Olfactometer ip

.gitignore

@@ -0,0 +1,5 @@
+Calibration Files/**
+Data/**
+Protocols/**
+.gitmodules
+*BpodUserPath.txt

Functions/Internal Functions/BpodObject.m

@@ -32,6 +32,7 @@
         ProtocolSettings
         Data
         BpodPath
+        BpodUserPath % FS MOD
         SettingsPath
         DataPath
         ProtocolPath
@@ -117,31 +118,54 @@
 
             obj.HostOS = system_dependent('getos');
             obj.BpodPath = BpodPath;
-            dir_calfiles = dir( fullfile(obj.BpodPath,'Calibration Files') );
-            if length(dir_calfiles) == 0, %then Cal Folder didn't exist.
-                mkdir(fullfile(obj.BpodPath,'Calibration Files'));
-                obj.CalibrationTables.LiquidCal = [];
-                obj.CalibrationTables.SoundCal = [];
+            %% FS MOD
+            if exist(fullfile(obj.BpodPath,'BpodUserPath.txt'),'file') == 2
+                UserFile = fopen(fullfile(obj.BpodPath,'BpodUserPath.txt'),'r');
+                BpodUserPath = fscanf(UserFile,'%s');
+                fclose(UserFile);
             else
-                % Liquid
-                try
-                    LiquidCalibrationFilePath = fullfile(obj.BpodPath, 'Calibration Files', 'LiquidCalibration.mat');
-                    load(LiquidCalibrationFilePath);
-                    obj.CalibrationTables.LiquidCal = LiquidCal;
-                catch
-                  obj.CalibrationTables.LiquidCal = [];  
-                end
-                % Sound
-                try
-                    SoundCalibrationFilePath = fullfile(obj.BpodPath, 'Calibration Files', 'SoundCalibration.mat');
-                    load(SoundCalibrationFilePath);
-                    obj.CalibrationTables.SoundCal = SoundCal;
-                catch
-                  obj.CalibrationTables.SoundCal = [];  
+                if ispc
+                    import java.lang.*;
+                    BpodUserPath = fullfile(char(System.getProperty('user.home')), 'BpodUser');
+                else
+                    BpodUserPath = fullfile('~', 'BpodUser');
                 end
+                UserFile = fopen(fullfile(obj.BpodPath,'BpodUserPath.txt'),'w');
+                fprintf(UserFile,'%s',BpodUserPath);
+                fclose(UserFile);
+            end
+            obj.BpodUserPath = BpodUserPath;
+            if ~isdir(obj.BpodUserPath)
+                mkdir(obj.BpodUserPath);
+                warning(['Bpod user directory not found. Directory created at ' obj.BpodUserPath]);
+            end
+            %setting up costum folders
+            if ~isdir(fullfile(obj.BpodUserPath,'Calibration Files')) %then Cal Folder didn't exist.
+                copyfile(fullfile(obj.BpodPath, 'Calibration Files'),fullfile(obj.BpodUserPath,'Calibration Files')); % FS MOD
             end
+            if ~isdir(fullfile(obj.BpodUserPath,'Settings Files'))
+                copyfile(fullfile(obj.BpodPath, 'Settings Files'), fullfile(obj.BpodUserPath, 'Settings Files'));
+            end
+
+            % Liquid
+            try
+                LiquidCalibrationFilePath = fullfile(obj.BpodUserPath, 'Calibration Files', 'LiquidCalibration.mat'); % FS MOD
+                load(LiquidCalibrationFilePath);
+                obj.CalibrationTables.LiquidCal = LiquidCal;
+            catch
+                obj.CalibrationTables.LiquidCal = [];
+            end
+            % Sound
+            try
+                SoundCalibrationFilePath = fullfile(obj.BpodUserPath, 'Calibration Files', 'SoundCalibration.mat'); % FS MOD
+                load(SoundCalibrationFilePath);
+                obj.CalibrationTables.SoundCal = SoundCal;
+            catch
+                obj.CalibrationTables.SoundCal = [];
+            end
+
             % Load input channel settings
-            obj.InputConfigPath = fullfile(obj.BpodPath, 'Settings Files', 'BpodInputConfig.mat');
+            obj.InputConfigPath = fullfile(obj.BpodUserPath, 'Settings Files', 'BpodInputConfig.mat'); % FS MOD
             load(obj.InputConfigPath);
             obj.InputsEnabled = BpodInputConfig;
 
