* Use progress bar instead of listing files in Normalise:Write (impro…

…vements still required for 4D files) * Allow syntax: spm_check_registration img1.nii img2.nii img3.nii * Highlight current volume when using spm_orthviews' browser plugin SVN r5700
spm · Oct 17, 2013 · 8cdf53b · 8cdf53b
1 parent 977f72b
commit 8cdf53b
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Showing 6 changed files with 213 additions and 174 deletions.
diff --git a/config/spm_cfg_norm.m b/config/spm_cfg_norm.m
diff --git a/config/spm_run_norm.m b/config/spm_run_norm.m
@@ -7,9 +7,10 @@
 % Output:
 % out    - computation results, usually a struct variable.
 %__________________________________________________________________________
-% Copyright (C) 2005-2011 Wellcome Trust Centre for Neuroimaging
+% Copyright (C) 2005-2013 Wellcome Trust Centre for Neuroimaging
+
+% $Id: spm_run_norm.m 5700 2013-10-17 14:59:50Z guillaume $
 
-% $Id: spm_run_norm.m 5261 2013-02-19 16:37:37Z john $
 
 for i=1:numel(job.subj)
 
@@ -85,25 +86,24 @@ function write_norm(job)
 defs.out{1}.pull.mask    = 1;
 defs.out{1}.pull.fwhm    = [0 0 0];
 
-for i=1:numel(job.subj),
+for i=1:numel(job.subj)
     defs.out{1}.pull.fnames = job.subj(i).resample;
     if ~isfield(job.subj(i),'def')
-        defs.comp{1}.def  = {spm_file(char(job.subj(i).vol), 'prefix','y_', 'ext','.nii')};
+        defs.comp{1}.def = {spm_file(char(job.subj(i).vol), 'prefix','y_', 'ext','.nii')};
     else
-        defs.comp{1}.def  = job.subj(i).def;
+        defs.comp{1}.def = job.subj(i).def;
     end
 
     Nii = nifti(defs.comp{1}.def);
-    vx = sqrt(sum(Nii.mat(1:3,1:3).^2));
-    o  = Nii.mat\[0 0 0 1]';
-    o  = o(1:3)';
-    dm = size(Nii.dat);
-    bb = [-vx.*(o-1) ; vx.*(dm(1:3)-o)];
+    vx  = sqrt(sum(Nii.mat(1:3,1:3).^2));
+    o   = Nii.mat\[0 0 0 1]';
+    o   = o(1:3)';
+    dm  = size(Nii.dat);
+    bb  = [-vx.*(o-1) ; vx.*(dm(1:3)-o)];
 
     defs.comp{2}.idbbvox.vox = job.woptions.vox;
     defs.comp{2}.idbbvox.bb  = job.woptions.bb;
     defs.comp{2}.idbbvox.vox(~isfinite(defs.comp{2}.idbbvox.vox)) = vx(~isfinite(defs.comp{2}.idbbvox.vox));
     defs.comp{2}.idbbvox.bb(~isfinite(defs.comp{2}.idbbvox.bb)) = bb(~isfinite(defs.comp{2}.idbbvox.bb));
     spm_deformations(defs);
 end
-
diff --git a/spm_check_registration.m b/spm_check_registration.m
@@ -1,7 +1,7 @@
-function spm_check_registration(images, captions, varargin)
+function spm_check_registration(varargin)
 % A visual check of image registration quality
 % FORMAT spm_check_registration
-% FORMAT spm_check_registration(images, captions)
+% FORMAT spm_check_registration(images)
 % Orthogonal views of one or more images are displayed. Clicking in
 % any image moves the centre of the orthogonal views. Images are
 % shown in orientations relative to that of the first selected image.
@@ -12,28 +12,55 @@ function spm_check_registration(images, captions, varargin)
 % Copyright (C) 1997-2013 Wellcome Trust Centre for Neuroimaging
 
 % John Ashburner
-% $Id: spm_check_registration.m 5360 2013-03-27 13:59:27Z guillaume $
+% $Id: spm_check_registration.m 5700 2013-10-17 14:59:50Z guillaume $
 
+SVNid = '$Rev: 5700 $';
 
