fmtomo2vtk merged with fmtomoUtils
This commit is contained in:
Marcel Paffrath
parent
8893a8ec6b
commit
f906211064
@ -1,236 +0,0 @@
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# -*- coding: utf-8 -*-
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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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:param: absOrRel, can be "abs" or "rel" for absolute or relative velocities. if "rel" inputfileref must be given
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:type: str
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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. There is one file created for each ray.
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:param: fdirout, output directory, must exist before
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:type: str
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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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@ -43,15 +43,32 @@ def vgrids2VTK(inputfile = 'vgrids.in', outputfile = 'vgrids.vtk', absOrRel = 'a
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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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if absOrRel == 'relDepth':
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outfile.writelines('SCALARS velocity2depthMean 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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pointsPerR = nTheta * nPhi
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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 == 'relDepth':
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print("Writing velocity values to VTK file relative to mean of each depth...")
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index = 0; count = 0
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veldepth = []
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for velocity in vel:
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count += 1
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veldepth.append(velocity)
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if count%pointsPerR == 0:
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velmean = np.mean(veldepth)
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#print velmean, count, count/pointsPerR
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for vel in veldepth:
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outfile.writelines('%10f\n' %(vel - velmean))
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veldepth = []
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elif absOrRel == 'rel':
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nref, dref, sref, velref = _readVgrid(inputfileref)
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nR_ref, nTheta_ref, nPhi_ref = nref
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