/usr/share/doc/pycorrfit/examples/external_model_functions/ExampleFunc_CS_2D+2D+S+T.txt is in pycorrfit 0.9.5+dfsg-1.
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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 | # CS-FCS 2D+2D+S+T (Confocal)
# Circular Scanninf FCS model function for two 2D-diffusing species
# including triplet component.
# Further reading:
# Precise Measurement of Diffusion Coefficients using Scanning
# Fluorescence Correlation Spectroscopy
# Petrasek and Schwille, BiophysJ 2008, 1437-1448
# http://dx.doi.org/10.1529/biophysj.107.108811
# Visit http://fcstools.dyndns.org/pyscanfcs/ for more information.
# The first line of this file will be treated as the name of the model
# inside PyCorrFit. PyCorrFit will enumerate user imported models with IDs
# starting at 7001. You can save a session and the user defined models
# like this one will be saved as well. Lines starting with a hash "#"
# are treated as comments. Empty lines and lines with only white space
# characters are ignored.
# Note that if your code does not work, it might be that some variables
# have other meaning. This includes using "n" instead of "N".
# If you get some Syntax Error it might be that your starting variables
# are not set to a reasonable starting function. PyCorrFit is testing the
# function with sympy (for safety) and calculates the function for
# different values of tau.
## Definition of parameters:
# First, define the parameters and their starting values for you model
# function. If the parameter has a unit of measurement, then it may be
# added separated by a white space before the "=" sign. The starting
# value should be a floating point number. You may use abbreviations
# like "1e-3" instead of "0.001".
# Note that PyCorrFit has it's own unit system:
# unit of time : 1 ms
# unit of inverse time: 1000 /s
# unit of distance : 100 nm
# unit of diff.coeff : 10 µm²/s
# unit of inverse area: 100 /µm²
# unit of inv. volume : 1000 /µm³
# Diffusion coefficient of first component
D1 [10 µm²/s] = 200.0
# Diffusion coefficient of second component
D2 [10 µm²/s] = 20.0
# Fraction of species One
F1 = 1.0
# Half waist of the lateral detection area (w0 = 2*a)
a [100 nm] = 1.0
# Particle number
n = 5.0
# Scan radius
R [100 nm] = 3.850
# Frequency
f [kHz] = .2
# Triplet fraction
T = 0.1
# Triplet time
tautrip [ms] = 0.001
# You may choose to substitute certain parts of the correlation function
# with other values for easy reading. This can be done by using the
# prefix "g". You may use all common mathematical functions,
# such as "sqrt()" or "exp()". For convenience, "pi" and "e" may also
# be used. If you are paranoid, you always use float numbers with a dot "."
# to be sure the program doesn't accidently do integer division.
gTriplet = 1. + T/(1-T)*exp(-tau/tautrip)
gScan1 = exp(-(R*sin(pi*f*tau))**2/(a**2+D1*tau))
gScan2 = exp(-(R*sin(pi*f*tau))**2/(a**2+D2*tau))
gTwoD1 = F1/(1.+D1*tau/a**2)
gTwoD2 = (1-F1)/(1.+D2*tau/a**2)
# The final line with the correlation function should start with a "G"
# before the "=" sign.
G = 1./n * (gTwoD1 * gScan1 + gTwoD2 * gScan2) * gTriplet
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