Get rid of some id19 functions, import the others

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@794 4c865b51-4357-4376-afb4-474e03ccb993

5_reconstruction/gtMakeHSTParfile.m

@@ -47,11 +47,11 @@ if isfield(acq,'scantype')
         scanrange=180;
     end
 elseif isfield(acq,'type')
-        if strcmp(acq.type,'360degree') || strcmp(acq.type,'360')
-            scanrange=360;
-        else
-            scanrange=180;
-        end
+    if strcmp(acq.type,'360degree') || strcmp(acq.type,'360')
+        scanrange=360;
+    else
+        scanrange=180;
+    end
 else
     disp('can not read scan range');
     return;
@@ -71,14 +71,13 @@ if ~isfield(acq,'interlaced_turns') || acq.interlaced_turns==0
     par.last=num2str(acq.nproj-1);
 	par.prefix=sprintf('%s/1_preprocessing/abs/abs',acq.dir);
     par.angle_between_projections=num2str(scanrange/2/acq.nproj);   %quick fix (2*acq.nproj) wolfgang 04/2008
-else if acq.interlaced_turns==1
-        par.last=num2str((acq.interlaced_turns+1)*acq.nproj-1); 
-		par.prefix=sprintf('%s/1_preprocessing/abs/abs_renumbered',acq.dir);
-        par.angle_between_projections=num2str(scanrange/((acq.interlaced_turns+1)*acq.nproj))
-    else
-        disp('to be adjsuted')
-        return
-    end
+elseif acq.interlaced_turns==1
+    par.last=num2str((acq.interlaced_turns+1)*acq.nproj-1); 
+	par.prefix=sprintf('%s/1_preprocessing/abs/abs_renumbered',acq.dir);
+    par.angle_between_projections=num2str(scanrange/((acq.interlaced_turns+1)*acq.nproj));
+else
+    disp('to be adjusted');
+    return;
 end
 % fin modif sabine
 par.image_pixel_size_1=num2str(acq.pixelsize);
@@ -93,4 +92,6 @@ par.end_voxel_2=num2str(acq.bb(3));
 par.end_voxel_3=num2str(acq.bb(4));
 par.output_file=sprintf('%s/%s.vol',acq.dir,acq.name);
 
-par_write(par);
+par.zeroclipvalue = acq.zeroclipvalue;
\ No newline at end of file
+
+gtHSTParamWriter(par);

initialise_gt.m

@@ -134,6 +134,7 @@ function initialise_gt(ignore_id19)
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_GVF'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Help'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ICP'));
+    addpath(fullfile(GT_MATLAB_HOME, 'zUtil_ID19'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Imaging'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Imaging', 'pmedf'));
     addpath(fullfile(GT_MATLAB_HOME, 'zUtil_Indexter'));

zUtil_Distortion/distortion_example.m

@@ -12,8 +12,8 @@ distortion=distortion_read('shifts_12_sfit56.dat');
 %   distortion.y = horizontal (!!) displacement field  
 
 % read your weird EDFs here
-im=edfread('holeX_corrected_Z0.edf');
-
+im=edf_read('holeX_corrected_Z0.edf');
+im=im';
 % correct them like this (image and distortion maps have to be of the same type!)
 
