LUMO integration

phoebe.m

@@ -256,6 +256,25 @@ function togglebutton_scan_Callback(hObject, ~, handles, FileName, PathName)
             end
              [SD,hb_streamed] = parse_fnirs_channels_oxysoft(inlet);
              lambda = [760,840];
+
+        case 4  % LUMO
+            pred = ' starts-with(name,''LUMO'') and type=''NIRS''' ;
+            result = lsl_resolve_bypred(lib, pred);
+
+            if ~isempty(result) 
+                inlet = lsl_inlet(result{1});
+                [~,~] = inlet.pull_chunk();
+            else
+                uiwait(warndlg(sprintf('LSL stream not found.\n\nPlease check if LSL Stream is enabled.'),'PHOEBE'))
+                set(handles.togglebutton_scan,'String','START MONITORING');
+                set(handles.togglebutton_scan,'Value',0);
+                set(handles.radiobutton_singleview,'Enable','on');
+                set(handles.radiobutton_doubleview,'Enable','on');
+                guidata(hObject,handles)
+                return
+            end
+            [SD,hb_streamed] = parse_fnirs_channels_lumo(inlet);
+            lambda = [735,850];
     end
 
     % extinction coefficients
@@ -354,6 +373,22 @@ function togglebutton_scan_Callback(hObject, ~, handles, FileName, PathName)
     nirs_data1 = lsl_buffer(:,SD(:,3));
     nirs_data2 = lsl_buffer(:,SD(:,4));
 
+    % Confirm that LUMO stream has valid data
+    if (get(handles.popupmenu_device,'value') == 4) 
+
+        % Check for potential saturation in LUMO data
+        if (sum(any(nirs_data1 < 1e-10)) > 0)
+            warning('Saturated signals');
+            continue
+        end
+
+        % Check for any incomplete frames
+        if (sum(any(isnan(nirs_data1))) > 0)
+            warning('Some frames are incomplete');
+            continue
+        end
+    end
+
     if hb_streamed
         [nirs_data1,nirs_data2] = hb2raw(nirs_data1,nirs_data2,ext);
     end

subfunctions/parse_fnirs_channels_lumo.m

@@ -0,0 +1,117 @@
+function [measurement_matrix,type] = parse_fnirs_channels_lumo(inlet)
+% PARSE_FNIRS_CHANNELS_LUMO Parse fNIRS channels from a LUMO LSL stream
+% 
+% [measurement_matrix,type] = PARSE_FNIRS_CHANNELS_LUMO(inlet)
+%
+% PARSE_FNIRS_CHANNELS_LUMO is used to parse fNIRS channel enumeration from
+% a LUMO LSL stream. 
+% 
+% The code checks if the LUMO LSL stream contains valid channel enumeration 
+% structure, and will return an error if invalid data is found.
+% 
+% Parameters
+%   inlet: an open LUMO LSL inlet
+%
+% Returns
+%   meausurement_matrix:    [#channels x 4] contains the S-D pairings (cols 1-2)
+%                           and the LSL vector indices (cols 3-4) for either wavelength 1-2 
+%
+%   type: 0 for raw data, 1 for hemoglobin
+% 
+% ND, Gowerlabs, October 2024
+
+% LUMO transmits raw data
+type = 0; 
+
+% Get information about the stream
+stream_info = inlet.info();
+
+% Get individual stream attributes
+stream_mac= stream_info.type();  %Type NIRS
+stream_n_channels = stream_info.channel_count(); %Get total channel count
+
+% Validate stream attributes
+if ~strcmp(stream_mac, 'NIRS') 
+    error('Chosen LSL stream is not a fNIRS LUMO stream.');
+end
+
+%% Scan LSL metadata to parse information about fNIRS channels only 
+ch = stream_info.desc().child('channels').child('channel');
+
+% Fill measurement list channel-by-channel
+% Columns: [s d wl lsl_vector_index) 
+nirs_channel = 1;
+meas_list = zeros(stream_n_channels,4); %Prepare for efficiency
+
+for k = 1:(stream_n_channels)
+    if strcmp(ch.child_value('type'),'Intensity')   
+
+        % extract source information
+        source = ch.child_value('source');
+        rg1= regexp(source,'N(?<node>\d+)/(?<idx>\w)','names');
+        src_node = str2double(rg1.node);
+
+        if (src_node < 1 || src_node > 54)
+            error('Chosen LSL stream has inconsistent source enumeration.');
+        end
+
+        switch(rg1.idx)
+            case 'A'
+                source_idx = 1;
+            case 'B'
+                source_idx = 2;
+            case 'C'
+                source_idx = 3;
+            otherwise
+                error('Chosen LSL stream has inconsistent source enumeration.');
+        end
+
+        % extract detector information
+        detector = ch.child_value('detector');
+        rg2= regexp(detector,'N(?<node>\d+)/(?<idx>\d)','names');
+        det_node = str2double(rg2.node);
+        det_idx = str2double(rg2.idx);
+
+        if (det_node < 1 || det_node > 54) || (det_idx < 1 || det_idx > 4)
+            error('Chosen LSL stream has inconsistent detector enumeration.');
+        end
+
+        % extract wavelength information 
+        wavelen = ch.child_value('wavelen');
+        if strcmp(wavelen,'735.000000')
+           wl = 0;
+        elseif strcmp(wavelen,'850.000000')
+           wl = 1;
+        else
+           error('Chosen LSL stream has inconsistent wavelength information.');
+        end
+
+        meas_list(nirs_channel,1) = (src_node - 1)*3 + source_idx;
+        meas_list(nirs_channel,2) = (det_node - 1)*4 + det_idx;
+        meas_list(nirs_channel,3) = wl;
+        meas_list(nirs_channel,4) = k;   % This is the index(position) of channel in the LSL vector being streamed
+        nirs_channel = nirs_channel +1;   % Increase nirs channel counter 
+    end
+    ch = ch.next_sibling(); % Move to next LSL channel
+end
+
+%% Convert to measurement_matrix: [s d wl1_lsl_index wl2_lsl_index]
+
+% Extract list of all wavelengths streamed by this device
+wl_list = unique(meas_list(:,3));
+%If wl_list is only two wavelengths, we are good. 
+if size(wl_list, 1) ~= 2
+    error('Chosen LSL stream has inconsistent number of wavelengths.');
+end
+
+measurement_matrix = zeros(size(meas_list,1)/length(wl_list),4); %Prepare for efficiency
+channel_list = unique(meas_list(:,1:2),'rows');   % Pull unique list of s-d pairings
+
+% For all occurrences of each s-d pairings, copy LSL index into column 3 and 4 of new matrix 
+for i = 1: size(channel_list,1)
+   [r1,~] = find(ismember(meas_list(:,1:3),[channel_list(i,:) wl_list(1)],'rows'));   % Find row where s-d pairing at wl1 is
+   [r2,~] = find(ismember(meas_list(:,1:3),[channel_list(i,:) wl_list(2)],'rows'));   % Find row where s-d pairing at wl2 is
+   measurement_matrix(i,1:2) = channel_list(i,:);   % Place unique s-d pairings
+   measurement_matrix(i,3) = meas_list(r1,4);       % Place lsl_index of wl1
+   measurement_matrix(i,4) = meas_list(r2,4);       % Place lsl_index of wl2
+end