.. _alligator-internal-parameters:

AlliGator Exposed Internal Parameters
+++++++++++++++++++++++++++++++++++++

AlliGator exposed internal parameters' JSON strings with default values
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+ # Folds:1
+ # Gates:100
+ # Logical Processors Used:8
+ 1-Normalize Decay:false
+ Additional Points:100
+ All Image ROIs:false
+ All Phasor Plot ROIs:false
+ Available Gate Names:["Gate"]
+ Average Dataset Sum:false
+ Average Lifetime Options:{"Use Local IRF ":true,"Use IRF Offset":true,"Use Fixed Offset":false,"Fixed Offset":0,"Baseline %":50}
+ Background Definition Range:{"Min Gate":0,"Max Gate":8.00000000000000E-10}
+ Background File:""
+ Background File Subtraction:false
+ Background Pile-up Correction:false
+ Background Pixel Well Capacity:1020
+ Background Scaling Factor:1
+ Background Subtraction:false
+ Backup Calibration Type:"Nearest Valid Calibration"
+ Baseline Subtraction Method:"Min"
+ Beep after Script:true
+ Beep on Error:true
+ Calibration Lifetime:0
+ Calibration Type:"No"
+ Constant Background:0
+ Cumulative Phasor Plot:false
+ Decay & IRF Parameters:{"Lifetime":1,"IRF Offset":0,"IRF Period":1.25000000000000E-8,"Normalized Decays":false,"IRF Model":"Dirac","IRF Parameter 1":0.1}
+ Decay Analysis Parameters:{"Type":"Default","Shift":0,"Threshold":0,"Rotate":true}
+ Decay Graph Active:true
+ Decay Graph Color Array:[1985280,16711680,6618880]
+ Decay Shift Parameters:{"Type":"Default","Shift":0,"Threshold":0.1,"Rotate":false}
+ Define Gates to:"Item 0"
+ Define Shortest Lifetime as:"Item 0"
+ Display Parameters:{"# Points":1000,"Ramp Type":"Logarithmic","Type of Series":"1-Exp Decays","Min tau":1.00000000000000E-12,"Max tau":1.00000000000000E-7,"Include 0":true,"Include Infinity":true}
+ Displayed Fit Parameters:[]
+ Exponential Fading:true
+ Export Tabulated Results:false
+ Exported Gate Image Settings:{"bitness":true," Min Value":-Infinity," Max Value":Infinity}
+ Extract IRF instead of Decay:false
+ Extrapolate Decay:false
+ Fit Options:{"Show Fit Residuals":true,"Fit Model":"1-Exponential","Residual Type":"Standard","Max Decay Percentile":1,"Min Decay Percentile":0,"Show Full Decay":true,"Weights":"1/Variance","Fitting Method":"Least Square","Compute Parameter Uncertainties":true,"Periodic Boundaries":true,"Model Calculation":"Convolution","Period":1.25000000000000E-8,"Termination Criteria":{"Max Iterations":1000,"Max Function Calls":10000,"Max Time":1000,"Function Tolerance":1.00000000000000E-9,"Parameter Tolerance":1.00000000000000E-9,"Gradient Tolerance":1.00000000000000E-9,"Min Lambda":1.00000000000000E-9,"Max Lambda":1000000000,"Initial Tick Count":0},"Offset Resolution":5.00000000000000E-11,"Use Local IRF":false,"Fitting Algorithm":"Levenberg-Marquardt"}
+ Fit Parameter Constraints:[]
+ Fold Decay:false
+ Gate Arithmetic:"None"
+ Gate Duration:3.00000000000000E-10
+ Gate Name:0
+ Gate Parameters:{"First Gate Start":0,"Use Gate Center":false,"Gate Width":0,"Gate Step":0,"# Gates":Infinity,"Gate Type":"Square","Edge Width":0,"Top Slope":0,"Reversed Sawtooth?":false,"Analytical Computation":false,"Integration":"Item 0","Tolerance":0.001,"# Steps":1000,"Type of User-defined Function":"IRF","Use Gate Step":false}
+ Gate Separation:4.00000000000000E-11
+ Gate Step:1
+ Gates to Keep:{"First":0,"Last":4294967295}
+ Gates to Skip:{"Start":0,"End":0}
+ Guess Parameter Names:[]
+ Guess Parameters:[]
+ Head Fraction:0.5
+ High Count Pixels Rejection Options:{"Background High Threshold Factor":0,"Fixed High Background Threshold":Infinity,"Reject High Count Pixels":false,"High Percentile":0}
+ Histogram Options:{"Bin Size":NaN,"Min Value":-Infinity,"Max Value":Infinity,"Filter NaN & Infinite Values":true,"Frequency Plot":false,"Align Bins":true,"Bin Location":"Left","Project Outside Values":false,"Max Histogram Size":100000}
