Changed: Made many changes for octave compatibility.

Fixed:   Corrected wrong arguments in sprintf command in
         cat_main_updateSPM1639.m
Fixed:   Contrasts were sometimes not recognized in cat_spm_results_ui.m because
         we have to go into the analysis folder.
Fixed:   Clipping should be ignored for cat_vol_slice_overlay if lower and upper
         clipping values are equal.
Fixed:   Figure in cat_vol_slice_overlay_ui.m was set to unvisible.

Changed paths:
 M CHANGES.txt
 M cat_io_cprintf.m
 M cat_io_xml.m
 M cat_main_reportfig.m
 M cat_main_reportstr.m
 M cat_main_updateSPM1639.m
 M cat_run.m
 M cat_spm_results_ui.m
 M cat_stat_check_cov_old.m
 M cat_surf_createCS2.m
 M cat_surf_results.m
 M cat_vbdist.c
 M cat_vol_approx.m
 M cat_vol_slice_overlay.m
 M compile.m
 M spm_cat12.m

CHANGES.txt

@@ -1,4 +1,33 @@
 ------------------------------------------------------------------------
+r2166 | gaser | 2023-01-22 23:40:08
+
+Changed paths:
+ M CHANGES.txt
+ M cat_io_cprintf.m
+ M cat_io_xml.m
+ M cat_main_reportfig.m
+ M cat_main_reportstr.m
+ M cat_main_updateSPM1639.m
+ M cat_run.m
+ M cat_spm_results_ui.m
+ M cat_stat_check_cov_old.m
+ M cat_surf_createCS2.m
+ M cat_surf_results.m
+ M cat_vbdist.c
+ M cat_vol_approx.m
+ M cat_vol_slice_overlay.m
+ M compile.m
+ M spm_cat12.m
+
+Changed: Made many changes for octave compatibility.
+Fixed:   Corrected wrong arguments in sprintf command in 
+         cat_main_updateSPM1639.m
+Fixed:   Contrasts were sometimes not recognized in cat_spm_results_ui.m because
+         we have to go into the analysis folder.
+Fixed:   Clipping should be ignored for cat_vol_slice_overlay if lower and upper 
+         clipping values are equal.
+Fixed:   Figure in cat_vol_slice_overlay_ui.m was set to unvisible.
+------------------------------------------------------------------------
 r2164 | gaser | 2023-01-14 21:46:06
 
 Changed paths:

cat_io_cprintf.m

@@ -215,7 +215,7 @@
   end
   % The following is for debug use only:
   %global docElement el debugData
-  if ~exist('el','var') || isempty(el),  el=handle([]);  end  %#ok mlint short-circuit error ("used before defined")
+  if ~strcmpi(spm_check_version,'octave') && (~exist('el','var') || isempty(el)),  el=handle([]);  end  %#ok mlint short-circuit error ("used before defined")
   if nargin<1, showDemo(majorVersion,minorVersion); return;  end
   if isempty(style),  return;  end
   % #### begin extended styles ####

cat_io_xml.m

@@ -52,28 +52,6 @@
 % ______________________________________________________________________
 
   onlyxml = 0; 
-  if strcmpi(spm_check_version,'octave')
-    pkglist = pkg('list'); 
-    if isempty(pkglist) || all( strfind( [pkglist{:}.name] , 'io') == 0 )  
-      pkg install -forge io
-    end
-    pkg load io
-    try 
-      % add java files
-      xmljava{1} = fullfile(fileparts(mfilename('fullpath')),'Octave','xercesImpl.jar'); 
-      xmljava{2} = fullfile(fileparts(mfilename('fullpath')),'Octave','xml-apis.jar'); 
-      % call them
-      for xi=1:numel(xmljava), eval(sprintf('javaaddpath("%s");',xmljava{xi})); end
-      % test function 
-      xmlread;
-    catch e
-      if strcmp(e.message,'xmlread: no Java JRE or JDK detected, exiting')
-        onlyxml = 1; 
-      end
-    end
-
-  end
-
 
