = (pstar_dot_m1.*p0star_dot_m3 - ...
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pstar_dot_m3.*p0star_dot_m1)./rho_squared;
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phi = atan2(sin_phi,cos_phi)*180/pi;
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pstar = [m1(1)*pstar_dot_m1 + m2(1)*pstar_dot_m2 + m3(1)*pstar_dot_m3,...
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m1(2)*pstar_dot_m1 + m2(2)*pstar_dot_m2 + m3(2)*pstar_dot_m3,...
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m1(3)*pstar_dot_m1 + m2(3)*pstar_dot_m2 + m3(3)*pstar_dot_m3];
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S_dot_d1 = (pstar(:,1) + s0(1))*d1(1) + ...
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(pstar(:,2) + s0(2))*d1(2) + ...
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(pstar(:,3) + s0(3))*d1(3);
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S_dot_d2 = (pstar(:,1) + s0(1))*d2(1) + ...
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(pstar(:,2) + s0(2))*d2(2) + ...
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(pstar(:,3) + s0(3))*d2(3);
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S_dot_d3 = (pstar(:,1) + s0(1))*d3(1) + ...
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(pstar(:,2) + s0(2))*d3(2) + ...
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(pstar(:,3) + s0(3))*d3(3);
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x = f*S_dot_d1./S_dot_d3;
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y = f*S_dot_d2./S_dot_d3;
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c1 = [phi,x,y,pstar];
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pstar_dot_m1 = -1*sqrt(rho_squared - pstar_dot_m3.*pstar_dot_m3);
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pstar_dot_m1(isoutside) = NaN;
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cos_phi = (pstar_dot_m1.*p0star_dot_m1 + ...
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pstar_dot_m3.*p0star_dot_m3)./rho_squared;
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sin_phi = (pstar_dot_m1.*p0star_dot_m3 - ...
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pstar_dot_m3.*p0star_dot_m1)./rho_squared;
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phi = atan2(sin_phi,cos_phi)*180/pi;
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pstar = [m1(1)*pstar_dot_m1 + m2(1)*pstar_dot_m2 + m3(1)*pstar_dot_m3,...
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m1(2)*pstar_dot_m1 + m2(2)*pstar_dot_m2 + m3(2)*pstar_dot_m3,...
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m1(3)*pstar_dot_m1 + m2(3)*pstar_dot_m2 + m3(3)*pstar_dot_m3];
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S_dot_d1 = (pstar(:,1) + s0(1))*d1(1) + ...
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(pstar(:,2) + s0(2))*d1(2) + ...
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(pstar(:,3) + s0(3))*d1(3);
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S_dot_d2 = (pstar(:,1) + s0(1))*d2(1) + ...
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(pstar(:,2) + s0(2))*d2(2) + ...
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(pstar(:,3) + s0(3))*d2(3);
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S_dot_d3 = (pstar(:,1) + s0(1))*d3(1) + ...
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(pstar(:,2) + s0(2))*d3(2) + ...
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(pstar(:,3) + s0(3))*d3(3);
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x = f*S_dot_d1./S_dot_d3;
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y = f*S_dot_d2./S_dot_d3;
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c2 = [phi,x,y,pstar];
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end

‎+geom/@Scattering/ewald2hkl.m

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% apply symmetry limits
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indh = indh(sum((indh*Binv).^2,2) <= smax^2,:);
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% unique list of miller indices with edges that intersect the ewald sphere
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hkl = unique([indh;indk;indl],'rows');
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