added checkerboard to fmtomo utils and added different checkerboard ampl. functions
This commit is contained in:
Marcel Paffrath
parent
165419cb88
commit
0a0ab4bfa9
417
pylot/core/active/fmtomoUtils.py
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417
pylot/core/active/fmtomoUtils.py
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# -*- coding: utf-8 -*-
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import sys
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import numpy as np
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def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'abs', inputfileref = 'vgridsref.in'):
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'''
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Generate a vtk-file readable by e.g. paraview from FMTOMO output vgrids.in
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'''
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def getDistance(angle):
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PI = np.pi
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R = 6371.
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distance = angle / 180 * (PI * R)
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return distance
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def readNumberOfPoints(filename):
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fin = open(filename, 'r')
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vglines = fin.readlines()
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nR = int(vglines[1].split()[0])
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nTheta = int(vglines[1].split()[1])
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nPhi = int(vglines[1].split()[2])
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print('readNumberOf Points: Awaiting %d grid points in %s'
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%(nR*nTheta*nPhi, filename))
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fin.close()
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return nR, nTheta, nPhi
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def readDelta(filename):
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fin = open(filename, 'r')
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vglines = fin.readlines()
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dR = float(vglines[2].split()[0])
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dTheta = float(vglines[2].split()[1])
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dPhi = float(vglines[2].split()[2])
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fin.close()
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return dR, dTheta, dPhi
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def readStartpoints(filename):
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fin = open(filename, 'r')
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vglines = fin.readlines()
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sR = float(vglines[3].split()[0])
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sTheta = float(vglines[3].split()[1])
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sPhi = float(vglines[3].split()[2])
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fin.close()
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return sR, sTheta, sPhi
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def readVelocity(filename):
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'''
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Reads in velocity from vgrids file and returns a list containing all values in the same order
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'''
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vel = []; count = 0
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fin = open(filename, 'r')
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vglines = fin.readlines()
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for line in vglines:
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count += 1
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if count > 4:
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vel.append(float(line.split()[0]))
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print("Read %d points out of file: %s" %(count - 4, filename))
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return vel
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R = 6371. # earth radius
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outfile = open(outputfile, 'w')
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# Theta, Phi in radians, R in km
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nR, nTheta, nPhi = readNumberOfPoints(inputfile)
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dR, dTheta, dPhi = readDelta(inputfile)
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sR, sTheta, sPhi = readStartpoints(inputfile)
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vel = readVelocity(inputfile)
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nX = nPhi; nY = nTheta; nZ = nR
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sZ = sR - R
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sX = getDistance(np.rad2deg(sPhi))
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sY = getDistance(np.rad2deg(sTheta))
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dX = getDistance(np.rad2deg(dPhi))
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dY = getDistance(np.rad2deg(dTheta))
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nPoints = nX * nY * nZ
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dZ = dR
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# write header
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print("Writing header for VTK file...")
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outfile.writelines('# vtk DataFile Version 3.1\n')
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outfile.writelines('Velocity on FMTOMO vgrids.in points\n')
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outfile.writelines('ASCII\n')
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outfile.writelines('DATASET STRUCTURED_POINTS\n')
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outfile.writelines('DIMENSIONS %d %d %d\n' %(nX, nY, nZ))
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outfile.writelines('ORIGIN %f %f %f\n' %(sX, sY, sZ))
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outfile.writelines('SPACING %f %f %f\n' %(dX, dY, dZ))
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outfile.writelines('POINT_DATA %15d\n' %(nPoints))
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if absOrRel == 'abs':
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outfile.writelines('SCALARS velocity float %d\n' %(1))
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elif absOrRel == 'rel':
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outfile.writelines('SCALARS velChangePercent float %d\n' %(1))
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outfile.writelines('LOOKUP_TABLE default\n')
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# write velocity
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if absOrRel == 'abs':
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print("Writing velocity values to VTK file...")
