Ephys: DeriveLFP now available as a plugin and in the compiled distri…

…bution

doc/updates.txt

@@ -1,5 +1,6 @@
 --------------------------------------------------------------
 November 2021
+- Ephys: DeriveLFP now available as a plugin and in the compiled distribution
 - GUI: 3D MRI display: Moving slice by clicking on it
 - GUI: Automatic registration reports the distance headpoints/scalp
 --------------------------------------------------------------

toolbox/core/bst_plugin.m

@@ -69,7 +69,8 @@
 %     - InstalledFcn   : String to eval or function handle to call after installing the plugin
 %     - UninstalledFcn : String to eval or function handle to call after uninstalling the plugin
 %     - LoadedFcn      : String to eval or function handle to call after loading the plugin
-%     - UnloadedFcn    : String to eval or function handle to call after unloading the plugin 
+%     - UnloadedFcn    : String to eval or function handle to call after unloading the plugin
+%     - DeleteFiles    : List of files to delete after installation
 %
 %     Fields set when installing the plugin
 %     =====================================
@@ -173,7 +174,7 @@
     PlugDesc(end).CompiledStatus = 0;
     PlugDesc(end).UnloadPlugs    = {'spm12', 'iso2mesh'};
     PlugDesc(end).LoadFolders    = {'lib/spm12', 'lib/iso2mesh', 'lib/cvx', 'lib/ncs2daprox', 'lib/NIFTI_20110921'};
-    
+
     % === FORWARD: OPENMEEG ===
     PlugDesc(end+1)              = GetStruct('openmeeg');
     PlugDesc(end).Version        = '2.4.1';
@@ -339,6 +340,19 @@
     PlugDesc(end).LoadFolders    = {'*'};
     PlugDesc(end).InstalledFcn   = 'd=pwd; cd(fileparts(which(''make''))); make; cd(d);';
 
+    % === ELECTROPHYSIOLOGY: DERIVELFP ===
+    PlugDesc(end+1)              = GetStruct('derivelfp');
+    PlugDesc(end).Version        = '1.0';
+    PlugDesc(end).Category       = 'e-phys';
+    PlugDesc(end).AutoUpdate     = 0;
+    PlugDesc(end).URLzip         = 'http://packlab.mcgill.ca/despikingtoolbox.zip';
+    PlugDesc(end).URLinfo        = 'https://journals.physiology.org/doi/full/10.1152/jn.00642.2010';
+    PlugDesc(end).TestFile       = 'despikeLFP.m';
+    PlugDesc(end).ReadmeFile     = 'readme.txt';
+    PlugDesc(end).CompiledStatus = 2;
+    PlugDesc(end).LoadFolders    = {'toolbox'};
+    PlugDesc(end).DeleteFiles    = {'ExampleDespiking.m', 'appendixpaper.pdf', 'downsample2x.m', 'examplelfpdespiking.mat', 'sta.m'};
+
     % === NIRSTORM ===
     PlugDesc(end+1)              = GetStruct('nirstorm');
     PlugDesc(end).Version        = 'github-master';
@@ -733,22 +747,35 @@ function Configure(PlugDesc)
     % Compiled: do not look for unreferenced plugins
     if isCompiled
         PlugList = [];
-    % Get folders in Brainstorm user folder
+    % Get a specific unlisted plugin
     elseif ~isempty(SelPlug)
+        % Get plugin name
         if ischar(SelPlug)
-            PlugList = dir(bst_fullfile(UserPluginsDir, SelPlug));
+            PlugName = SelPlug;
+        else
+            PlugName = SelPlug.Name;
+        end
+        % If plugin is already referenced: skip
+        if ismember(PlugName, {PlugDesc.Name})
+            PlugList = [];
+        % Else: Try to get target plugin as unreferenced
         else
-            PlugList = dir(bst_fullfile(UserPluginsDir, SelPlug.Name));
+            PlugList = struct('name', SelPlug);
         end
+    % Get all folders in Brainstorm plugins folder
     else
         PlugList = dir(UserPluginsDir);
     end
     % Process folders containing a plugin.mat file
     for iDir = 1:length(PlugList)
-        % Process only folders containing a 'plugin.mat' file and not already referenced
+        % Process only folders
         PlugDir = bst_fullfile(UserPluginsDir, PlugList(iDir).name);
+        if ~isdir(PlugDir) || (PlugList(iDir).name(1) == '.')
+            continue;
+        end
+        % Process only folders containing a 'plugin.mat' file
         PlugMatFile = bst_fullfile(PlugDir, 'plugin.mat');
-        if ~isdir(PlugDir) || (PlugList(iDir).name(1) == '.') || ~file_exist(PlugMatFile) || ismember(PlugList(iDir).name, {PlugDesc.Name})
+        if ~file_exist(PlugMatFile)
             continue;
         end
         % If selecting only one plugin
@@ -1169,7 +1196,8 @@ function Configure(PlugDesc)
             end
     end
     file_delete(pkgFile, 1, 3);
-    % Save plugin.mat
+
+    % === SAVE PLUGIN.MAT ===
     PlugDesc.Path = PlugPath;
     PlugMatFile = bst_fullfile(PlugDesc.Path, 'plugin.mat');
     excludedFields = {'LoadedFcn', 'UnloadedFcn', 'InstalledFcn', 'UninstalledFcn', 'Path', 'isLoaded', 'isManaged'};
@@ -1200,6 +1228,26 @@ function Configure(PlugDesc)
     PlugDescSave = rmfield(PlugDesc, excludedFields);
     bst_save(PlugMatFile, PlugDescSave, 'v6');
 
