SPM8 r5236

@gifti/private/isintent.m

@@ -9,7 +9,7 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: isintent.m 4382 2011-07-06 14:59:41Z guillaume $
+% $Id: isintent.m 4717 2012-04-19 11:02:50Z guillaume $
 
 a = [];
 b = [];
@@ -51,12 +51,12 @@
             fprintf('Intent %s is ignored.\n',this.data{i}.attributes.Intent);
     end
 end
-[d,i] = unique(a);
-if length(d) < length(a)
-    warning('Several fields match intent type. Using first.');
-    a = a(i);
-    b = b(i);
-end
+%[d,i] = unique(a);
+%if length(d) < length(a)
+%    warning('Several fields match intent type. Using first.');
+%    a = a(i);
+%    b = b(i);
+%end
 
 function c = cdata
 

@gifti/struct.m

@@ -7,9 +7,10 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Guillaume Flandin
-% $Id: struct.m 2076 2008-09-10 12:34:08Z guillaume $
+% $Id: struct.m 4717 2012-04-19 11:02:50Z guillaume $
 
 names = fieldnames(this);
+names = unique(names);
 values = cell(length(names), length(this(:)));
 
 for i=1:length(names)

@meeg/badtrials.m

@@ -0,0 +1,42 @@
+function res = badtrials(this, varargin)
+% Method for getting/setting bad trials
+% FORMAT res = badtrials(this)
+% _______________________________________________________________________
+% Copyright (C) 2011-2012 Wellcome Trust Centre for Neuroimaging
+
+% Christophe Phillips
+% $Id: badtrials.m 5059 2012-11-15 13:48:35Z vladimir $
+
+
+if length(varargin) == 2 && ~isempty(varargin{1})
+    % make sure that the two inputs for set are the same length
+    if ~(length(varargin{2}) == 1 || (length(varargin{1}) == length(varargin{2})))
+        error('Use either same vector length or scalar for value');
+    end
+end
+
+if numel(varargin) >= 1  && ~isempty(varargin{1})  
+    if ~(all(varargin{1} >= 1) && all(varargin{1} <= ntrials(this)))
+        error('Trial number out of range.');
+    end
+end
+
+if numel(varargin) >= 2
+    ubad = unique(varargin{2});
+    if isempty(ubad) || ~all(ismember(ubad, [0 1]))
+        error('Illegal bad flags (should be 0 or 1)');
+    end
+end
+
+res = getset(this, 'trials', 'bad', varargin{:});
+
+
+% Return trial indices if called without arguments and [0, 1] if called
+if numel(varargin) <= 1 % get
+    if iscell(res)
+        res = [res{:}];
+    end
+    if isempty(varargin)
+        res = find(res);
+    end
+end

@meeg/clone.m

@@ -11,14 +11,14 @@
 % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
 
 % Stefan Kiebel, Vladimir Litvak
-% $Id: clone.m 4207 2011-02-22 10:48:36Z christophe $
+% $Id: clone.m 4781 2012-07-10 15:59:45Z vladimir $
 
 if nargin < 4
     reset = 0;
 end
 
 if nargin < 3
-    if ~strcmp(transformtype(this), 'TF')
+    if ~strncmpi(transformtype(this), 'TF', 2) 
         dim = [nchannels(this), nsamples(this), ntrials(this)];
     else
         dim = [nchannels(this), nfrequencies(this), nsamples(this), ntrials(this)];

@meeg/ftraw.m

@@ -1,66 +1,69 @@
-function raw = ftraw(this, memmap)
+function raw = ftraw(this, chanind, timeind, trialind)
 % Method for converting meeg object to Fieldtrip raw struct
-% FORMAT raw = ftraw(this, memmap)
-%        memmap - 1 (default) memory map the data with file_array
-%                 0 load the data into memory
+% FORMAT raw  =  ftraw(this, chanind, timeind, trialind)
 % _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+% Copyright (C) 2008-2012 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: ftraw.m 1742 2008-05-28 11:58:04Z vladimir $
+% $Id: ftraw.m 5063 2012-11-16 12:10:41Z vladimir $
 
