Release of BioPatRec FRA

BioPatRec.m

@@ -24,6 +24,7 @@
 % ------------------------- Updates & Contributors ------------------------
 % 2009-04-02 / Max Ortiz  / Creation of EMG_AQ
 % 2011-22-06 / Max Ortiz  / Software name changed from EMG_AQ to BioPatRec
+% 20XX-XX-XX / Author     / Comments
 
 close all;
 clear all;

Comm/AFE/Acquire_tWs.m

@@ -23,46 +23,84 @@
                             % SetDeviceStartAcquisition(),
                             % Acquire_tWs(), StopAcquisition(). This functions 
                             % has been moved to COMM/AFE folder, into this new script.
-
+% 2015-1-19 / Enzo Mastinu / The ADS1299 part has been modified in way to be 
+                            % compatible with the new ADS1299 acquisition mode (DSP + FPU) 
+% 2015-4-10 / Enzo Mastinu / The ADS1299_DSP acquisition has been optimized, only desired
+                            % channels are transmitted to PC, not all as before
+% 2016-7-08 / Enzo Mastinu / The ADS_DSP/Neuromotus acquisition has been
+                            % optimized introducing the re-synchronization
+                            % in case the signal got lost
 % 20xx-xx-xx / Author  / Comment
 
 
 
 % It acquire tWs samples from the selected device
-function cData = Acquire_tWs(deviceName, obj, nCh, tWs)
+function [cData, error] = Acquire_tWs(deviceName, obj, nCh, tWs)
  
-    cData     = zeros(tWs,nCh);                                            % this is the data structure that the function must return
-    ampPP = 0.0005;
-    offVector = 0:nCh-1;
-    offVector = offVector .* ampPP;
-    
+    error = 0;
+    cData = zeros(tWs,nCh);                                                % this is the data structure that the function must return
     
-    %%%%% ADS1299 %%%%%
-    if strcmp(deviceName, 'ADS1299')
-        LSBweight = double(4.5/(24*8388607));                              % ADS1299: if gain is set on 24 V/V
-        for sampleNr = 1:tWs
-            % 27bytes package mode
-            byteData = fread(obj,27,'char');                               % Acquire 27 bytes packet from Tiva (and from ADS1299), 3 status bytes + 3 byte (24bit) for each channel
-            value = [65536 256 1]*reshape(byteData(4:end), 3, 8);          % all channels data are now available on value vector, byteData(4:end) means throw away status bytes
-            for k = 1:nCh  
-                if value(k) > 8388607                                      % the data must be converted from 2's complement
-                    value(k) = value(k) - 2^24;
+    % Set warnings to temporarily issue error (exceptions)
+    s = warning('error', 'instrument:fread:unsuccessfulRead');
+    try
+        %%%%% ADS1299 %%%%%
+        if strcmp(deviceName, 'ADS1299')
+        %   LSBweight = double(4.5/(24*8388607));                            % ADS1299: we always use the gain of 24 V/V
+            LSBweight = double(4.5/(8388607));                                 % It is better to plot data with gain scaling effect
+            for sampleNr = 1:tWs
+                % 27bytes package mode
+                byteData = fread(obj,27,'char');                               % Acquire 27 bytes packet from Tiva (and from ADS1299), 3 status bytes + 3 byte (24bit) for each channel
+                value = [65536 256 1]*reshape(byteData(4:end), 3, 8);          % all channels data are now available on value vector, byteData(4:end) means throw away status bytes
+                for k = 1:nCh  
+                    if value(k) > 8388607                                      % the data must be converted from 2's complement
+                        value(k) = value(k) - 2^24;
+                    end
+                    cData(sampleNr,k) = value(k) * LSBweight;                  
+                end 
+            end
+        end
+        if strcmp(deviceName, 'ADS_BP')   
+            for sampleNr = 1:tWs
+                go = 0;
+                while go == 0
+                    % nCh*4 bytes (float) mode
+                    byteData = fread(obj,nCh,'float32');                             % float data mode (4bytes X nCh channels)
+                    if byteData < 10
+                        go = 1;
+                    else
+                        % Synchronize the device again
+                        fwrite(obj,'T','char');
+                        % Read available data and discard it
+                        if obj.BytesAvailable > 1
+                            fread(obj,obj.BytesAvailable,'uint8');        
+                        end
+                        fwrite(obj,'G','char');
+                        fwrite(obj,nCh,'char');
+                        fread(obj,1,'char');
+                        go = 0;
+                    end
                 end
-                cData(sampleNr,k) = value(k) * LSBweight;                  
-            end 
+                cData(sampleNr,:) = byteData(1:nCh,:)';
+            end
         end
-    end
+
+       %%%%% INTAN RHA2216 %%%%%
+       if strcmp(deviceName, 'RHA2216')   
+    %        LSBweight = double(2.5/(200*65535));                              % Intan differential gain is 200 V/V
+            LSBweight = double(2.5/(65535));                                   % It is better to plot data with gain scaling effect
+            for sampleNr = 1:tWs                  
+                value16 = fread(obj,nCh,'uint16');
+                for k = 1:nCh
+    %                 cData(sampleNr,k) = value16(k) - 16384;                  % Centers data and scales it to fit the graphs
+                    cData(sampleNr,k) = value16(k)*LSBweight;                  % Convert data into volt
+                end
+            end 
+       end
    