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for velocity in vel:
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outfile.writelines('%10f\n' %velocity)
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elif absOrRel == 'rel':
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velref = readVelocity(inputfileref)
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if not len(velref) == len(vel):
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print('ERROR: Number of gridpoints mismatch for %s and %s'%(inputfile, inputfileref))
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return
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#velrel = [((vel - velref) / velref * 100) for vel, velref in zip(vel, velref)]
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velrel = []
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for velocities in zip(vel, velref):
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v, vref = velocities
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if not vref == 0:
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velrel.append((v - vref) / vref * 100)
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else:
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velrel.append(0)
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nR_ref, nTheta_ref, nPhi_ref = readNumberOfPoints(inputfileref)
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if not nR_ref == nR and nTheta_ref == nTheta and nPhi_ref == nPhi:
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print('ERROR: Dimension mismatch of grids %s and %s'%(inputfile, inputfileref))
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return
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print("Writing velocity values to VTK file...")
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for velocity in velrel:
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outfile.writelines('%10f\n' %velocity)
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print('Pertubations: min: %s %%, max: %s %%'%(min(velrel), max(velrel)))
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outfile.close()
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print("Wrote velocity grid for %d points to file: %s" %(nPoints, outputfile))
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return
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def rays2VTK(fnin, fdirout = './vtk_files/', nthPoint = 50):
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'''
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Writes VTK file(s) for FMTOMO rays from rays.dat
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:param: nthPoint, plot every nth point of the ray
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:type: integer
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'''
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def getDistance(angle):
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PI = np.pi
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R = 6371.
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distance = angle / 180 * (PI * R)
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return distance
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infile = open(fnin, 'r')
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R = 6371
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rays = {}
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raynumber = 0
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nPoints = 0
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### NOTE: rays.dat seems to be in km and radians
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while True:
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raynumber += 1
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firstline = infile.readline()
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if firstline == '': break # break at EOF
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raynumber = int(firstline.split()[0])
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shotnumber = int(firstline.split()[1])
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rayValid = int(firstline.split()[4]) # is zero if the ray is invalid
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if rayValid == 0:
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print('Invalid ray number %d for shot number %d'%(raynumber, shotnumber))
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continue
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nRayPoints = int(infile.readline().split()[0])
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if not shotnumber in rays.keys():
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rays[shotnumber] = {}
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rays[shotnumber][raynumber] = []
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for index in range(nRayPoints):
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if index % nthPoint is 0 or index == (nRayPoints - 1):
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rad, lat, lon = infile.readline().split()
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rays[shotnumber][raynumber].append([getDistance(np.rad2deg(float(lon))), getDistance(np.rad2deg(float(lat))), float(rad) - R])
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else:
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dummy = infile.readline()
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infile.close()
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for shotnumber in rays.keys():
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fnameout = fdirout + 'rays%03d.vtk'%(shotnumber)
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outfile = open(fnameout, 'w')
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nPoints = 0
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for raynumber in rays[shotnumber]:
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for ray in rays[shotnumber][raynumber]:
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nPoints += 1
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# write header
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#print("Writing header for VTK file...")
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print("Writing shot %d to file %s" %(shotnumber, fnameout))
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outfile.writelines('# vtk DataFile Version 3.1\n')
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outfile.writelines('FMTOMO rays\n')
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outfile.writelines('ASCII\n')
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outfile.writelines('DATASET POLYDATA\n')
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outfile.writelines('POINTS %15d float\n' %(nPoints))
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# write coordinates
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#print("Writing coordinates to VTK file...")
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for raynumber in rays[shotnumber].keys():
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for raypoint in rays[shotnumber][raynumber]:
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outfile.writelines('%10f %10f %10f \n' %(raypoint[0], raypoint[1], raypoint[2]))
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outfile.writelines('LINES %15d %15d\n' %(len(rays[shotnumber]), len(rays[shotnumber]) + nPoints))
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# write indices
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#print("Writing indices to VTK file...")