+ Hot Pixel Removal:{"Remove Screamers":false,"Delta":Infinity,"Equalize Histogram":false,"Percentile":0}
+ IRF Extraction Options:{"Time Constant for IRF Extraction":1.00000000000000E-9,"IRF Order":132,"Fourier Series Smoothing":"None","Noise Threshold":0.1,"Smoothing Width":1,"Fourier Series Truncation":"Automatic","Truncation Order":0,"Save Power Spectrum":false,"Smoothing":true,"Smoothing Parameter":-1,"Smoothing Order":10,"Method":"Direct"}
+ IRF Optimization Options:{"Search Range":5.00000000000000E-10,"Search Step":1.00000000000000E-12,"Tail threshold (%)":5,"Regularized IRF":false,"Export Plot":true,"Export Data":false,"Smooth Metrics":true,"S-G Side Points":6,"S-G Polynomial Order":3}
+ IRF Order:1
+ IRF Time Constants:[]
+ Image Binning Options:{"Use Image Binning":false,"X Bin":1,"Y Bin":1}
+ Image Histogram Active:true
+ Image Smoothing Options:{"Use Image Smoothing":false,"Kernel Type":"Uniform","Bin":1,"Algorithm":"Rapid"}
+ Include Loading in Timing:false
+ Intensity Correction File:""
+ Intensity Threshold:500
+ Invert Binary Mask:false
+ Laser Period:1.00000000000000E-8
+ Last Run Version:false
+ Lifetime Map Active:false
+ Low Count Pixels Rejection Options:{"Background Low Threshold Factor":0,"Fixed Low Background Threshold":20000,"Reject Low Count Pixels":false,"Low Percentile":0}
+ Max Peak Value:Infinity
+ Min Peak Value:500
+ Operations Order:["Background subtraction","Revert","Smoothen","Straighten","Shift","Extrapolate","Normalize","Fold"]
+ Peak Threshold:500
+ Phasor Frequency:80000000
+ Phasor Graph Active:true
+ Phasor Parameters:{"Harmonic Frequency":80000000,"Use f* = 1/D Frequency":false,"Calibrated Phasor":true,"Calibration Lifetime":0,"Phasor Calculation":"Analytical Formula","SEPL Type":"UC","# Gates":1000,"Square Gate Width":0,"Show Ticks":false}
+ Phasor Plot Active:true
+ Phasor Plot Graphics Options:{"UC Color":0,"Show UC Tau Ticks":false,"SEPL Color":7171459,"Show SEPL Tau Ticks":false,"Axes Color":0,"Show (g,s) Ticks":true,"Show UC":true,"Show SEPL":false,"Show Axes":true,"Show UC Tau Labels":false,"Show SEPL Tau Labels":false,"Show (g,s) Labels":true}
+ Phasor Plot Size:{"H":512,"V":512,"Margin":0.5}
+ Phasor Plot Smoothing Options:{"Use Phasor Plot Smoothing":false,"Kernel Type":"Uniform","Bin":1,"Algorithm":"Rapid"}
+ Phasor Ratio Color Map:"Rainbow"
+ Phasor Ratio Color Map Type:"Interpolate Reference Colors"
+ Phasor Ratio Color-Coded Quantity:"Phasor Ratio"
+ Phasor Ratio Decay Range:0.02
+ Phasor Ratio Display Range:{"Min":0,"Max":1}
+ Phasor Ratio Reference Colors:{"Reference 1":6618880,"Reference 2":16711680,"Boundary":9868950}
+ Phasor Ratio Type:"Item 0"
+ Pile-up Correction:false
+ Pixel Well Capacity:1020
+ Pixel-Normalize Decay:false
+ Pixel-level Phasor Computation:false
+ Python Settings:{"Python Version":"3.9","Use PATH definition":true,"Python.exe Path":""}
+ ROI Center Color:16711680
+ ROI Diameter:12
+ Reference Radius:3
+ Reject High Decay Peak Pixels:false
+ Reject Low Decay Peak Pixels:false
+ Reverse Gates:false
+ SYNC Period:1.00000000000000E-8
+ Save Phasor Graph:false
+ Save Phasor Plot:false
+ Saved Image File Format:"PNG"
+ Selected Image ROI(s):false
+ Selected Phasor Plot ROI(s):false
+ Shift Decay:false
+ Show Color Map Vertices:false
+ Show Last Decay Only:false
+ Show References:false
+ Smoothen Decay:false
+ Smoothing Parameter:-1
+ Square Pulse Options:{"Method":"Mode","# Bins":100,"Threshold %":10,"Center on Midpoint":true,"Smoothen Plot":false}
+ Straighten Decay:false
+ Tail Fraction:0.5
+ Time Step:1
+ Use Backup Calibration if needed:false
+ Use Cursors:false
+ Use Decay Pre-Processing:false
+ Use File Timestamp:true
+ Use Fixed ROI Diameter:false
+ Use Guess Parameters:false
