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BpodObject.m
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BpodObject.m
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%{
----------------------------------------------------------------------------
This file is part of the Sanworks Bpod repository
Copyright (C) Sanworks LLC, Rochester, New York, USA
----------------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3.
This program is distributed WITHOUT ANY WARRANTY and without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
%}
% BpodObject is a class representing the Bpod behavior measurement system.
% Bpod() creates BpodSystem, an instance of BpodObject that is global and
% accessed by user code, and internally throughout the code base.
%
% User-facing fields and functions of BpodObject are documented on the wiki,
% at https://sanworks.github.io/Bpod_Wiki/function-reference/
classdef BpodObject < handle
properties
MachineType % 1 = Bpod 0.5, 2 = Bpod 0.7+, 3 = 2.X, 4 = 2+
FirmwareVersion % An integer specifying the firmware on the connected device
SerialPort % ArCOM serial port object
AnalogSerialPort % On state machine r2+ or newer, this is a dedeicated USB serial port to handle analog data
HW % Hardware description
Modules % Connected UART serial module description
ModuleUSB % Struct containing paired USB port name for each connected module, (e.g. ModuleUSB.ModuleName = 'COM3')
Status % Struct with system status variables
Path % Struct with paths to Bpod root folder and specific sub-folders
Data % Struct storing all data collected in the current session. SaveBpodSessionData saves this to the current data file.
FlexIOConfig % Struct with Flex I/O channel config (FSM 2+). Changes to this field are automatically synced to the device.
AnalogDataFile % On Bpod FSM 2+ or newer, a memory-mapped MAT file containing analog data (see matfile() MATLAB docs)
StateMatrix % Struct of matrices describing current (running) state machine
StateMatrixSent % StateMatrix sent to the state machine, for the next trial. At run, this replaces StateMatrix.
LastStateMatrix % Last state matrix completed. This is updated each time a trial run completes.
HardwareState % Current state of I/O lines and serial codes
StateMachineInfo % Struct with information about state machines (customized for connected hardware)
GUIHandles % Struct with graphics handles
GUIData % Struct with graphics data
InputsEnabled % Struct storing input channels that are connected to something. This is modified from the settings menu UI.
SyncConfig % Struct storing the sync channel and mode (modified from settings menu UI)
PluginSerialPorts % Struct with serial port objects for plugins (modules)
PluginFigureHandles % Struct with figure handles for plugins
PluginObjects % Struct with plugin objects
SystemSettings % Struct with miscellaneous system settings
SoftCodeHandlerFunction % The path to a user m-file triggered by the state machine to run PC-side tasks (play video, etc.)
ProtocolFigures % A struct of figure handles used by the current protocol. Figs are auto-closed when the session ends.
ProtocolSettings % The settings struct selected by the user in the launch manager, when launching a protocol
Emulator % A struct with the internal variables of the emulator (mirror of state machine workspace in Arduino)
ManualOverrideFlag % Used in the emulator to indicate an override that needs to be handled
VirtualManualOverrideBytes % Stores emulated event byte codes generated by manual override
CalibrationTables % Struct for liquid, sound, etc.
BlankStateMachine % Holds a blank state machine to use with AddState().
ProtocolStartTime % The time when the current protocol was started.
BonsaiSocket % An object containing a TCP/IP socket for communication with Bonsai
EmulatorMode % 0 if actual device connected, 1 if emulator
HostOS % Holds a string naming the host operating system (i.e. 'Microsoft Windows 10')
Timers % A struct containing MATLAB timer objects
LiveTimestamps % Set to 1 if a timestamp is sent with each event, 0 if sent after the trial is complete
end
properties (Access = private)
CurrentFirmware % Struct of current firmware versions for state machine + curated modules
SplashData % Splash screen frames
LastHardwareState % Last known state of I/O lines and serial codes
CycleMonitoring % 0 = off, 1 = on. Measures min and max actual hardware timer callback execution time
IsOnline % 1 if connection to Internet is available, 0 if not
end
methods
function obj = BpodObject
% Constructor, run when creating an instance of BpodObject
% Notify the user of the installed software version
ver = BpodSoftwareVersion_Semantic;
disp(['Starting Bpod Console v' ver])
% Check path for duplicate Bpod installations
matlabPath = path;
nInstallations = length([strfind(matlabPath, 'Bpod_Gen2;') strfind(matlabPath, 'Bpod_Gen2-develop;')]);
if nInstallations > 1
error(['Duplicate Bpod_Gen2 folders found in the MATLAB path. ' char(10)...