 
   verbose = 0;
@@ -188,8 +166,9 @@
       try
         if usejava('jvm')
           xml_write(file,S);
-        elseif strcmpi(spm_check_version,'octave') && ~onlyxml
-          xmlwrite(file,S);
+        elseif strcmpi(spm_check_version,'octave')
+          warning off all
+          savexml(file,'S');
         end
       catch %#ok<*NASGU> % can write xml file??
         % This can be a warning as far as we have the mat.
@@ -211,8 +190,8 @@
             try
               if usejava('jvm')
                 S = xml_read(file);
-              elseif strcmpi(spm_check_version,'octave') && ~onlyxml
-                S = xmlread(file);
+              elseif strcmpi(spm_check_version,'octave')
+                S = loadxml(file);
               end
             catch 
               error('MATLAB:cat_io_xml:write+ReadErr','Can''t read XML-file ''%s'' for update!\n',file);
@@ -223,8 +202,8 @@
         try
           if usejava('jvm')
             S = xml_read(file);
-          elseif strcmpi(spm_check_version,'octave') && ~onlyxml
-            S = xmlread(file);
+          elseif strcmpi(spm_check_version,'octave')
+            S = loadxml(file);
           end
         catch 
           error('MATLAB:cat_io_xml:write+ReadErr','Can''t read XML-file ''%s'' for update!\n',file);
@@ -248,8 +227,9 @@
       try
         if usejava('jvm')
           xml_write(file,S);
-        elseif strcmpi(spm_check_version,'octave') && ~onlyxml
-          xmlwrite(file,S);
+        elseif strcmpi(spm_check_version,'octave')
+          warning off all
+          savexml(file,'S');
         end
       catch 
         warning('MATLAB:cat_io_xml:writeErr','Can''t write XML-file ''%s''!\n',file);
@@ -271,7 +251,7 @@
           if usejava('jvm')
             S = xml_read(file);
           elseif strcmpi(spm_check_version,'octave') 
-            S = xmlread(file);
+            S = loadxml(file);
           end
           warning on
         catch 

cat_main_reportfig.m

@@ -970,7 +970,7 @@ function cat_main_reportfig(Ym,Yp0,Yl1,Psurf,job,qa,res,str)
       % CAT atlas labeling
       LAB = job.extopts.LAB;
       NS  = @(Ys,s) Ys==s | Ys==s+1;
-      if job.extopts.report.useoverlay>1
+      if job.extopts.report.useoverlay>1 && ~strcmpi(spm_check_version,'octave')
         try spm_orthviews('window',hhp0,[0 2]); end
         V2 = VO;
         switch job.extopts.report.useoverlay

cat_main_reportstr.m

@@ -63,8 +63,8 @@
 % red version in case of old version?
   % 1 line: Matlab, SPM12, CAT12 version number and GUI and experimental mode 
   if strcmpi(spm_check_version,'octave')
-    str{1} = [str{1} struct('name', 'Version: OS / Octave / SPM12 / CAT12:','value',...
-      sprintf('%s / %s / %s / %s (%s)',qa.software.system,qa.software.version_octave,...
+    str{1} = [str{1} struct('name', 'Version: OS / SPM12 / CAT12:','value',...
+      sprintf('%s / %s / %s (%s)',qa.software.system,...
       qa.software.version_spm,qa.software.version_cat,catv))];
     % native2unicode is working on the command line but not in the figure
     cub = '^3';

cat_main_updateSPM1639.m

@@ -94,7 +94,7 @@
     abs(diff(res.spmP0.hsti(1:2:3,:))) ./ max(eps,sum(res.spmP0.hsti(1:2:3,:))); 
     ]));
   res.spmP0.help = [res.spmP0.help; {
-    sprintf('The hsti is the histogram of the T1 image for each class (prob>%0.2%%,%d buckets) ',minprob/255,hbuckets)};
+    sprintf('The hsti is the histogram of the T1 image for each class (prob>%0.2f,%d buckets) ',minprob/255,hbuckets)};
     'that are combined into the average intensity difference between classes histidiff with 1 for the ideal case without overlap and 0 for high overlap. '];
   if job.extopts.expertgui>1 && res.spmP0.hstidiff<0.5
       cat_io_addwarning('cat_main_updateSPM:highIntOverlapBetweenClasses',...