@@ -155,9 +179,9 @@
                 obj.UsesPsychToolbox = 0;
             end
             %Check for Data folder
-            dir_data = dir(fullfile(obj.BpodPath,'Data'));
+            dir_data = dir(fullfile(obj.BpodUserPath,'Data')); % FS MOD
             if length(dir_data) == 0, %then Data didn't exist.
-                mkdir(fullfile(obj.BpodPath, 'Data'));
+                mkdir(fullfile(obj.BpodUserPath, 'Data'));
             end
         end
         function obj = InitializeHardware(obj, portString)
@@ -425,7 +449,12 @@
             set(obj.GUIHandles.MainFig,'handlevisibility','off');
 
             % Load protocols into selector
-            ProtocolPath = fullfile(obj.BpodPath,'Protocols');
+ %% FS MOD             
+            ProtocolPath = fullfile(obj.BpodUserPath,'Protocols');
+            if ~isdir(ProtocolPath)
+                mkdir(ProtocolPath)
+            end
+%%            
             Candidates = dir(ProtocolPath);
             ProtocolNames = cell(1);
             nCandidates = length(Candidates)-2;

Functions/Internal Functions/SaveBpodSystemSettings.m

@@ -1,4 +1,4 @@
 function SaveBpodSystemSettings
 global BpodSystem
 BpodSystemSettings = BpodSystem.SystemSettings;
-save(fullfile(BpodSystem.BpodPath, 'Settings Files', 'BpodSystemSettings.mat'), 'BpodSystemSettings');
+save(fullfile(BpodSystem.BpodUserPath, 'Settings Files', 'BpodSystemSettings.mat'), 'BpodSystemSettings'); % FS MOD

Functions/Launch manager/LaunchManager.m

@@ -91,9 +91,9 @@ function LaunchManager_OpeningFcn(hObject, eventdata, handles, varargin)
 % Check to see if a folder for this protocol's name exists, and if not, make one
 % along with default files for the default test subject named "Test Session"
 
-DataPath = fullfile(BpodSystem.BpodPath,'Data',DummySubjectString);
+DataPath = fullfile(BpodSystem.BpodUserPath,'Data',DummySubjectString);
 ProtocolName = BpodSystem.CurrentProtocolName;
-ProtocolPath = fullfile(BpodSystem.BpodPath,'Protocols',ProtocolName);
+ProtocolPath = fullfile(BpodSystem.BpodUserPath,'Protocols',ProtocolName);
 SettingsPath = fullfile(DataPath,ProtocolName,'Session Settings');
 DefaultSettingsPath = fullfile(ProtocolPath,'SessionSettings.mat');
 
@@ -113,7 +113,7 @@ function LaunchManager_OpeningFcn(hObject, eventdata, handles, varargin)
 % Make a list of the names of all subjects who already have a folder for this
 % protocol.
 
-DataPath = fullfile(BpodSystem.BpodPath,'Data');
+DataPath = fullfile(BpodSystem.BpodUserPath,'Data');
 CandidateSubjects = dir(DataPath);
 SubjectNames = cell(1);
 nSubjects = 1;
@@ -133,7 +133,7 @@ function LaunchManager_OpeningFcn(hObject, eventdata, handles, varargin)
 end
 set(handles.listbox1,'String',SubjectNames);
 