'Please remove duplicates of Bpod_Gen2 and any duplicate subfolders before running Bpod.'])
end
% Add Bpod code to MATLAB path
bpodPath = fileparts(which('Bpod'));
addpath(genpath(fullfile(bpodPath, 'Assets')));
rmpath(genpath(fullfile(bpodPath, 'Assets', 'BControlPatch', 'ExperPort')));
addpath(genpath(fullfile(bpodPath, 'Examples', 'State Machines')));
load BpodSplashData;
if exist('rng','file') == 2
rng('shuffle', 'twister'); % Seed the random number generator by CPU clock
else
rand('twister', sum(100*fliplr(clock))); % For older versions of MATLAB
end
% Check for Internet Connection
obj.IsOnline = obj.check4Internet();
% Validate software version
if obj.IsOnline
obj.ValidateSoftwareVersion();
end
% Initialize fields
obj.LiveTimestamps = 0;
obj.SplashData = SplashData;
obj.Status.BpodStartTime = now;
obj.Status = struct;
obj.Status.Initialized = false;
obj.Status.LastTimestamp = 0;
obj.Status.CurrentStateCode = 0;
obj.Status.LastStateCode = 0;
obj.Status.CurrentStateName = '';
obj.Status.LastStateName = '';
obj.Status.LastEvent = 0;
obj.Status.Live = 0;
obj.Status.Pause = 0;
obj.Status.InStateMatrix = 0;
obj.Status.BeingUsed = 0;
obj.Status.BpodStartTime = 0;
obj.Status.CurrentProtocolName = '';
obj.Status.CurrentSubjectName = '';
obj.Status.SerialPortName = '';
obj.Status.NewStateMachineSent = 0;
obj.Status.SessionStartFlag = 0;
obj.Status.AnalogViewer = 0;
obj.Status.nAnalogSamples = 0;
obj.Status.RecordAnalog = 1;
% Initialize paths
obj.Path = struct;
obj.Path.BpodRoot = bpodPath;
obj.Path.ParentDir = fileparts(bpodPath);
obj.Path.LocalDir = fullfile(obj.Path.ParentDir, 'Bpod Local');
obj.Path.SettingsDir = fullfile(obj.Path.LocalDir, 'Settings');
obj.Path.Settings = '';
obj.Path.DataFolder = '';
obj.Path.CurrentDataFile = '';
obj.Path.CurrentProtocol= '';
obj.Path.InputConfig = fullfile(obj.Path.SettingsDir, 'InputConfig.mat');
obj.Path.FlexConfig = fullfile(obj.Path.SettingsDir, 'FlexConfig.mat');
obj.Path.SyncConfig = fullfile(obj.Path.SettingsDir, 'SyncConfig.mat');
obj.Path.ModuleUSBConfig = fullfile(obj.Path.SettingsDir, 'ModuleUSBConfig.mat');
% Initialize state machine info, to be populated in SetupStateMachine()
obj.StateMachineInfo = struct;
obj.StateMachineInfo.nEvents = 0; % Number of events the state machine can respond to
obj.StateMachineInfo.EventNames = 0; % Cell array of strings with names for each event
obj.StateMachineInfo.InputChannelNames = 0; % cell array of strings with names for input channels
obj.StateMachineInfo.nOutputChannels = 0; % Number of output channels
obj.StateMachineInfo.OutputChannelNames = 0; % Cell array of strings with output channel names
obj.StateMachineInfo.MaxStates = 0; % Maximum number of states the attached Bpod can store
% Ensure that settings, data, protocol and calibration folders exist
if ~exist(obj.Path.LocalDir)
mkdir(obj.Path.LocalDir);
end
if ~exist(obj.Path.SettingsDir)
mkdir(obj.Path.SettingsDir);
end
addpath(genpath(obj.Path.SettingsDir));
if exist('BpodSettings.mat') > 0
load BpodSettings;
obj.SystemSettings = BpodSettings;
else
obj.SystemSettings = struct;
end
obj.Path.ProtocolFolder = '';
if isfield(obj.SystemSettings, 'ProtocolFolder')
if exist(obj.SystemSettings.ProtocolFolder)
obj.Path.ProtocolFolder = obj.SystemSettings.ProtocolFolder;
end
end
obj.Path.DataFolder = '';
if isfield(obj.SystemSettings, 'DataFolder')
if exist(obj.SystemSettings.DataFolder)
obj.Path.DataFolder = obj.SystemSettings.DataFolder;
end
end
obj.Path.BcontrolRootFolder = '';
if isfield(obj.SystemSettings, 'BcontrolRootFolder')
if exist(obj.SystemSettings.BcontrolRootFolder) == 7
obj.Path.BcontrolRootFolder = obj.SystemSettings.BcontrolRootFolder;
ExperPortFolder = fullfile(obj.Path.BcontrolRootFolder, 'ExperPort');
if exist(ExperPortFolder) == 7
addpath(ExperPortFolder);
end
end
end
% Get info about the PC
obj.HostOS = system_dependent('getos');
if ~isempty(strfind(obj.HostOS, 'Windows 7'))
disp(['Bpod Startup: Windows 7 detected.' char(10)...
'Please consider updating to Windows 10 or 11 for improved stability.' char(10)])
end
% Verify calibration folder and copy example calibration if none exist
% (so that users can validate the system and develop protocols before running calibration)
calFolder = fullfile(obj.Path.LocalDir,'Calibration Files');
if ~exist(calFolder)
mkdir(calFolder);
copyfile(fullfile(obj.Path.BpodRoot, 'Examples', 'Example Calibration Files'), calFolder);
questdlg('Calibration folder created in /BpodLocal/. Replace example calibration files soon.', ...