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count = 0
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for raynumber in rays[shotnumber].keys():
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outfile.writelines('%d ' %(len(rays[shotnumber][raynumber])))
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for index in range(len(rays[shotnumber][raynumber])):
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outfile.writelines('%d ' %(count))
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count += 1
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outfile.writelines('\n')
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# outfile.writelines('POINT_DATA %15d\n' %(nPoints))
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# outfile.writelines('SCALARS rays float %d\n' %(1))
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# outfile.writelines('LOOKUP_TABLE default\n')
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# # write velocity
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# print("Writing velocity values to VTK file...")
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# for velocity in vel:
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# outfile.writelines('%10f\n' %velocity)
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# outfile.close()
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# print("Wrote velocity grid for %d points to file: %s" %(nPoints, outputfile))
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def addCheckerboard(spacing = 10., pertubation = 0.1, inputfile = 'vgrids.in',
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outputfile = 'vgrids_cb.in', ampmethod = 'linear', rect = (None, None)):
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'''
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Add a checkerboard to an existing vgrids.in velocity model.
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:param: spacing, size of the tiles
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type: float
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:param: pertubation, pertubation (default: 0.1 = 10%)
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type: float
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'''
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def readNumberOfPoints(filename):
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fin = open(filename, 'r')
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vglines = fin.readlines()
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nR = int(vglines[1].split()[0])
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nTheta = int(vglines[1].split()[1])
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nPhi = int(vglines[1].split()[2])
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print('readNumberOf Points: Awaiting %d grid points in %s'
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%(nR*nTheta*nPhi, filename))
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fin.close()
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return nR, nTheta, nPhi
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def readDelta(filename):
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fin = open(filename, 'r')
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vglines = fin.readlines()
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dR = float(vglines[2].split()[0])
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dTheta = float(vglines[2].split()[1])
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dPhi = float(vglines[2].split()[2])
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fin.close()
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return dR, dTheta, dPhi
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def readStartpoints(filename):
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fin = open(filename, 'r')
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vglines = fin.readlines()
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sR = float(vglines[3].split()[0])
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sTheta = float(vglines[3].split()[1])
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sPhi = float(vglines[3].split()[2])
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fin.close()
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return sR, sTheta, sPhi
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def readVelocity(filename):
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'''
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Reads in velocity from vgrids file and returns a list containing all values in the same order
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'''
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vel = []; count = 0
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fin = open(filename, 'r')
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vglines = fin.readlines()
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for line in vglines:
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count += 1
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if count > 4:
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vel.append(float(line.split()[0]))
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print("Read %d points out of file: %s" %(count - 4, filename))
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return vel
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def correctSpacing(spacing, delta, disttype = None):
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if spacing > delta:
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spacing_corr = round(spacing / delta) * delta
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elif spacing < delta:
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spacing_corr = delta
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print('The spacing of the checkerboard of %s (%s) was corrected to '
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'a value of %s to fit the grid spacing of %s.' %(spacing, disttype, spacing_corr, delta))
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return spacing_corr
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def linearAmp(InCell):
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decimal = InCell - np.floor(InCell)
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return (-abs(decimal - 0.5) + 0.5) * 2
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def rectAmp(InCell, rect):
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decimal = InCell - np.floor(InCell)
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r1, r2 = rect
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if r1 <= decimal <= r2:
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return 1
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else:
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return 0
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def ampFunc(InCell, method = 'linear', rect = None):
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if method == 'linear':
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return linearAmp(InCell)
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if method == 'rect' and rect is not None:
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return rectAmp(InCell, rect)
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else:
