forked from kavli-ntnu/MINI2P_toolbox
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMachine_Data_File_2000Hz.m
204 lines (158 loc) · 11.7 KB
/
Machine_Data_File_2000Hz.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
% Most Software Machine Data File
%% scanimage.SI (ScanImage)
% Global microscope properties
objectiveResolution = 27.5; % Resolution of the objective in microns/degree of scan angle
% Data file location
% Custom Scripts
startUpScript = 'ScanImageStartScript'; % Name of script that is executed in workspace 'base' after scanimage initializes
shutDownScript = ''; % Name of script that is executed in workspace 'base' after scanimage exits
fieldCurvatureZs = []; % Field curvature for mesoscope
fieldCurvatureRxs = []; % Field curvature for mesoscope
fieldCurvatureRys = []; % Field curvature for mesoscope
useJsonHeaderFormat = false; % Use JSON format for TIFF file header
fieldCurvatureTip = 0;
fieldCurvatureTilt = 0;
%% scanimage.components.Motors (SI Motors)
% SI Stage/Motor Component.
motorXYZ = {'ScopeHolder' 'ScopeHolder' 'ScopeHolder'}; % Defines the motor for ScanImage axes X Y Z.
motorAxisXYZ = [2 1 3]; % Defines the motor axis used for Scanimage axes X Y Z.
scaleXYZ = [1 -1 1]; % Defines scaling factors for axes.
backlashCompensation = [0 0 0]; % Backlash compensation in um (positive or negative)
%% scanimage.components.scan2d.RggScan (MINI2P_001)
acquisitionDeviceId = 'vDAQ0'; % RDI Device ID
acquisitionEngineIdx = 1;
resonantScanner = 'MEMS2000Hz'; % Name of the resonant scanner
xGalvo = ''; % Name of the x galvo scanner
yGalvo = 'MEMS2000Hz_slowaxis'; % Name of the y galvo scanner
beams = {'920nm AOM'}; % beam device names
fastZs = {'TLens'}; % fastZ device names
shutters = {'Laser' 'MEMS' 'PMT' 'LED'}; % shutter device names
channelsInvert = [true true false false]; % Logical: Specifies if the input signal is inverted (i.e., more negative for increased light signal)
keepResonantScannerOn = false; % Always keep resonant scanner on to avoid drift and settling time issues
externalSampleClock = false; % Logical: use external sample clock connected to the CLK IN terminal of the FlexRIO digitizer module
externalSampleClockRate = 8e+07; % [Hz]: nominal frequency of the external sample clock connected to the CLK IN terminal (e.g. 80e6); actual rate is measured on FPGA
externalSampleClockMultiplier = 1; % Multiplier to apply to external sample clock
extendedRggFov = 0; % If true and x galvo is present, addressable FOV is combination of resonant FOV and x galvo FOV.
% Advanced/Optional
PeriodClockDebounceTime = 1e-07; % [s] time the period clock has to be stable before a change is registered
TriggerDebounceTime = 5e-07; % [s] time acquisition, stop and next trigger to be stable before a change is registered
reverseLineRead = 0; % flips the image in the resonant scan axis
defaultFlybackTimePerFrame = 0.001; % [s] default time to allow galvos to fly back after one frame is complete. overridden by cfg file
defaultFlytoTimePerScanfield = 0.001; % [s] time to allow galvos to fly from one scanfield to the next. overridden by cfg file
% Aux Trigger Recording, Photon Counting, and I2C are mutually exclusive
% Aux Trigger Recording
auxTriggersTimeDebounce = 1e-07; % [s] time after an edge where subsequent edges are ignored
auxTriggerLinesInvert = [false false false false]; % [logical] 1x4 vector specifying polarity of aux trigger inputs
auxTrigger1In = ''; % Digital input lines for aux trigger 1
auxTrigger2In = ''; % Digital input lines for aux trigger 2
auxTrigger3In = ''; % Digital input lines for aux trigger 3
auxTrigger4In = ''; % Digital input lines for aux trigger 4
% Signal Conditioning
disableMaskDivide = [false false false false]; % disable averaging of samples into pixels; instead accumulate samples
% I2C
i2cEnable = false;
i2cSdaPort = '';
i2cSclPort = '';
i2cAddress = 0; % [byte] I2C address of the FPGA
i2cDebounce = 1e-07; % [s] time the I2C signal has to be stable high before a change is registered
i2cStoreAsChar = false; % if false, the I2C packet bytes are stored as a uint8 array. if true, the I2C packet bytes are stored as a string. Note: a Null byte in the packet terminates the string
i2cSendAck = true; % When enabled FPGA confirms each packet with an ACK bit by actively pulling down the SDA line
% Laser Trigger
LaserTriggerPort = ''; % Digital input where laser trigger is connected.