'Calibration folder not found', ...
'Ok', 'Ok');
end
% Load liquid calibration
try
liquidCalibrationFilePath = fullfile(obj.Path.LocalDir, 'Calibration Files', 'LiquidCalibration.mat');
load(liquidCalibrationFilePath);
obj.CalibrationTables.LiquidCal = LiquidCal;
catch
obj.CalibrationTables.LiquidCal = [];
end
% Load sound calibration
try
soundCalibrationFilePath = fullfile(obj.Path.LocalDir, 'Calibration Files', 'SoundCalibration.mat');
load(soundCalibrationFilePath);
obj.CalibrationTables.SoundCal = SoundCal;
catch
obj.CalibrationTables.SoundCal = [];
end
% Load input channel settings
if ~exist(obj.Path.InputConfig)
copyfile(fullfile(obj.Path.BpodRoot, 'Examples', 'Example Settings Files', 'InputConfig.mat'), obj.Path.InputConfig);
end
load(obj.Path.InputConfig);
obj.InputsEnabled = BpodInputConfig;
% Load sync settings
if ~exist(obj.Path.SyncConfig)
copyfile(fullfile(obj.Path.BpodRoot, 'Examples',...
'Example Settings Files', 'SyncConfig.mat'), obj.Path.SyncConfig);
end
load(obj.Path.SyncConfig);
obj.SyncConfig = BpodSyncConfig;
% Create module USB port config file (if not present)
if ~exist(obj.Path.ModuleUSBConfig)
copyfile(fullfile(obj.Path.BpodRoot, 'Examples',...
'Example Settings Files', 'ModuleUSBConfig.mat'), obj.Path.ModuleUSBConfig);
end
% Load list of current firmware versions
cf = CurrentFirmwareList; % Located in /Functions/Internal Functions/, returns list of current firmware
obj.CurrentFirmware = cf;
% Create timer objects
obj.Timers = struct;
obj.Timers.PortRelayTimer = timer('TimerFcn', 'UpdateSerialTerminals()',...
'ExecutionMode', 'fixedRate', 'Period', 0.1);
obj.Timers.AnalogTimer = timer('TimerFcn',@(h,e)obj.ProcessAnalogSamples(),...
'ExecutionMode', 'fixedRate', 'Period', 0.1);
obj.BpodSplashScreen(1);
end
function obj = resetSessionClock(obj)
% Resets the state machine session clock, used for event and state timestamps.
if obj.EmulatorMode == 0
obj.SerialPort.write('*', 'uint8'); % Reset session clock
confirmed = obj.SerialPort.read(1,'uint8');
if confirmed ~= 1
error('Error: confirm not returned after resetting session clock.')
end
end
end
function obj = setupFolders(obj)
% setupFolders() Launches a GUI for the user to set the locations of data and protocol folders
% This is called from the settings menu's 'Folder' button
if isfield(obj.GUIHandles, 'FolderConfigFig') && ~verLessThan('MATLAB', '8.4')
if isgraphics(obj.GUIHandles.FolderConfigFig)
figure(obj.GUIHandles.FolderConfigFig);
return
end
end
if ispc
FigHeight = 130; Label1Ypos = 28; Label2Ypos = 68;
else
FigHeight = 150; Label1Ypos = 38; Label2Ypos = 75;
end
obj.GUIHandles.FolderConfigFig = figure('Position', [350 480 600 FigHeight],...
'name', 'Setup folders', 'numbertitle', 'off', 'MenuBar', 'none', 'Resize', 'off');
ha = axes('units','normalized', 'position',[0 0 1 1]);
uistack(ha,'bottom');
BG = imread('SettingsMenuBG2.bmp');
imagesc(BG); axis off; drawnow;
text(10, Label1Ypos,'Protocols','Parent', ha , 'FontName', 'OCRAStd', 'FontSize', 13, 'Color', [0.8 0.8 0.8]);
text(10, Label2Ypos,'Data Root','Parent', ha , 'FontName', 'OCRAStd', 'FontSize', 13, 'Color', [0.8 0.8 0.8]);
if isfield(obj.SystemSettings, 'ProtocolFolder')
if isempty(obj.SystemSettings.ProtocolFolder)
protocolPath = fullfile(obj.Path.LocalDir, 'Protocols',filesep);
else
protocolPath = obj.SystemSettings.ProtocolFolder;
end
else
protocolPath = fullfile(obj.Path.LocalDir, 'Protocols',filesep);
end
if isfield(obj.SystemSettings, 'DataFolder')
if isempty(obj.SystemSettings.DataFolder)
dataPath = fullfile(obj.Path.LocalDir, 'Data',filesep);
else
dataPath = obj.SystemSettings.DataFolder;
end
else
dataPath = fullfile(obj.Path.LocalDir, 'Data',filesep);
end
ImportButtonGFX = imread('ImportButton.bmp');
obj.GUIHandles.setupFoldersButton = uicontrol(obj.GUIHandles.FolderConfigFig,...