+ Use Image Brightness:false
+ Use Image Histogram for Contrast:true
+ Use Intensity Correction File:false
+ Use Last Fitted Parameters:false
+ Use Periodicity:false
+ Use Phasor Brightness:false
+ Use Phasor Plot Binning:false
+ User-defined Gate:{"X Array":[],"Y Array":[]}
+ User-defined IRF:{"X Array":[],"Y Array":[]}
+ Verbose Decay Pre-Processing:true
+ Verbose Error Mode:true
+ Verbose Mode:false
+ Verbose Settings Mode:false
+ Visible Settings Tab:""
+ Wavelet Analysis Options:{"Wavelet":"db02","Option for Approximate Coefficients":"Threshold","# Levels":-1,"Threshold Settings":{"Thresholding Rule":"Universal","Rescaling Method":"Single level","Soft Threshold?":true},"Wavelet Transform Type":"Discrete"}
+ [0-1]-Normalize Decay:false


AlliGator exposed internal variables JSON strings with values
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+ Source Image Display Range:{"Min Value":-Infinity,"Max Value":Infinity}
+ Source Image Palette Information:{"Palette Name [# Colors,int?,inv?]":"Grayscale","Palette Type":5,"Palette Colors":[0,65793,131586,197379,263172,328965,394758,460551,526344,592137,657930,723723,789516,855309,921102,986895,1052688,1118481,1184274,1250067,1315860,1381653,1447446,1513239,1579032,1644825,1710618,1776411,1842204,1907997,1973790,2039583,2105376,2171169,2236962,2302755,2368548,2434341,2500134,2565927,2631720,2697513,2763306,2829099,2894892,2960685,3026478,3092271,3158064,3223857,3289650,3355443,3421236,3487029,3552822,3618615,3684408,3750201,3815994,3881787,3947580,4013373,4079166,4144959,4210752,4276545,4342338,4408131,4473924,4539717,4605510,4671303,4737096,4802889,4868682,4934475,5000268,5066061,5131854,5197647,5263440,5329233,5395026,5460819,5526612,5592405,5658198,5723991,5789784,5855577,5921370,5987163,6052956,6118749,6184542,6250335,6316128,6381921,6447714,6513507,6579300,6645093,6710886,6776679,6842472,6908265,6974058,7039851,7105644,7171437,7237230,7303023,7368816,7434609,7500402,7566195,7631988,7697781,7763574,7829367,7895160,7960953,8026746,8092539,8158332,8224125,8289918,8355711,8421504,8487297,8553090,8618883,8684676,8750469,8816262,8882055,8947848,9013641,9079434,9145227,9211020,9276813,9342606,9408399,9474192,9539985,9605778,9671571,9737364,9803157,9868950,9934743,10000536,10066329,10132122,10197915,10263708,10329501,10395294,10461087,10526880,10592673,10658466,10724259,10790052,10855845,10921638,10987431,11053224,11119017,11184810,11250603,11316396,11382189,11447982,11513775,11579568,11645361,11711154,11776947,11842740,11908533,11974326,12040119,12105912,12171705,12237498,12303291,12369084,12434877,12500670,12566463,12632256,12698049,12763842,12829635,12895428,12961221,13027014,13092807,13158600,13224393,13290186,13355979,13421772,13487565,13553358,13619151,13684944,13750737,13816530,13882323,13948116,14013909,14079702,14145495,14211288,14277081,14342874,14408667,14474460,14540253,14606046,14671839,14737632,14803425,14869218,14935011,15000804,15066597,15132390,15198183,15263976,15329769,15395562,15461355,15527148,15592941,15658734,15724527,15790320,15856113,15921906,15987699,16053492,16119285,16185078,16250871,16316664,16382457,16448250,16514043,16579836,16645629,16711422,16777215],"Interpolate?":false}
+ Time Gate Slider:0
+ Type of Displayed Image:"Sum of All Gates"


AlliGator exposed internal data JSON strings with values
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+ Calibration Phasor:{"m":0,"phi":0,"Phasor Frequency":0,"Reference Lifetime":0}
+ Phasor Calibration Map:{"m Array":[],"phi Array":[],"Phasor Frequency":80000000,"Calibration Lifetime":1.00000000000000E-9,"ROI Centers":[],"ROI Descriptors":[],"Map Resolution X":0,"Map Resolution Y":0}
+ ROIs:[]
+ Reference Decay:{"t Array":[],"I Array":[]}
+ Reference Decay Plot Name:""
+ IRF Array:[]
+ IRF Array Time Axis:[]