 turns = 50

zUtil_ID19/correlate.m

+% function c=correlate(z1,z2,varargin)
+% 
+% looks for the maximum correlation between z1 and z2
+% 
+% c=correlate(z1,z2,flag)
+% flag should be zero if z1 and z2 are in real (default)       space
+%                one                      reciprocal
+% 
+% c=correlate(z1,z2,flag,size_part)
+% limits de maximum displacement to a given value (default: no limit)
+%                               
+% uses fourier transformation to calculate the cross-correlation between z1 and z2
+% searches the maximum trough interpolation between the pixels
+% max is max of parabol through 9 points around the abs. max
+% result is c=[row column]
+% z2 should go column columns to the right (or z1 column columns to the left)
+% z2 should go row rows down (or z1 row rows up)
+% to compensate drift: interpolate(z2,row,column)
+% 
+% see also INTERPOLATE, TRANSLATE
+% 
+% origin: peter
+
+function c=correlate(z1,z2,varargin)
+
+switch nargin
+case 2
+	flag=0;
+	part=0;
+case 3
+	flag=varargin{1};
+	part=0;
+case 5
+	flag=varargin{1};
+	if isempty(flag)
+		flag=0;
+	end
+	part=1;
+	part_pos = varargin{2};
+	part_size = varargin{3};
+end
+
+
+[n m]=size(z1);
+
+if flag
+	% matrices are fft'ed
+	cc=abs(ifft2(z1.*conj(z2)));
+else
+	% matrices are not fft'ed
+	cc=abs(ifft2(fft2(z1).*conj(fft2(z2))));
+end %if
+
+if part
+	part_pos=round(part_pos);
+	if (length(part_size)==1)
+		part_size(2) = part_size(1);
+	end
+	w=zeros(size(z1));
+	
+% 	w([n-part_size:n 1:1+part_size],[m-part_size:m 1:1+part_size])=1;
+	w(mod(-part_size(1)+part_pos(1):part_size(1)+part_pos(1),n)+1,mod(-part_size(2)+part_pos(2):part_size(2)+part_pos(2),m)+1)=1;
+	cc=cc.*w-1e20.*(1-w);
+end
+
+
+[a,b]=max(cc);
+[d,c(2)]=max(a);
+c(1)=b(c(2));
+
+c=c+min2par(cc([mod(c(1)-2,n)+1 c(1) mod(c(1),n)+1],[mod(c(2)-2,m)+1 c(2) mod(c(2),m)+1]));
+c=rem(c+ceil([n/2 m/2])-[2 2],[n m])-ceil([n/2 m/2])+[1 1];
+
+
+% subfunctions
+%-------------------------
+function mi=min2par(arg)
+
+[X,Y]=meshgrid(-1:1,-1:1);
+r=Y(:);
+c=X(:);
+xt=quad2func(r,c);
+a=xt\arg(:);
+mi=[-a(2) -a(3)]/[2*a(5) a(4);a(4) 2*a(6)];
+
+%-------------------------
+% function xt=quad2func(x,y)
+% quadratic function of 2 parameters x and y
+% size(xt)=[n 6] with n the number of observations
+% for functions linear in the parameters:
+% z = xt*a with size(a)=[6 1]
+% i.e. z=a(1)+a(2)*x+a(3)*y+a(4)*x.*y+a(5)*x.^2+a(6)*y.^2
+% if one has n observations given by z (size(z)=[n 1])
+% the least squares estimation of a is
+% a=xt\z;
+
+
+function xt=quad2func(x,y)
+
+xt=[ones(size(x)) x y x.*y x.^2 y.^2];

zUtil_ID19/correlate1.m

+% function c=correlate1(z1,z2)
+% looks for the shift giving maximum correlation between (column) vectors z1 and z2
+% uses Fourier transformation to calculate the cross-correlation between z1 and z2
+% searches the maximum trough interpolation between the pixels
+% uses parabolic fit around the absolute maximum
+% result is c
+% z2 should go c rows down (or z1 c rows up)
+% to correct use interpolate1(f)(z2,c)
+% if z1 and z2 are matrices the correlation is determined between the corresponding columns
+%
+% may not work for very short vectors (length 3 and so on)
+% length of the vectors should be even
+%
+% assumes that the shift is less then half the number of rows of z1
+% returns NaN if not successful for a given row
+%
+% origin: peter
+%
+% see also INTERPOLATE1, CORRELATE
+
+function c=correlate1(z1,z2)
+
+[n,m]=size(z1);
+% m is the number of columns in z1 (and z2)
+% n is the number of rows in z1
+if rem(n,2)
+	disp('Please use an even number of rows in correlate1!')
+	return
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%   Calculation of cross-correlation function  %%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+cc=abs(ifft(fft(z1).*conj(fft(z2))));
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%   Determination maximum of cc function       %%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% starting from absolute maximum
+[a,c]=max(cc);
+
+% translation of the zero displacement to the center of the vector because this is where the maximum will be
+% to avoid to look at start and end of the vector
+c=rem(c+n/2-1,n)+1;
+cc=roll(cc,n/2,0);
+
+% parabolic fit using w points around the maximum to go sub-pixel
+w=3;
+wb=floor((w-1)/2);
+we=ceil((w-1)/2);
+xt=quadfunc((1:w)');
+xt2=xt'*xt;
+for k=1:m 
+	if (c(k)-wb<1)|(c(k)+we>n)
+		disp(sprintf('Correlation was not successful for row %d',m))
+		c(k)=NaN;
+	else
+		a=xt2\(xt'*cc(c(k)-wb:c(k)+we,k));
+		c(k)=c(k)+(-a(2)/2/a(3));
+	end
+end
+
+% correction for translation made
+c=c-n/2-2-wb;
+
+
+
+
+
+
+
+
+
+