'Style', 'pushbutton',...
'String', 'Ok',...
'Position', [270 10 60 25],...
'Callback', @(h,e)obj.setFolders(),...
'BackgroundColor', [.4 .4 .4],...
'ForegroundColor', [1 1 1]);
obj.GUIHandles.dataFolderEdit = uicontrol(obj.GUIHandles.FolderConfigFig,...
'Style', 'edit',...
'String', dataPath,...
'Position', [140 50 410 25],...
'HorizontalAlignment', 'Left',...
'BackgroundColor', [.8 .8 .8],...
'FontSize', 10,...
'FontName', 'Arial');
obj.GUIHandles.dataFolderNav = uicontrol(obj.GUIHandles.FolderConfigFig,...
'Style', 'pushbutton',...
'String', '',...
'Position', [560 50 25 25],...
'BackgroundColor', [.8 .8 .8],...
'CData', ImportButtonGFX,...
'Callback', @(h,e)obj.folderSetupUIGet('Data'));
obj.GUIHandles.protocolFolderEdit = uicontrol(obj.GUIHandles.FolderConfigFig,...
'Style', 'edit',...
'String', protocolPath,...
'Position', [140 90 410 25],...
'HorizontalAlignment', 'Left',...
'BackgroundColor', [.8 .8 .8],...
'FontSize', 10,...
'FontName', 'Arial');
obj.GUIHandles.protocolFolderNav = uicontrol(obj.GUIHandles.FolderConfigFig,...
'Style', 'pushbutton',...
'String', '',...
'Position', [560 90 25 25],...
'BackgroundColor', [.8 .8 .8],...
'CData', ImportButtonGFX,...
'Callback', @(h,e)obj.folderSetupUIGet('Protocol'));
end
function obj = folderSetupUIGet(obj, type)
% folderSetupUIGet() is a callback function triggered by the "select folder" button on the setupFolders() GUI.
% Arguments: type (char array) - a string indicating which folder type to select, 'Data' or 'Protocol'
switch type
case 'Data'
originalFolder = get(obj.GUIHandles.dataFolderEdit, 'String');
chosenFolder = uigetdir(obj.Path.LocalDir, 'Select Bpod data folder');
if chosenFolder == 0
chosenFolder = originalFolder;
end
set(obj.GUIHandles.dataFolderEdit, 'String', fullfile(chosenFolder, filesep));
case 'Protocol'
originalFolder = get(obj.GUIHandles.protocolFolderEdit, 'String');
chosenFolder = uigetdir(obj.Path.LocalDir, 'Select Bpod protocol folder');
if chosenFolder == 0
chosenFolder = originalFolder;
end
set(obj.GUIHandles.protocolFolderEdit, 'String', fullfile(chosenFolder, filesep));
end
end
function obj = setFolders(obj)
% setFolders() is a callback function triggered by the 'Ok' button on the setupFolders() GUI.
% It saves the selected data and protocol folders to the system settings file.
dataFolder = get(obj.GUIHandles.dataFolderEdit, 'String');
protocolFolder = get(obj.GUIHandles.protocolFolderEdit, 'String');
if exist(dataFolder) == 0
mkdir(dataFolder);
end
if exist(protocolFolder) == 0
mkdir(protocolFolder);
end
contents = dir(protocolFolder);
if length(contents) == 2
choice = questdlg('Copy example protocols to new protocol folder?', ...
'Protocol folder is empty', ...
'Yes', 'No', 'No');
if strcmp(choice, 'Yes')
copyfile(fullfile(obj.Path.BpodRoot, 'Examples', 'Protocols'), protocolFolder);
end
end
obj.Path.ProtocolFolder = protocolFolder;
obj.Path.DataFolder = dataFolder;
obj.SystemSettings.ProtocolFolder = protocolFolder;
obj.SystemSettings.DataFolder = dataFolder;
obj.SaveSettings;
close(obj.GUIHandles.FolderConfigFig);
end
function obj = Wiki(obj)
% Launches the Bpod wiki
% Triggered by the '?' button on the Bpod Console GUI
if ispc || ismac
web ('https://sanworks.github.io/Bpod_Wiki/', '-browser');
else
disp(['**NOTE** If MATLAB is running as root, your browser may fail to open. '...
