[format] automatic format all matlab script with miss_hit

.miss_hit

@@ -0,0 +1,11 @@
+project_root
+
+suppress_rule: "redundant_brackets"
+suppress_rule: "line_length"
+suppress_rule: "file_length"
+suppress_rule: "copyright_notice"
+suppress_rule: "naming_functions"
+suppress_rule: "naming_parameters"
+suppress_rule: "naming_scripts"
+suppress_rule: "unicode"
+indent_function_file_body: false

example/masktest/plotresults.m

@@ -1,16 +1,15 @@
-fid=fopen('mtest.mask','rb'); 
-dat=fread(fid,inf,'uchar');
+fid = fopen('mtest.mask', 'rb');
+dat = fread(fid, inf, 'uchar');
 fclose(fid);
 
-dat=reshape(dat,[8 8 8]);
-pcolor(dat(:,:,1)')
+dat = reshape(dat, [8 8 8]);
+pcolor(dat(:, :, 1)');
 
-r=3;
-s=0:pi/20:2*pi;
-c0=[4.9,4.1];
-x=c0(1)+r*cos(s);
-y=c0(2)+r*sin(s);
-
-hold on
-plot(x,y,'y-');
+r = 3;
+s = 0:pi / 20:2 * pi;
+c0 = [4.9, 4.1];
+x = c0(1) + r * cos(s);
+y = c0(2) + r * sin(s);
 
+hold on;
+plot(x, y, 'y-');

example/multipattern/plotresults.m

@@ -1,11 +1,11 @@
-dat=loadjson('multipattern.jnii',[3 60 60 60]);
+dat = loadjson('multipattern.jnii', [3 60 60 60]);
 figure;
 subplot(131);
-imagesc(squeeze(log10(abs(dat(1,:,:,10))))')
-axis equal
+imagesc(squeeze(log10(abs(dat(1, :, :, 10))))');
+axis equal;
 subplot(132);
-imagesc(squeeze(log10(abs(dat(2,:,:,10))))')
-axis equal
+imagesc(squeeze(log10(abs(dat(2, :, :, 10))))');
+axis equal;
 subplot(133);
-imagesc(squeeze(log10(abs(dat(3,:,:,10))))')
-axis equal
+imagesc(squeeze(log10(abs(dat(3, :, :, 10))))');
+axis equal;

example/polarized/onelayer_plot_results.m

@@ -5,62 +5,78 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %% load mcx input and output file
-data=loadjson("onelayer_detp.jdat");
-cfg=loadjson("onelayer.json");
+data = loadjson("onelayer_detp.jdat");
+cfg = loadjson("onelayer.json");
 
 %% compute total reflectance
-nphotons=cfg.Session.Photons;
+nphotons = cfg.Session.Photons;
 
 % extract simulation settings needed for post-processing
-unitinmm=cfg.Domain.LengthUnit; % dx,dy,dz in mm
+unitinmm = cfg.Domain.LengthUnit; % dx,dy,dz in mm
 
 % default ambient medium
-prop=[0 0 1 1];
+prop = [0 0 1 1];
 
 % absorption coefficent (in 1/mm) of each tissue type
-mua=cellfun(@(f)getfield(f,'mua'),cfg.Domain.MieScatter)';
-prop=[prop;mua, zeros(size(mua,1),3)];
+mua = cellfun(@(f)getfield(f, 'mua'), cfg.Domain.MieScatter)';
+prop = [prop; mua, zeros(size(mua, 1), 3)];
 
 % photon exiting direction
-u=data(:,6:8);
-phi=atan2(u(:,2),u(:,1));
+u = data(:, 6:8);
+phi = atan2(u(:, 2), u(:, 1));
 
 % photon exiting Stokes Vector
-s=data(:,10:13);
-S2=[s(:,1),s(:,2).*cos(2.*phi)+s(:,3).*sin(2.*phi),...
-   -s(:,2).*sin(2.*phi)+s(:,3).*cos(2.*phi),s(:,4)];
+s = data(:, 10:13);
+S2 = [s(:, 1), s(:, 2) .* cos(2 .* phi) + s(:, 3) .* sin(2 .* phi), ...
+      -s(:, 2) .* sin(2 .* phi) + s(:, 3) .* cos(2 .* phi), s(:, 4)];
 
 % final weight of exiting photons
-detphoton=struct();
-detphoton.ppath=data(:,2);
-w=mcxdetweight(detphoton,prop,unitinmm);
+detphoton = struct();
+detphoton.ppath = data(:, 2);
+w = mcxdetweight(detphoton, prop, unitinmm);
 
 % total reflected IQUV
-R=S2'*w/nphotons;
+R = S2' * w / nphotons;
 
 %% plot 2-D images for I, Q, U, V
 % extract x and y values of the exiting positions.
-x=data(:,3);
-y=data(:,4);
+x = data(:, 3);
+y = data(:, 4);
 
 % define image dimension
-NN=100;
+NN = 100;
 
 % 2D exiting positions are binned on the 2D plane (z=0)
-xedges=0:cfg.Domain.Dim(1,1)/NN:cfg.Domain.Dim(1,1);
-yedges=0:cfg.Domain.Dim(1,2)/NN:cfg.Domain.Dim(1,2);
-ix=discretize(x,xedges);
-iy=discretize(y,yedges);
-idx1d=sub2ind([NN,NN],iy,ix); % x and y is flipped to match Jessica's code
+xedges = 0:cfg.Domain.Dim(1, 1) / NN:cfg.Domain.Dim(1, 1);
+yedges = 0:cfg.Domain.Dim(1, 2) / NN:cfg.Domain.Dim(1, 2);
+ix = discretize(x, xedges);
+iy = discretize(y, yedges);
+idx1d = sub2ind([NN, NN], iy, ix); % x and y is flipped to match Jessica's code
 