zUtil_ID19/findshifts3.m

+function findshifts2(varargin);
+% function shift=findshifts(im1,im2)
+% allows to to determine visually the relative shift between two images
+% KEYS:
+% arrows (cursor keys) - one pixel shift
+% shift-arrows - ten pixel shift
+% 1 (2)  - increase (decrease) image contrast
+% 3 (4)  - increase (decrease) image brightness
+%
+% press    t       to toggle between images
+% press    s       to return to to image subtraction mode
+% press    z       to select graphically a region of interest (4 times oversampling)
+% press    r       to return to full image')
+% press  enter     to accept current value')
+% 
+% OTHER STARTUP OPTIONS
+% findshifts2(im1,im1,parameter,value)
+% where parameter and value pairs can be:
+%   'roix',[minimum maximum]  - set the horizontal region of interest
+%   'roiy',[minimum maximum]  - vertical ROI
+%   'clims',[minimum maximum] - preset the colour limits
+%   'precorrelate','yes'      - attempt to correlate the images before
+%                               interaction
+
+% origin: Wolfgang  12/05
+  warning('off','Images:initSize:adjustingMag');
+  %% startup
+  app=[];
+  app.view.h=figure; % create a new figure
+  app.mode='subtract';
+  app.togglestate=true;
+  app.vshift=0;
+  app.hshift=0;
+  app.voffset=0;
+  app.hoffset=0;
+  app.rot=0;
+  app.zoom=1;
+  app.view.h=gcf;
+  app.clims=[-0.1 0.1];
+  app.climt=[0 1];
+  app.clima=[0 2];
+  app.im0=varargin{1};
+ 
+  app.im1=varargin{2};
+  app.im1nr=app.im1;
+  app.roix=[1 size(app.im0,2)];
+  app.roiy=[1 size(app.im0,1)];
+  app.precorrelate='off';
+  app.block='off';
+  app.quit=0;
+  app.firsttime=true;
+  if nargin>2
+    if iscell(varargin{3})
+      app=parse_pv_pairs(app,varargin{3});
+    else
+      app=parse_pv_pairs(app,{varargin{3:end}});
+    end
+  end
+  % precrop the image 
+  app.im0=app.im0(app.roiy(1):app.roiy(2),app.roix(1):app.roix(2));
+  app.im1=app.im1(app.roiy(1):app.roiy(2),app.roix(1):app.roix(2));
+  
+  % then pre-correlate if requested
+  if strcmpi(app.precorrelate,'yes') || strcmpi(app.precorrelate,'on')
+    fprintf('Pre-correlating images\n')
+
+    tmp=correlate(app.im0,app.im1);
+    app.voffset = tmp(1);app.hoffset=tmp(2);
+  end
+  
+  set(app.view.h,'KeyPressFcn',@sfKeyPress)
+  %  help(mfilename)
+  iptsetpref('imtoolinitialmagnification','fit')
+  sfUpdateFigure;
+  if strcmp(app.block,'on')
+    % if user wants nothing to return until findshift is finished
+    while 1
+      drawnow
+      if app.quit==1
+        break
+      end
+    end
+  end
+
+function sfKeyPress(varargin)
+  c=varargin{2};
+  switch c.Key
+    case 'uparrow'    
+      if strcmp(c.Modifier,'shift')
+        app.vshift=app.vshift+10/app.zoom;
+      else
+        app.vshift=app.vshift+1/app.zoom;
+      end
+      sfUpdateFigure;
+
+    case 'downarrow'
+      if strcmp(c.Modifier,'shift')
+        app.vshift=app.vshift-10/app.zoom;
+      else
+        app.vshift=app.vshift-1/app.zoom;
+      end
+      sfUpdateFigure;
+    
+    case 'rightarrow'
+      if ~isempty(c.Modifier)
+	  if strcmp(c.Modifier,'shift')
+        app.hshift=app.hshift+10/app.zoom;
+	  elseif strcmp(c.Modifier,'control')
+		app.rot=app.rot+1;
+		app.im1=imrotate(app.im1nr,app.rot,'bicubic','crop');
+		
+	  elseif strcmp(c.Modifier,{'shift' 'control'})
+		app.rot=app.rot+0.1;
+		app.im1=imrotate(app.im1nr,app.rot,'bicubic','crop');
+	    
+	  end	
+      else
+        app.hshift=app.hshift+1/app.zoom;
+      end
+      sfUpdateFigure;
+
+    case 'leftarrow'
+      if ~isempty(c.Modifier)
+	  if strcmp(c.Modifier,'shift')
+        app.hshift=app.hshift-10/app.zoom;
+	  elseif strcmp(c.Modifier,'control')
+		app.rot=app.rot-1;
+		app.im1=imrotate(app.im1nr,app.rot,'bicubic','crop');
+		
+	  elseif strcmp(c.Modifier,{'shift' 'control'})
+		app.rot=app.rot-0.1;
+		app.im1=imrotate(app.im1nr,app.rot,'bicubic','crop');
+		
+	  end
+	  else
+        app.hshift=app.hshift-1/app.zoom;
+      end
+      sfUpdateFigure;
+    
+    case 'return'
+      %exit interactive mode and return current shift
+      set(app.view.h,'KeyPressFcn','');
+      assignin('base','shift',[app.vshift+app.voffset app.hshift+app.hoffset app.rot]);
+      fprintf('Shift is: [%.2fv %.2fh]\n',app.vshift+app.voffset,app.hshift+app.hoffset);
+      app.quit=1;
+      return;
+
+    case 'a'
+      disp('changing to adding mode');
+      app.mode='add';
+      sfUpdateFigure;
+