'The wiki is at: https://sanworks.github.io/Bpod_Wiki/']);
web ('https://sanworks.github.io/Bpod_Wiki/');
end
end
function obj = SaveSettings(obj)
% Saves the BpodObject.SystemSettings struct to the Bpod settings file
BpodSettings = obj.SystemSettings;
save(fullfile(obj.Path.LocalDir, 'Settings', 'BpodSettings.mat'), 'BpodSettings');
end
function obj = BeingUsed(obj)
% A notice to the user for obsolete protocol syntax
error('Error: "BpodSystem.BeingUsed" is now "BpodSystem.Status.BeingUsed" - Please update your protocol!')
end
function obj = setStatusLED(obj, status)
% Enable/Disable the State Machine status LED. This is useful for experiments requiring
% mitigation of ambient light sources. Requires state machine firmware v23 or newer
% Arguments: status (int) 0 = disabled, 1 = enabled
if obj.EmulatorMode == 0
if obj.FirmwareVersion < 23
error('Error: status LED enable/disable requires firmware v23+');
end
if (status == 1) || (status == 0)
obj.SerialPort.write([':' status], 'uint8');
confirmed = obj.SerialPort.read(1, 'uint8');
else
error('Error: LED status must be 0 (disabled) or 1 (enabled)')
end
end
end
function obj = SetStatusLED(obj, status)
% A notice to the user for obsolete protocol syntax
error('Case syntax error. setStatusLED needs a lowercase ''s''') % For users on the develop branch
end
function StartModuleRelay(obj, module)
% BpodObject.StartModuleRelay sets the state machine to relay bytes arriving from a Bpod module to the PC.
% While the relay is active, read incoming bytes with ModuleRead()
% To disable the relay use BpodObject.StopModuleRelay(). The relay must be stopped before running a trial.
%
% Arguments: module, the module index (int) or name (char array). Module names are given in BpodObject.Modules.Name
if ischar(module)
moduleNum = find(strcmp(module, obj.Modules.Name));
end
if ~isempty(moduleNum)
if (moduleNum <= length(obj.Modules.Connected))
if (sum(obj.Modules.RelayActive)) == 0
obj.SerialPort.write(['J' moduleNum-1 1], 'uint8');
obj.Modules.RelayActive(moduleNum) = 1;
else
error('Error: You must stop the active module relay with StopModuleRelay() before starting another one.')
end
end
end
end
function StopModuleRelay(obj, varargin)
% Stops the active module relay
for i = 1:length(obj.Modules.RelayActive)
obj.SerialPort.write(['J' i 0], 'uint8');
end
runningState = get(obj.Timers.PortRelayTimer, 'Running');
if strcmp(runningState, 'on')
stop(obj.Timers.PortRelayTimer);
while strcmp(runningState, 'on')
runningState = get(obj.Timers.PortRelayTimer, 'Running');
pause(.001);
end
end
nAvailable = obj.SerialPort.bytesAvailable;
if nAvailable > 0
obj.SerialPort.read(nAvailable, 'uint8');
end
obj.Modules.RelayActive(1:end) = 0;
end
function set.FlexIOConfig(obj, config)
% This method is called when BpodObject.FlexIOConfig is set. It
% verifies the new config struct and updates the device.
% Assert that config is struct
if ~isstruct(config)
error('Error setting FlexIOConfig: the configuration must be a struct.')
end
% Check for expected fields
expectedFields = {'about','channelTypes', 'analogSamplingRate', 'nReadsPerSample','threshold1','threshold2',...
'polarity1','polarity2','thresholdMode'}';
providedFields = fields(config);
if length(providedFields) > length(expectedFields)
error(['Error setting FlexIOConfig: ''' providedFields{end} ''' is not a FlexIO Config property'])
elseif length(providedFields) < length(expectedFields)
error(['Error setting FlexIOConfig: incorrect number of fields provided'])
end
fieldMatch = strcmp(expectedFields, providedFields);
mismatch = find(fieldMatch == 0, 1);
if ~isempty(mismatch)
error(['Error setting FlexIOConfig: expected field ' expectedFields(mismatch) ' was not provided.'])
end
configMessage = []; % Initialize byte message to configure FlexIO channels
nAcks = 0; % Number of acknowledgement bytes to read
% Set channel types
% ChannelTypes: 0 = DI, 1 = DO, 2 = ADC, 3 = DAC 4 = Disabled (Tri-State / High Z)
if length(config.channelTypes) ~= obj.HW.n.FlexIO
error(['Error using setFlexIO: the channelTypes vector must specify one type for each of the '...
num2str(obj.HW.n.FlexIO) ' FlexIO channels.']);
end
if (sum(config.channelTypes > 4) > 0) || (sum(config.channelTypes < 0) > 0)
error(['Error using setFlexIO: invalid channel type specified. Valid channel types are: ' ...