-   %%%%% INTAN RHA2216 %%%%%
-   if strcmp(deviceName, 'RHA2216')   
-       LSBweight = double(2.5/(200*65535));                                % Intan differential gain is 200 V/V
-        for sampleNr = 1:tWs                  
-            value16 = fread(obj,nCh,'uint16');
-            for k = 1:nCh
-%                 cData(sampleNr,k) = value16(k) - 16384;                  % Centers data and scales it to fit the graphs
-                cData(sampleNr,k) = value16(k)*LSBweight;                  % Convert data into volt
-            end
-        end 
-   end
+    catch exception
+       error = 1;
+    end
+    %Set warning back to normal state
+    warning(s);
    
 end

Comm/AFE/ConnectDevice.m

@@ -23,6 +23,8 @@
                             % SetDeviceStartAcquisition(),
                             % Acquire_tWs(), StopAcquisition(). This functions 
                             % has been moved to COMM/AFE folder, into this new script.
+% 2015-1-19 / Enzo Mastinu / The ADS1299 part has been modified in way to be 
+                            % compatible with the new ADS1299 acquisition mode (DSP + FPU)
                             
 
 % 20xx-xx-xx / Author  / Comment
@@ -41,23 +43,17 @@
     sT          = handles.sT;
     nCh         = handles.nCh;
     sTall       = handles.sTall;
-    
-    % Delete previous connection objects
-    if exist('obj')
-        fclose(obj);
-        delete(obj);
-    end
 
     %%%%% WiFi %%%%%
     if strcmp(ComPortType, 'WiFi')
         %%%%% TI ADS1299 %%%%%
-        if strcmp(deviceName, 'ADS1299')
-           obj = tcpip('192.168.100.10',65100,'NetworkRole','client');     % WIICOM                       
-           obj.InputBufferSize = sTall*sF*27;                              % 27bytes data package
+        if strcmp(deviceName, 'ADS_BP')
+            obj = tcpip('192.168.100.10',65100,'NetworkRole','client');        % ADS1299
+            obj.InputBufferSize = sTall*sF*nCh*4;  
         end
         %%%%% INTAN RHA2216 %%%%%
         if strcmp(deviceName, 'RHA2216')
-            obj = tcpip('192.168.100.10',65100,'NetworkRole','client');    % WIICOM
+            obj = tcpip('192.168.100.10',65100,'NetworkRole','client');        % WIICOM
             obj.InputBufferSize = sT*sF*nCh*2;  
         end
     end
@@ -66,8 +62,12 @@
     if strcmp(ComPortType, 'COM')
         %%%%% TI ADS1299 %%%%%
         if strcmp(deviceName, 'ADS1299')
-           obj = serial (ComPortName, 'baudrate', 2500000, 'databits', 8, 'byteorder', 'bigEndian');                       
-           obj.InputBufferSize = sTall*sF*27;                              % 27bytes data package
+           obj = serial (ComPortName, 'baudrate', 2000000, 'databits', 8, 'byteorder', 'bigEndian');                       
+           obj.InputBufferSize = sTall*sF*27;                                 % 27bytes data package
+        end
+        if strcmp(deviceName, 'ADS_BP')
+           obj = serial (ComPortName, 'baudrate', 460800, 'databits', 8, 'byteorder', 'bigEndian');
+           obj.InputBufferSize = sTall*sF*nCh*4;     
         end
         %%%%% INTAN RHA2216 %%%%%
         if strcmp(deviceName, 'RHA2216')

