Final version of field_import.m
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shiroka
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[x y z bx by bz] = textread('sep_0nl.lis','%f %f %f %f %f %f', 'headerlines', 13);
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function field_import(varargin)
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[nx ny nz] = textread('sep_0nl.lis','%*s %*s %*s %*s %u %u %u', 1, 'headerlines', 10);
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%FIELD_IMPORT Imports B-field maps calculated by Opera in G4.
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% B-field maps calculated by Opera in the first (positive) octant
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% are extended to all octants and modified for importing in Geant4.
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% Notice that the variable export order in Opera is x->y->z, while
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% Geant4 expects variables to vary in the opposite order z->y->x.
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% Notice that the original By values have been multiplied by -1.
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% USAGE: field_import or field_import(B_map).
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% OUTPUT: Extended B-map with name B_map_G4.dat
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%
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% See also ELMAT, FLIPDIM, CAT, SUB2IND, PERMUTE.
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% Copyright (c) 2008 by Toni Shiroka
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% $Revision: 1.0 $ $Date: 2008/12/31 13:45:13 $
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error(nargchk(0,1,nargin));
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wd=cd;
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if nargin == 0,
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%[filename, pathname] = uigetfile('*.lis', 'Choose a B-field map to read');%, 10, 24);
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[filename, pathname] = uigetfile({'*.lis';'*.dat';'*.txt';'*.*'}, 'Choose a B-field map to read');
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fnam=filename; direc=pathname;
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if filename==0,
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disp(' '); disp('No file loaded ...');
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disp(' '); cd(wd); return
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end
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end
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if nargin == 1,
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fnam = char(varargin);
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if ~exist(fnam,'file'),
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disp(' '); disp(['File ',fnam,' does not exist. No file loaded ...']);
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disp(' '); cd(wd); return
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end
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end
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%Read variables, step sizes and number of points
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[x y z bx by bz] = textread(fnam,'%f %f %f %f %f %f', 'headerlines', 13);
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[units sx sy sz] = textread(fnam,'%*s %s %*s %f %f %f', 1, 'headerlines', 9);
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[nx ny nz] = textread(fnam,'%*s %*s %*s %*s %u %u %u', 1, 'headerlines', 10);
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disp(' '); disp(['File ',fnam,' read successfully. Processing data ...']);
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% Prepare length units for later use
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% Use length units as mm, cm or m, but NOT dm!
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units = char(units);
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str_s = findstr(units,'['); str_e = findstr(units,']');
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l_unit = units(str_s+1:str_e-1);
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% Recreate B field in the first octant
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Bx = reshape(bx,nx,ny,nz);
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Bx = reshape(bx,nx,ny,nz);
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By = reshape(by,nx,ny,nz);
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By = reshape(by,nx,ny,nz);
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Bz = reshape(bz,nx,ny,nz);
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Bz = reshape(bz,nx,ny,nz);
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x1 = reshape(x,nx,ny,nz);
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y1 = reshape(y,nx,ny,nz);
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z1 = reshape(z,nx,ny,nz);
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i=1:32;
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% Extend B-field map in negative x direction:
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test = [x1(i);y1(i);z1(i)]'
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Bx_extx = -flipdim(Bx,1); % Notice the NEGATIVE sign!
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By_extx = flipdim(By,1);
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Bz_extx = flipdim(Bz,1);
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%min(x) max(x)
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%The (1:end-1) argument is to avoid repeating the origin Bx_extx(end) twice!
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Bx_X = cat(1, Bx_extx(1:end-1,:,:), Bx); % Extend Bx in X direction
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By_X = cat(1, By_extx(1:end-1,:,:), By); % Extend By in X direction
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Bz_X = cat(1, Bz_extx(1:end-1,:,:), Bz); % Extend Bz in X direction
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sx = max(diff(x)); % read step size along x
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sy = max(diff(y)); % read step size along y
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sz = max(diff(z)); % read step size along z
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x2 = -x(end:-1:1);
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% Extend B-field map in negative y direction:
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x3 = -x(end:-1:1);
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Bx_exty = flipdim(Bx_X,2);
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x4 = -x(end:-1:1);
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By_exty = flipdim(By_X,2); % Notice the ABSENCE of negative sign due to -1 in orig. file!