-SettingsPath = fullfile(BpodSystem.BpodPath,'Data',DummySubjectString, ProtocolName,'Session Settings');
+SettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',DummySubjectString, ProtocolName,'Session Settings');
 Candidates = dir(SettingsPath);
 nSettingsFiles = 0;
 SettingsFileNames = cell(1);
@@ -211,7 +211,7 @@ function listbox1_Callback(hObject, eventdata, handles)
     else
         SelectedName = NameList;
     end
-SettingsPath = fullfile(BpodSystem.BpodPath,'Data',SelectedName,ProtocolName,'Session Settings');
+SettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',SelectedName,ProtocolName,'Session Settings');
 Candidates = dir(SettingsPath);
 nSettingsFiles = 0;
 SettingsFileNames = cell(1);
@@ -268,7 +268,7 @@ function pushbutton1_Callback(hObject, eventdata, handles)
     if ~isempty(SettingsFileName) && ~isempty(NameList)
         ProtocolName = BpodSystem.CurrentProtocolName;
         FormattedDate = [datestr(now, 3) datestr(now, 7) '_' datestr(now, 10)];
-        DataFolder = fullfile(BpodSystem.BpodPath,'Data',SubjectName,ProtocolName, 'Session Data');
+        DataFolder = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName,ProtocolName, 'Session Data');
         Candidates = dir(DataFolder);
         nSessionsToday = 0;
         for x = 1:length(Candidates)
@@ -278,11 +278,11 @@ function pushbutton1_Callback(hObject, eventdata, handles)
                 end
             end
         end
-        DataPath = fullfile(BpodSystem.BpodPath,'Data',SubjectName,ProtocolName,'Session Data',[SubjectName '_' ProtocolName '_' FormattedDate '_Session' num2str(nSessionsToday+1) '.mat']);
-        SettingsPath = fullfile(BpodSystem.BpodPath,'Data',SubjectName,ProtocolName, 'Session Settings',[SettingsFileName '.mat']);
+        DataPath = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName,ProtocolName,'Session Data',[SubjectName '_' ProtocolName '_' FormattedDate '_Session' num2str(nSessionsToday+1) '.mat']);
+        SettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName,ProtocolName, 'Session Settings',[SettingsFileName '.mat']);
         BpodSystem.DataPath = DataPath;
         BpodSystem.SettingsPath = SettingsPath;
-        ProtocolPath = fullfile(BpodSystem.BpodPath,'Protocols',ProtocolName,[ProtocolName '.m']);
+        ProtocolPath = fullfile(BpodSystem.BpodUserPath,'Protocols',ProtocolName,[ProtocolName '.m']);
         close(LaunchManager)
         BpodSystem.Live = 1;
         BpodSystem.GUIData.ProtocolName = ProtocolName;
@@ -331,9 +331,9 @@ function pushbutton2_Callback(hObject, eventdata, handles)  % ------------------
 NewName = Spaces2Underscores(NewName);
 % Check to see if subject already exists
 ProtocolName = BpodSystem.CurrentProtocolName;
-Testpath = fullfile(BpodSystem.BpodPath,'Data',NewName);
+Testpath = fullfile(BpodSystem.BpodUserPath,'Data',NewName);
 Testpath2 = fullfile(Testpath,ProtocolName);
-ProtocolPath = fullfile(BpodSystem.BpodPath,'Protocols',ProtocolName);
+ProtocolPath = fullfile(BpodSystem.BpodUserPath,'Protocols',ProtocolName);
 NewAnimal = 0;
 if exist(Testpath) ~= 7
     mkdir(Testpath);
@@ -397,7 +397,7 @@ function pushbutton3_Callback(hObject, eventdata, handles)
     catch
     end
