kleine aenderungen im template

examples/template_tomo_analysis_GINIX.m

@@ -29,16 +29,9 @@ addpath(genpath(toolboxPath));
 
 %% Add ASTRA-toolbox to path
 if ispc
-    astraPath = 'S:/Projects_X-ray_Imaging/holotomotoolbox/ASTRAToolbox/windows';
+    astraPath = 'S:/Projects_X-ray_Imaging/ASTRAToolbox/windows';
 elseif isunix
-    computerName = char(java.net.InetAddress.getLocalHost.getHostName);
-    % If name is of the form 'santa0.roentgen.physik.uni-goettingen.de',
-    % only take prefix until first point:
-    pointIdx = strfind(computerName, '.');
-    if ~isempty(pointIdx)
-        computerName = computerName(1:pointIdx(1)-1);
-    end
-    astraPath = ['/IRP/AG_Salditt/Projects_X-ray_Imaging/ASTRAToolbox/', computerName];
+    astraPath = '/IRP/AG_Salditt/Projects_X-ray_Imaging/ASTRAToolbox/linux';
 end    
 
 if ~exist(astraPath,'dir')
@@ -90,13 +83,15 @@ switch(lower(detector))
         dx = 6.5e-6;
 end
 
-fileName = [dataPath,'/',filePrefix,fileEnding];
-dumpName = [dataPath,'/dump/',filePrefix,dumpEnding];
+fileName = [filePrefix,fileEnding];
+dumpName = [filePrefix,dumpEnding];
 
+getFileName = @(number) fullfile(dataPath, sprintf(fileName,number));
+getDumpName = @(number) fullfile(dataPath,'dump',sprintf(dumpName,number));
 
 %% Read one image to check if path is correct
 number = 100;
-raw0 = imageReader(sprintf(fileName,number));
+raw0 = imageReader(getFileName(number));
 
 showImage(raw0);
 colormap gray
@@ -149,13 +144,13 @@ darknum = flatFilenum(2,end,end)+1:flatFilenum(2,end,end)+numDarks;
 fprintf('... please check flat, projection and dark... \n' ) ;
 
 for iii = 1 : numDistances
-    tmp = imageReader(sprintf(fileName,flatFilenum(1,iii,1)));
+    tmp = imageReader(getFileName(flatFilenum(1,iii,1)));
     showImage(tmp);
     title('Is this a flatfield? (Y- enter) (N - Ctr+c)')
     colormap gray
     pause()
     
-    tmp = imageReader(sprintf(fileName,projFilenum(iii,1)));
+    tmp = imageReader(getFileName(projFilenum(iii,1)));
     showImage(tmp);
     title('Is this a projection? (Y- enter) (N - Ctr+c)')
     colormap gray
@@ -163,7 +158,7 @@ for iii = 1 : numDistances
     
 end
 
-tmp = imageReader(sprintf(fileName,darknum(1)));
+tmp = imageReader(getFileName(darknum(1)));
 showImage(tmp);
 title('Is this a darkfield? (Y- enter) (N - Ctr+c)')
 colormap gray
@@ -179,7 +174,7 @@ for indDistance = 1:numDistances
     for indEmpty = 1:size(flatFilenum,1)
         emptyTmp = zeros([size(raw0,1),size(raw0,2),numFlats], 'single');
         for indImg = 1:numFlats
-            emptyTmp(:,:,indImg) = imageReader(sprintf(fileName,flatFilenum(indEmpty,indDistance,indImg)));
+            emptyTmp(:,:,indImg) = imageReader(getFileName(flatFilenum(indEmpty,indDistance,indImg)));
             fprintf('.');
         end
         % take median of all emptys
@@ -194,7 +189,7 @@ fprintf('... read darkfields... \n' ) ;
 
 darkTmp = zeros(size(raw0,1),size(raw0,2),numDarks);
 for indImg = 1:numDarks
-    darkTmp(:,:,indImg) = imageReader(sprintf(fileName,darknum(indImg)));
+    darkTmp(:,:,indImg) = imageReader(getFileName(darknum(indImg)));
     fprintf('.');
 end
 % take median of all darkfield images
@@ -208,7 +203,7 @@ fprintf('... calculate geometry parameters... \n' ) ;
 % Read defocus distances from dump files
 stx = zeros([1,numDistances]);
 for distIdx = 1:numDistances
-    stx(distIdx) = wwas(sprintf(dumpName,projFilenum(distIdx,2)),xmotor);
+    stx(distIdx) = wwas(getDumpName(projFilenum(distIdx,2)),xmotor);
 end
 