Comm/AFE/SBI/InitSBI_NI.m

@@ -28,13 +28,16 @@
 %                           job
 % 2012-05-29 / Max Ortiz  / Removed the routine for sequentially adding
 %                           channels to a loop.
+% 2016-02-10 / Max Ortiz  / Modifed routine to use chAI directly as a
+%                           string of numbers identifying each channels
+%                           as in the GUI
 % 20xx-xx-xx / Author    / Comment on update
 
 function [s] = InitSBI_NI(sF, sT, chAI, chAO)
 
 % Auxiliar variables
-nChAI = size(chAI,2);
-chAIidx = find(chAI);
+% nChAI = size(chAI,2);
+% chAIidx = find(chAI);
 
 % Close possible daq objects running
 if (~isempty(daqfind))
@@ -50,8 +53,8 @@
 
 % Add channels in a loop
 
-for i = 1 : size(chAIidx,2)
-    chID = ['ai' num2str(chAIidx(i)-1)];    
+for i = 1 : size(chAI,2)
+    chID = ['ai' num2str(chAI(i)-1)];    
     s.addAnalogInputChannel(dev.ID,chID,'Voltage');
     s.Channels(i).InputType ='SingleEnded';
     s.Channels(i).Range = [-5 5];    

Comm/AFE/SetDeviceStartAcquisition.m

@@ -23,7 +23,16 @@
                             % SetDeviceStartAcquisition(),
                             % Acquire_tWs(), StopAcquisition(). This functions 
                             % has been moved to COMM/AFE folder, into this new script.
-                            
+% 2015-1-19 / Enzo Mastinu / The ADS1299 part has been modified in way to be 
+                            % compatible with the new ADS1299 acquisition mode (DSP + FPU)
+% 2015-4-10 / Enzo Mastinu / The ADS1299_DSP acquisition has been optimized, only desired
+                            % channels are transmitted to PC, not all as
+                            % before. To do that PC sends start command
+                            % followed by the number of channels requested
+% 2016-5-9 / Enzo Mastinu / The ADS_BP acquisition has been optimized. Now
+%                           % sF will be set before starting the recording.
+%                           % Only some values of sF are allowed. 
+
 % 20xx-xx-xx / Author  / Comment
 
 
@@ -35,13 +44,12 @@ function SetDeviceStartAcquisition(handles, obj)
     nCh         = handles.nCh;
     sTall       = handles.sTall;
     sF          = handles.sF;
-    
-
+     
     %%%%% INTAN RHA2216 %%%%%
     if strcmp(deviceName, 'RHA2216')
 