+    case '1'
+      disp('Increasing contrast')
+      switch app.mode
+        case 'subtract'
+          app.clims=app.clims*0.9;
+          disp(sprintf('clim is %f %f',app.clims(1),app.clims(2)));
+        case 'toggle'
+          app.climt=app.climt*0.95;
+          disp(sprintf('clim is %f %f',app.climt(1),app.climt(2)));
+        case 'add'
+          app.clima=app.clima*0.9;
+          disp(sprintf('clim is %f %f',app.clima(1),app.clima(2)));
+      end
+      sfUpdateFigure;
+      
+    case '2'
+      disp('Decreasing contrast')
+      switch app.mode
+        case 'subtract'
+          app.clims=app.clims*1.1;
+          disp(sprintf('clim is %f %f',app.clims(1),app.clims(2)));
+        case 'toggle'
+          app.climt=app.climt*1.05;
+          disp(sprintf('clim is %f %f',app.climt(1),app.climt(2)));
+        case 'add'
+          app.clima=app.clima*1.1;
+          disp(sprintf('clim is %f %f',app.clima(1),app.clima(2)));
+      end
+      sfUpdateFigure;
+    case '3'
+      disp('Colormap brighter')
+      switch app.mode
+        case 'subtract'
+          app.clims=app.clims-max(app.clims)*0.1;
+          disp(sprintf('clim is %f %f',app.clims(1),app.clims(2)));
+        case 'toggle'
+          app.climt=app.climt-mean(app.climt)*0.05;
+          disp(sprintf('clim is %f %f',app.climt(1),app.climt(2)));
+        case 'add'
+          app.clima=app.clima-mean(app.clima)*0.1;
+          disp(sprintf('clim is %f %f',app.clima(1),app.clima(2)));
+      end
+      sfUpdateFigure;
+    case '4'
+      disp('Colormap darker')
+      switch app.mode
+        case 'subtract'
+          app.clims=app.clims+max(app.clims)*0.1;
+          disp(sprintf('clim is %f %f',app.clims(1),app.clims(2)));
+        case 'toggle'
+          app.climt=app.climt+mean(app.climt)*0.05;
+          disp(sprintf('clim is %f %f',app.climt(1),app.climt(2)));
+        case 'add'
+          app.clima=app.clima+mean(app.clima)*0.1;
+          disp(sprintf('clim is %f %f',app.clima(1),app.clima(2)));
+      end
+      sfUpdateFigure;
+    case 's'
+      disp('changing to subtraction mode');
+      app.mode='subtract';
+      app.clim=app.clims;
+      sfUpdateFigure;
+    case 'z'
+      disp('Select region of interest');
+      title('Select region of interest');
+      [toto,r]=imcrop;
+      disp('Zooming...')
+      title('Zooming...')
+      r=round(r);
+      sfZoom(r)
+      sfUpdateFigure;
+    case 'r'
+      disp('reset full image');
+      app.zoom=1;
+      app.im0=app.orig0;
+      app.im1=app.orig1;
+      app.vshift=round(app.vshift+app.voffset);
+      app.hshift=round(app.hshift+app.hoffset);
+      app.voffset=0;
+      app.hoffset=0;
+      sfUpdateFigure;
+    case 't'
+      app.mode='toggle';
+      app.togglestate= not(app.togglestate);
+      app.clim=app.climt;
+      sfUpdateFigure;
+    case 'h'
+      help(mfilename)
+  end
+
+end
+
+
+
+function sfZoom(roi)
+  
+  app.orig0=app.im0;
+  app.orig1=app.im1;
+  app.zoom=4;
+  app.im0=imresize(imcrop(app.im0,roi),4,'bicubic');
+  app.im1=imresize(imcrop(app.im1,[roi(1)-app.hshift,roi(2)-app.vshift,roi(3),roi(4)]),4,'bicubic');
+  app.voffset=app.vshift;
+  app.hoffset=app.hshift;
+  app.vshift=0;
+  app.hshift=0;
+end
+
+function sfUpdateFigure
+  colormap gray;
+  im_tmp=roll(app.im1,app.vshift*app.zoom,app.hshift*app.zoom);
+  switch app.mode
+    case 'add'
+      imshow(app.im0+im_tmp,app.clima);
+      title(sprintf('vertical shift: %.2f\t horizontal shift: %.2f',app.vshift+app.voffset,app.hshift+app.hoffset));
+    case 'subtract'
+      %imagesc(app.im0-im_tmp,app.clims);
+      if app.firsttime
+        app.h_im=imshow(app.im0-im_tmp,app.clims);
+        %app.firsttime=false;
+      else
+        set(app.h_im,'cdata',app.im0-im_tmp)
+        set(get(app.h_im,'parent'),'clim',app.clims);
+      end
+%      keyboard
+%      axis image
+      title(sprintf('vertical shift: %.2f\t horizontal shift: %.2f',app.vshift+app.voffset,app.hshift+app.hoffset));
+    case 'toggle'
+      if app.togglestate == true
+        imagesc(app.im0,app.climt);
+        axis image
+        title('first image (fixed position)');
+      else
+        imagesc(im_tmp,app.climt);
+        axis image
+        title(sprintf('second image: vertical shift: %.2f\t horizontal shift: %.2f, rotation: %.2f',app.vshift+app.voffset,app.hshift+app.hoffset,app.rot));
+      end
+  end
+  drawnow
+end
+
+
+
+end
+