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Bz_exty = flipdim(Bz_X,2);
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x2 = reshape(x2,nx,ny,nz);
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Bx_XY = cat(2, Bx_exty(:,1:end-1,:), Bx_X); % Extend Bx_X in Y direction
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x3 = reshape(x3,nx,ny,nz);
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By_XY = cat(2, By_exty(:,1:end-1,:), By_X); % Extend By_X in Y direction
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x4 = reshape(x4,nx,ny,nz);
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Bz_XY = cat(2, Bz_exty(:,1:end-1,:), Bz_X); % Extend Bz_X in Y direction
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%p = [x(:)'; y(:)'; z(:)'];
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%ind2sub
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% Extend B-field map in negative z direction:
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%[i j] = ind2sub(3,x1);
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Bx_extz = -flipdim(Bx_XY,3); % Notice the NEGATIVE sign!
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By_extz = flipdim(By_XY,3); % Notice the ABSENCE of negative sign due to -1 in orig. file!
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Bz_extz = flipdim(Bz_XY,3);
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Bx_XYZ = cat(3, Bx_extz(:,:,1:end-1), Bx_XY); % Extend Bx_XY in Z direction
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By_XYZ = cat(3, By_extz(:,:,1:end-1), By_XY); % Extend By_XY in Z direction
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Bz_XYZ = cat(3, Bz_extz(:,:,1:end-1), Bz_XY); % Extend Bz_XY in Z direction
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% The final B-field map is stored in Bx_XYZ, By_XYZ, Bz_XYZ.
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% The coordinates are reconstructed using the number of points and the step size.
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% Test plots: By is the main magnetic field component
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k = 45;
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figure(1) % plot original By field map (xy projection)
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Byo_plot = squeeze(By(:,:,k));
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[c,h] = contourf(Byo_plot); clabel(c,h);
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axis('square')
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figure(2) % plot extended By field map (xy projection)
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Bye_plot = squeeze(By_XYZ(:,:,nz + k)); % nz +/- k
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[x_plot, y_plot] = meshgrid(-x(end):sx:x(end), -y(end):sy:y(end));
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[c,h] = contourf(x_plot, y_plot, Bye_plot); clabel(c,h);
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axis('square')
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xlabel('x-axis (cm)','FontSize',14)
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ylabel('y-axis (cm)','FontSize',14)
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title(['xy section of the extended B_y-field map at z = ',num2str(sz*k),' cm'],'FontSize',16)
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%for kk = 1:4:2*nz;
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% Bye_plot = squeeze(By_XYZ(:,:,kk));
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% [c,h] = contourf(Bye_plot); clabel(c,h);
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% axis('square')
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% hold on
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% quiver(squeeze(Bx_XYZ(:,:,nz+k)),squeeze(By_XYZ(:,:,nz+k)));
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% drawnow
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%end
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p = 3;
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figure(3) % plot Bz original field map (yz projection)
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Bzo_plot = squeeze(Bz(p,:,:));
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[c,h] = contourf(Bzo_plot); clabel(c,h);
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axis('equal','tight')
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figure(4) % plot Bz extended field map (yz projection)
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Bze_plot = squeeze(Bz_XYZ(nx+p,:,:));
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[y_plot, z_plot] = meshgrid(-y(end):sy:y(end), -z(end):sz:z(end));
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[c,h] = contourf(y_plot, z_plot, Bze_plot'); clabel(c,h);
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view(90,90)
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axis('equal','tight')
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xlabel('y-axis (cm)','FontSize',14)
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ylabel('z-axis (cm)','FontSize',14)
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title(['yz section of the extended B_z-field map at x = ',num2str(sx*p),' cm'],'FontSize',16)
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%for pp = 1:2*nx,
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% Bze_plot = squeeze(Bz_XYZ(pp,:,:));
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% [c,h] = contourf(Bze_plot); clabel(c,h); pause(1)
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% axis('equal','tight')
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% hold on
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% quiver(squeeze(By_XYZ(nx+p,:,:)),squeeze(Bz_XYZ(nx+p,:,:)));
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% drawnow
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%end
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figure(5) % plot By extended field map (yz projection)
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Bye_plot = squeeze(By_XYZ(nx+p,:,:));
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%[c,h] = contourf(Bye_plot); clabel(c,h);
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[c,h] = contourf(y_plot, z_plot, Bye_plot'); clabel(c,h);
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view(90,90)
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axis('equal','tight')
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xlabel('y-axis (cm)','FontSize',14)
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ylabel('z-axis (cm)','FontSize',14)
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title(['yz section of the extended B_y-field map at x = ',num2str(sx*p),' cm'],'FontSize',16)
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figure(6) % plot By extended field map along the z-axis
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Bye_zplot = squeeze(By_XYZ(nx,ny,:));
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plot(-z(end):sz:z(end),Bye_zplot);
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xlabel('z-axis (cm)','FontSize',14)
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ylabel('Field value (arb. units)','FontSize',14)
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title('Extended B_y-field map along {\itz} axis','FontSize',16)
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%Prepare extended coord. and field maps for writing into the final file.
