Merge pull request #99 from thomas-vincent/surface_glm

Surface glm
- add import/export of manual markings: events and bad channel tagging
- add computation of HbT after projection
- fix negative values introduced during motion correction

bst_plugin/MANIFEST

@@ -1,3 +1,7 @@
+nst_bst_import_channel_flags.m
+nst_bst_export_channel_flags.m
+nst_bst_export_events.m
+nst_bst_import_events.m
 nst_io_fetch_sample_data.m
 nst_bst_set_template_anatomy.m
 nst_core_get_available_templates.m

bst_plugin/nst_bst_export_channel_flags.m

@@ -0,0 +1,19 @@
+function nst_bst_export_channel_flags(sFile,  channel_flags_fn)
+%NST_BST_EXPORT_CHANNEL_FLAGS Save channel flags from given sFile 
+%                             into given channel_flags_fn.
+% TODO: also save list of channels
+if ischar(sFile)
+    bst_chan_data = load(file_fullpath(sFile), 'ChannelFlag');
+    bst_chan_flags = bst_chan_data.ChannelFlag;
+end
+[root, bfn, ext] = fileparts(channel_flags_fn);
+switch ext
+    case '.mat'
+        s.channel_flags = bst_chan_flags;
+        bst_save(channel_flags_fn, s, 'v7');
+    otherwise
+        error(sprintf('Unsupported extension for channel file: "%s"', ext));
+end
+end
+
+

bst_plugin/nst_bst_export_events.m

@@ -0,0 +1,20 @@
+function nst_bst_export_events(sFile, event_fn)
+% Wrapper around bst functions to export events.
+
+if ischar(sFile)
+    bst_evt_data = load(file_fullpath(sFile), 'Events');
+    bst_events = bst_evt_data.Events;
+else
+    bst_events = sFile.Events;
+end
+
+
+[root, bfn, ext] = fileparts(event_fn);
+switch ext
+    case '.mat'
+        s.events = bst_events;
+        bst_save(event_fn, s, 'v7');
+    otherwise
+        error(sprintf('Unsupported extension for event file: "%s"', ext));
+end
+end

bst_plugin/nst_bst_import_channel_flags.m

@@ -0,0 +1,63 @@
+function sFileUpdated = nst_bst_import_channel_flags(sFile,  channel_flags_fn)
+%NST_BST_EXPORT_CHANNEL_FLAGS Save channel flags from given sFile 
+%                             into given channel_flags_fn.
+% TODO: also save list of channels to always insure that chan flags array
+% is aligned with channel info
+%
+%  Inputs:
+%      - sFile (struct or str): data to import into. 
+%              either a brainstorm data structure or a mat file containing
+%              the data structure
+%      - events_fn (str): channel flags file
+%              Channel flag information. Suported format: .mat
+%
+%  Outputs:
+%      - sFile (struct or str): same type as sFile intput
+%
+% TODO: utest with struct input
+
+STRUCT = 1;
+FILE = 2;
+if isstruct(sFile)
+    obj_type = STRUCT;
+else
+    assert(ischar(sFile));
+
+    sFile_fn = sFile;
+    obj_type = FILE;
+
+    isRaw = ~isempty(strfind(sFile_fn, '_0raw'));
+    if isRaw
+        DataMat = in_bst_data(sFile_fn, 'F');
+        sFile = DataMat.F;
+    else
+        DataMat = in_fopen_bstmat(sFile_fn);
+        sFile = DataMat;
+    end    
+end
+
+[root, bfn, ext] = fileparts(channel_flags_fn);
+sFileUpdated = sFile;
+switch ext
+    case '.mat'
+        chan_flags_data = load(channel_flags_fn);
+        sFileUpdated.ChannelFlag = chan_flags_data.channel_flags;
+        %TODO: save channel flags properly -> should be in channel header
+        %file, not data file!
+    otherwise
+        error(sprintf('Unsupported extension for channel file: "%s"', ext));
+end
+
+if obj_type == FILE   
+    % Report changes in .mat structure
+    DataMat.ChannelFlag = sFileUpdated.ChannelFlag;
+    if isRaw
+        DataMat.F.channelflag = chan_flags_data.channel_flags;
+    end
+    % Save file definition
+    bst_save(file_fullpath(sFile_fn), DataMat, 'v6', 1);
+
+    sFileUpdated = sFile_fn;
+end
+
+end

bst_plugin/nst_bst_import_events.m

@@ -0,0 +1,59 @@
+function sFileUpdated = nst_bst_import_events(sFile, events_fn)
+% Wrapper around bst functions to import events from given file event_fn into 
+% given sFile (file or struct), in a backward compatible way.
+% Load according to format based on extension
+%
+%  Inputs:
+%      - sFile (struct or str): data to import into. 
+%              either a brainstorm data structure or a mat file containing
+%              the data structure
+%      - events_fn (str): event file
+%              Event information. Suported format: .mat
+%
+%  Outputs:
+%      - sFile (struct or str): same type as sFile intput
+%
+% TODO: utest with struct input
+
+STRUCT = 1;
+FILE = 2;
+if isstruct(sFile)
+    obj_type = STRUCT;
+else
+    assert(ischar(sFile));
+
+    sFile_fn = sFile;
+    obj_type = FILE;
+
+    isRaw = ~isempty(strfind(sFile_fn, '_0raw'));
+    if isRaw
+        DataMat = in_bst_data(sFile_fn, 'F');
+        sFile = DataMat.F;
+    else
+        DataMat = in_fopen_bstmat(sFile_fn);
+        sFile = DataMat;
+    end    
+end
+
+[root, bfn, ext] = fileparts(events_fn);
+switch ext
+    case '.mat'
+        sFileUpdated = import_events(sFile, [], events_fn, 'BST');
+    otherwise
+        error(sprintf('Unsupported extension for event file: "%s"', ext));
+end
+
+if obj_type == FILE   
+    % Report changes in .mat structure
+    if isRaw
+        DataMat.F = sFileUpdated;
+    else
+        DataMat.Events = sFileUpdated.events;
+    end
+    % Save file definition
+    bst_save(file_fullpath(sFile_fn), DataMat, 'v6', 1);
+
+    sFileUpdated = sFile_fn;
+end
+
+end

bst_plugin/nst_bst_load_events.m

@@ -0,0 +1,15 @@
+function  bst_events = nst_bst_load_events(event_fn)
+% Wrapper around bst functions to save events in a backward compatible mode
+% Save according to format based on extension
+wrapper.events = [];
+[root, bfn, ext] = fileparts(event_fn);
+switch ext
+    case '.mat'
+        % Use dummy sampling frequency high enough so that times are not rounded
+        wrapper.prop.sfreq = 1e6;
+        wrapper = import_events(wrapper, [], event_fn, 'BST');
+        bst_events = wrapper.events;
+    otherwise
+        error(sprintf('Unsupported extension for event file: "%s"', ext));
+end
+end

bst_plugin/nst_bst_save_events.m

@@ -0,0 +1,15 @@
+function nst_bst_save_events(bst_events, event_fn)
+% Wrapper around bst functions to load event in a backward compatible mode
+% Load according to format based on extension
+
+[root, bfn, ext] = fileparts(event_fn);
+switch ext
+    case '.mat'
+        wrapper.events = bst_events;
+        % Emulate sampling frequency high enough to avoid rounding of times
+        % wrapper.prop.sfreq = 2.0 / min(diff(sort([bst_events.times])));
+        export_events(wrapper, [], event_fn);
+    otherwise
+        error(sprintf('Unsupported extension for event file: "%s"', ext));
+end
+end