-SVNid = '$Rev: 5360 $';
-
-if ~nargin
+%-Get input
+%--------------------------------------------------------------------------
+if nargin
+    if nargin > 1 && iscellstr(varargin{2})
+        images = varargin{1};
+    elseif isstruct(varargin{1})
+        images = [varargin{:}];
+    else
+        images = char(varargin);
+    end
+else
     [images, sts] = spm_select([1 24],'image','Select images');
     if ~sts, return; end
 end
 
 if ischar(images), images = spm_vol(images); end
+images = images(1:min(numel(images),24));
 
+%-Print
+%--------------------------------------------------------------------------
 spm('FnBanner',mfilename,SVNid);                                        %-#
+exactfname  = @(f) [f.fname ',' num2str(f.n(1))];
 if desktop('-inuse')
-    dispf = @(f) sprintf('<a href="matlab:spm_image(''display'',''%s'');">%s</a>',f,f);
-else dispf = @(f) f;
+    href    = '<a href="matlab:%s;">%s</a>';
+    cmd     = 'spm_image(''display'',''%s'')';
+    dispone = @(f) sprintf(href,sprintf(cmd,f),f);
+    cmd     = 'spm_check_registration(%s)';
+    str     = [];
+    for i=1:numel(images)
+        str = [str sprintf('''%s'',',exactfname(images(i)))];
+    end
+    dispall = @(f) sprintf([' (' href ')  '],sprintf(cmd,str(1:end-1)),'all');
+else
+    dispone = @(f) f;
+    dispall = @(f) '        ';
 end
 for i=1:numel(images)
-    if i==1, fprintf('Display '); else fprintf('        '); end         %-#
-    fprintf('%s\n',dispf([images(i).fname ',' num2str(images(i).n(1))]));%-#
+    if i==1,     fprintf('Display ');                                   %-#
+    elseif i==2, fprintf('%s',dispall(images));
+    else         fprintf('        '); end
+    fprintf('%s\n',dispone(exactfname(images(i))));                     %-#
 end
 
+%-Display
+%--------------------------------------------------------------------------
 spm_figure('GetWin','Graphics');
 spm_figure('Clear','Graphics');
 spm_orthviews('Reset');
@@ -51,11 +78,13 @@ function spm_check_registration(images, captions, varargin)
         [j+ds/2 i+ds/2 w-ds h-ds]);
     if ij==1, spm_orthviews('Space'); end
     spm_orthviews('AddContext',handle);
-    if nargin > 1 && ~isempty(captions)
-        captions = cellstr(captions);
-        mn = numel(captions);
-        if ij <= mn
-            spm_orthviews('Caption', ij, captions{ij}, varargin{:});
-        end
-    end
+end
+
+%-Backward compatibility with spm_check_registration(images,captions)
+%--------------------------------------------------------------------------
+if nargin > 1 && iscellstr(varargin{2})
+    spm_orthviews('Caption',varargin{2}, varargin{3:end});
+    %for ij=1:numel(varargin{2})
+    %    spm_orthviews('Caption', ij, varargin{2}{ij}, varargin{3:end});
+    %end
 end
diff --git a/spm_deformations.m b/spm_deformations.m
@@ -8,10 +8,10 @@
 %
 % See spm_cfg_deformations.m for more information.
 %__________________________________________________________________________
-% Copyright (C) 2005-2012 Wellcome Trust Centre for Neuroimaging
+% Copyright (C) 2005-2013 Wellcome Trust Centre for Neuroimaging
 
 % John Ashburner
-% $Id: spm_deformations.m 5668 2013-10-03 18:34:18Z guillaume $
+% $Id: spm_deformations.m 5700 2013-10-17 14:59:50Z guillaume $
 
 
 [Def,mat] = get_comp(job.comp);
@@ -406,6 +406,7 @@
 end
 
 oM = zeros(4,4);
+spm_progress_bar('Init',numel(PI),'Resampling','volumes completed');
 for m=1:numel(PI)
 