     if ((OkToDelete == 1) && (~isempty(SelectedName)))
-        DeletePath = fullfile(BpodSystem.BpodPath,'Data',SelectedName);
+        DeletePath = fullfile(BpodSystem.BpodUserPath,'Data',SelectedName);
          rmdir(DeletePath,'s')
         BpodErrorSound;
          msgbox(['       Entry  for ' SelectedName ' deleted!'], 'Modal');
@@ -459,7 +459,7 @@ function pushbutton4_Callback(hObject, eventdata, handles)
 SubjectName = SubjectNameList{SubjectNameValue};
 % Check to see if subject already exists
 ProtocolName = BpodSystem.CurrentProtocolName;
-Testpath = 			fullfile(BpodSystem.BpodPath,'Data',SubjectName,ProtocolName,'Session Settings',[NewSettingsName '.mat' ]);
+Testpath = 			fullfile(BpodSystem.BpodUserPath,'Data',SubjectName,ProtocolName,'Session Settings',[NewSettingsName '.mat' ]);
 if exist(Testpath) == 0
     SettingsPath = Testpath;
     ProtocolSettings = struct;
@@ -502,13 +502,13 @@ function pushbutton5_Callback(hObject, eventdata, handles)
 Selected = get(handles.listbox2, 'Value');
 SettingsFileName = NameList{Selected};
 ProtocolName = BpodSystem.CurrentProtocolName;
-SettingsPath = fullfile(BpodSystem.BpodPath,'Data',SubjectName,ProtocolName,'Session Settings',[ SettingsFileName '.mat']);
+SettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName,ProtocolName,'Session Settings',[ SettingsFileName '.mat']);
 delete(SettingsPath);
 BpodErrorSound;
 msgbox(['Settings file ' SettingsFileName ' deleted!'], 'Modal');
 set(handles.listbox2, 'Value', 1);
 % Update UI with new settings
-SettingsPath = fullfile(BpodSystem.BpodPath,'Data',SubjectName, ProtocolName,'Session Settings');
+SettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName, ProtocolName,'Session Settings');
 Candidates = dir(SettingsPath);
 nSettingsFiles = 0;
 SettingsFileNames = cell(1);
@@ -549,7 +549,7 @@ function pushbutton6_Callback(hObject, eventdata, handles)
 Selected = get(handles.listbox2, 'Value');
 SettingsFileName = NameList{Selected};
 ProtocolName = BpodSystem.CurrentProtocolName;
-SettingsPath = fullfile(BpodSystem.BpodPath,'Data',SubjectName,ProtocolName,'Session Settings',[ SettingsFileName '.mat']);
+SettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName,ProtocolName,'Session Settings',[ SettingsFileName '.mat']);
 BpodSystem.SettingsPath = SettingsPath;
 evalin('base', ['load(''' SettingsPath ''')'])
 clc
@@ -567,7 +567,7 @@ function pushbutton7_Callback(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 global BpodSystem;
-SearchStartPath = fullfile(BpodSystem.BpodPath, 'Data');
+SearchStartPath = fullfile(BpodSystem.BpodUserPath, 'Data');
 [Filename Pathname Junk] = uigetfile('*.mat', 'Select settings to import', SearchStartPath);
 SettingsName = Filename(1:(length(Filename)-4));
 TargetSettingsPath = [Pathname Filename];
@@ -582,7 +582,7 @@ function pushbutton7_Callback(hObject, eventdata, handles)
 Selected = get(handles.listbox1, 'Value');
 SubjectName = NameList{Selected};
 ProtocolName = BpodSystem.CurrentProtocolName;
-DestinationSettingsPath = fullfile(BpodSystem.BpodPath,'Data',SubjectName,ProtocolName,'Session Settings',[ SettingsName '.mat']);
+DestinationSettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName,ProtocolName,'Session Settings',[ SettingsName '.mat']);
 
