mirror of
https://github.com/wassname/simpeg.git
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Major overhaul of Survey and Problem class.
Create SrcField and RxObs retrotfit I/O to use survey Forward matrix as property Inversion running again but needs cleanup
This commit is contained in:
D Fournier
+48
-349
@@ -105,6 +105,54 @@ class BaseMagSurvey(Survey.BaseSurvey):
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return np.r_[bfx, bfy, bfz]
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class LinearSurvey(Survey.BaseSurvey):
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"""Base Magnetics Survey"""
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rxLoc = None #: receiver locations
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rxType = None #: receiver type
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def __init__(self, srcField, **kwargs):
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self.srcField = srcField
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Survey.BaseSurvey.__init__(self, **kwargs)
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def eval(self, u):
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return u
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@property
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def nD(self):
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return self.prob.G.shape[0]
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@property
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def nRx(self):
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return self.srcField.rxList[0].locs.shape[0]
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# def setBackgroundField(self, SrcField):
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# if getattr(self, 'B0', None) is None:
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# self._B0 = SrcField.param[0] * dipazm_2_xyz(SrcField.param[1],SrcField.param[2])
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# return self._B0
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class SrcField(Survey.BaseSrc):
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""" Define the inducing field """
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param = None #: Inducing field param (Amp, Incl, Decl)
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def __init__(self, rxList, A, I, D, **kwargs):
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self.param = (A,I,D)
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super(SrcField, self).__init__(rxList, **kwargs)
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class RxObs(Survey.BaseRx):
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"""A station location must have be located in 3-D"""
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def __init__(self, locsXYZ, **kwargs):
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locs = locsXYZ
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assert locsXYZ.shape[1] == 3, 'locs must in 3-D (x,y,z).'
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super(RxObs, self).__init__(locs, 'tmi', storeProjections=False, **kwargs)
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@property
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def nD(self):
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"""Number of data in the receiver."""
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return self.locs[0].shape[0]
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class MagSurveyBx(object):
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"""docstring for MagSurveyBx"""
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def __init__(self, **kwargs):
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@@ -144,352 +192,3 @@ class WeightMap(Maps.IdentityMap):
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return Utils.sdiag(self.weight)
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def readUBCmagObs(obs_file):
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"""
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Read and write UBC mag file format
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INPUT:
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:param fileName, path to the UBC obs mag file
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OUTPUT:
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:param dobs, observation in (x y z [data] [wd])
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:param B, primary field information (BI, BD, B0)
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:param M, magnetization orentiaton (MI, MD)
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"""
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fid = open(obs_file,'r')
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# First line has the inclination,declination and amplitude of B0
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line = fid.readline()
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B = np.array(line.split(),dtype=float)
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# Second line has the magnetization orientation and a flag
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line = fid.readline()
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M = np.array(line.split(),dtype=float)
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# Third line has the number of rows
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line = fid.readline()
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ndat = np.array(line.split(),dtype=int)
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# Pre-allocate space for obsx, obsy, obsz, data, uncert
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line = fid.readline()
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temp = np.array(line.split(),dtype=float)
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dobs = np.zeros((ndat,len(temp)), dtype=float)
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for ii in range(ndat):
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dobs[ii,:] = np.array(line.split(),dtype=float)
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line = fid.readline()
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return B, M, dobs
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def read_MAGfwr_inp(input_file):
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"""Read input files for forward modeling MAG data with integral form
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INPUT:
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input_file: File name containing the forward parameter
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OUTPUT:
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mshfile
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obsfile
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modfile
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magfile
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topofile
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# All files should be in the working directory, otherwise the path must
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# be specified.
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Created on Jul 17, 2013
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@author: dominiquef
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"""
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fid = open(input_file,'r')
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line = fid.readline()
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l_input = line.split('!')
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mshfile = l_input[0].rstrip()
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line = fid.readline()
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l_input = line.split('!')
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obsfile = l_input[0].rstrip()
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line = fid.readline()
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l_input = line.split('!')
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modfile = l_input[0].rstrip()
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line = fid.readline()
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l_input = line.split('!')
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if l_input=='null':
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magfile = []
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else:
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magfile = l_input[0].rstrip()
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line = fid.readline()
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l_input = line.split('!')
