Re-work of spikedetection so it can deal with inconsistent sampling frequencies.

Anthony Boyer
Commit 0541c2773b72917d20b078e151d3af1d27d5e919 1 parent 839f9b2e
Showing 1 changed file with 109 additions and 80 deletions
toolbox/ImaGIN_SpikesDetection.m
--- a/toolbox/ImaGIN_SpikesDetection.m
View file @0541c27
+++ b/toolbox/ImaGIN_SpikesDetection.m
View file @0541c27
@@ -2,8 +2,8 @@ function ImaGIN_SpikesDetection(S)
 % This function extracts and concatenates the baselines from cropped, qualitatively controlled, stimulation files.
 % It runs Delphos' spike detection on extracted baselines after bipolar montage computation.
 % It then computes corrected spike rates for each bipolar recording channel.
-% /!\ Cropped files CAN have a variable number of channels and thus the monopolar <-> bipolar mapping has to be established for each cropped file
-% and taken into account during baseline concatenation for consistency. /!\
+% /!\ Cropped files CAN have a variable number of channels AND different sampling rates, the monopolar <-> bipolar mapping has to be established for each cropped file
+% and taken into account during baseline concatenation for consistency AND cropped files with the same sampling rate have to be concatenated together. /!\
     %% Vars parsing
     stims_files = S.stims_files;
@@ -88,58 +88,134 @@ function ImaGIN_SpikesDetection(S)
         end    
     end   
-    %% Create the new monopolar baseline object
-    for nn=1:numel(global_montage)
-        channel{nn} = global_montage{nn};
-        timeseries(nn,:) =  [channels.(global_montage{nn}).timeserie{:}];
-        zeroed(nn,:) =  [channels.(global_montage{nn}).zeroed{:}];  
-        all_coordinates = cell2mat(channels.(global_montage{nn}).coordinates(:));
-        [lines cols] = find(~isnan(all_coordinates));        
-        coordinates_with_values = all_coordinates(unique(lines),:);           
-        if isempty(coordinates_with_values)
-            coordinates(nn,:) = NaN(1,3);  
-        elseif sum(all(coordinates_with_values == coordinates_with_values(1,:))) == 3  
-            coordinates(nn,:) = coordinates_with_values(1,:);
+    %% Create monopolar baseline objects
+    unique_srates = unique(sampling);
+    
+    for ss=1:numel(unique_srates) 
+        clear srate labels timeseries zeroed coordinates; 
+        srate = unique_srates(ss);
+        for nn=1:numel(global_montage)
+            labels{nn} = global_montage{nn};
+            timeseries(nn,:) =  [channels.(global_montage{nn}).timeserie{find(sampling==srate)}];
+            zeroed(nn,:) =  [channels.(global_montage{nn}).zeroed{find(sampling==srate)}];         
+            all_coordinates = cell2mat(channels.(global_montage{nn}).coordinates(:));
+            [lines cols] = find(~isnan(all_coordinates));        
+            coordinates_with_values = all_coordinates(unique(lines),:);           
+            if isempty(coordinates_with_values)
+                coordinates(nn,:) = NaN(1,3);  
+            elseif sum(all(coordinates_with_values == coordinates_with_values(1,:))) == 3  
+                coordinates(nn,:) = coordinates_with_values(1,:);
+            else
+                error('Inconsistent electrodes coordinates between cropped files.');
+            end 
+        end        
+        rates_tables{ss} = spikes_from_monopolar(srate,labels,timeseries,zeroed,coordinates,path_out);       
+    end 
+    
+    rates_labels = {};
+    rates_scores = [];
+    for rr=1:numel(rates_tables)  
+        rates_labels = [rates_labels rates_tables{rr}{:,1}];        
+        current_rates = rates_tables{rr}{:,2};
+        current_rates(isinf(current_rates)) = NaN;        
+        rates_scores = [rates_scores current_rates];
+    end
+    
+    for ll=1:size(rates_labels,1)