'0 = DI, 1 = DO, 2 = ADC, 3 = DAC, 4 = Disabled']);
end
configMessage = uint8([configMessage 'Q' config.channelTypes]);
nAcks = nAcks + 1;
% Set FlexIO analog input sampling rate (Hz). Permitted range = [1, 1000]
nCyclesPerSample = obj.HW.CycleFrequency/config.analogSamplingRate; % state machine cycles per analog sample
if nCyclesPerSample < 10 || nCyclesPerSample > (obj.HW.CycleFrequency/10)
error('Error configuring FlexIO analog input sampling rate: Rate must be in range [1, 1000]');
end
configMessage = uint8([configMessage '^' typecast(uint32(nCyclesPerSample), 'uint8')]);
nAcks = nAcks + 1;
% Set FlexIO ADC reads per sample
if config.nReadsPerSample > 4 || config.nReadsPerSample < 1
error('FlexIO readsPerSample must be in range [1, 4]')
end
configMessage = uint8([configMessage 'o' config.nReadsPerSample]);
nAcks = nAcks + 1;
% Set analog voltage thresholds
if sum(config.threshold1 > 5) > 0 || sum(config.threshold1 < 0) > 0
error('FlexIO threshold1 must be in range [0, 5] Volts')
end
if sum(config.threshold2 > 5) > 0 || sum(config.threshold2 < 0) > 0
error('FlexIO threshold2 must be in range [0, 5] Volts')
end
thresholdBits1 = (config.threshold1/5)*4095;
thresholdBits2 = (config.threshold1/5)*4095;
configMessage = uint8([configMessage 't' typecast(uint16([thresholdBits1 thresholdBits2]), 'uint8')]);
nAcks = nAcks + 1;
% Set analog threshold polarity
if sum(config.polarity1 < 0) > 0 || sum(config.polarity1 > 1) > 0
error('FlexIO polarity1 must be in range [0, 1]')
end
if sum(config.polarity2 < 0) > 0 || sum(config.polarity2 > 1) > 0
error('FlexIO polarity2 must be in range [0, 1]')
end
configMessage = uint8([configMessage 'p' config.polarity1 config.polarity2]);
nAcks = nAcks + 1;
% Set analog threshold mode
if sum(config.thresholdMode < 0) > 0 || sum(config.thresholdMode > 1) > 0
error('FlexIO thresholdMode must be in range [0, 1]')
end
configMessage = uint8([configMessage 'm' config.thresholdMode]);
nAcks = nAcks + 1;
% Send FlexIO Config to device and receive ACK
if obj.Status.InStateMatrix
error('Error: FlexIO channels cannot be reconfigured while the state machine is running.');
end
obj.SerialPort.write(configMessage, 'uint8');
ok = obj.SerialPort.read(nAcks, 'uint8');
if sum(ok) ~= length(ok) || isempty(ok)
error('Error configuring FlexIO channels: confirm code not returned');
end
% Update registries of behavior events and outputs
if sum(obj.HW.FlexIO_ChannelTypes == config.channelTypes) < obj.HW.n.FlexIO
obj.HW.FlexIO_ChannelTypes = config.channelTypes;
obj.HW.FlexIO_SamplingRate = config.analogSamplingRate;
inputChannelNames = cell(1,obj.HW.n.FlexIO);
outputChannelNames = cell(1,obj.HW.n.FlexIO);
flexEventPos = obj.HW.Pos.Event_FlexIO;
flexInputPos = obj.HW.Pos.Input_FlexIO;
flexOutputPos = obj.HW.Pos.Output_FlexIO;
for i = 1:obj.HW.n.FlexIO
switch config.channelTypes(i)
case 0
inputChannelNames{i} = ['Flex' num2str(i)];
outputChannelNames{i} = '---';
obj.StateMachineInfo.EventNames{flexEventPos} = [inputChannelNames{i} 'High'];
obj.StateMachineInfo.EventNames{flexEventPos+1} = [inputChannelNames{i} 'Low'];
flexEventPos = flexEventPos + 2;
case 1
inputChannelNames{i} = '---';
outputChannelNames{i} = ['Flex' num2str(i) 'DO'];
obj.StateMachineInfo.EventNames{flexEventPos} = '---';
obj.StateMachineInfo.EventNames{flexEventPos+1} = '---';
flexEventPos = flexEventPos + 2;
case 2
inputChannelNames{i} = ['Flex' num2str(i)];
outputChannelNames{i} = '---';
obj.StateMachineInfo.EventNames{flexEventPos} = [inputChannelNames{i} 'Trig1'];
obj.StateMachineInfo.EventNames{flexEventPos+1} = [inputChannelNames{i} 'Trig2'];
flexEventPos = flexEventPos + 2;
case 3
inputChannelNames{i} = '---';
outputChannelNames{i} = ['Flex' num2str(i) 'AO'];
obj.StateMachineInfo.EventNames{flexEventPos} = '---';
obj.StateMachineInfo.EventNames{flexEventPos+1} = '---';
flexEventPos = flexEventPos + 2;
case 4
inputChannelNames{i} = '---';
outputChannelNames{i} = '---';
obj.StateMachineInfo.EventNames{flexEventPos} = '---';
obj.StateMachineInfo.EventNames{flexEventPos+1} = '---';
flexEventPos = flexEventPos + 2;
end
end
obj.StateMachineInfo.InputChannelNames(flexInputPos:flexInputPos+obj.HW.n.FlexIO-1) = inputChannelNames;
obj.StateMachineInfo.OutputChannelNames(flexOutputPos:flexOutputPos+obj.HW.n.FlexIO-1) = outputChannelNames;
end
if isfield (obj.Data, 'Analog')
obj.Data.Analog.nChannels = sum(config.channelTypes == 2);
obj.Data.Analog.channelNumbers = find(config.channelTypes == 2);
end
obj.FlexIOConfig = config;
end
function PhoneHomeOpt_In_Out(obj)
% Launches a GUI for registration with the Bpod Phone Home program
obj.GUIHandles.BpodPhoneHomeFig = figure('Position', [550 180 400 350],...