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if l_input=='null':
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topofile = []
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else:
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topofile = l_input[0].rstrip()
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return mshfile, obsfile, modfile, magfile, topofile
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def read_MAGinv_inp(input_file):
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"""Read input files for forward modeling MAG data with integral form
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INPUT:
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input_file: File name containing the forward parameter
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OUTPUT:
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mshfile
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obsfile
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topofile
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start model
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ref model
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mag model
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weightfile
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chi_target
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as, ax ,ay, az
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upper, lower bounds
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lp, lqx, lqy, lqz
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# All files should be in the working directory, otherwise the path must
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# be specified.
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Created on Dec 21th, 2015
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@author: dominiquef
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"""
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fid = open(input_file,'r')
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# Line 1
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line = fid.readline()
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l_input = line.split('!')
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mshfile = l_input[0].rstrip()
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# Line 2
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line = fid.readline()
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l_input = line.split('!')
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obsfile = l_input[0].rstrip()
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# Line 3
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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if l_input=='null':
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topofile = []
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else:
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topofile = l_input[0].rstrip()
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# Line 4
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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if l_input[0]=='VALUE':
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mstart = float(l_input[1])
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else:
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mstart = l_input[0].rstrip()
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# Line 5
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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if l_input[0]=='VALUE':
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mref = float(l_input[1])
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else:
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mref = l_input[0].rstrip()
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# Line 6
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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if l_input=='DEFAULT':
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magfile = []
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else:
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magfile = l_input[0].rstrip()
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# Line 7
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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if l_input=='DEFAULT':
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wgtfile = []
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else:
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wgtfile = l_input[0].rstrip()
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# Line 8
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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chi = float(l_input[0])
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# Line 9
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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val = np.array(l_input[0:4])
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alphas = val.astype(np.float)
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# Line 10
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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if l_input[0]=='VALUE':
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val = np.array(l_input[1:3])
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bounds = val.astype(np.float)
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else:
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bounds = l_input[0].rstrip()
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# Line 11
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line = fid.readline()
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l_input = re.split('[!\s]',line)
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if l_input[0]=='VALUE':
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val = np.array(l_input[1:6])
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lpnorms = val.astype(np.float)
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else:
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lpnorms = l_input[0].rstrip()
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return mshfile, obsfile, topofile, mstart, mref, magfile, wgtfile, chi, alphas, bounds, lpnorms
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def read_GOCAD_ts(tsfile):
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"""Read GOCAD triangulated surface (*.ts) file
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INPUT:
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tsfile: Triangulated surface
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OUTPUT:
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vrts : Array of vertices in XYZ coordinates [n x 3]
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trgl : Array of index for triangles [m x 3]. The order of the vertices
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is important and describes the normal
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n = cross( (P2 - P1 ) , (P3 - P1) )
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Created on Jan 13th, 2016
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Author: @fourndo
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"""
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fid = open(tsfile,'r')
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line = fid.readline()
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# Skip all the lines until the vertices
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while re.match('TFACE',line)==None:
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line = fid.readline()
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line = fid.readline()
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vrtx = []
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# Run down all the vertices and save in array
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while re.match('VRTX',line):
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l_input = re.split('[\s*]',line)
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temp = np.array(l_input[2:5])
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vrtx.append(temp.astype(np.float))
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# Read next line
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line = fid.readline()
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vrtx = np.asarray(vrtx)
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# Skip lines to the triangles
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while re.match('TRGL',line)==None:
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line = fid.readline()
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# Run down the list of triangles
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trgl = []
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# Run down all the vertices and save in array
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while re.match('TRGL',line):
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l_input = re.split('[\s*]',line)
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temp = np.array(l_input[1:4])
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trgl.append(temp.astype(np.int))
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# Read next line
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line = fid.readline()
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trgl = np.asarray(trgl)
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return vrtx, trgl
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def gocad2vtk(gcFile,mesh,bcflag,inflag):
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""""
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Function to read gocad polystructure file and output indexes of mesh with in the structure.
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"""
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import vtk, vtk.util.numpy_support as npsup
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print "Reading GOCAD ts file..."