% Trigger Outputs
frameClockOut = '/vDAQ0/D3.7'; % Output line for the frame clock
lineClockOut = ''; % Output line for the line clock
beamModifiedLineClockOut = ''; % Output line for beam clock
volumeTriggerOut = ''; % Output line for the volume clock
% Calibration data
scannerToRefTransform = [1 0 0;0 1 0;0 0 1];
virtualChannelSettings = [];
LaserTriggerDebounceTicks = 1;
enableHostPixelCorrection = false;
hostPixelCorrectionMultiplier = 500;
%% dabs.mirrorcle.ResonantAxis (MEMS2000Hz)
hAOZoom = '/vDAQ0/AO1'; % Analog output channel to be used to control resonant axis of the mirror e.g. '/vDAQ0/AO0'
hDOSync = '/vDAQ0/D1.7'; % String identifying the digital output for the sync signal e.g. '/vDAQ0/D0.1
hDOFilterX = '/vDAQ0/D3.2'; % String identifying the digital output for the X filter clock e.g. '/vDAQ0/D0.2
hDOFilterY = '/vDAQ0/D3.1'; % String identifying the digital output for the Y filter clock e.g. '/vDAQ0/D0.3
inputVoltageRange_Vpp = 8; % Max input voltage range of the controller
angularRange_deg = 16; % Max angular range of the device
% Default scan settings
syncPhase_deg = 100;
rampTime_s = 0;
xFilterClockFreq_Hz = 300000;
yFilterClockFreq_Hz = 150000;
xFilterClockEnable = 1;
yFilterClockEnable = 1;
nominalFrequency_Hz = 2000;
% Calibration Settings
amplitudeToLinePhaseMap = [4 -2.912e-06;4.5 -3.144e-06;5 -3.056e-06;5.333 -3.48e-06;5.714 -2.56e-06;6 -3.432e-06;6.154 -3.48e-06;6.667 -3.352e-06;7.273 -5.7912e-05;7.5 -3.416e-06;7.692 -3.504e-06;7.727 -3.416e-06;7.72727 0;8 -3.512e-06;8.182 6.3208e-05;8.333 -3.472e-06;8.5 -3.728e-06;8.636 -3.48e-06;9 -3.576e-06;9.091 -3.48e-06;9.5 -3.576e-06;10 0.00011808;11 -3.072e-06]; % translates an amplitude (degrees) to a line phase (seconds)
amplitudeLUT = zeros(0,2); % translates a nominal amplitude (degrees) to an output amplitude (degrees)
%% dabs.generic.DigitalShutter (Laser)
DOControl = '/vDAQ0/D0.0'; % control terminal e.g. '/vDAQ0/DIO0'
invertOutput = false; % invert output drive signal to shutter
openTime_s = 0.1; % settling time for shutter in seconds
%% dabs.generic.DigitalShutter (MEMS)
DOControl = '/vDAQ0/D0.1'; % control terminal e.g. '/vDAQ0/DIO0'
invertOutput = false; % invert output drive signal to shutter
openTime_s = 0.1; % settling time for shutter in seconds
%% dabs.generic.DigitalShutter (PMT)
DOControl = '/vDAQ0/D0.2'; % control terminal e.g. '/vDAQ0/DIO0'
invertOutput = false; % invert output drive signal to shutter
openTime_s = 0.1; % settling time for shutter in seconds
%% dabs.generic.DigitalShutter (LED)
DOControl = '/vDAQ0/D0.3'; % control terminal e.g. '/vDAQ0/DIO0'
invertOutput = false; % invert output drive signal to shutter
openTime_s = 0.1; % settling time for shutter in seconds
%% dabs.generic.BeamModulatorFastAnalog (920nm AOM)
AOControl = '/vDAQ0/AO2'; % control terminal e.g. '/vDAQ0/AO0'
AIFeedback = ''; % feedback terminal e.g. '/vDAQ0/AI0'
outputRange_V = [0 2]; % Control output range in Volts
feedbackUsesRejectedLight = false; % Indicates if photodiode is in rejected path of beams modulator.
