[WIP] update transparent plotting demo

demos/MoAE/moae_03_slice_display.m

@@ -18,104 +18,15 @@
 
 this_dir = fileparts(mfilename('fullpath'));
 
-subLabel = '01';
-
 opt.pipeline.type = 'stats';
 
-opt.dir.raw = fullfile(this_dir, 'inputs', 'raw');
 opt.dir.derivatives = fullfile(this_dir, 'outputs', 'derivatives');
 opt.dir.preproc = fullfile(opt.dir.derivatives, 'bidspm-preproc');
 
-opt.dir.roi = fullfile(opt.dir.derivatives, 'bidspm-roi');
-opt.dir.stats = fullfile(opt.dir.derivatives, 'bidspm-stats');
-
 opt.model.file = fullfile(this_dir, 'models', 'model-MoAE_smdl.json');
 
-% Specify the result to compute
-opt.results(1).nodeName = 'run_level';
-
-opt.results(1).name = 'listening';
-% MONTAGE FIGURE OPTIONS
-opt.results(1).montage.do = true();
-opt.results(1).montage.slices = -4:2:16; % in mm
-% axial is default 'sagittal', 'coronal'
-opt.results(1).montage.orientation = 'axial';
-% will use the MNI T1 template by default but the underlay image can be changed.
-opt.results(1).montage.background = ...
-    fullfile(spm('dir'), 'canonical', 'avg152T1.nii');
+opt.subjects = {'01'};
 
 opt = checkOptions(opt);
 
-use_schema = false;
-BIDS_ROI = bids.layout(opt.dir.roi, 'use_schema', use_schema);
-
-filter = struct('sub', subLabel, ...
-                'hemi', 'R', ...
-                'desc', 'auditoryCortex');
-
-rightRoiFile = bids.query(BIDS_ROI, 'data', filter);
-
-filter.hemi = 'L';
-
-leftRoiFile = bids.query(BIDS_ROI, 'data', filter);
-
-% we get the con image to extract data
-ffxDir = getFFXdir(subLabel, opt);
-maskImage = spm_select('FPList', ffxDir, '^.*_mask.nii$');
-bf = bids.File(spm_file(maskImage, 'filename'));
-conImage = spm_select('FPList', ffxDir, ['^con_' bf.entities.label '.nii$']);
-
-%% Layers to put on the figure
-layers = sd_config_layers('init', {'truecolor', 'dual', 'contour', '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.map = gray(256);
-
-%% Layer 2: Dual-coded layer
-%
-%   - contrast estimates color-coded;
-
-layers(2).color.file = conImage;
-
-color_map_folder = fullfile(fileparts(which('map_luminance')), '..', 'mat_maps');
-load(fullfile(color_map_folder, 'diverging_bwr_iso.mat'));
-layers(2).color.map = diverging_bwr;
-
-layers(2).color.range = [-4 4];
-layers(2).color.label = '\beta_{listening} - \beta_{baseline} (a.u.)';
-
-%% Layer 2: Dual-coded layer
-%
-%   - t-statistics opacity-coded
-
-spmTImage = spm_select('FPList', ffxDir, ['^spmT_' bf.entities.label '.nii$']);
-layers(2).opacity.file = spmTImage;
-
-layers(2).opacity.range = [2 3];
-layers(2).opacity.label = '| t |';
-
-%% Layer 3 and 4: Contour of ROI
-
-layers(3).color.file = rightRoiFile{1};
-layers(3).color.map = [0 0 0];
-layers(3).color.line_width = 2;
-
-layers(4).color.file = leftRoiFile{1};
-layers(4).color.map = [1 1 1];
-layers(4).color.line_width = 2;
-
-%% Settings
-settings = sd_config_settings('init');
-
-% we reuse the details for the SPM montage
-settings.slice.orientation = opt.results(1).montage.orientation;
-settings.slice.disp_slices = -15:3:18;
-settings.fig_specs.n.slice_column = 4;
-settings.fig_specs.title = opt.results(1).name;
-
-%% Display the layers
-[settings, p] = sd_display(layers, settings);
+transparentMontage(opt);

src/bids_model/BidsModel.m

@@ -312,6 +312,7 @@
     end
 
     function results = getResults(obj)
+      %    return results from all nodes
 
       results = struct([]);
       idx = 1;

src/defaults/defaultResultsStructure.m

@@ -32,16 +32,16 @@
   %   load(fullfile(color_map_folder, 'diverging_bwr_iso.mat'));
 
   layers{2} = struct('color', struct('file', [], ... % con image
-                                     'map', 'diverging_bwr_iso', ...
-                                     'range', [-4 4]), ...
-                     'label', '\beta_{listening} - \beta_{baseline} (a.u.)', ...
-                     'opacity', struct('file', [], ... % spmT image
+                                     'range', [-4 4], ...
+                                     'label', ''), ...
+                     'opacity', struct('file', [], ... % assume spmT image
                                        'range', [2 3], ...
-                                       'label', '| t |'));
+                                       'label', ''), ...
+                     'type', 'dual');
 
   layers{3} = struct('color', struct('file', [], ... % spmT mask thresholded at 0.05 FWD
-                                     'map', [0 0 0], ...
-                                     'line_width', 2));
+                                     'map', 'w', ...
+                                     'line_width', 1));
 
   result.sdConfig.layers = layers;
 

src/stats/results/checkMontage.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/renameSpmT.m

@@ -8,18 +8,23 @@ function renameSpmT(result)
   %
 
   % (C) Copyright 2023 bidspm developers
-  outputFiles = spm_select('FPList', result.dir, '^spmT_[0-9].*_sub-.*nii$');
+  prefixes = {'spmT', 'spmF'};
+  for i_prefix = 1:numel(prefixes)
 
-  for iFile = 1:size(outputFiles, 1)
+    outputFiles = spm_select('FPList', result.dir, ['^' prefixes{i_prefix} '_[0-9].*_sub-.*nii$']);
 
-    source = deblank(outputFiles(iFile, :));
+    for iFile = 1:size(outputFiles, 1)
 
-    basename = spm_file(source, 'basename');
-    split = strfind(basename, '_sub');
-    bf = bids.File(basename(split + 1:end));
+      source = deblank(outputFiles(iFile, :));
 
-    target = spm_file(source, 'basename', bf.filename);
+      basename = spm_file(source, 'basename');
+      split = strfind(basename, '_sub');
+      bf = bids.File(basename(split + 1:end));
+
+      target = spm_file(source, 'basename', bf.filename);
+
+      movefile(source, target);
+    end
 
-    movefile(source, target);
   end
 end