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vrtx, trgl = read_GOCAD_ts(gcFile)
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# Adjust the index
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trgl = trgl - 1
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# Make vtk pts
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ptsvtk = vtk.vtkPoints()
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ptsvtk.SetData(npsup.numpy_to_vtk(vrtx,deep=1))
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# Make the polygon connection
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polys = vtk.vtkCellArray()
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for face in trgl:
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poly = vtk.vtkPolygon()
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poly.GetPointIds().SetNumberOfIds(len(face))
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for nrv, vert in enumerate(face):
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poly.GetPointIds().SetId(nrv,vert)
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polys.InsertNextCell(poly)
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# Make the polydata, structure of connections and vrtx
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polyData = vtk.vtkPolyData()
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polyData.SetPoints(ptsvtk)
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polyData.SetPolys(polys)
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# Make implicit func
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ImpDistFunc = vtk.vtkImplicitPolyDataDistance()
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ImpDistFunc.SetInput(polyData)
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# Convert the mesh
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vtkMesh = vtk.vtkRectilinearGrid()
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vtkMesh.SetDimensions(mesh.nNx,mesh.nNy,mesh.nNz)
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vtkMesh.SetXCoordinates(npsup.numpy_to_vtk(mesh.vectorNx,deep=1))
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vtkMesh.SetYCoordinates(npsup.numpy_to_vtk(mesh.vectorNy,deep=1))
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vtkMesh.SetZCoordinates(npsup.numpy_to_vtk(mesh.vectorNz,deep=1))
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# Add indexes
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vtkInd = npsup.numpy_to_vtk(np.arange(mesh.nC),deep=1)
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vtkInd.SetName('Index')
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vtkMesh.GetCellData().AddArray(vtkInd)
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extractImpDistRectGridFilt = vtk.vtkExtractGeometry() # Object constructor
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extractImpDistRectGridFilt.SetImplicitFunction(ImpDistFunc) #
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extractImpDistRectGridFilt.SetInputData(vtkMesh)
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if bcflag is True:
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extractImpDistRectGridFilt.ExtractBoundaryCellsOn()
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else:
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extractImpDistRectGridFilt.ExtractBoundaryCellsOff()
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if inflag is True:
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extractImpDistRectGridFilt.ExtractInsideOn()
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else:
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extractImpDistRectGridFilt.ExtractInsideOff()
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print "Extracting indices from grid..."
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# Executing the pipe
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extractImpDistRectGridFilt.Update()
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# Get index inside
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insideGrid = extractImpDistRectGridFilt.GetOutput()
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insideGrid = npsup.vtk_to_numpy(insideGrid.GetCellData().GetArray('Index'))
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# Return the indexes inside
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return insideGrid
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+558
-19
@@ -1,18 +1,43 @@
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from SimPEG import *
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import BaseMag
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import BaseMag as MAG
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from scipy.constants import mu_0
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from MagAnalytics import spheremodel, CongruousMagBC
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import re
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class MagneticIntegral(Problem.BaseProblem):
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surveyPair = Survey.LinearSurvey
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#surveyPair = Survey.LinearSurvey
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def __init__(self, mesh, G, mapping=None, **kwargs):
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storeG = True #: Store the forward matrix by default, otherwise just compute d
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actInd = None #: Active cell indices provided
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M = None #: Magnetization matrix provided, otherwise all induced
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def __init__(self, mesh, mapping=None, **kwargs):
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Problem.BaseProblem.__init__(self, mesh, mapping=mapping, **kwargs)
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self.G = G
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def fwr_ind(self):
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# Add forward function
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# kappa = self.curModel.kappa TODO
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kappa = self.mapping*self.curModel
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return self.G.dot(kappa)
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def fwr_rem(self):
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#TODO check if we are inverting for M
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return self.G.dot(self.mapping(m))
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def fields(self, m):
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return self.G.dot(self.mapping*(m))
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self.curModel = m
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total = np.zeros(self.survey.nRx)
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induced = self.fwr_ind()
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# rem = self.rem
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if induced is not None:
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total += induced
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return total
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# return self.G.dot(self.mapping*(m))
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def Jvec(self, m, v, u=None):
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dmudm = self.mapping.deriv(m)
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@@ -22,15 +47,171 @@ class MagneticIntegral(Problem.BaseProblem):
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dmudm = self.mapping.deriv(m)
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return dmudm.T * (self.G.T.dot(v))
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@property
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def G(self):
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if not self.ispaired:
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raise Exception('Need to pair!')
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if getattr(self,'_G', None) is None:
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self._G = self.Intrgl_Fwr_Op( 'ind' )
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return self._G
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# @property
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# def Grem(self):
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# if not self.ispaired:
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# raise Exception('Need to pair!')