zUtil_ID19/fwhm.m

+% function [y,f]=fwhm(cc,c)
+% looks for the maximum around the position given by c
+% y corresponds to position of  maximum
+% f corresponds to fwhm (no background)
+% m corresponds to the maximum (parabolic fit)
+%
+  
+function [y,f,m]=fwhm(cc,varargin)
+
+switch nargin
+case 1
+	[m,c]=max(cc);
+case 2
+	c=varargin{1};
+end
+
+
+w=3;
+wb=floor((w-1)/2);
+we=ceil((w-1)/2);
+xt=quadfunc((1:w)');
+xt2=xt'*xt;
+
+a=xt2\(xt'*cc(c-wb:c+we));
+y=c+(-a(2)/2/a(3))-wb-1;
+m=(a(1)-a(2)^2/4/a(3))/2;
+
+% looking for left crossing of half of maximum
+index=floor(y);
+while cc(index)>m
+	index=index-1;
+end
+yl=index+(m-cc(index))/(cc(index+1)-cc(index));
+
+% looking for right crossing of half of maximum
+index=ceil(y);
+while cc(index)>m
+	index=index+1;
+end
+yr=index-(m-cc(index))/(cc(index-1)-cc(index));	
+
+f=yr-yl;	
+m=2*m;
+

zUtil_ID19/interpolatef.m

+% function r=interpolate1f(p,r,c)
+% interpolates each column of p according to the translation-fault given by fault (column vector)
+% a positive fault corresponds to translating down the column
+% method for interpolation is Fourier-transformation
+% supposes periodic signals for the edges
+
+function r=interpolatef(p,r,c)
+
+[n m]=size(p);
+
+r=real(ifft2(fft2(p).*translate(r,c,n,m)));

zUtil_ID19/quadfunc.m

+% function x=quadfunc(arg)
+% used by correlate1, ...
+% for implementing parabolic fit
+% returns x=[ones(length(arg),1) arg arg.^2];
+% origin: peter
+
+function x=quadfunc(arg)
+
+x=[ones(length(arg),1) arg arg.^2];