         % Setup the selected channels
-        vCh = 0:nCh'-1;                                                    % Vector of channels    
+        vCh = 0:nCh'-1;  
         fwrite(obj,'C','char');
         fwrite(obj,nCh,'uint8');
         for i = 1 : nCh    
@@ -97,5 +105,58 @@ function SetDeviceStartAcquisition(handles, obj)
             return
         end
     end
+    if strcmp(deviceName, 'ADS_BP')
+        % Set the ADS_BP datarate output
+        if(sF~=500 && sF~=1000 && sF~=2000)
+            disp('The selected sampling frequency is not valid for the ADS_BP. Errors may occur!');
+            errordlg('The selected sampling frequency is not valid for the ADS_BP. Errors may occur!','Erroneous sampling frequency');
+        end
+        fwrite(obj,'T','char');
+        % Read available data and discard it
+        if obj.BytesAvailable > 1
+            fread(obj,obj.BytesAvailable,'uint8');       
+        end
+        fwrite(obj,'r','char');
+        replay = char(fread(obj,1,'char'));
+        if strcmp(replay,'r')
+            fwrite(obj,sF,'uint32');
+            replay = char(fread(obj,1,'char'));
+            if strcmp(replay,'r');
+                set(handles.t_msg,'String','sampling frequency set');
+            else
+                set(handles.t_msg,'String','Error Setting sampling frequency'); 
+                fclose(obj);
+                return
+            end
+        else
+            set(handles.t_msg,'String','Error Setting sampling frequency'); 
+            fclose(obj);
+            return
+        end
+        % Send the START command
+        fwrite(obj,'G','char');
+        fwrite(obj,nCh,'char');
+        replay = char(fread(obj,1,'char'));
+        switch replay
+            case 'G'
+                set(handles.t_msg,'String','EMG Start');
+            case 'L'
+                set(handles.t_msg,'String','Error: Neuromotus locked');
+                fclose(obj);
+                return
+            case 'B'
+                set(handles.t_msg,'String','Error: Battery Low!');
+                fclose(obj);
+                return
+        end
+        % the digital filtering introduce a transient not needed in recording
+        % session. To avoid that transient we can just skip the first
+        % samples coming from the device
+        settlingTime = 1;
+        settlingSamples = settlingTime*sF;
+        for sampleNr = 1:settlingSamples
+            fread(obj,nCh,'float32');
+        end
+    end
          
 end

Comm/AFE/StopAcquisition.m

@@ -42,5 +42,9 @@ function StopAcquisition(deviceName, obj)
         fwrite(obj,'G','char');                                        % Stop the aquisition  ´
         fclose(obj);                                                   % Close connection
     end
+    if strcmp(deviceName, 'ADS_BP')
+        fwrite(obj,'T','char');                                        % Stop the aquisition  ´
+        fclose(obj);                                                   % Close connection
+    end
         
 end

Comm/ALC/VCP_Piccolo/Connect_ALC.m

@@ -1,39 +0,0 @@
-% ---------------------------- Copyright Notice ---------------------------
-% This file is part of BioPatRec © which is open and free software under 
-% the GNU Lesser General Public License (LGPL). See the file "LICENSE" for 
-% the full license governing this code and copyrights.
-%
-% BioPatRec was initially developed by Max J. Ortiz C. at Integrum AB and 
-% Chalmers University of Technology. All authors’ contributions must be kept
-% acknowledged below in the section "Updates % Contributors". 
-%
-% Would you like to contribute to science and sum efforts to improve 
-% amputees’ quality of life? Join this project! or, send your comments to:
-% maxo@chalmers.se.
-%
-% The entire copyright notice must be kept in this or any source file 
-% linked to BioPatRec. This will ensure communication with all authors and
-% acknowledge contributions here and in the project web page (optional).
-% ------------------- Function Description ------------------
-% Function to create the communicatio object
-
-% --------------------------Updates--------------------------
-% 2011-11-09 / Max Ortiz  / Creation
-% 20xx-xx-xx / Author  / Comment
-
-
-
-function obj = Connect_ALC(conn)
-    %conn, Connection String
-    %Find serial port objects with specified property values
-    obj.io=instrfind('Status','open');
-    if isempty(obj.io)
-        obj.io=serial(conn, 'BaudRate', 14400);
-        pause(1)
-        % Open io for read and write access
-        set(obj.io,'InputBuffer',1024*64)
-        fopen(obj.io)
-        pause(1)
-    end
-
-end