Merge pull request #15 from tincala91/nb_plugins

Implementation of plugins

COFFEE_BREAK_FDGPET.m

@@ -50,6 +50,9 @@
 addpath(fullfile(baseDir, 'OTHER_FUNCTIONS', 'TFCE'));
 addpath(fullfile(baseDir, 'OTHER_FUNCTIONS', 'export_fig-master'));
 
+% Initialize plugins
+%plugins.init()
+
 %selects the directory containing only dicoms 
 dir_path = spm_select(1,'dir', 'Select directory where DICOM files are'); %% input directory
 
@@ -151,7 +154,7 @@
       %creates render in MRIcron style
       sub_info = I_SUV_GM_script(dir_path, sub_info);
 
-      K_Create_Report(dir_path, sub_info);  
+      run_plugin('K', dir_path, sub_info);
 
   end
 
@@ -160,7 +163,7 @@
   rmpath(fullfile(baseDir, 'OTHER_FUNCTIONS', 'TFCE'));
   rmpath(fullfile(baseDir, 'OTHER_FUNCTIONS', 'export_fig-master'));
   cd(cur_path);
-  save('workspace_dump.m');
+  save('workspace_dump.mat');
   rethrow(ME);
 end
 

OTHER_FUNCTIONS/ViewSUV3D.m

@@ -5,7 +5,8 @@ function ViewSUV3D(filename, sub_info)
 
 %filename = 'wSUV_ScCh_19591229_20210510.nii'
 %Load image
-img_SUV = double(load_nii(filename).img);
+nii = load_nii(filename);
+img_SUV = double(nii.img);
 
 %Get image shape
 [xdim, ydim, zdim] = size(img_SUV);

Plugins/.gitignore

@@ -0,0 +1 @@
+*/

Plugins/README.md

@@ -0,0 +1,3 @@
+Place the plugins in this folder.
+
+The folders in this directory will be added to path at runtime.

private/E_STAT_script.m

@@ -1,7 +1,6 @@
 function mat_file = E_STAT_script(files, render, mask, controls)
   %declaring useful variables
   global JOB_DIR
-  global xSPM
 
   files = cellstr(files);
   controls = cellstr(controls);
@@ -31,12 +30,12 @@
   export_fig 'Hypo.jpg';
 
   %spm_render_DOC(struct('XYZ', xSPM.XYZ, 't',xSPM.Z,'mat', xSPM.M,'dim', xSPM.DIM),1,render,1)
-  spm_render_DOC(get_renderer(xSPM),1,render,1)
+  spm_render_DOC(get_renderer(),1,render,1);
   %saveas(gcf, 'Render_hypo_new.jpg');
   export_fig 'Render_hypo_new.jpg';
 
   %spm_render_DOC(struct('XYZ', xSPM.XYZ, 't',xSPM.Z,'mat', xSPM.M,'dim', xSPM.DIM),nan,render)
-  spm_render_DOC(get_renderer(xSPM),nan,render)
+  spm_render_DOC(get_renderer(),nan,render);
   spm_figure('colormap','gray-cool');
   %saveas(gcf, 'Render_hypo_old.jpg');
   export_fig 'Render_hypo_old.jpg';

private/E_STAT_script_addon.m

@@ -1,7 +1,6 @@
 function files = E_STAT_script_addon(spm_mat_file, render, template)
   %declaring useful variables
   global JOB_DIR
-  global xSPM
 
   [pth, ~, ~] = fileparts(spm_mat_file);
   cur_dir = pwd();
@@ -23,11 +22,11 @@
   export_fig 'Pres.jpg'
 
   %spm_render_DOC(struct('XYZ', xSPM.XYZ, 't',xSPM.Z,'mat', xSPM.M,'dim', xSPM.DIM), 1, render, 0);
-  spm_render_DOC(get_renderer(xSPM), 1, render, 0);
+  spm_render_DOC(get_renderer(), 1, render, 0);
   export_fig 'Render_pres_new.jpg'; %saves render as jpeg (get current figure!)
 
   %spm_render_DOC(struct('XYZ', xSPM.XYZ, 't',xSPM.Z,'mat', xSPM.M,'dim', xSPM.DIM), nan, render);
-  spm_render_DOC(get_renderer(xSPM), nan, render);
+  spm_render_DOC(get_renderer(), nan, render);
   export_fig 'Render_pres_old.jpg'
 
   hypo_nii = 'spmT_0001_Hypo.nii';

OTHER_FUNCTIONS/get_renderer.m → private/get_renderer.m

@@ -1,7 +1,8 @@
-function params = get_renderer(xSPM)
-
-  params.XYZ = xSPM.XYZ;
-  params.t = xSPM.Z;
-  params.mat = xSPM.M;
-  params.dim = xSPM.DIM;
-end
+function params = get_renderer()
+  global xSPM;
+
+  params.XYZ = xSPM.XYZ;
+  params.t = xSPM.Z;
+  params.mat = xSPM.M;
+  params.dim = xSPM.DIM;
+end

private/run_plugin.m

@@ -0,0 +1,42 @@
+function run_plugin(index, varargin)
+  % Simple wrapper to run function from Plugins directory
+  % with same letter index and given parameters
+  %
+  % The plugin script must have same name as folder, including the index
+
+  cur_dir = pwd();
+  paths = path();
+  cleanup = onCleanup(@()restorePaths(paths, cur_dir));
+
+  pth = fileparts(mfilename('fullpath'));
+  plugins_path = fullfile(pth, '..', 'Plugins');
+
+  plugins = dir(fullfile(plugins_path, [index, '_*']));
+
+  if numel(plugins) == 0
+    return;
+  end
+
+  if numel(plugins) > 1
+    warning('Plugin %s: Found several plugins, will run only first', index);
+  end
+
+  plugin_path = fullfile(plugins(1).folder, plugins(1).name);
+  plugin_script = fullfile(plugin_path, 'plugin.m');
+  if ~exist(plugin_script, 'file')
+    warning('Plugin %s: Can''t find script plugin.m', index);
+    return;
+  end
+
+  fprintf('Plugin %s: Running from %s\n', index, plugin_path);
+
+  addpath(plugin_path);
+  plugin(varargin{:});
+
+end
+
+
+function restorePaths(search_paths, current_path)
+  path(search_paths);
+  cd(current_path);
+end