Updated the use of the new version of gtModifyStructure to a general list of...

Updated the use of the new version of gtModifyStructure to a general list of options to be checked with user...
Only FED code is missing from this update...

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

5_reconstruction/gtSetupAssembleVolume.m

@@ -9,22 +9,14 @@ par.list                    = [];            % if list is [], load all grains.
 par.display_error_messages  = true;          % show error messages
 
 % check with user
-list{1,1} = 'savefilename';
-list{1,2} = 'filename to save volume (goes into 5_reconstruction/)';
-
-list{2,1} = 'overlaps';
-list{2,2} = 'how to treat overlapping grain labels ("zeros" or "summed")';
-
-list{3,1} = 'add_to_filename';
-list{3,2} = 'to add grains to an existing reconstruction (filename, path/filename)';
-
-list{4,1} = 'list';
-list{4,2} = 'list of grains to add to volume, or "all"';
-
-list{5,1} = 'display_error_messages';
-list{5,2} = 'display error messages?';
-
-par = gtModifyStructure(par, list);
+list = cell(0,4);
+list(end+1,:) = [{'savefilename'},{'filename to save volume (goes into 5_reconstruction/)'},{'char'},{1}];
+list(end+1,:) = [{'overlaps'},{'how to treat overlapping grain labels ("zeros" or "summed")'},{'char'},{1}];
+list(end+1,:) = [{'add_to_filename'},{'to add grains to an existing reconstruction (filename, path/filename)'},{'char'},{1}];
+list(end+1,:) = [{'list'},{'list of grains to add to volume, or empty if "all" grains'},{'double'},{1}];
+list(end+1,:) = [{'display_error_messages'},{'display error messages?'},{'logical'},{1}];
+
+par = gtModifyStructure(par, list, [], 'Check with user:');
 
 if ~exist('update_cb', 'var')
     [output, redo_list] = GtAssembleVol3D('savefilename', par.savefilename, ...

zUtil_Indexter/gtSetupIndexing.m

@@ -43,44 +43,32 @@ else
 
     % Work through the various INDEXTER parameters
 
-    % Get parameters template
-    list = build_list_v2;
+    oplist = cell(0,4);
+    oplist(end+1,:) = [{'phase_ID'},{'Which phase should be indexed?'},{'double'},{1}];
+    oplist(end+1,:) = [{'input_file'},{'Use input file?'},{'logical'},{2}];
+    oplist(end+1,:) = [{'flag_update'},{'Update ''parameters.mat'', ''index.mat'', database with the results ?'},{'logical'},{3}];
+    oplist(end+1,:) = [{'flag_log'},{'Write log and output file with current date ?'},{'logical'},{3}];
+    oplist(end+1,:) = [{'forcemerge'},{'Run INDEXTER only merging grains as written in parameters.index.forcemerge'},{'logical'},{3}];
 
+    
     % Select phase to be indexed
+    options = [];
     options.phase_ID    = phase_id;
-    header = 'INDEXTER OPTIONS';
-
-
-    oplist{1,1} = 'phase_ID';
-    oplist{1,2} = 'Which phase should be indexed?';
-
-    options = gtModifyStructure(options, oplist, header);
-
+    options = gtModifyStructure(options, oplist, 1, 'INDEXTER options:');
+    % Input file name
+    fname = fullfile('4_grains',sprintf('phase_%02d',options.phase_ID),'index_input.mat');
 
-    % Update and log
+    % Update and log: check existence of file 'fname'
+    % TO DO: better handle the existence of input file?
+    options.input_file  = exist(fname,'file') == 2;
     options.flag_update = true;
     options.flag_log    = true;
+    options.forcemerge  = false;
 
-    % Input file name
-    fname = sprintf('4_grains/phase_%02d/index_input.mat',options.phase_ID);
-
-    if exist(fname,'file')
-        header = 'An input file already exists.';
-        options.input_file = true;
-        oplist{1,1} = 'input_file';
-        oplist{1,2} = 'Use input file?';
-        oplist{2,1} = 'flag_update';
-        oplist{2,2} = 'Update ''parameters.mat'', ''index.mat'', database with the results ?';
-        oplist{3,1} = 'flag_log';
-        oplist{3,2} = 'Write log and output file with current date ?';
-        options = gtModifyStructure(options, oplist, header);
+    if (options.input_file)
+        options = gtModifyStructure(options, oplist, [2 3], 'An input file already exists:');
     else
-        oplist{1,1} = 'flag_update';
-        oplist{2,2} = 'Update ''parameters.mat'', ''index.mat'', database with the results ?';
-        oplist{2,1} = 'flag_log';
-        oplist{2,2} = 'Write log and output file with current date ?';
-        options = gtModifyStructure(options, oplist);
-        options.input_file = false;
+        options = gtModifyStructure(options, oplist, 2, 'The input file does not exist:');
     end
 
     % Get parameters template
@@ -134,7 +122,7 @@ else
     check = inputwdefault('Start gtINDEXTER now? [y/n]', 'y');
     if strcmpi(check, 'y')
         gtINDEXTER(options.phase_ID, options.flag_update, ...
-            options.input_file, options.flag_log, 0, parameters);
+            options.input_file, options.flag_log, options.forcemerge, parameters);
     end
 
 end % end of function