 if (exist(DestinationSettingsPath) == 2)
     msgbox(['"' SettingsName '"' ' already exists in the target folder. Import aborted.'])
@@ -593,7 +593,7 @@ function pushbutton7_Callback(hObject, eventdata, handles)
 copyfile(TargetSettingsPath, DestinationSettingsPath);
 
 % Update UI with new settings
-SettingsPath = fullfile(BpodSystem.BpodPath,'Data',SubjectName, ProtocolName,'Session Settings');
+SettingsPath = fullfile(BpodSystem.BpodUserPath,'Data',SubjectName, ProtocolName,'Session Settings');
 Candidates = dir(SettingsPath);
 nSettingsFiles = 0;
 SettingsFileNames = cell(1);

Functions/Launch manager/RunProtocol.m

@@ -27,7 +27,7 @@ function RunProtocol(Opstring)
             SelectedProtocol = get(BpodSystem.GUIHandles.ProtocolSelector, 'Value');
             SelectedProtocolName = ProtocolNames{SelectedProtocol};
             BpodSystem.CurrentProtocolName = SelectedProtocolName;
-            addpath(fullfile(BpodSystem.BpodPath, 'Protocols', SelectedProtocolName));
+            addpath(fullfile(BpodSystem.BpodUserPath, 'Protocols', SelectedProtocolName));
             LaunchManager;
         else
             if BpodSystem.Pause == 0
@@ -41,11 +41,17 @@ function RunProtocol(Opstring)
             end
         end
     case 'Stop'
+        %execute user kill script
+        try
+            [~,Protocol]=fileparts(fileparts(fileparts(BpodSystem.DataPath)));
+            run(fullfile(BpodSystem.BpodUserPath,'Protocols',Protocol,'UserKillScript.m'));
+        catch
+        end
         if ~isempty(BpodSystem.CurrentProtocolName)
             disp(' ')
             disp([BpodSystem.CurrentProtocolName ' ended.'])
         end
-        rmpath(fullfile(BpodSystem.BpodPath, 'Protocols', BpodSystem.CurrentProtocolName));
+        rmpath(fullfile(BpodSystem.BpodUserPath, 'Protocols', BpodSystem.CurrentProtocolName));
         BpodSystem.BeingUsed = 0;
         BpodSystem.CurrentProtocolName = '';
         BpodSystem.SettingsPath = '';

Functions/Launch manager/SaveBpodProtocolSettings.m

@@ -19,4 +19,8 @@
 %}
 function SaveBpodProtocolSettings
 global BpodSystem
-save(BpodSystem.SettingsPath, 'BpodSystem.ProtocolSettings');
+
+% now compatible with recent matlab versions in which you can't save a
+% structure field directly (FS MOD)
+ProtocolSettings = BpodSystem.ProtocolSettings;
+save(BpodSystem.SettingsPath, 'ProtocolSettings');

Functions/LiquidCalibrator/BpodLiquidCalibration.m

@@ -40,7 +40,7 @@
 
         % Setup calibration
         BpodSystem.PluginObjects.LiquidCal.PendingMeasurements = cell(1,8);
-        CalibrationFilePath = fullfile(BpodSystem.BpodPath, 'Calibration Files', 'LiquidCalibration.mat');
+        CalibrationFilePath = fullfile(BpodSystem.BpodUserPath, 'Calibration Files', 'LiquidCalibration.mat');
         if exist(CalibrationFilePath) == 2
             load(CalibrationFilePath);
         else
@@ -329,11 +329,11 @@ function RemoveMeasurement(varargin)
         BpodSystem.PluginObjects.LiquidCal.CalData(CurrentValve).Coeffs = [];
     end
     % Save file
-    TestSavePath = fullfile(BpodSystem.BpodPath, 'Calibration Files');
+    TestSavePath = fullfile(BpodSystem.BpodUserPath, 'Calibration Files');
     if exist(TestSavePath) ~= 7
         mkdir(TestSavePath);
     end
-    SavePath = fullfile(BpodSystem.BpodPath, 'Calibration Files', 'LiquidCalibration.mat');
+    SavePath = fullfile(BpodSystem.BpodUserPath, 'Calibration Files', 'LiquidCalibration.mat');
     LiquidCal = BpodSystem.PluginObjects.LiquidCal.CalData;
     LiquidCal(1).LastDateModified = now;
     save(SavePath, 'LiquidCal');
@@ -696,11 +696,11 @@ function AddCalMeasurements(varargin)
     % LiquidCalibrationManager to reflect the new pending measurements vector
 
     % Save file
-    TestSavePath = fullfile(BpodSystem.BpodPath, 'Calibration Files');
+    TestSavePath = fullfile(BpodSystem.BpodUserPath, 'Calibration Files');
     if exist(TestSavePath) ~= 7
         mkdir(TestSavePath);
     end
-    SavePath = fullfile(BpodSystem.BpodPath, 'Calibration Files', 'LiquidCalibration.mat');
+    SavePath = fullfile(BpodSystem.BpodUserPath, 'Calibration Files', 'LiquidCalibration.mat');
     LiquidCal = BpodSystem.PluginObjects.LiquidCal.CalData;
     LiquidCal(1).LastDateModified = now;
     save(SavePath, 'LiquidCal');