 % calculate derived parameters: (suffixes 'x' and 'y' account for
@@ -223,20 +218,20 @@ z12x = z02-z01x;
 z12y = z02-z01y;
 %
 % magnifications
-Mx = z02/z01x;
-My = z02/z01y;
+Mx = z02./z01x;
+My = z02./z01y;
 %
 % effective distance between object and detetor
-z_effx = z12x/Mx;
-z_effy = z12y/My;
+z_effx = z12x./Mx;
+z_effy = z12y./My;
 %
 % effective pixel size
-dxeffx = dx/Mx;
-dxeffy = dx/My;
+dxeffx = dx./Mx;
+dxeffy = dx./My;
 %
 % Fresnel numbers in the effective geometry
-Fx = dxeffx.^2/(z_effx*lambda);
-Fy = dxeffy.^2/(z_effy*lambda);
+Fx = dxeffx.^2./(z_effx*lambda);
+Fy = dxeffy.^2./(z_effy*lambda);
 
 
 % Magnifications and Fresnel numbers for all defocus distances (columns), 
@@ -247,10 +242,10 @@ F = [Fy(:).'; Fx(:).'];
 
 %% Read, rescale and align holograms
 
-% which distances should be read
+% Which distances should be read?
 distToUse = 1:numDistances;      
 
-% Settings for alignment of the different defocussed images. See
+% Settings for alignment of the different defocused images. See
 % documentation of rescaleDefocusSeries for details and additional options
 alignSettings = rescaleDefocusSeries;
 alignSettings.alignMethod = 'dftregistration';
@@ -264,7 +259,7 @@ ctfsettingsAlign.betaDeltaRatio = 1/10;
 ctfsettingsAlign.lim2 = 0.1;
 alignSettings.ctfsettings = ctfsettingsAlign;
 
-
+% no changes below this point
 fprintf('... reading holograms... \n' ) ;
 holograms = zeros([size(raw0,1), size(raw0,2), numel(distToUse), numAngles], 'single');
 thetas = zeros([numAngles,1]);
@@ -282,7 +277,7 @@ parfor indProj = 1:numAngles
         emptyInterpolated = a*empty(:,:,indDistance,1)+(1-a)*empty(:,:,indDistance,2);
         
         % read in data and perform empty beam correction
-        tmp = imageReader(sprintf(fileName,projFilenum(indDistance,indProj)));
+        tmp = imageReader(getFileName(projFilenum(indDistance,indProj)));
         tmpCorr=(tmp-dark)./(emptyInterpolated-dark);
         
         % remove hot pixels
@@ -292,7 +287,7 @@ parfor indProj = 1:numAngles
     
     % read rotation angle
     if indProj~=1
-        thetas(indProj) = wwas(sprintf(dumpName,projFilenum(distToUse(1),indProj)),'stzrot');
+        thetas(indProj) = wwas(getDumpName(projFilenum(distToUse(1),indProj)),'stzrot');
     else
         thetas(indProj)=0;
     end
@@ -312,16 +307,14 @@ end
 %% Show all holograms for a random tomographic angle to check results
 projIdx = randi(numAngles);
 for jj = 1:size(holograms,3)
-    figure; showImage(holograms(:,:,jj,projIdx));
+    showImage(holograms(:,:,jj,projIdx));
+    colormap gray
+    pause(1)
 end
 
-
 %% Show full tomographic data set for first distance to check results
 figure; showStack(squeeze(holograms(:,:,1,:)));
 
-
-
-
 %% OPTIONAL: delete corrupted holograms due to missing wedge from data
 missingWedge = [];      % Enter range of corrupted holograms here
 holograms(:,:,:,missingWedge) = [];