calibrationOpenShutters = {}; % List of shutters to open during the calibration. (e.g. {'Shutter1' 'Shutter2'}
powerFractionLimit = 1; % Maximum allowed power fraction (between 0 and 1)
% Calibration data for the laser
powerFraction2ModulationVoltLut = [0 0;0.0157 0.2;0.0541 0.4;0.1165 0.6;0.2009 0.8;0.3047 1;0.4247 1.2;0.5583 1.4;0.7005 1.6;0.8493 1.8;1 2];
powerFraction2PowerWattLut = [0 0;1 164.6];
powerFraction2FeedbackVoltLut = zeros(0,2);
feedbackOffset_V = 0;
% Advanced Settings. Note: these settings are unused for vDAQ based systems
modifiedLineClockIn = ''; % Terminal to which external beam trigger is connected. Leave empty for automatic routing via PXI/RTSI bus
frameClockIn = ''; % Terminal to which external frame clock is connected. Leave empty for automatic routing via PXI/RTSI bus
referenceClockIn = ''; % Terminal to which external reference clock is connected. Leave empty for automatic routing via PXI/RTSI bus
referenceClockRate = 1e+07; % if referenceClockIn is used, referenceClockRate defines the rate of the reference clock in Hz. Default: 10e6Hz
%% dabs.legacy.motor.LegacyMotor (ScopeHolder)
% Motor used for X/Y/Z motion, including stacks.
controllerType = 'PI C884/C863'; % If supplied, one of {'sutter.mp285', 'sutter.mpc200', 'thorlabs.mcm3000', 'thorlabs.mcm5000', 'scientifica', 'pi.e665', 'pi.e816', 'npoint.lc40x', 'bruker.MAMC'}.
comPort = ''; % Integer identifying COM port for controller, if using serial communication
customArgs = {}; % Additional arguments to stage controller. Some controller require a valid stageType be specified
invertDim = '$$$''---'''; % string with one character for each dimension specifying if the dimension should be inverted. '+' for normal, '-' for inverted
positionDeviceUnits = [-0.001 -0.001 -0.001]; % 1xN array specifying, in meters, raw units in which motor controller reports position. If unspecified, default positionDeviceUnits for stage/controller type presumed.
velocitySlow = []; % Velocity to use for moves smaller than motorFastMotionThreshold value. If unspecified, default value used for controller. Specified in units appropriate to controller type.
velocityFast = []; % Velocity to use for moves larger than motorFastMotionThreshold value. If unspecified, default value used for controller. Specified in units appropriate to controller type.
moveCompleteDelay = 0.1; % Delay from when stage controller reports move is complete until move is actually considered complete. Allows settling time for motor
moveTimeout = ''; % Default: 2s. Fixed time to wait for motor to complete movement before throwing a timeout error
moveTimeoutFactor = ''; % (s/um) Time to add to timeout duration based on distance of motor move command
%% dabs.generic.FastZPureAnalog (TLens)
AOControl = '/vDAQ0/AO3'; % control terminal e.g. '/vDAQ0/AO0'
AIFeedback = ''; % feedback terminal e.g. '/vDAQ0/AI0'
FrameClockIn = ''; % frame clock input terminal e.g. '/Dev1/PFI0'
parkPositionUm = 0; % park position in micron
travelRangeUm = [-250 10]; % travel range in micron
voltsPerUm = -0.032; % volts per micron
voltsOffset = 0; % volts that sets actuator to zero position
% Calibration Data for uTLens
positionLUT = [-240 -267.5;-230 -250.625;-220 -233.75;-210 -217.5;-200 -205;-190 -191.25;-180 -180;-170 -168.958;-160 -159.167;-150 -150;-140 -139.375;-130 -130;-120 -121.25;-110 -113.542;-100 -104.583;-90 -96.25;-80 -86.875;-70 -80;-60 -71.925;-50 -65;-40 -56.2;-30 -46.2;-20 -34.95;-10 -21.2;0 0;10 25]; % Position LUT
feedbackVoltLUT = zeros(0,2); % [Nx2] lut translating feedback volts into position volts
%% dabs.generic.GalvoPureAnalog (MEMS2000Hz_slowaxis)
AOControl = '/vDAQ0/AO0'; % control terminal e.g. '/vDAQ0/AO0'
AOOffset = ''; % control terminal e.g. '/vDAQ0/AO0'
AIFeedback = ''; % feedback terminal e.g. '/vDAQ0/AI0'
angularRange = 6; % total angular range in optical degrees (e.g. for a galvo with -20..+20 optical degrees, enter 40)
voltsPerOpticalDegrees = 1.3; % volts per optical degrees for the control signal
parkPosition = 0; % park position in optical degrees
slewRateLimit = Inf; % Slew rate limit of the analog output in Volts per second
% Calibration settings
feedbackVoltLUT = zeros(0,2); % [Nx2] lut translating feedback volts into position volts
offsetVoltScaling = 1; % scalar factor for offset volts
voltsOffset = -0.3;