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% Extend x, y, z coordinates to negative values.
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% Use ndgrid for reverse order, or meshgrid for mixed order!
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% Variation order: ndgrd: z -> y -> x, ndgrid: x -> y -> z
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[x_ext, y_ext, z_ext] = ndgrd(-x(end):sx:x(end), -y(end):sy:y(end), -z(end):sz:z(end));
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%Change also the B order according to the same coord. order, i.e.: z -> y -> x
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Bx_ext = permute(Bx_XYZ, [3 2 1]);
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By_ext = permute(By_XYZ, [3 2 1]);
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Bz_ext = permute(Bz_XYZ, [3 2 1]);
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%Export coordinates and field values
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data = [x_ext(:) y_ext(:) z_ext(:) Bx_ext(:) By_ext(:) Bz_ext(:)];
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%Export field values only
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%data = [Bx_ext(:) By_ext(:) Bz_ext(:)];
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imax = find(data(:,1)==0 & data(:,2)==0 & data(:,3)==0); % Center of magnet
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M = data(imax,5); % Consider as max. the By field value at magnet center!
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%M = max(max(data(:,4:6))); % consider only the last three columns (Bx, By and Bz)
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norm_fact = 1/M; % normalization factor
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% The filename of the extended field map
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fname = [strtok(fnam,'.'),'_ext.map'];
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% Prepare data for writing
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header1 = sprintf('%d\t%d\t%d\t%s\t%.8f', 2*nx-1, 2*ny-1, 2*nz-1, l_unit, norm_fact);
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header2 = sprintf('%s\t%s\t%s\t%s\t%s', '%nx', 'ny', 'nz', 'length_unit', 'norm_fact');
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disp(' ')
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disp('Data being written to the extended field map. Please wait ...')
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%Write data to the extended field map file
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fid = fopen(fname,'w');
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fprintf(fid,'%s\n',header1);
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fprintf(fid,'%s\n',header2);
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fprintf(fid,'%s\n','%');
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fprintf(fid,'%2.5g\t%2.5g\t%2.5g\t%2.5g\t%2.5g\t%2.5g\n',data');
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fclose(fid);
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% This works only in more advanced matlab versions!
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% dlmwrite(filename,header,'delimiter','')
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% dlmwrite(filename,data,'delimiter','\t','precision','%-2.5g','-append');
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% try also f, or e instead of g, or fprintf
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disp(['Data successfully written to ',fname,'.'])
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disp(' ')
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return
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% Initial check of correctness
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%[Bx_extx(:,2,13),Bx(end:-1:1,2,13)]
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%[By_extx(:,2,13),By(end:-1:1,2,13)]
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%[Bz_extx(:,2,13),Bz(end:-1:1,2,13)]
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% Final Check of correctness
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% Extended data
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%data(237000,:)
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%4.0 2.0 1.5 -2.46 128.60 -3.06
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%data(237002,:)
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%4.0 2.0 2.5 -2.42 129.63 -5.13
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% Original data!
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%datao = [x(:) y(:) z(:) bx(:) by(:) bz(:)];
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%datao(744,:)
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%4.0 2.0 1.5 -2.46 128.60 -3.06
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%datao(1194,:)
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%4.0 2.0 2.5 -2.42 129.63 -5.13
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