cat_run.m

@@ -1006,18 +1006,6 @@
   end
 
 
-  if strcmpi(spm_check_version,'octave') && job.extopts.regstr > 0
-    warning('cat_run:noShooting','No Shooting registration possible under Octave yet. Switch to Dartel registration.')
-    job.extopts.regstr = 0; 
-    if isfield(job.extopts,'regmethod')
-      job.extopts.regmethod = rmfield(job.extopts.regmethod,'shooting');
-    else
-      job.extopts = rmfield(job.extopts,'shooting');
-    end
-    job.extopts.dartel.darteltpm = cat_get_defaults('extopts.darteltpm');
-  end
-
-
   %% set Dartel/Shooting templates
   if isfield(job.extopts,'regmethod') 
     if isfield(job.extopts.regmethod,'dartel')

cat_spm_results_ui.m

@@ -294,8 +294,9 @@
       if exist(fullfile(fileparts(fileparts(mfilename('fullpath'))),'TFCE'),'dir')
         [spmmatfile, sts] = spm_select(1,'^SPM\.mat$','Select SPM.mat');
         swd = spm_file(spmmatfile,'fpath');
+        cd(swd)
         warning off
-        load(fullfile(swd,'SPM.mat'),'SPM','xSPM');
+        load('SPM.mat','SPM','xSPM');
         warning on
 
         [Ic,xCon] = spm_conman(SPM,'T&F',Inf,'    Select contrast(s)...','',1);

cat_stat_check_cov_old.m

@@ -1,4 +1,4 @@
-function varargout = cat_stat_check_cov(job)
+function varargout = cat_stat_check_cov_old(job)
 %cat_stat_check_cov. To check covariance across sample.
 %
 % Images have to be in the same orientation with same voxel size

cat_surf_createCS2.m

@@ -54,7 +54,7 @@
   cstime = clock; 
 
   if strcmpi(spm_check_version,'octave')
-    cat_io_addwarning('cat_surf_createCS:noSRP','Correction of surface collisions is not yet available under Octave.',2,[1 1])
+    cat_io_addwarning('cat_surf_createCS2:noSRP','Correction of surface collisions is not yet available under Octave.',2,[1 1])
     opt.SRP = 0; 
   end
 

cat_surf_results.m

@@ -127,7 +127,7 @@
     end
 
     % close old figures
-    if ishandle(12),close(12);end;if ishandle(21),close(21);end;
+    if ishandle(12),close(12);end;if ishandle(22),close(22);end;
 
     % remove any existing data
     if exist('H','var')
@@ -205,7 +205,7 @@
       'ovmin',  [0.050 0.125 0.425 0.100],'ovmax',   [0.525 0.125 0.425 0.100],... 
       'save',   [0.050 0.050 0.425 0.050],'close',   [0.525 0.050 0.425 0.050]);
 
-    H.figure = figure(22);
+    H.figure = figure(23);
     clf(H.figure);
 
     set(H.figure, 'MenuBar', 'none', 'Position', H.pos{1}.fig, ...
@@ -1847,8 +1847,8 @@ function disphist(type)
   OV.reference_range = [0.2 1.0];                        
 end
 
-% clipping if defined
-if ~isempty(H.clip)
+% clipping if (meaningful) defined
+if ~isempty(H.clip) && H.clip(2) ~= H.clip(3)
   if ~isnan(H.clip(2)) && ~isnan(H.clip(3))
     OV.clip = H.clip(2:3);
   else
@@ -1914,7 +1914,8 @@ function disphist(type)
 end
 
 % show MIP and keep position if window exists
-OV.fig = 21;
+OV.fig = 22;
+
 if ishandle(OV.fig)
   cat_vol_slice_overlay(OV);
 else
@@ -2805,19 +2806,19 @@ function select_data(obj, event_obj, P)
     P0{i} = Pout; 
     H.isvol(i) = 1;
     H.Pvol{i} = Pvol;
-    H.Pvol_sel = Pvol;
     vol = spm_read_vols(spm_vol(Pvol));
-    H.Pvol_mn{i} = min(vol(:));
-    H.Pvol_mx{i} = max(vol(:));
+    H.Pvol_mn{i} = min(vol(vol ~= 0));
+    H.Pvol_mx{i} = max(vol(vol ~= 0));
 