'name','Bpod Phone Home','numbertitle','off', 'MenuBar', 'none', 'Resize', 'off');
ha = axes('units','normalized', 'position',[0 0 1 1]);
uistack(ha,'bottom');
bg = imread('PhoneHomeBG.bmp');
image(bg); axis off; drawnow;
text(20, 40,'Bpod PhoneHome Program', 'FontName', 'Courier New', 'FontSize', 16, 'Color', [1 1 1]);
Pos = 80; Step = 25;
text(20, Pos,'Bpod PhoneHome is an opt-in', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
text(20, Pos,'program to send anonymous data', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
text(20, Pos,'about your Bpod software setup', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
text(20, Pos,'to Sanworks LLC on Bpod start.', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
text(20, Pos,'This will help us understand', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
text(20, Pos,'which MATLAB versions and OS', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
text(20, Pos,'flavors typically run Bpod', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
text(20, Pos,'+ how many rigs are out there.', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step+5;
text(140, Pos,'See BpodPhoneHome.m', 'FontName', 'Courier New', 'FontSize', 12, 'Color', [1 1 1]); Pos = Pos + Step;
BpodSystem.GUIHandles.PhoneHomeAcceptBtn = uicontrol('Style', 'pushbutton', 'String', 'Ok',...
'Position', [130 15 120 40], 'Callback', @(h,e)obj.phoneHomeRegister(1),...
'FontSize', 12,'Backgroundcolor',[0.29 0.29 0.43],'Foregroundcolor',[0.9 0.9 0.9], 'FontName', 'Courier New');
BpodSystem.GUIHandles.PhoneHomeAcceptBtn = uicontrol('Style', 'pushbutton', 'String', 'Decline',...
'Position', [260 15 120 40], 'Callback', @(h,e)obj.phoneHomeRegister(0),...
'FontSize', 12,'Backgroundcolor',[0.29 0.29 0.43],'Foregroundcolor',[0.9 0.9 0.9], 'FontName', 'Courier New');
end
function onlineStatus = check4Internet(obj)
% Check for Internet connectivity
% Returns: onlineStatus (double) = 1 if online, 0 if not
if ispc
[~,reply]=system('ping -n 1 -w 1000 www.google.com'); % Check for connection
ConnectConfirmString = 'Received = 1';
elseif ismac
[~,reply]=system('trap -SIGALRM; ping -c 1 -t 1 www.google.com'); % Check for connection
ConnectConfirmString = '1 packets received';
else
[~,reply]=system('timeout 1 ping -c 1 www.google.com'); % Check for connection
ConnectConfirmString = '1 received';
end
onlineStatus = 0;
if ~isempty(strfind(reply, ConnectConfirmString)) %#ok contains() requires r2016b but Bpod supports back to r2013a
onlineStatus = 1;
end
end
function startAnalogViewer(obj)
obj.analogViewer('init', []);
end
function delete(obj)
% Destructor
obj.SerialPort = []; % Trigger the ArCOM port's destructor function (closes and releases port)
if obj.MachineType > 3 && obj.FirmwareVersion > 22
obj.AnalogSerialPort = [];
end
end
end
methods (Access = private)
function phoneHomeRegister(obj, state)
% Callback from pushbutton of PhoneHomeOpt_In_Out() GUI
% Registers user with the Bpod Phone Home program
if ~isfield(obj.SystemSettings, 'PhoneHomeRigID')
obj.SystemSettings.PhoneHomeRigID = char(floor(rand(1,16)*25)+65);
end
switch state
case 0
obj.SystemSettings.PhoneHome = 0;
obj.BpodPhoneHome('Opt_Out');
case 1
obj.SystemSettings.PhoneHome = 1;
obj.BpodPhoneHome(0);
end
obj.SaveSettings;
close(obj.GUIHandles.BpodPhoneHomeFig);
end
function SwitchPanels(obj, panel)
% Callback triggered when switching between module tabs on the Bpod Console GUI
% Arguments: panel, the index of the panel selected
obj.GUIData.CurrentPanel = 0;
offPanels = 1:obj.HW.n.UartSerialChannels+1;
offPanels = offPanels(offPanels~=panel);
set(obj.GUIHandles.OverridePanel(panel), 'Visible', 'on');
uistack(obj.GUIHandles.OverridePanel(panel), 'top');
for i = offPanels
% Button -> gray
set(obj.GUIHandles.PanelButton(i), 'BackgroundColor', [0.37 0.37 0.37]);
set(obj.GUIHandles.OverridePanel(i), 'Visible', 'off');
end
