%% ScanImage

%Example with two scanning systems, one ResScan (named 'ResScanner'), one LinScan (named 'LinScanner')
scannerNames = {'ResScanner', 'LinScanner'}; % choose names freely (no spaces or special characters)
scannerTypes = {'Resonant',   'Linear'};     % types of scanners. Resonant = ResScan, Linear = LinScan
 
simulated = false;
components = {};
dataDir = '[MDF]\ConfigData'; % saves the configuration data in the subfolder 'ConfigData' located in the same directory as this Machine Data File
objectiveResolution = 15;
startUpScript = '';

%% Shutters
shutterNames = {'Shutter 1' 'Shutter 2'}; 
shutterDaqDevices = {'PXI1Slot3','Dev2'};
shutterChannelIDs = {'PFI12','PFI12'};
shutterOpenLevel = [true true];
shutterOpenTime = 0.1;

%% Beams
% Example configuring 3 Pockels cells on 2 different DAQ boards
beamDaqDevices = {'PXI1Slot4','Dev1'}; %'PXI1Slot4' is DAQ 1, 'Dev1' is DAQ 2

beamDaqs(1).modifiedLineClockIn = '';
beamDaqs(1).frameClockIn = '';
beamDaqs(1).referenceClockIn = '';
beamDaqs(1).chanIDs = [0,1];
beamDaqs(1).displayNames = {'Mai Tai 1','Mai Tai 2'};
beamDaqs(1).voltageRanges = 1.5;
beamDaqs(1).calInputChanIDs = [0,1];
beamDaqs(1).calOffsets = [];
beamDaqs(1).calUseRejectedLight = false;
beamDaqs(1).calOpenShutterIDs = [1];
 
beamDaqs(2).modifiedLineClockIn = 'PFI0';
beamDaqs(2).frameClockIn = 'PFI1';
beamDaqs(2).referenceClockIn = 'PFI14';
beamDaqs(2).chanIDs = [0];
beamDaqs(2).displayNames = {'Chameleon'};
beamDaqs(2).voltageRanges = 1.5;
beamDaqs(2).calInputChanIDs = [0];
beamDaqs(2).calOffsets = [];
beamDaqs(2).calUseRejectedLight = false;
beamDaqs(2).calOpenShutterIDs = [2];

%% ResScan
nominalResScanFreq = 7910;
beamDaqID = 1;                        Must be set to the beam DAQ ID defined in the beams section.
shutterIDs = 1;
digitalIODeviceName = 'PXI1Slot3';
fpgaModuleType = 'NI7961';
digitizerModuleType = 'NI5732';
rioDeviceID = 'RIO0';
channelsInvert = false;
externalSampleClock = false;
externalSampleClockRate = [];
galvoDeviceName = 'PXI1Slot3';
galvoDeviceFrameClockIn = '';
galvoAOChanIDX = [];
galvoAOChanIDY = 1;
xGalvoAngularRange = [];
yGalvoAngularRange = 15;
galvoVoltsPerOpticalDegreeX = 1.0;
galvoVoltsPerOpticalDegreeY = 1.0;
galvoParkDegreesX = -8;
galvoParkDegreesY = -8;
resonantAngularRange = 15;
resonantZoomDeviceName = '';
resonantZoomAOChanID = 0;
rScanVoltsPerOpticalDegree = 0.33;
resonantScannerSettleTime = 0.5;

%% LinScan
deviceNameAcq   = 'PXI1Slot4';
deviceNameGalvo = 'PXI1Slot4';
deviceNameAux   = 'PXI1Slot4';


channelsInvert = false;
beamDaqID = 1;                      Must be set to the beam DAQ ID defined in the beams section.
shutterIDs = 1;
resScanframeClockIn = '';
referenceClockIn = '';
enableRefClkOutput = 0;
XMirrorPosChannelID = [];
YMirrorPosChannelID = [];
XMirrorChannelID = 0;
YMirrorChannelID = 1;
xGalvoAngularRange = 15;
yGalvoAngularRange = 15;
scanParkAngleX = -7.5;
scanParkAngleY = -7.5;
voltsPerOpticalDegreeX = 1;
voltsPerOpticalDegreeY = 1;
scanOffsetAngleX = 0;
scanOffsetAngleY = 0;
channelIDs = [];

%Optional: mirror position offset outputs for motion correction
deviceNameOffset = 'Dev1';              
XMirrorOffsetChannelID = 0;         
YMirrorOffsetChannelID = 1;         
XMirrorOffsetMaxVoltage = 1;        
YMirrorOffsetMaxVoltage = 1;        
deviceNameGalvoFeedback = '';
internalRefClockSrc = '';

%% FastZ
fastZControllerType = 'pi.e665';
fastZCOMPort = 1;
fastZBaudRate = [];
fastZDeviceName = 'PXI1Slot5';
frameClockIn = '';
fastZAOChanID = 0;
fastZAIChanID = 0;

%% Motors
motorControllerType = '';
motorDimensions = '';
motorStageType = '';
motorCOMPort = [];
motorBaudRate = [];
motorZDepthPositive = true;
motorPositionDeviceUnits = [];
motorVelocitySlow = [];
motorVelocityFast = [];

%Secondary motor for Z motion, allowing either XY-Z or XYZ-Z hybrid configuration
motor2ControllerType = '';
motor2StageType = '';
motor2COMPort = [];
motor2BaudRate = [];
motor2ZDepthPositive = true;
motor2PositionDeviceUnits = [];
motor2VelocitySlow = [];
motor2VelocityFast = [];

moveCompleteDelay = 0;

%% Photostim
photostimScannerName = 'LinScanner';          
BeamAiId = 0;                  
loggingStartTrigger = 'PFI3';

%% IntegrationRoiOutputs
channelNames = {'My FIrst Channel' 'My Second Channel' 'My Software Channel'};    
deviceNames = {'Dev2' 'Dev2' ''};    
deviceChannels = {'PFI0' 'port0/line0' ''};    

%% Thorlabs BScope2
scannerName = 'ResScanner';                   
ecuComPort = 2;                   
galvoGalvoMirrorComPort = 3;       
galvoResonantMirrorComPort = 1;    
flipperMirrorComPort = 4;          
pmtDevAddresses = {'' '' '' ''};     

galvoGalvoMirrorInvert = true;
galvoResonantMirrorInvert = true;
flipperMirrorInvert = true;

%% Thorlabs ECU1
scannerName = 'ResScanner';                   
comPort = 1;                       

%% GenericPmtController
pmtNames = {'Green' 'Red'};                                 
pmtDaqDeviceName = {'Dev2' 'Dev2'};                         
pmtDaqGainAOChannels = [0 1];                               
pmtDaqPowerDOChannels = {'port0/line0' 'port0/line3'};      
pmtDaqTrippedDIChannels = {'port0/line1' 'port0/line4'};    
pmtDaqTripResetDOChannels = {'port0/line2' 'port0/line5'};  
pmtDaqAOVoltageRange = {[0 5] [0 5]};                    
pmtMaxGainValue = [1250 1250];                             

%% LSC Pure Analog