 % accumulate I Q U V
-HIQUV=zeros(4,NN,NN);
-for i=1:4
-    HIQUV(i,:,:)=reshape(accumarray(idx1d,S2(:,i)),[NN,NN]);
+HIQUV = zeros(4, NN, NN);
+for i = 1:4
+    HIQUV(i, :, :) = reshape(accumarray(idx1d, S2(:, i)), [NN, NN]);
 end
 
 % plot
-subplot(2,2,1);imagesc(squeeze(HIQUV(1,:,:)));axis equal;title("HI");colorbar;
-subplot(2,2,2);imagesc(squeeze(HIQUV(2,:,:)));axis equal;title("HQ");colorbar;
-subplot(2,2,3);imagesc(squeeze(HIQUV(3,:,:)));axis equal;title("HU");colorbar;
-subplot(2,2,4);imagesc(squeeze(HIQUV(4,:,:)));axis equal;title("HV");colorbar;
+subplot(2, 2, 1);
+imagesc(squeeze(HIQUV(1, :, :)));
+axis equal;
+title("HI");
+colorbar;
+subplot(2, 2, 2);
+imagesc(squeeze(HIQUV(2, :, :)));
+axis equal;
+title("HQ");
+colorbar;
+subplot(2, 2, 3);
+imagesc(squeeze(HIQUV(3, :, :)));
+axis equal;
+title("HU");
+colorbar;
+subplot(2, 2, 4);
+imagesc(squeeze(HIQUV(4, :, :)));
+axis equal;
+title("HV");
+colorbar;

example/shapetest/plotshapemask.m

@@ -1,9 +1,8 @@
-fid=fopen('jsonshape.mask','rb');
-dat=fread(fid,inf,'uchar');
+fid = fopen('jsonshape.mask', 'rb');
+dat = fread(fid, inf, 'uchar');
 fclose(fid);
 
-dat=reshape(dat,[40 60 50]);
+dat = reshape(dat, [40 60 50]);
 figure;
-imagesc(squeeze(dat(:,:,15)));
-axis equal
-
+imagesc(squeeze(dat(:, :, 15)));
+axis equal;

example/sphbox/plotresults.m

@@ -1,56 +1,55 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% add paths to the necessary toolboxes
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-addpath('~/space/Projects/mcx/utils/')
-addpath('~/space/Projects/mmc/matlab/')
+addpath('~/space/Projects/mcx/utils/');
+addpath('~/space/Projects/mmc/matlab/');
 
-c0=299792458000;
-twin=[5e-11:1e-10:5e-9];
-gates=50;
-clines=[-1:0.5:8];
+c0 = 299792458000;
+twin = [5e-11:1e-10:5e-9];
+gates = 50;
+clines = [-1:0.5:8];
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% load MCX results
-%%-----------------------------------------------------------------
-mcx=loadmc2('spherebox.mc2', [60 60 60 gates]);
-cwmcx=sum(mcx,4);
+%% -----------------------------------------------------------------
+mcx = loadmc2('spherebox.mc2', [60 60 60 gates]);
+cwmcx = sum(mcx, 4);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate/load analytical solution for sphere inside infinite slab
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%[phi_ana,xa,ya,za]=sphdiffusionslab(0,0,60,-22:0.8:22,0,-30:0.8:10);
-%save sphdiffsemiinf.mat phi_ana xa ya za
+% [phi_ana,xa,ya,za]=sphdiffusionslab(0,0,60,-22:0.8:22,0,-30:0.8:10);
+% save sphdiffsemiinf.mat phi_ana xa ya za
 
-load sphdiffsemiinf.mat
-idx=find((xa(:)<-12 | xa(:)>12) & za(:)>-5);
-phi_ana(idx)=nan;
-idx=find((xa(:)<-10 | xa(:)>10) & za(:)>0);
-phi_ana(idx)=nan;
+load sphdiffsemiinf.mat;
+idx = find((xa(:) < -12 | xa(:) > 12) & za(:) > -5);
+phi_ana(idx) = nan;
+idx = find((xa(:) < -10 | xa(:) > 10) & za(:) > 0);
+phi_ana(idx) = nan;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate the contour of the inclusion
-%%-----------------------------------------------------------------
-
-[xcirc,ycirc] = cylinder(10,200);
-xcirc=xcirc(1,:)+30;
-ycirc=ycirc(1,:)+30;
-
-figure
-hold on
-[cc,hc]=contour(xa+30,za+31,log10(abs(phi_ana))+10,clines,'color',[0.7 0.7 0.7],'linewidth',2);
-contour(log10(squeeze(abs(cwmcx(:,30,:)))'),clines,'b-')
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'ylim',[1 60]);
-set(gca,'fontsize',18)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MCX')
+%% -----------------------------------------------------------------
+
+[xcirc, ycirc] = cylinder(10, 200);
+xcirc = xcirc(1, :) + 30;
+ycirc = ycirc(1, :) + 30;
+
+figure;
+hold on;
+[cc, hc] = contour(xa + 30, za + 31, log10(abs(phi_ana)) + 10, clines, 'color', [0.7 0.7 0.7], 'linewidth', 2);
+contour(log10(squeeze(abs(cwmcx(:, 30, :)))'), clines, 'b-');
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'ylim', [1 60]);
+set(gca, 'fontsize', 18);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MCX');
 legend boxoff;
 box on;
-set(gcf,'PaperPositionMode','auto');
-
+set(gcf, 'PaperPositionMode', 'auto');