Add spacing and comments to files

+tools/convert2grid.m

@@ -4,7 +4,7 @@
 % Author: Timothy Sipkens, 2020-07-16
 %=========================================================================%
 
-function [grid,idx] = convert2grid(sp_m, d_star)
+function [grid,idx] = convert2grid(sp_m, d_star, b)
 
 % adjust mass setpoint
 if isstruct(sp_m); m_star = [sp_m.m_star] .* 1e18; % if setpoint structure

+tools/fit_mm_median.m

@@ -26,15 +26,20 @@
 %-- Fit normal distribution to data in log(d) space --------%
 opts = optimset('Display','none');
 for bb=length(grid_b.edges{1}):-1:1
-    fun0 = @(x) x(1).*normpdf(log10(grid_b.edges{2}),x(2),x(3));
-    x0 = [max(b_plot_rs(bb,:))/5,log10(d_med(bb)),0.1];
+    % Function to fit, normal in log-space.
+    fun0 = @(x) x(1) .* normpdf(log10(grid_b.edges{2}),x(2),x(3));
+
+    % Initialize x0, using max. in scan.
+    x0 = [max(b_plot_rs(bb,:))/5 , log10(d_med(bb)), 0.1];
+
+    % Fitting procedure.
     [x2(bb,:),~,~,~,~,~,jacob] = ...
-        lsqnonlin(@(x) (fun0(x)-b_plot_rs(bb,:)).^2,x0,[],[],opts);
+        lsqnonlin(@(x) (fun0(x) - b_plot_rs(bb,:)).^2, x0, [], [], opts);
 
-    t0 = inv(jacob'*jacob);
+    t0 = inv(jacob' * jacob);  % use jacobian to get uncertainties
     sx2(bb,1) = sqrt(t0(2,2)); % error in median, used to weight other analysis
 end
-d_med = 10.^x2(:,2);
+d_med = 10 .^ x2(:,2);
 
 
 %-- Linear regression on median/mode diameter --------------%

+tools/overlay_phantom.m

@@ -6,16 +6,15 @@
 function [pha, N, ci] = overlay_phantom(x_pha,grid,iso_levels,varargin)
 
 %-- Parse inputs ---------------------------------------------------------%
-if isa(x_pha,'Phantom')
+if isa(x_pha, 'Phantom')
     pha = x_pha;
     grid = pha.grid;
     N = [];
 else
     [pha, N, ~, ci] = Phantom.fit(x_pha, grid);
 end
 
-if ~exist('iso_levels','var'); iso_levels = []; end
-if isempty(iso_levels); iso_levels = [1,2,3]; end % plot 1, 2, and 3 sigma
+if ~exist('iso_levels', 'var'); iso_levels = [1,2,3]; end  % plot 1, 2, and 3 sigma
 
 if isempty(varargin); varargin = {'Color',[1,1,0,1]}; end
     % specify line properties (default: yellow, no transparency)

@Phantom/Phantom.m

@@ -307,7 +307,7 @@
 
             %-- OPTION 2: Using a mass-mobility parameter set (p) ----%
             case {'mass-mobility'} % for custom mass-mobility phantom
-                                   % sepcified using a p structure
+                                   % specified using a p structure
                 obj.type = 'mass-mobility';
                 obj.modes = Sigma_modes;
                 obj.p = obj.fill_p(mu_p); % fill out p structure