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print('ampFunc: Could not amplify cb pattern')
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R = 6371. # earth radius
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decm = 0.3 # diagonal elements of the covariance matrix (grid3dg's default value is 0.3)
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outfile = open(outputfile, 'w')
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# Theta, Phi in radians, R in km
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nR, nTheta, nPhi = readNumberOfPoints(inputfile)
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dR, dThetaRad, dPhiRad = readDelta(inputfile)
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sR, sThetaRad, sPhiRad = readStartpoints(inputfile)
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vel = readVelocity(inputfile)
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dTheta, dPhi = np.rad2deg((dThetaRad, dPhiRad))
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sTheta, sPhi = np.rad2deg((dThetaRad, dPhiRad))
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eR = sR + (nR - 1) * dR
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ePhi = sPhi + (nPhi - 1) * dPhi
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eTheta = sTheta + (nTheta - 1) * dTheta
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nPoints = nR * nTheta * nPhi
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thetaGrid = np.linspace(sTheta, eTheta, num = nTheta)
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phiGrid = np.linspace(sPhi, ePhi, num = nPhi)
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rGrid = np.linspace(sR, eR, num = nR)
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# write header for velocity grid file (in RADIANS)
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outfile.writelines('%10s %10s \n' %(1, 1))
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outfile.writelines('%10s %10s %10s\n' %(nR, nTheta, nPhi))
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outfile.writelines('%10s %10s %10s\n' %(dR, dThetaRad, dPhiRad))
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outfile.writelines('%10s %10s %10s\n' %(sR, sThetaRad, sPhiRad))
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spacR = correctSpacing(spacing, dR, '[meter], R')
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spacTheta = correctSpacing(_getAngle(spacing), dTheta, '[degree], Theta')
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spacPhi = correctSpacing(_getAngle(spacing), dPhi, '[degree], Phi')
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count = 0
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evenOdd = 1
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even = 0; odd = 0
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# In the following loop it is checked whether the positive distance from the border of the model
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# for a point on the grid divided by the spacing is even or odd and then pertubated.
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# The position is also shifted by half of the delta so that the position is directly on the point and
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# not on the border between two points.
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# "InCell" points e.g. rInCell are floats with their integer number corresponding to the cell number and
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# their decimal place (0 - 1) corresponding to the position inside the cell.
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# The amplification factor ampFactor comes from a linear relationship and ranges between 0 (cell border)
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# and 1 (cell middle)
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for radius in rGrid:
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rInCell = (radius - sR - dR/2) / spacR
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ampR = ampFunc(rInCell, ampmethod, rect)
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if np.floor(rInCell) % 2:
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evenOddR = 1
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else:
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evenOddR = -1
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for theta in thetaGrid:
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thetaInCell = (theta - sTheta - dTheta/2) / spacTheta
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ampTheta = ampFunc(thetaInCell, ampmethod, rect)
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if np.floor(thetaInCell) % 2:
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evenOddT = 1
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else:
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evenOddT = -1
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for phi in phiGrid:
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phiInCell = (phi - sPhi - dPhi/2) / spacPhi
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ampPhi = ampFunc(phiInCell, ampmethod, rect)
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if np.floor(phiInCell) % 2:
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evenOddP = 1
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else:
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evenOddP = -1
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velocity = vel[count]
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ampFactor = (ampR + ampTheta + ampPhi) / 3
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evenOdd = evenOddR * evenOddT * evenOddP * ampFactor
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velocity += evenOdd * pertubation * velocity
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outfile.writelines('%10s %10s\n'%(velocity, decm))
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count += 1
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progress = float(count) / float(nPoints) * 100
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_update_progress(progress)
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print('Added checkerboard to the grid in file %s with a spacing of %s and a pertubation of %s %%. '
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'Outputfile: %s.'%(inputfile, spacing, pertubation, outputfile))
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outfile.close()
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def _update_progress(progress):
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sys.stdout.write("%d%% done \r" % (progress) )
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sys.stdout.flush()
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def _getAngle(distance):
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'''
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Function returns the angle on a Sphere of the radius R = 6371 [km] for a distance [km].
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'''
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PI = np.pi
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R = 6371.
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angle = distance * 180. / (PI * R)
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return angle
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