refactor

Author: Remi-Gau

demos/MoAE/moae_03_slice_display.m

@@ -31,15 +31,25 @@
 
 opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
 
+opt.subjects = [subLabel];
+
 % read the model
 opt = checkOptions(opt);
 
-opt.results = opt.model.bm.Nodes{1}.Model.Software.bidspm.Results{1};
+iRes = 1;
+
+opt.results = opt.model.bm.Nodes{iRes}.Model.Software.bidspm.Results{1};
+
+node = opt.model.bm.Nodes{iRes};
+[opt, BIDS] = checkMontage(opt, iRes, node, struct([]), subLabel);
 
 opt = checkOptions(opt);
 
+opt.results(iRes).montage = setMontage(opt.results(iRes));
+
 % we get the con image to extract data
 ffxDir = getFFXdir(subLabel, opt);
+
 maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
 bf = bids.File(spm_file(maskImage, 'filename'));
 conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
@@ -48,9 +58,12 @@
 layers = sd_config_layers('init', {'truecolor', 'dual', 'contour'});
 
 % Layer 1: Anatomical map
-[anat_normalized_file, anatRange] = return_normalized_anat_file(opt, subLabel);
-layers(1).color.file = anat_normalized_file;
-layers(1).color.range = [0 anatRange(2)];
+layers(1).color.file = opt.results(iRes).montage.background{1};
+
+hdr = spm_vol(layers(1).color.file);
+[max_val, min_val] = slover('volmaxmin', hdr);
+layers(1).color.range = [0 max_val];
+
 layers(1).color.map = gray(256);
 
 %% Layer 2: Dual-coded layer

demos/MoAE/return_normalized_anat_file.m

@@ -0,0 +1,70 @@
+function [opt, BIDS] = checkMontage(opt, iRes, node, BIDS, subLabel)
+  % 
+  % Check values for create a slice montage.
+  % 
+  % Set default values if they are missing.
+  %
+  % USAGE::
+  %
+  %   [opt, BIDS] = checkMontage(opt, iRes, node, BIDS, subLabel)
+  %
+  %
+
+  % (C) Copyright 2019 bidspm developers
+
+  if nargin < 4
+    BIDS = '';
+    subLabel = '';
+  end
+
+  if isfield(opt.results(iRes), 'montage') && any(opt.results(iRes).montage.do)
+
+    background = opt.results(iRes).montage.background;
+
+    % TODO refactor with getInclusiveMask
+    if isstruct(background)
+
+      if ismember(lower(node.Level), {'run', 'session', 'subject'})
+
+        if isempty(BIDS)
+          BIDS =  bids.layout(opt.dir.preproc, ...
+                              'use_schema', false, ...
+                              'index_dependencies', false, ...
+                              'filter', struct('sub', {opt.subjects}));
+        end
+
+        background.sub = subLabel;
+        background.space = opt.space;
+        file = bids.query(BIDS, 'data', background);
+
+        if iscell(file)
+          if isempty(file)
+            % let checkMaskOrUnderlay figure it out
+            file = '';
+
+          elseif numel(file) == 1
+            file = file{1};
+
+          elseif numel(file) > 1
+            file = file{1};
+
+            msg = sprintf('More than 1 overlay image found for %s.\n Taking the first one.', ...
+                          bids.internal.create_unordered_list(background));
+            id = 'tooManyMontageBackground';
+            logger('WARNING', msg, 'id', id, 'options', opt, 'filename', mfilename());
+          end
+
+        end
+
+        background = file;
+
+      end
+
+    end
+
+    background = checkMaskOrUnderlay(background, opt, 'background');
+    opt.results(iRes).montage.background = background;
+
+  end
+  
+end

src/stats/results/checkMontage.m

@@ -547,62 +547,3 @@
   matlabbatch{end}.result = result;
 
 end
-
-function [opt, BIDS] = checkMontage(opt, iRes, node, BIDS, subLabel)
-
-  if nargin < 4
-    BIDS = '';
-    subLabel = '';
-  end
-
-  if isfield(opt.results(iRes), 'montage') && any(opt.results(iRes).montage.do)
-
-    background = opt.results(iRes).montage.background;
-
-    % TODO refactor with getInclusiveMask
-    if isstruct(background)
-
-      if ismember(lower(node.Level), {'run', 'session', 'subject'})
-
-        if isempty(BIDS)
-          BIDS =  bids.layout(opt.dir.preproc, ...
-                              'use_schema', false, ...
-                              'index_dependencies', false, ...
-                              'filter', struct('sub', {opt.subjects}));
-        end
-
-        background.sub = subLabel;
-        background.space = opt.space;
-        file = bids.query(BIDS, 'data', background);
-
-        if iscell(file)
-          if isempty(file)
-            % let checkMaskOrUnderlay figure it out
-            file = '';
-
-          elseif numel(file) == 1
-            file = file{1};
-
-          elseif numel(file) > 1
-            file = file{1};
-
-            msg = sprintf('More than 1 overlay image found for %s.\n Taking the first one.', ...
-                          bids.internal.create_unordered_list(background));
-            id = 'tooManyMontageBackground';
-            logger('WARNING', msg, 'id', id, 'options', opt, 'filename', mfilename());
-          end
-
-        end
-
-        background = file;
-
-      end
-
-    end
-
-    background = checkMaskOrUnderlay(background, opt, 'background');
-    opt.results(iRes).montage.background = background;
-
-  end
-
-end