+    % === DELETE UNWANTED FILES ===
+    if ~isempty(PlugDesc.DeleteFiles) && iscell(PlugDesc.DeleteFiles)
+        for iDel = 1:length(PlugDesc.DeleteFiles)
+            if ~isempty(PlugDesc.SubFolder)
+                fileDel = bst_fullfile(PlugDesc.Path, PlugDesc.SubFolder, PlugDesc.DeleteFiles{iDel});
+            else
+                fileDel = bst_fullfile(PlugDesc.Path, PlugDesc.DeleteFiles{iDel});
+            end
+            if file_exist(fileDel)
+                try
+                    file_delete(fileDel, 1, 3);
+                catch
+                    disp(['BST> Plugin ' PlugName ': Could not delete file: ' PlugDesc.DeleteFiles{iDel}]);
+                end
+            else
+                disp(['BST> Plugin ' PlugName ': Missing file: ' PlugDesc.DeleteFiles{iDel}]);
+            end
+        end
+    end
+
     % === CALLBACK: POST-INSTALL ===
     [isOk, errMsg] = ExecuteCallback(PlugDesc, 'InstalledFcn');
     if ~isOk

toolbox/db/db_template.m

@@ -1185,6 +1185,7 @@
             'UninstalledFcn',[], ...  % String to eval or function handle to call after uninstalling the plugin
             'LoadedFcn',     [], ...  % String to eval or function handle to call after loading the plugin
             'UnloadedFcn',   [], ...  % String to eval or function handle to call after unloading the plugin
+            'DeleteFiles',   [], ...  % Cell-array of files to delete after unzipping the plugin package (path relative to the plugin folder)
             ... % Set when installing or loading the plugin 
             'SubFolder',     '', ...  % If all the code is in a subfolder: detect this at installation time
             'Path',          [], ...  % Set at runtime: Installation path for this plugin

toolbox/process/functions/process_convert_raw_to_lfp.m

@@ -23,6 +23,7 @@
 % =============================================================================@
 %
 % Authors: Konstantinos Nasiotis 2018
+%          Francois Tadel, 2021
 
 eval(macro_method);
 end
@@ -100,25 +101,12 @@
         end
 
         %% Check for dependencies
-        % If DespikeLFP is selected, check if it is already installed
+        % If DespikeLFP is selected: Install DeriveLFP plugin
         if sProcess.options.despikeLFP.Value
-            % Ensure we are including the DeriveLFP folder in the Matlab path
-            DeriveLFPDir = bst_fullfile(bst_get('BrainstormUserDir'), 'DeriveLFP');
-            if exist(DeriveLFPDir, 'dir')
-                addpath(genpath(DeriveLFPDir));
-            end
-
-            % Install DeriveLFP if missing
-            if ~exist('despikeLFP.m', 'file')
-                rmpath(genpath(DeriveLFPDir));
-                isOk = java_dialog('confirm', ...
-                    ['The DeriveLFP toolbox is not installed on your computer.' 10 10 ...
-                         'Download and install the latest version?'], 'DeriveLFP');
-                if ~isOk
-                    bst_report('Error', sProcess, sInput, 'This process requires the DeriveLFP toolbox.');
-                    return;
-                end
-                downloadAndInstallDeriveLFP();
+            [isInstalled, errMsg] = bst_plugin('Install', 'derivelfp');
+            if ~isInstalled
+                bst_report('Error', sProcess, [], errMsg);
+                return;
             end
         end
 
@@ -269,7 +257,7 @@
         data = sMat.data';
     end
 
-    % Aplly final filter
+    % Apply final filter
     data = bst_bandpass_hfilter(data, Fs, filterBounds(1), filterBounds(2), 0, 0);
     data = downsample(data, round(Fs/1000));  % The file now has a different sampling rate (fs/30) = 1000Hz.
 end
@@ -364,36 +352,3 @@
 end
 
 
-
-%% ===== DOWNLOAD AND INSTALL DeriveLFP =====
-function downloadAndInstallDeriveLFP()
-    DeriveLFPDir = bst_fullfile(bst_get('BrainstormUserDir'), 'DeriveLFP');
-    DeriveLFPTmpDir = bst_fullfile(bst_get('BrainstormUserDir'), 'DeriveLFP_tmp');
-    url = 'http://packlab.mcgill.ca/despikingtoolbox.zip';
-    % If folders exists: delete
-    if isdir(DeriveLFPDir)
-        file_delete(DeriveLFPDir, 1, 3);
-    end
-    if isdir(DeriveLFPTmpDir)
-        file_delete(DeriveLFPTmpDir, 1, 3);
-    end
-    % Create folder
-	mkdir(DeriveLFPTmpDir);
-    % Download file
-    zipFile = bst_fullfile(DeriveLFPTmpDir, 'despikingtoolbox.zip');
-    errMsg = gui_brainstorm('DownloadFile', url, zipFile, 'DeriveLFP download'); % This line downloads the file
-    if ~isempty(errMsg)
-        error(['Impossible to download DeriveLFP:' errMsg]);
-    end
-    % Unzip file
-    bst_progress('start', 'DeriveLFP', 'Installing DeriveLFP...');
-    unzip(zipFile, DeriveLFPTmpDir);
-    newDeriveLFPDir = bst_fullfile(DeriveLFPTmpDir);
-    % Move directory to proper location
-    file_move(newDeriveLFPDir, DeriveLFPDir);
-    % Delete unnecessary files
-    file_delete(DeriveLFPTmpDir, 1, 3);
-    % Add to Matlab path
-    addpath(genpath(DeriveLFPDir));
-end
-