+        if all(strcmp(rates_labels(ll,:),rates_labels{ll,1})==1)
+            bipolar_labels{ll} = rates_labels{ll,1};
         else
-            error('Inconsistent electrodes coordinates between cropped files.');
-        end  
-    end   
+            error('Inconsistent labels between bipolar baselines');
+        end
+    end          
+    mean_rates = mean(rates_scores,2,'omitnan');
+    
+    % Store rate table in an individual files for easy extraction
+    rate_table_file = 'SPK_bBaseline_rates.mat';
+    spike_rates = [bipolar_labels',num2cell(mean_rates)];
+    save(fullfile(path_out,rate_table_file), 'spike_rates');
+    
+    % Ending step
+    set_final_status('OK');
+    disp('Done');    
+
+end
+
+function channels_map = monopolar_to_bipolar_mapping(monopolar_file,path_out)
+    mono_stimulation_obj = spm_eeg_load(monopolar_file);
+    monopolar_sensors = sensors(mono_stimulation_obj,'EEG');
+    [mono_path,mono_name,mono_ext] = fileparts(monopolar_file);
+    Sbp.Fname = monopolar_file;
+    Sbp.FileOut = fullfile(path_out,['b' mono_name]);
+    bp_stimulation_obj = ImaGIN_BipolarMontage(Sbp);     
+    for cc=1:nchannels(bp_stimulation_obj)
+        bipolar_chan = chanlabels(bp_stimulation_obj,cc);   
+        mono_chans = regexp(bipolar_chan,'-','split');  
+        channels_map(cc).bp_chan = bipolar_chan;
+        channels_map(cc).bp_idx = cc;
+        channels_map(cc).mono_chan1 = mono_chans{1}{1};
+        channels_map(cc).mono_chan2 = mono_chans{1}{2};        
+        % Get the monopolar channels idxes.
+        chan1_idx = find(strcmp(monopolar_sensors.label,mono_chans{1}{1})); 
+        chan2_idx = find(strcmp(monopolar_sensors.label,mono_chans{1}{2}));        
+        % Test and correct for duplicated labels in the monopolar object
+        if numel(chan1_idx) == 0
+            error('Could not find the monopolar channel from the bipolar montage.');
+        elseif numel(chan1_idx) == 1 % If 1 match, as expected, do nothing
+            %pass        
+        else
+            error('2 or more channels with the same label')        
+        end
+        % Same logic as for chan1_idx
+        if numel(chan2_idx) == 0
+            error('Could not find the monopolar channel from the bipolar montage.');
+        elseif numel(chan2_idx) == 1
+            %pass       
+        else
+            error('2 or more channels with the same label')        
+        end
+        channels_map(cc).mono_idx1 = chan1_idx;
+        channels_map(cc).mono_idx2 = chan2_idx;        
+    end    
+    delete([Sbp.FileOut '.mat']);delete([Sbp.FileOut '.dat']);delete([Sbp.FileOut '_log.txt']); 
+end
+
+function rates_table = spikes_from_monopolar(srate,labels,timeseries,zeroed,coordinates,path_out)    
+    
     % Create the new sensor
     new_sensors_info.balance.current = 'none';
     new_sensors_info.chanpos = coordinates;
-    new_sensors_info.chantype = cell(1,numel(global_montage)); new_sensors_info.chantype(:) = {'eeg'};
-    new_sensors_info.chanunit = cell(1,numel(global_montage)); new_sensors_info.chanunit(:) = {'V'};
+    new_sensors_info.chantype = cell(1,numel(labels)); new_sensors_info.chantype(:) = {'eeg'};
+    new_sensors_info.chanunit = cell(1,numel(labels)); new_sensors_info.chanunit(:) = {'V'};
     new_sensors_info.elecpos = coordinates;
-    new_sensors_info.label = channel;
+    new_sensors_info.label = labels;
     new_sensors_info.type = 'ctf';
     new_sensors_info.unit = 'mm';
+    
     % Create the new files 
-    file_header = fullfile(path_out,'monopolar_baseline.mat');
-    file_data = fullfile(path_out,'monopolar_baseline.dat');    
+    file_header = fullfile(path_out,['monopolar_baseline_' num2str(srate) 'Hz.mat']);
+    file_data = fullfile(path_out,['monopolar_baseline_' num2str(srate) 'Hz.dat']);    
     if exist(file_header, 'file') == 2