     % print warning if no SPM.mat file was found
-    if ~exist(fullfile(pp, 'SPM.mat'), 'file') || ~exist(fullfile(pp, 'vSPM.mat'), 'file')
+    if ~exist(fullfile(pp, 'SPM.mat'), 'file') && ~exist(fullfile(pp, 'vSPM.mat'), 'file')
       fprintf('Warning: Please ensure that %s is spatially registered to the new MNI152NLin2009cAsym template space.\n',[ff ee]);
     end
   else
     P0{i} = deblank(P(i,:));
   end
 end
+H.Pvol_sel = H.Pvol{1};
 
 P0   = char(P0);
 info = cat_surf_info(P0,0);

cat_vbdist.c

@@ -150,7 +150,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
     /* such as cat_run_job.APRGs:196 where the old call "Ymx  = Ybgd./(Ybd+Ybgd);" was working but 
      * the new version caused a treshold in an image with INF that lead to an empty brainmask 
      * Although, this can be solved by "Ymx  = min(1,Ybgd./(Ybd+Ybgd));" I do not know other 
-     * problematic call now and this should maybe change later. 
+     * problematic call now and this should maybe changed later. 
      */
     if (L[i]>=0.5) D[i]=0.0; else D[i]=FLT_MAX; 
     if (L[i]>255.0)  

cat_vol_approx.m

@@ -199,7 +199,7 @@
   PM{1} = (cat_vbdist(PM{1},true(size(PM{1})),[1.5 1 1]) + ...
           cat_vol_smooth3X(rand(PTsize)*20,2) + cat_vol_smooth3X(randn(PTsize)*20)) <PTsize(1)/2; 
 
-  ds('d2','',[1 1 1],PT{1},PT{2},PT{1}.*PM{1},PT{2}.*PM{1},32)
+  ds('d2','',[1 1 1],PT{1},PT{2},PT{1}.*PM{1},PT{2}.*PM{1},32);
 
 
   %%

cat_vol_slice_overlay.m

@@ -77,7 +77,7 @@
 end
 
 % clip colorbar
-if isfield(OV,'clip') && all(isfinite(OV.clip))
+if isfield(OV,'clip') && all(isfinite(OV.clip)) && OV.clip(2) ~= OV.clip(1)
   ncol = length(OV.cmap);
   col_step = (OV.range(2) - OV.range(1)) / ncol;
   cmin = max([1, ceil((OV.clip(1) - OV.range(1)) / col_step)]);
@@ -409,7 +409,7 @@
     'PaperPositionMode', 'auto', ...
     'NumberTitle', 'off', ...
     'Name', nm, ...
-    'Visible', 'off');
+    'Visible', 'on');
 
 SO.figure = h;
 SO.area.units = 'pixels';
@@ -938,7 +938,7 @@
 corners = T * [vcorners; ones(1, 8)];
 
 SO.slices = spm_input('Slices to display (mm)', '+1', 'e', XYZ_unique{orientn});
-SO.figure = figure(21);
+SO.figure = figure(22);
 
 % and do the display
 if dispf, slice_overlay; end

compile.m

@@ -94,9 +94,12 @@
       'cat_sanlm.c sanlm_float.c'
     };
     % internal c-functions
-    nc{2} = {
-      'cat_vol_cMRegularizarNLM3D.c'
-    };
+    % does not yet work for octave
+    if  ~strcmpi(spm_check_version,'octave')
+        nc{2} = {
+        'cat_vol_cMRegularizarNLM3D.c'
+      };
+    end
     rc   = cell(1,2);   % results of c-function comiling
     rcc  = cell(1,2);   % results of c-function comiling
     nce  = cell(1,2);   % number of errors

spm_cat12.m

@@ -39,7 +39,11 @@ function spm_cat12(varargin)
 try
   feval(@cat_sanlm,single(rand(6,6,6)),1,3);
 catch
-  if ismac 
+  if strcmpi(spm_check_version,'octave')
+    cd(pth)
+    compile
+    feval(@cat_sanlm,single(rand(6,6,6)),1,3);
+  elseif ismac 
     CATDir = fullfile(catdir);
     web('https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)#Troubleshooting');
     cat_io_cmd(sprintf('\nThe following commands will be executed as administrator to allow execution of CAT12 binaries and mex-files.\n Please now type admin password to call sudo\n'),'warning');