-if nargin < 2
-    memmap = 1;
+if ~isequal(transformtype(this), 'time')
+    raw = fttimelock(this, chanind, timeind, trialind);
+    return;
 end
 
-nchans  = nchannels(this);
-ntime   = nsamples(this);
-ntrl =    ntrials(this);
+% chanind == 0 is accepted for backward compatibility
+if nargin < 2 || isempty(chanind) || chanind == 0
+    chanind = 1:nchannels(this);
+end
+
+if nargin < 3 || isempty(timeind)
+    timeind = 1:nsamples(this);
+end
+
+if nargin < 4 || isempty(trialind)
+    trialind = 1:ntrials(this);
+end
 
 raw = [];
-raw.fsample = fsample(this);
-raw.label   = chanlabels(this)';
-
-wsize=wordsize(this.data.datatype);
-
-for i=1:ntrl
-    if memmap
-        offset = (i-1)*nchans*ntime*wsize;
-        trialdim = [nchans ntime];
-        raw.trial{i} = file_array(fullfile(this.path, this.data.fnamedat),trialdim,this.data.datatype,offset,1,0,'ro');
-    else
-        raw.trial{i} = this.data.y(:, :, i);
-    end
+
+raw.label   = chanlabels(this, chanind)';
+
+raw.trial   = cell(1, length(trialind));
+
+for i =  1:length(trialind) 
+    raw.trial{i} = this.data.y(chanind, timeind, trialind(i));
+end
+
+raw.time = repmat({time(this, timeind)}, 1, length(trialind));
+
+clist      =  condlist(this);
+
+condlabels = conditions(this, trialind);
+
+raw.trialinfo = 0*trialind;
+for k = 1:numel(clist)
+  fprintf('mapping condition label "%s" to condition code %d\n', clist{k}, k);
+  sel = strcmp(clist{k}, condlabels);
+  raw.trialinfo(sel) = k;
+end
+
+if ~isempty(sensors(this, 'MEG'))
+    raw.grad = sensors(this, 'MEG');
+end
+
+if ~isempty(sensors(this, 'EEG'))
+    raw.elec = sensors(this, 'EEG');
+end
+
+if isfield(this.other, 'origheader')
+    raw.hdr = this.other.origheader;
+end
+
+onsets = trialonset(this, trialind);
+
+if all(onsets>0)
+    onsets = round(onsets(:)*fsample(this));
+    raw.sampleinfo = [onsets+timeind(1) onsets+timeind(end)]-1;
 end
 
-raw.time = repmat({time(this)}, 1, ntrl);
-
-function s = wordsize(datatype)
-
-datatype = strtok(datatype, '-');
-
-switch datatype
-    case 'int8'
-        s = 1;
-    case 'int16'
-        s = 2;
-    case 'int32'
-        s = 4;
-    case 'uint8'
-        s = 1;
-    case 'uint16'
-        s = 2;
-    case 'uint32'
-        s = 4;
-    case 'float'
-        s = 4;
-    case 'double'
-        s = 8;
-    case 'float32'
-        s = 4;
-    case 'float64'
-        s = 8;
-    otherwise
-        error('unrecognized datatype');
-        % FIXME, add support for le and be versions
-end

@meeg/fttimelock.m

@@ -1,26 +1,95 @@
-function timelock = fttimelock(this)
+function timelock = fttimelock(this, chanind, timeind, trialind, freqind)
 % Method for converting meeg object to Fieldtrip timelock/freq struct
-% FORMAT  timelock = fttimelock(this)
+% FORMAT timelock = fttimelock(this, chanind, timeind, trialind, freqind)
+%
+% The method support both time and TF data and outputs different variants
+% of timelock or freq FT struct depending on the dataset type and requested
+% data dimensions.
 % _______________________________________________________________________
-% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+% Copyright (C) 2008-2012 Wellcome Trust Centre for Neuroimaging
 
