fixing grain Thresholing on OAR; couple of small fixes

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

1_preprocessing/gtFillCrystFields.m

@@ -370,8 +370,8 @@ function cryst = sfUpdateReflections(cryst, energy)
 	cryst.thetasp = asind(0.5*lambda./cryst.dspacingsp);
 	
 	% Update the intensity info: MISSING !
-	cryst.int   = ones(1, numel(cryst.dspacing);
-	cryst.intsp = ones(1, numel(cryst.dspacingsp);
-    cryst.usedfam = true(1, numel(cryst.dspacing);
+	cryst.int   = ones(1, numel(cryst.dspacing));
+	cryst.intsp = ones(1, numel(cryst.dspacingsp));
+    cryst.usedfam = true(1, numel(cryst.dspacing));
 end
 

1_preprocessing/gtFindRotationAxis.m

@@ -25,6 +25,7 @@ try
     name_next = fullfile(raw_data_dir, sprintf('%s%04d.edf', acq.name, indx_next) );
 
     if exist(name_next,'file')
+      sprintf('Using images AFTER scan for determination of rotation axis posistion\n')
         % FIRST CHOICE: IMAGES AFTER SCAN
       indx_curr = 2*acq.nproj;
 
@@ -32,6 +33,7 @@ try
       name_ref0 = fullfile(raw_data_dir, sprintf('ref0000_%04d.edf', indx_curr) );
       name_ref1 = name_ref0;
     else
+      sprintf('Using images DURING scan for determination of rotation axis posistion\n')
         % SECOND CHOICE: IMAGES DURING SCAN
       % WL May 2009
       % changed to use per default the images at end of scan - should be more accurate;

5_reconstruction/gtAstraReconstructGrain.m

@@ -31,6 +31,10 @@ function varargout = gtAstraReconstructGrain(grainID, phaseID, parameters)
         gr_extra = gtLoadGrain(phaseID, grainID, 'fields', {'selected'});
         gr.proj.selected = gr_extra.selected;
     end
+    if isempty(find(gr.proj.selected))
+        warning('No projection has been selected - skipping grain')
+        return
+    end
     gr.proj.num_iter = rec_opts.num_iter;
 
     gr.proj.stack = gr.proj.stack(:, gr.proj.selected, :);

5_reconstruction/gtChangeThreshold3D.m

-function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, parameters, varargin)
+function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, ~, varargin)
 % GTCHANGETHRESHOLD3D
 %     seg = gtChangeThreshold3D(firstID, lastID, ~, phaseID, varargin)
 %     ----------------------------------------------------------------
@@ -11,6 +11,9 @@ function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, paramete
 %       varargin = to modify parameters.rec
 %
 
+    args = struct('list', [], 'verbose', false);
+    args = parse_pv_pairs(args, varargin);
+
     if (isdeployed)
         global GT_DB
         global GT_MATLAB_HOME
@@ -23,14 +26,20 @@ function [varargout] = gtChangeThreshold3D(firstID, lastID, ~, phaseID, paramete
             warning('OAR:unexpected_behavior', ...
                 'We should expect only strings from shell environment')
         end
+
+        args.list = str2num(args.list); %#ok<ST2NM>
     end
+    % This handles OAR's habbit of passing lists of IDs in a field called
+    % 'list'
+    args.grain_ids = args.list;
+    args = rmfield(args, 'list');
 
-    args = [varargin, 'verbose', false];
+    args = [fieldnames(args), struct2cell(args)]';
     thresh = GtThreshold(args{:});
-    if (nargin >= 1)
+    if (nargout >= 1)
         varargout{1} = thresh.batchThreshold(phaseID, firstID, lastID);
     else
-        thresh.batchThreshold(phaseID, firstID, lastID)
+        thresh.batchThreshold(phaseID, firstID, lastID);
     end
 end
 