      delete(file_header);      
     end
     if exist(file_data, 'file') == 2
      delete(file_data);          
     end   
+    
     % Create the new object    
     D = meeg(size(timeseries,1),size(timeseries,2),1);
-    D = fname(D,'monopolar_baseline');
+    D = fname(D,['monopolar_baseline_' num2str(srate) 'Hz']);
     D = path(D,path_out);
-    if all(sampling == sampling(1))
-        D = fsample(D,sampling(1));
-    else
-        error('Inconsistent sampling frequency across cropped files.');
-    end
+    D = fsample(D,srate); 
     D = sensors(D,'EEG',new_sensors_info)    
     D = blank(D) ;
     D = link(D,file_data);   
     D(:,:,1) = timeseries;   
-    save(D);    
-    
+    save(D);
+
     %% Compute bipolar montage on baseline object to get the bipolar baseline object
     Sbp.Fname = file_header;
-    Sbp.FileOut = fullfile(path_out,'bipolar_baseline');
+    Sbp.FileOut = fullfile(path_out,['bipolar_baseline_' num2str(srate) 'Hz']);
     bp_baseline_obj = ImaGIN_BipolarMontage(Sbp);     
     global_mapping = monopolar_to_bipolar_mapping(Sbp.Fname,path_out);
@@ -179,53 +255,6 @@ function ImaGIN_SpikesDetection(S)
     spkFile.markers   = spks_table;
     spkFile.baseline  = ['Total duration of ' num2str((nsamples(bp_baseline_obj)/fsample(bp_baseline_obj))/60)  ' minutes'];
     spkFile.comment   = 'Spike rate is number of spikes per minute whithin a bipolar channel';
-    save(fullfile(path_out,spkFileName), 'spkFile');
-    
-    % Store rate table in an individual files for easy extraction
-    rate_table_file = 'SPK_bBaseline_rates.mat';
-    spike_rates = [chans,num2cell(rates)];
-    save(fullfile(path_out,rate_table_file), 'spike_rates');
-    
-    % Ending step
-    set_final_status('OK');
-    disp('Done');
-end
-
-function channels_map = monopolar_to_bipolar_mapping(monopolar_file,path_out)
-    mono_stimulation_obj = spm_eeg_load(monopolar_file);
-    monopolar_sensors = sensors(mono_stimulation_obj,'EEG');
-    [mono_path,mono_name,mono_ext] = fileparts(monopolar_file);
-    Sbp.Fname = monopolar_file;
-    Sbp.FileOut = fullfile(path_out,['b' mono_name]);
-    bp_stimulation_obj = ImaGIN_BipolarMontage(Sbp);     
-    for cc=1:nchannels(bp_stimulation_obj)
-        bipolar_chan = chanlabels(bp_stimulation_obj,cc);   
-        mono_chans = regexp(bipolar_chan,'-','split');  
-        channels_map(cc).bp_chan = bipolar_chan;
-        channels_map(cc).bp_idx = cc;
-        channels_map(cc).mono_chan1 = mono_chans{1}{1};
-        channels_map(cc).mono_chan2 = mono_chans{1}{2};        
-        % Get the monopolar channels idxes.
-        chan1_idx = find(strcmp(monopolar_sensors.label,mono_chans{1}{1})); 
-        chan2_idx = find(strcmp(monopolar_sensors.label,mono_chans{1}{2}));        
-        % Test and correct for duplicated labels in the monopolar object
-        if numel(chan1_idx) == 0
-            error('Could not find the monopolar channel from the bipolar montage.');
-        elseif numel(chan1_idx) == 1 % If 1 match, as expected, do nothing
-            %pass        
-        else
-            error('2 or more channels with the same label')        
-        end
-        % Same logic as for chan1_idx
-        if numel(chan2_idx) == 0
-            error('Could not find the monopolar channel from the bipolar montage.');
-        elseif numel(chan2_idx) == 1
-            %pass       
-        else
-            error('2 or more channels with the same label')        
-        end
-        channels_map(cc).mono_idx1 = chan1_idx;
-        channels_map(cc).mono_idx2 = chan2_idx;        
-    end    
-    delete([Sbp.FileOut '.mat']);delete([Sbp.FileOut '.dat']);delete([Sbp.FileOut '_log.txt']); 
+    results_file = fullfile(path_out,spkFileName);
+    save(results_file, 'spkFile');
 end