 % Vladimir Litvak
-% $Id: fttimelock.m 3210 2009-06-17 13:46:25Z vladimir $
+% $Id: fttimelock.m 5063 2012-11-16 12:10:41Z vladimir $
+
+if nargin < 2 || isempty(chanind)
+    chanind = 1:nchannels(this);
+end
+
+if nargin < 3 || isempty(timeind)
+    timeind = 1:nsamples(this);
+end
+
+if nargin < 4 || isempty(trialind)
+    trialind = 1:ntrials(this);
+end
+
+if strncmpi(transformtype(this),'TF',2) && ...
+        (nargin < 5 || isempty(freqind))
+     freqind = 1:nfrequencies(this);
+end
 
 timelock             = [];
-timelock.label       = chanlabels(this);
-timelock.label       = timelock.label(:);
+timelock.label       = chanlabels(this, chanind)';
+
 if isequal(transformtype(this), 'time')
-    timelock.dimord  = 'rpt_chan_time';
-    timelock.fsample = fsample(this);
-    timelock.trial   = permute(this.data.y(:, :, :), [3 1 2]);
-    timelock.dimord  = 'rpt_chan_time';
+   if isequal(type(this), 'continuous')
+            error('For continuous data use ftraw method');
+   end
+
+   if isequal(type(this), 'single') || length(trialind)>1
+       timelock.dimord  = 'rpt_chan_time';
+       timelock.trial   =  permute(this.data.y(chanind, timeind, trialind), [3 1 2]);
+   else
+       timelock.dimord  = 'chan_time';
+       timelock.avg     =  spm_squeeze(this.data.y(chanind, timeind, trialind), 3);
+   end
+
+   timelock.time       = time(this, timeind);
+
 elseif strncmpi(transformtype(this),'TF',2)
-    timelock.dimord  = 'rpt_chan_freq_time';
-    timelock.powspctrm = permute(this.data.y(:, :, :, :), [4 1 2 3]);
-    timelock.freq    =  frequencies(this);
+    if length(timeind)>1
+        if isequal(type(this), 'single') || length(trialind)>1
+            timelock.dimord    = 'rpt_chan_freq_time';
+            timelock.powspctrm = permute(this.data.y(chanind, freqind, timeind, trialind), [4 1 2 3]);
+        else
+            timelock.dimord     = 'chan_freq_time';
+            timelock.powspctrm  =  spm_squeeze(this.data.y(chanind, freqind, timeind, trialind), 3);
+        end
+
+        timelock.time       = time(this, timeind);
+    else
+        if isequal(type(this), 'single') || length(trialind)>1
+            timelock.dimord    = 'rpt_chan_freq';
+            timelock.powspctrm = spm_squeeze(permute(this.data.y(chanind, freqind, timeind, trialind), [4 1 2 3]), 4);
+        else
+            timelock.dimord     = 'chan_freq';
+            timelock.powspctrm  =  spm_squeeze(this.data.y(chanind, freqind, timeind, trialind), [3 4]);
+        end
+    end
+
+    timelock.freq      = frequencies(this, freqind);
 else
-  error('Unknown transform type.');
+    error('Unknown transform type.');
+end   
+
+if length(trialind)>1
+
+    clist      =  condlist(this);
+    condlabels = conditions(this, trialind);
+    timelock.trialinfo = 0*trialind;
+
+    for k = 1:numel(clist)
+        fprintf('mapping condition label "%s" to condition code %d\n', clist{k}, k);
+        sel = strcmp(clist{k}, condlabels);
+        timelock.trialinfo(sel) = k;
+    end
+
 end
 
-timelock.time       = time(this);
+if ~isempty(sensors(this, 'MEG'))
+    timelock.grad = sensors(this, 'MEG');
+end
+
+if ~isempty(sensors(this, 'EEG'))
+    timelock.elec = sensors(this, 'EEG');
+end