set(obj.GUIHandles.PanelButton(panel), 'BackgroundColor', [0.45 0.45 0.45]);
if isempty(strfind(obj.HostOS, 'Linux')) && ~verLessThan('matlab', '8.0.0') && verLessThan('matlab', '9.5.0')
for i = 1:obj.HW.n.UartSerialChannels+1
jButton = findjobj(obj.GUIHandles.PanelButton(i));
jButton.setBorderPainted(false);
end
end
obj.GUIData.CurrentPanel = panel;
if obj.EmulatorMode == 0
% Set module byte stream relay to current module
obj.StopModuleRelay;
if panel > 1
if obj.Status.BeingUsed == 0 && obj.GUIData.DefaultPanel(panel) == 1
obj.SerialPort.write(['J' panel-2 1], 'uint8');
obj.Modules.RelayActive(panel-1) = 1;
% Start timer to scan port
start(obj.Timers.PortRelayTimer);
end
end
end
obj.FixPushbuttons;
end
function FixPushbuttons(obj)
% Remove all the nasty borders around pushbuttons on platforms besides win7
if isempty(strfind(obj.HostOS, 'Windows 7'))
warning off
handles = findjobj('class', 'pushbutton');
set(handles, 'border', []);
warning on
end
end
function BpodSplashScreen(obj, stage)
% Create / Update the Bpod splash screen, shown on startup
% Arguments: stage, the index of the startup stage (1-5)
if stage == 1
ySize = 970;
xSize = 600;
if ~isunix && ~verLessThan('matlab', '9') % Image scaling was not as graceful in prior MATLAB
ySize = floor(ySize*0.5);
xSize = floor(xSize*0.5);
end
SS = get(0,'screensize');
yOffset = round((SS(4)/2))-(xSize/2);
xOffset = round((SS(3)/2))-(ySize/2);
obj.GUIHandles.SplashFig = figure('Position',[xOffset yOffset ySize xSize],'name','Bpod',...
'numbertitle','off', 'MenuBar', 'none', 'Resize', 'off');
ha = axes('units','normalized', 'position',[0 0 1 1]);
uistack(ha,'bottom');
end
img = obj.SplashData(:,:,:,stage);
img(540:548, 86:885,:) = ones(9,800,3)*160;
startPos = 86;
endPos = 87;
StepSize = 5;
if ~verLessThan('matlab', '9')
StepSize = 10;
end
switch stage
case 1
while endPos < 246
endPos = endPos + StepSize;
img(540:548, startPos:endPos,1) = ones(9,(endPos-(startPos-1)),1)*200;
img(540:548, startPos:endPos,2) = ones(9,(endPos-(startPos-1)),1)*30;
img(540:548, startPos:endPos,3) = ones(9,(endPos-(startPos-1)),1)*30;
imagesc(img); colormap('gray'); set(gcf,'name','Bpod','numbertitle','off', 'MenuBar', 'none',...
'Resize', 'off'); axis off; drawnow;
end
case 2
endPos = 246;
while endPos < 406
endPos = endPos + StepSize;
img(540:548, startPos:endPos,1) = ones(9,(endPos-(startPos-1)),1)*200;
img(540:548, startPos:endPos,2) = ones(9,(endPos-(startPos-1)),1)*30;
img(540:548, startPos:endPos,3) = ones(9,(endPos-(startPos-1)),1)*30;
imagesc(img); colormap('gray'); set(gcf,'name','Bpod','numbertitle','off', 'MenuBar', 'none',...
'Resize', 'off'); axis off; drawnow;
end
case 3
endPos = 406;
while endPos < 566
endPos = endPos + StepSize;
img(540:548, startPos:endPos,1) = ones(9,(endPos-(startPos-1)),1)*200;
img(540:548, startPos:endPos,2) = ones(9,(endPos-(startPos-1)),1)*30;
img(540:548, startPos:endPos,3) = ones(9,(endPos-(startPos-1)),1)*30;
imagesc(img); colormap('gray'); set(gcf,'name','Bpod','numbertitle','off', 'MenuBar', 'none',...
'Resize', 'off'); axis off; drawnow;
end
case 4
endPos = 566;
while endPos < 726
endPos = endPos + StepSize;
img(540:548, startPos:endPos,1) = ones(9,(endPos-(startPos-1)),1)*200;
img(540:548, startPos:endPos,2) = ones(9,(endPos-(startPos-1)),1)*30;
img(540:548, startPos:endPos,3) = ones(9,(endPos-(startPos-1)),1)*30;
imagesc(img); colormap('gray'); set(gcf,'name','Bpod','numbertitle','off', 'MenuBar', 'none',...
'Resize', 'off'); axis off; drawnow;
end
case 5
endPos = 726;
while endPos < 886
endPos = endPos + StepSize;
img(540:548, startPos:endPos,1) = ones(9,(endPos-(startPos-1)),1)*200;
img(540:548, startPos:endPos,2) = ones(9,(endPos-(startPos-1)),1)*30;
img(540:548, startPos:endPos,3) = ones(9,(endPos-(startPos-1)),1)*30;
imagesc(img); colormap('gray'); set(gcf,'name','Bpod','numbertitle','off', 'MenuBar', 'none',...
'Resize', 'off'); axis off; drawnow;
end
pause(.5);
end
end
end
end