initial commit

2026-09-17 22:59:07 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
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+%   LOAD_ANGLES_APS  load tomopgrahy angles for given scan numbers 
+%   Directly load from original mda files. useful for BNP
+%   created by YJ based on PSI's function
+
+%   [par,  angles] = load_angles(par, scans, plot_angles)
+%   Inputs: 
+%       **par               tomo parameter structure 
+%       **scans           - list of loaded scan numbers 
+%       **tomo_id         - indetification number of the sample, default = []
+%       **plot_angles     - plot loaded angles, default == true 
+%   *returns*
+%       ++par               tomo parameter structure 
+%       ++angles            loaded angles 
+
+function [par,  angles] = load_angles_aps_bnp(par, scans, plot_angles)
+    warning on
+    Nscans = length(scans);
+    angles = nan(Nscans,1);
+    hasAngle = ones(Nscans,1);
+    %{
+    if isfield(par,par.angle.filesuffix) && ~isempty(par.angle.filesuffix)
+        file_suffix = par.angle.filesuffix;
+    else
+        file_suffix = '.mda'; %default for velociprobe data outputs
+    end
+    %}
+    file_suffix = '.mda'; %default for velociprobe data outputs
+    
+    %%
+    wb = waitbar(0,'1','Name','Loading ptycho-tomo projection angles...',...
+        'CreateCancelBtn','setappdata(gcbf,''canceling'',1)');
+    setappdata(wb,'canceling',0);
+    for i=1:Nscans
+         % Check for clicked Cancel button
+        if getappdata(wb,'canceling')
+            break
+        end
+        scan_string_format = 'bnp_fly%04d';
+        %disp(scans(i))
+        filename = strcat(par.base_path, 'mda/',sprintf(scan_string_format, scans(i)),file_suffix);
+        if ~isempty(filename)
+            try
+                %disp(filename)
+                xx=mdaload(filename);
+                a=(getfield(getfield(xx,'extra'),'pvs'));
+            	angles(i) = getfield(a(9),'values');
+                status = [sprintf(par.scan_string_format, scans(i)), ' angle = ',num2str(angles(i))];
+            catch
+                disp(['Reading angle failed for ', sprintf(par.scan_string_format, scans(i))]);
+                %disp(strcat('Check angle h5path:',h5path))
+                status = ['Reading angle failed for ', sprintf(par.scan_string_format, scans(i))];
+            end
+        else
+            hasAngle(i) = 0;
+            disp(['No angle found for ',sprintf(par.scan_string_format, scans(i))])
+            status = ['No angle found for ',sprintf(par.scan_string_format, scans(i))];
+
+        end
+        
+        % Update waitbar and message
+        %waitbar(i/Nscans,wb,sprintf(par.scan_string_format, scans(i)))
+        waitbar(i/Nscans,wb,status)
+        
+    end
+    delete(wb)
+
+    
+    % legacy code - read angles from processed h5 files
+    %{ 
+    for i=1:Nscans
+        file = find_projection_files_names_aps(par, scans(i));
+        if ~isempty(file)
+            angles(i) = h5read(file,'/angle');
+        else
+            hasAngle(i) = 0;
+            disp(strcat('No angle found for scan ',num2str(scans(i))))
+        end
+    end
+    %}
+    %% process angles
+    % remove scan without angle
+    angles = angles(hasAngle==1);
+    scans = scans(hasAngle==1);
+
+    % remove duplicted scan numbers 
+    [~,ind] = unique(scans, 'last');   % take the !last! occurence of the scan, assume that the second measurement was better 
+    angles = angles(ind);    % Angles not repeated in scan
+    scans = scans(ind);
+    %subtomos = subtomos(ind);
+
+    % take only unique angles, measure uniqueness
+    if par.remove_duplicated_angles 
+        [~,ind] = unique(angles, 'last');   % take the !last! occurence of the angle, assume that the second measurement was better 
+        if length(angles) ~= length(ind)
+            warning('Removed %i duplicated angles', length(angles) - length(ind))
+        end
+    else
+        [~,ind] = sort(angles);     
+    end
+    angles = angles(ind);    % Angles not repeated in scan
+    scans = scans(ind);
+    %subtomos = subtomos(ind);
+
+    if isfield(par,'angle_offset') && par.angle_offset ~=0 
+        angles = angles + par.angle_offset;  % avoid the angles to be too well aligned with pixels, ie avoid exact angles 0, 90, 180, ... 
+    end
+    
+    par.scanstomo = scans;
+    %par.subtomos = subtomos;
+
+    par.num_proj=numel(par.scanstomo);
+    [anglessort,indsortangle] = sort(angles);
+    
+    if par.sort_by_angle
+        angles = angles(indsortangle);
+        par.scanstomo = par.scanstomo(indsortangle);
+        %par.subtomos = par.subtomos(indsortangle);
+    else  % sort by scan number 
+        [~,indsortscan] = sort( par.scanstomo);
+        angles = angles(indsortscan);
+        par.scanstomo = par.scanstomo(indsortscan);
+        %par.subtomos = par.subtomos(indsortscan);
+    end
+
+    if par.verbose_level && plot_angles
+        plotting.smart_figure(1);
+        subplot(2,1,1)
+        plot(par.scanstomo,angles,'ob'); grid on; 
+        xlim(par.scanstomo([1,end]))
+        %legend('Tilt angles')
+        xlabel('Scan #')
+        ylabel('Tilt angles')
+
+        subplot(2,1,2)
+        plot(diff(anglessort))
+        ylabel('Angle increment')
+        %title('Angular spacing'); 
+        grid on; 
+        xlim([1,par.num_proj-1])
+        if par.windowautopos
+            screensize = get( groot, 'Screensize' );
+            win_size = [946 815]; 
+            set(gcf,'Outerposition',[139 min(163,screensize(4)-win_size(2))  win_size]);  %[left, bottom, width, height]
+        end
+        title('Measured angles')
+        drawnow 
+    end
+end