     % Generate headers etc for output images
@@ -416,7 +417,7 @@
     j_range = 1:size(NI.dat,4);
     k_range = 1:size(NI.dat,5);
     l_range = 1:size(NI.dat,6);
-    if ~isempty(num),
+    if ~isempty(num)
         num = sscanf(num,',%d');
         if numel(num)>=1, j_range = num(1); end
         if numel(num)>=2, k_range = num(2); end
@@ -448,7 +449,7 @@
     NO.mat0        = mat;
     NO.mat_intent  = 'Aligned';
     NO.mat0_intent = 'Aligned';
-    if isempty(num),
+    if isempty(num)
         out{m}     = NO.dat.fname;
     else
         out{m}     = [NO.dat.fname, ',', num2str(num(1))]; 
@@ -462,8 +463,8 @@
 
     % Loop over volumes within the file
     %----------------------------------------------------------------------
-    fprintf('%s',nam);
-    for j=j_range,
+    %fprintf('%s',nam);
+    for j=j_range
 
         M0 = NI.mat;
         if ~isempty(NI.extras) && isstruct(NI.extras) && isfield(NI.extras,'mat')
@@ -472,16 +473,16 @@
                 M0 = M1(:,:,j);
             end
         end
-        M   = inv(M0);
+        M  = inv(M0);
         if ~all(M(:)==oM(:))
             % Generate new deformation (if needed)
             Y     = affine(Def,M);
         end
-        oM  = M;
+        oM = M;
         % Write the warped data for this time point
         %------------------------------------------------------------------
-        for k=k_range,
-            for l=l_range,
+        for k=k_range
+            for l=l_range
                 C   = spm_diffeo('bsplinc',single(NI.dat(:,:,:,j,k,l)),intrp);
                 dat = spm_diffeo('bsplins',C,Y,intrp);
                 if job.mask
@@ -491,12 +492,14 @@
                     spm_smooth(dat,dat,krn); % Side effects
                 end
                 NO.dat(:,:,:,j,k,l) = dat;
-                fprintf('\t%d,%d,%d', j,k,l);
+                %fprintf('\t%d,%d,%d', j,k,l);
             end
         end
     end
-    fprintf('\n');
+    %fprintf('\n');
+    spm_progress_bar('Set',m);
 end
+spm_progress_bar('Clear');
 
 
 %==========================================================================

diff --git a/spm_orthviews.m b/spm_orthviews.m
@@ -151,7 +151,7 @@
 % Copyright (C) 1996-2013 Wellcome Trust Centre for Neuroimaging
 
 % John Ashburner et al
-% $Id: spm_orthviews.m 5542 2013-06-11 17:31:00Z guillaume $
+% $Id: spm_orthviews.m 5700 2013-10-17 14:59:50Z guillaume $
 
 
 % The basic fields of st are:
@@ -275,6 +275,17 @@
         redraw_all
 
     case 'caption'
+        if ~isnumeric(varargin{1})
+            varargin{1} = cellstr(varargin{1});
+            xlh = NaN(numel(varargin{1}),1);
+            for i=1:numel(varargin{1})
+                h = spm_orthviews('Caption',i,varargin{1}{i},varargin{3:end});
+                if ~isempty(h), xlh(i) = h; end
+            end
+            varargout{1} = xlh;
+            return;
+        end
+
         vh = valid_handles(varargin{1});
         nh = numel(vh);
 

diff --git a/spm_orthviews/spm_ov_browser.m b/spm_orthviews/spm_ov_browser.m
@@ -9,7 +9,7 @@
 % Copyright (C) 2013 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: spm_ov_browser.m 5585 2013-07-19 15:50:44Z guillaume $
+% $Id: spm_ov_browser.m 5700 2013-10-17 14:59:50Z guillaume $
 
 
 cmd = lower(varargin{1});
@@ -199,6 +199,10 @@ function browser_profile(hObj,event)
 end
 
 plot(hAx,Y);
+hold(hAx,'on')
+i =round(get(hS,'value'));
+plot(hAx,i,Y(i),'r*');
+hold(hAx,'off');
 ylabel(hAx,sprintf('[%.2f %.2f %.2f]',pos));
 st.vols{hC}.browser.fun = @browser_profile;
 st.vols{hC}.browser.h = hObj;