microscpsf / microscpsf-imagej Goto Github PK

// Oil thickness. I use only a single number for z (not an array),
// so you will need to change the line below.
ti = (this.ti0 + z);

double sqNA = this.NA * this.NA;
double rhoNA2;
for (int rhoi = 0; rhoi < this.numSamples; rhoi++) {
    rho = rhoi * deltaRho;
    rhoNA2 = rho * rho * sqNA;
                
    // OPD in the sample
    OPD = this.eZ * Math.sqrt(this.ns * this.ns - rhoNA2);
                
    // OPD in the immersion medium
    OPD += ti * Math.sqrt(this. ni * this.ni - rhoNA2) -
        this.ti0 * Math.sqrt(this.ni0 * this.ni0 - rhoNA2);

    // OPD in the coverslip
    OPD += this.tg * Math.sqrt(this.ng * this.ng - rhoNA2) -
        this.tg0 * Math.sqrt(this.ng0 * this.ng0 - rhoNA2);

    W = k0 * OPD;

    // You will need to change the second index back to that used in your notation
    Ffun[rhoi][0] = Math.cos(W);
    Ffun[rhoi][1] = Math.sin(W);
}