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PSPVPTest.py
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# -*- coding: utf-8 -*-
"""
Created on Thu Dec 1 08:55:11 2016
@author: dfs1
"""
# import libraries
import numpy as np
import CDSAXSfunctions as CD
import scoop.futures
#import matplotlib.pyplot as plt
import time
#from multiprocessing import Pool
# Import data
Intensity=np.loadtxt('Sat3N_Intensity.txt')
Qx = np.loadtxt('Sat3N_Qx.txt')
Qz = np.loadtxt('Sat3N_Qz.txt')
CutLengths=np.loadtxt('Sat3N_CutLength.txt')
Trapnumber = 5
Disc=18
DW = 1.69
I0 = 10
Bk = 1.2
Pitch = 84
SPAR=np.zeros([4])
SPAR[0]=DW; SPAR[1]=I0; SPAR[2]=Bk;SPAR[3]=Pitch;
Spline=np.zeros([Trapnumber,5])
Offset = np.zeros([7,1])
Offset[0,0]=20
Offset[1,0]=5
Offset[2,0]=10.5
Offset[3,0]=10.5
Offset[4,0]=10.5
Offset[5,0]=10.5
Offset[6,0]=10
Spline[0,0]=0; Spline[0,1]=0; Spline[0,2]=0; Spline[0,3]=0; Spline[0,4]=0;
Spline[1,0]=5; Spline[1,1]=3; Spline[1,2]=0; Spline[1,3]=0; Spline[1,4]=0;
Spline[2,0]=15; Spline[2,1]=3; Spline[2,2]=1; Spline[2,3]=1; Spline[2,4]=1;
Spline[3,0]=21; Spline[3,1]=3; Spline[3,2]=-1; Spline[3,3]=-0.5; Spline[3,4]=-1;
Spline[4,0]=24; Spline[4,1]=3; Spline[4,2]=-1; Spline[4,3]=-0.5; Spline[4,4]=-1;
MCoord=np.loadtxt('MCOORDPSPVP1.txt')
(Coord)= CD.PSPVPCoord(Spline,MCoord,Trapnumber, Disc,Pitch, Offset)
(FITPAR,FITPARLB,FITPARUB)=CD.PSPVP_PB(Offset,Spline,SPAR,Trapnumber,Disc)
np.savetxt('test.txt',FITPAR,delimiter=',')
MCPAR=np.zeros([7])
MCPAR[0] = 2 # Chainnumber
MCPAR[1] = len(FITPAR)
MCPAR[2] = 100 #stepnumber
MCPAR[3] = 0 #randomchains
MCPAR[4] = 5 # Resampleinterval
MCPAR[5] = 40 # stepbase
MCPAR[6] = 200 # steplength
def SimInt_PSPVP(FITPAR):
T=int(FITPAR[len(FITPAR)-3])
Disc=int(FITPAR[len(FITPAR)-2])
Pitch=int(FITPAR[len(FITPAR)-4])
Spline=np.reshape(FITPAR[0:T*5],(T,5))
Spline
Offset=FITPAR[T*5:T*5+7]
SPAR=FITPAR[T*5+7:T*5+11]
Coord=CD.PSPVPCoord(Spline,MCoord,Trapnumber, Disc,Pitch, Offset)
F1 = CD.FreeFormTrapezoid(Coord[:,:,0],Qx,Qz,Disc+1)
F2 = CD.FreeFormTrapezoid(Coord[:,:,1],Qx,Qz,Disc+1)
F3 = CD.FreeFormTrapezoid(Coord[:,:,2],Qx,Qz,Disc+1)
F4 = CD.FreeFormTrapezoid(Coord[:,:,3],Qx,Qz,Disc+1)
F5 = CD.FreeFormTrapezoid(Coord[:,:,4],Qx,Qz,Disc+1)
F6 = CD.FreeFormTrapezoid(Coord[:,:,5],Qx,Qz,Disc+1)
F7 = CD.FreeFormTrapezoid(Coord[:,:,6],Qx,Qz,Disc+1)
F8 = CD.FreeFormTrapezoid(Coord[:,:,7],Qx,Qz,Disc+1)
Formfactor=(F1+F2+F3+F4+F5+F6+F7+F8)
M=np.power(np.exp(-1*(np.power(Qx,2)+np.power(Qz,2))*np.power(SPAR[0],2)),0.5);
Formfactor=Formfactor*M
SimInt = np.power(abs(Formfactor),2)*SPAR[1]+SPAR[2]
return SimInt
def MCMCInit_PSPVP(FITPAR,FITPARLB,FITPARUB,MCPAR):
MCMCInit=np.zeros([int(MCPAR[0]),int(MCPAR[1])+1])
for i in range(int(MCPAR[0])):
if i <MCPAR[3]: #reversed from matlab code assigns all chains below randomnumber as random chains
for c in range(int(MCPAR[1])-3):
MCMCInit[i,c]=FITPARLB[c]+(FITPARUB[c]-FITPARLB[c])*np.random.random_sample()
MCMCInit[i,int(MCPAR[1])-3:int(MCPAR[1])]=FITPAR[int(MCPAR[1])-3:int(MCPAR[1])]
SimInt=SimInt_PSPVP(MCMCInit[i,:])
C=np.sum(CD.Misfit(Intensity,SimInt))
MCMCInit[i,int(MCPAR[1])]=C
else:
MCMCInit[i,0:int(MCPAR[1])]=FITPAR
SimInt=SimInt_PSPVP(MCMCInit[i,:])
C=np.sum(CD.Misfit(Intensity,SimInt))
MCMCInit[i,int(MCPAR[1])]=C
return MCMCInit
MCMCInit=MCMCInit_PSPVP(FITPAR,FITPARLB,FITPARUB,MCPAR)
MCMC_List=[0]*int(MCPAR[0])
for i in range(int(MCPAR[0])):
MCMC_List[i]=MCMCInit[i,:]
def MCMC_PSPVP(MCMC_List):
MCMCInit=MCMC_List
L = int(MCPAR[1])
Stepnumber= int(MCPAR[2])
SampleMatrix=np.zeros([Stepnumber,L+1])
SampleMatrix[0,:]=MCMCInit
Move = np.zeros([L+1])
ChiPrior = MCMCInit[L]
for step in np.arange(1,Stepnumber,1):
Temp = SampleMatrix[step-1,:]
print(Temp)
for p in range(L-3):
StepControl = MCPAR[5]+MCPAR[6]*np.random.random_sample()
Move[p] = (FITPARUB[p]-FITPARLB[p])/StepControl*(np.random.random_sample()-0.5) # need out of bounds check
Temp=Temp+Move
SimPost=SimInt_PSPVP(Temp)
ChiPost=np.sum(CD.Misfit(Intensity,SimPost))
if ChiPost < ChiPrior:
SampleMatrix[step,0:L]=Temp[0:L]
SampleMatrix[step,L]=ChiPost
else:
MoveProb = np.exp(-0.5*np.power(ChiPost-ChiPrior,2))
if np.random.random_sample() < MoveProb:
SampleMatrix[step,0:L]=Temp[0:L]
SampleMatrix[step,L]=ChiPost
else:
SampleMatrix[step,:]=SampleMatrix[step-1,:]
return SampleMatrix
start_time = time.perf_counter()
if __name__ == '__main__':
F=scoop.futures.map(MCMC_PSPVP,MCMC_List)
end_time=time.perf_counter()
print(F)
np.savetxt('Ptest.txt',F,delimiter=',')