| 1 | from sas.sascalc.data_util.calcthread import CalcThread |
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| 2 | from sas.sascalc.dataloader.data_info import Data1D |
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| 3 | from scipy.fftpack import dct |
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| 4 | from scipy.integrate import trapz |
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| 5 | import numpy as np |
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| 6 | from time import sleep |
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| 7 | |
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| 8 | class FourierThread(CalcThread): |
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| 9 | def __init__(self, raw_data, extrapolated_data, bg, updatefn=None, |
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| 10 | completefn=None): |
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| 11 | CalcThread.__init__(self, updatefn=updatefn, completefn=completefn) |
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| 12 | self.data = raw_data |
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| 13 | self.background = bg |
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| 14 | self.extrapolation = extrapolated_data |
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| 15 | |
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| 16 | def check_if_cancelled(self): |
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| 17 | if self.isquit(): |
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| 18 | self.update("Fourier transform cancelled.") |
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| 19 | self.complete(transforms=None) |
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| 20 | return True |
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| 21 | return False |
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| 22 | |
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| 23 | def compute(self): |
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| 24 | qs = self.extrapolation.x |
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| 25 | iqs = self.extrapolation.y |
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| 26 | q = self.data.x |
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| 27 | background = self.background |
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| 28 | |
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| 29 | xs = np.pi*np.arange(len(qs),dtype=np.float32)/(q[1]-q[0])/len(qs) |
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| 30 | |
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| 31 | self.ready(delay=0.0) |
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| 32 | self.update(msg="Fourier transform in progress.") |
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| 33 | self.ready(delay=0.0) |
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| 34 | |
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| 35 | if self.check_if_cancelled(): return |
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| 36 | try: |
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| 37 | # ----- 1D Correlation Function ----- |
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| 38 | gamma1 = dct((iqs-background)*qs**2) |
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| 39 | gamma1 = gamma1 / gamma1.max() |
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| 40 | |
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| 41 | if self.check_if_cancelled(): return |
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| 42 | |
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| 43 | # ----- 3D Correlation Function ----- |
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| 44 | # gamma3(R) = 1/R int_{0}^{R} gamma1(x) dx |
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| 45 | # trapz uses the trapezium rule to calculate the integral |
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| 46 | mask = xs <= 200.0 # Only calculate gamma3 up to x=200 (as this is all that's plotted) |
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| 47 | gamma3 = [trapz(gamma1[:n], xs[:n])/xs[n-1] for n in range(2, len(xs[mask]) + 1)] |
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| 48 | gamma3.insert(0, 1.0) # Gamma_3(0) is defined as 1 |
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| 49 | gamma3 = np.array(gamma3) |
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| 50 | |
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| 51 | if self.check_if_cancelled(): return |
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| 52 | |
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| 53 | # ----- Interface Distribution function ----- |
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| 54 | dmax = 200.0 # Max real space value to calculate IDF up to |
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| 55 | dstep = 0.5 |
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| 56 | qmax = 1.0 # Max q value to integrate up to when calculating IDF |
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| 57 | |
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| 58 | # Units of x axis depend on qmax (for some reason?). This scales |
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| 59 | # the xgamma array appropriately, since qmax was set to 0.6 in |
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| 60 | # the original fortran code. |
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| 61 | x_scale = qmax / 0.6 |
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| 62 | |
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| 63 | xgamma = np.arange(0, dmax/x_scale, step=dstep/x_scale) |
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| 64 | idf = np.zeros(len(xgamma)) |
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| 65 | |
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| 66 | # nth moment = integral(q^n * I(q), q=0, q=inf) |
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| 67 | moment = np.zeros(5) |
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| 68 | for n in range(5): |
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| 69 | integrand = qs**n * (iqs-background) |
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| 70 | moment[n] = trapz(integrand[qs < qmax], qs[qs < qmax]) |
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| 71 | if self.check_if_cancelled(): return |
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| 72 | |
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| 73 | # idf(x) = -integral(q^4 * I(q)*cos(qx), q=0, q=inf) / 2nd moment |
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| 74 | # => idf(0) = -integral(q^4 * I(q), 0, inf) / (2nd moment) |
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| 75 | # = -(4th moment)/(2nd moment) |
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| 76 | idf[0] = -moment[4] / moment[2] |
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| 77 | for i in range(1, len(xgamma)): |
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| 78 | d = xgamma[i] |
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| 79 | |
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| 80 | integrand = -qs**4 * (iqs-background) * np.cos(d*qs) |
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| 81 | idf[i] = trapz(integrand[qs < qmax], qs[qs < qmax]) |
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| 82 | idf[i] /= moment[2] |
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| 83 | if self.check_if_cancelled(): return |
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| 84 | |
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| 85 | xgamma *= x_scale |
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| 86 | |
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| 87 | except Exception as e: |
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| 88 | import logging |
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| 89 | logger = logging.getLogger(__name__) |
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| 90 | logger.error(e) |
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| 91 | |
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| 92 | self.update(msg="Fourier transform failed.") |
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| 93 | self.complete(transforms=None) |
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| 94 | return |
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| 95 | if self.isquit(): |
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| 96 | return |
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| 97 | self.update(msg="Fourier transform completed.") |
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| 98 | |
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| 99 | transform1 = Data1D(xs, gamma1) |
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| 100 | transform3 = Data1D(xs[xs <= 200], gamma3) |
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| 101 | idf = Data1D(xgamma, idf) |
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| 102 | |
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| 103 | transforms = (transform1, transform3, idf) |
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| 104 | |
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| 105 | self.complete(transforms=transforms) |
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| 106 | |
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| 107 | class HilbertThread(CalcThread): |
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| 108 | def __init__(self, raw_data, extrapolated_data, bg, updatefn=None, |
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| 109 | completefn=None): |
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| 110 | CalcThread.__init__(self, updatefn=updatefn, completefn=completefn) |
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| 111 | self.data = raw_data |
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| 112 | self.background = bg |
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| 113 | self.extrapolation = extrapolated_data |
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| 114 | |
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| 115 | def compute(self): |
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| 116 | qs = self.extrapolation.x |
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| 117 | iqs = self.extrapolation.y |
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| 118 | q = self.data.x |
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| 119 | background = self.background |
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| 120 | |
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| 121 | self.ready(delay=0.0) |
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| 122 | self.update(msg="Starting Hilbert transform.") |
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| 123 | self.ready(delay=0.0) |
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| 124 | if self.isquit(): |
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| 125 | return |
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| 126 | |
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| 127 | # TODO: Implement hilbert transform |
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| 128 | |
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| 129 | self.update(msg="Hilbert transform completed.") |
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| 130 | |
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| 131 | self.complete(transforms=None) |
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