5_reconstruction/gtReconstructGrains.m

@@ -96,8 +96,12 @@ function gtReconstructGrains(first, last, workingdirectory, phaseID, parameters,
                 gtReconstructGrainOrientation(gr_id, phaseID, parameters);
         end
         if (~isdeployed)
-            t.singleGrainAutoThreshold(phaseID, gr_id);
-            fprintf(repmat('\b', [1 num_chars]))
+            try
+                t.singleGrainAutoThreshold(phaseID, gr_id);
+                fprintf(repmat('\b', [1 num_chars]))
+            catch
+                sprintf('Segmentation of grain %d failed - check reconstruction!', gr_id)
+            end
         end
     end
     fprintf('Done (in %f seconds).\n', toc(c))

5_reconstruction/gtSetupReconstruction.m

@@ -177,18 +177,7 @@ if (~isempty(conf.grain_ids))
                 launch_on_OAR('gtChangeThreshold3D', first, last, ...
                     phaseID_str, parameters, 'core', 4, 'distribute', true, 'list', conf.grain_ids);
             else
-                if isempty(conf.grain_ids)
-                    gtChangeThreshold3D(first, last, [], phase_id);
-                else
-                    t=GtThreshold();
-                    for i = 1 : numel(conf.grain_ids)
-                        if sample.phases{phase_id}.getSelected(conf.grain_ids(i))
-                            t.singleGrainAutoThreshold(phase_id, conf.grain_ids(i));
-                        else
-                            sprintf('skipping deselected grain %d\n',conf.grain_ids(i))
-                        end
-                    end
-                end
+                gtChangeThreshold3D(first, last, [], phase_id, [], 'list', conf.grain_ids);
             end
         end
     end

6_rendering/gtDrawGrainUnitCells.m

@@ -98,8 +98,9 @@ app.linecolor = app.linecolor(1:numel(grains));
 parameters = [];
 load('parameters.mat');
 labgeo  = parameters.labgeo;
+detgeo  = parameters.detgeo;
 if isempty(app.pxsize{1})
-    app.pxsize{1}  = (labgeo.pixelsizeu + labgeo.pixelsizev)/2;
+    app.pxsize{1}  = (detgeo.pixelsizeu + detgeo.pixelsizev)/2;
 end
 
 if isempty(app.hf)

zUtil_Indexter/gtINDEXMatchGrains.m

-function [match, dev, dcm, drotm, conflicts, toBeChecked] = gtINDEXMatchGrains(...
+function [match, dev, dcm, drotm, conflicts, toBeChecked, tol] = gtINDEXMatchGrains(...
                       grain1, grain2, ph1, dc, drot, tol)
 % GTINDEXMATCHGRAINS  Matches multiple indexed grains between two datasets; 
 %                     can also be used to find unmerged grains.
@@ -178,7 +178,7 @@ disp('Loading pixelsize and crystallographic info from parameters.mat ...')
 parameters = [];
 load parameters
 cryst   = parameters.cryst(ph1);
-pixsize = 0.5*(parameters.labgeo.pixelsizeu + parameters.labgeo.pixelsizev);
+pixsize = 0.5*(parameters.detgeo.pixelsizeu + parameters.detgeo.pixelsizev);
 
 
 match      = NaN(nof_grains1,2);
@@ -224,6 +224,10 @@ dev.rot = NaN(3,3,nof_grains1);
 % Extension to Rodrigues fundamental zone
 % Rext = 0;
 Rext = tol.Rdist;
+spacegroup = cryst.spacegroup;
+fzone_acc = gtCrystRodriguesFundZone(spacegroup,0);
+fzone_ext = gtCrystRodriguesFundZone(spacegroup,Rext);
+
 
 if (any(gtIndexAllGrainValues(grain1,'R_onedge',[],1,[])) || ~isempty(drot))
         

zUtil_Python/oar/oar_api.py

@@ -17,6 +17,7 @@ except ImportError as exc:
     from yaml import YamlLoader
 
 try:
+    raise ImportError('requests has been disabled')
     import requests
     from requests.exceptions import ConnectionError, HTTPError
     from urllib2 import URLError