Add defaults for transparent plots (#1355)

* add local path

* add local path

* add chagelog CI script

* add code

* add mock change

* update changelog workflow

* fix typo

* fix syntax

* fix CI error

* saved UNDO information for reset changes and discarded files

* update bids-matlab submodule to latest commit in main

* update gitmodule file to track main branch in bids-matlab

* rm files we do not know where they are coming from

* add defaults for transparent plots

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* Update src/defaults/defaultResultsStructure.m

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

* Update src/defaults/defaultResultsStructure.m

* assign the sd structures to the result one

* fix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* add test and update

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Remi Gau <remi_gau@hotmail.com>
Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

Author: 4 people

src/defaults/defaultResultsStructure.m

@@ -23,4 +23,35 @@
 
   result.nidm = true();
 
+  % transparent plot
+  layers{1} = struct('color', struct('file', result.montage.background, ...
+                                     'range', [0 1], ...
+                                     'map', gray(256)));
+
+  %   color_map_folder = fullfile(fileparts(which('map_luminance')), '..', 'mat_maps');
+  %   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', [2 3], ...
+                                       'label', '| t |'));
+
+  layers{3} = struct('color', struct('file', [], ... % spmT mask thresholded at 0.05 FWD
+                                     'map', [0 0 0], ...
+                                     'line_width', 2));
+
+  result.sdConfig.layers = layers;
+
+  settings = sd_config_settings('init');
+
+  settings.slice.orientation = result.montage.orientation;
+  settings.slice.disp_slices = -50:10:50;
+  settings.fig_specs.n.slice_column = 4;
+  settings.fig_specs.title = [];
+
+  result.sdConfig.settings = settings;
+
 end

tests/tests_defaults/test_defaultResultsStructure.m

@@ -37,6 +37,35 @@ function test_defaultResultsStructure_basic()
 
   expected.nidm = true();
 
+  layers{1} = struct('color', struct('file', expected.montage.background, ...
+                                     'range', [0 1], ...
+                                     'map', gray(256)));
+
+  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', [2 3], ...
+                                       'label', '| t |'));
+
+  layers{3} = struct('color', struct('file', [], ... % spmT mask thresholded at 0.05 FWD
+                                     'map', [0 0 0], ...
+                                     'line_width', 2));
+
+  expected.sdConfig.layers = layers;
+
+  settings = sd_config_settings('init');
+
+  settings = sd_config_settings('init');
+
+  settings.slice.orientation = expected.montage.orientation;
+  settings.slice.disp_slices = -50:10:50;
+  settings.fig_specs.n.slice_column = 4;
+  settings.fig_specs.title = [];
+
+  expected.sdConfig.settings = settings;
+
   assertEqual(results, expected);
 
 end