zUtil_ID19/roll.m

+% function rm=roll(matrix,r,c)
+% cycles a matrix (or vector) r rows down and c columns to the right
+% rm(i,j)=rm(i-r,j-c)
+% origin: peter
+
+function rm=roll(matrix,r,c)
+[n,m]=size(matrix);
+
+
+if r>0
+      rm=[matrix(n-r+1:n,:) ; matrix(1:n-r,:)];
+elseif r<0
+      rm=[matrix(1-r:n,:) ; matrix(1:-r,:)];
+else
+      rm=matrix;
+end
+
+if c>0
+      rm=[rm(:,m-c+1:m) rm(:,1:m-c)];
+elseif c<0
+      rm=[rm(:,1-c:m) rm(:,1:-c)];
+end
+
+
+
+
+
+
+
+

zUtil_ID19/translate.m

+% function t=translate(r,c,n,m)
+% creates matrix for interpolation using Fourier-transformation
+% r: translation in the direction of the rows, positive is down
+% c: translation in the direction of the columns, positive is to the right
+% n: number of rows in the resulting matrix
+% m: number of columns in the resulting matrix
+% if an image im(x1,x2) must be translated of r and c in direction x1 and x2
+% one can use:
+% fft2( im(x1-r,x2-c) ) = translate(r,c,n,m) .* fft2( im(x1,x2) )
+% or
+% im(x1-r,x2-c) = real( ifft2( translate(r,c,n,m) .* fft2( im(x1,x2) ) ) 
+% real is to avoid a small imaginary part in the result (only for real images)
+% origin: peter
+
+function t=translate(r,c,n,m)
+
+
+f=r*2*pi/n*(0:floor(n/2))';
+f=cos(f)-i*sin(f);
+%f=exp(-i*f);
+f=repmat([f;flipud(conj(f(2:ceil(n/2))))],1,m);
+
+g=c*2*pi/m*(0:floor(m/2));
+g=cos(g)-i*sin(g);
+%g=exp(-i*g);
+g=repmat([g fliplr(conj(g(2:ceil(m/2))))],n,1);
+
+t=f.*g;

zUtil_ID19/utilExtractFilenameParts.m

+function parts=utilExtractFilenameParts(fname)
+% UTILEXTRACTFILENAMEPARTS.M
+% Given a filename, extracts the prefix, index, and extension
+% Greg Johnson, May 2006
+%
+% Bugs: only deals with files having four or five digits in the number
+% see fileparts for a more general purpose tool
+
+% used to have . after \w*).
+
+pattern='(?<prefix>\w*)(?<index>\d{4,5}+).(?<extension>\w*)';
+parts=regexp(fname,pattern,'names');
+try
+    parts.index=str2num(parts.index);
+catch
+end

zUtil_ID19/utilStripExtensionandFormat.m

+function [fnameroot,fnameformatstring,fnameextension]=utilStripExtensionandFormat(full_fname)
+% removes, if necessary, the .edf extension of a file name
+  if strcmpi(full_fname(end-3:end),'.edf')
+      fname=full_fname(1:end-4);
+  else
+    fname=full_fname;
+  end
+  [fnameroot,fnameformatstring]=sfStripFormatting(fname);
+  fnameextension='.edf';
+end
+  
+
+function [root,fmt]=sfStripFormatting(fname)
+% removes, if it can, any formatting at the end of the fname (%04d, for example)
+
+ndx=find(fname=='%');
+if ndx
+  root=fname(1:ndx-1);
+  fmt=fname(ndx:end);
+else
+  root=fname;
+  fmt='';
+end
+end

zUtil_TomoUtils/gtHSTParamWriter.m

@@ -116,7 +116,9 @@ if isfield(par, 'prefix')
     fprintf(fid, 'DO_AXIS_CORRECTION = %s # Axis correction\n', par.correct_axis);
     fprintf(fid, 'AXIS_CORRECTION_FILE = %s\n', par.correct_axis_file);
     fprintf(fid, 'OPTIONS= { ''padding'':''%s'' , ''axis_to_the_center'':''%s''} # Padding and position axis\n', par.padding, par.axis_to_the_center);
-    fprintf(fid, 'ZEROCLIPVALUE = %s # Minimum value of radiographs after flat / before log\n', par.zeroclipvalue);
+    if isfield(par, 'zeroclipvalue')
+        fprintf(fid, 'ZEROCLIPVALUE = %s # Minimum value of radiographs after flat / before log\n', par.zeroclipvalue);
+    end
 
     fprintf(fid, '\n# Parameters defining output file / format\n');
     fprintf(fid, 'OUTPUT_FILE = %s\n', par.output_file);