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# if getattr(self,'_Grem', None) is None:
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# self._Grem = Intrgl_Fwr_Op('full')
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# return self._Grem
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def Intrgl_Fwr_Op(self, flag):
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"""
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Magnetic forward operator in integral form
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flag = 'ind' | 'full'
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1- ind : Magnetization fixed by user
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3- full: Full tensor matrix stored with shape([3*ndata, 3*nc])
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Return
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_G = Linear forward modeling operation
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Created on March, 13th 2016
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@author: dominiquef
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"""
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# Find non-zero cells
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#inds = np.nonzero(actv)[0]
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if getattr(self, 'actInd', None) is not None:
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if self.actInd.dtype=='bool':
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inds = np.asarray([inds for inds, elem in enumerate(self.actInd, 1) if elem], dtype = int) - 1
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else:
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inds = self.actInd
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else:
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inds = np.asarray(range(self.mesh.nC))
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nC = len(inds)
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# Create active cell projector
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P = sp.csr_matrix((np.ones(nC),(inds, range(nC))),
|
||||
shape=(self.mesh.nC, nC))
|
||||
|
||||
|
||||
|
||||
|
||||
# Create vectors of nodal location (lower and upper coners for each cell)
|
||||
xn = self.mesh.vectorNx;
|
||||
yn = self.mesh.vectorNy;
|
||||
zn = self.mesh.vectorNz;
|
||||
|
||||
yn2,xn2,zn2 = np.meshgrid(yn[1:], xn[1:], zn[1:])
|
||||
yn1,xn1,zn1 = np.meshgrid(yn[0:-1], xn[0:-1], zn[0:-1])
|
||||
|
||||
Yn = P.T*np.c_[mkvc(yn1), mkvc(yn2)]
|
||||
Xn = P.T*np.c_[mkvc(xn1), mkvc(xn2)]
|
||||
Zn = P.T*np.c_[mkvc(zn1), mkvc(zn2)]
|
||||
|
||||
rxLoc = self.survey.srcField.rxList[0].locs
|
||||
ndata = rxLoc.shape[0]
|
||||
|
||||
survey = self.survey
|
||||
|
||||
# Pre-allocate space and create magnetization matrix if required
|
||||
if (flag=='ind'):
|
||||
|
||||
# # If assumes uniform magnetization direction
|
||||
# if M.shape != (nC,3):
|
||||
|
||||
# print 'Magnetization vector must be Nc x 3'
|
||||
# return
|
||||
if getattr(self, 'M', None) is None:
|
||||
M = dipazm_2_xyz(np.ones(nC) * survey.srcField.param[1],np.ones(nC) * survey.srcField.param[2])
|
||||
|
||||
|
||||
Mx = Utils.sdiag(M[:,0]*survey.srcField.param[0])
|
||||
My = Utils.sdiag(M[:,1]*survey.srcField.param[0])
|
||||
Mz = Utils.sdiag(M[:,2]*survey.srcField.param[0])
|
||||
|
||||
Mxyz = sp.vstack((Mx,My,Mz))
|
||||
|
||||
|
||||
|
||||
if survey.srcField.rxList[0].rxType == 'tmi':
|
||||
G = np.zeros((ndata, nC))
|
||||
|
||||
# Convert Bdecination from north to cartesian
|
||||
D = (450.-float(survey.srcField.param[2]))%360.
|
||||
I = survey.srcField.param[1]
|
||||
# Projection matrix
|
||||
Ptmi = mkvc(np.r_[np.cos(np.deg2rad(I))*np.cos(np.deg2rad(D)),
|
||||
np.cos(np.deg2rad(I))*np.sin(np.deg2rad(D)),
|
||||
np.sin(np.deg2rad(I))],2).T;
|
||||
|
||||
elif survey.srcField.rxList[0].rxType == 'xyz':
|
||||
|
||||
G = np.zeros((int(3*ndata), nC))
|
||||
|
||||
elif flag == 'full':
|
||||
G = np.zeros((int(3*ndata), int(3*nC)))
|
||||
|
||||
|
||||
else:
|
||||
print """Flag must be either 'tmi' | 'xyz' | 'full', please revised"""
|
||||
return
|
||||
|
||||
|
||||
# Loop through all observations and create forward operator (ndata-by-nC)
|
||||
print "Begin calculation of forward operator: " + flag
|
||||
|
||||
# Add counter to dsiplay progress. Good for large problems
|
||||
count = -1;
|
||||
for ii in range(ndata):
|
||||
|
||||
|
||||
tx, ty, tz = get_T_mat(Xn,Yn,Zn,rxLoc[ii,:])
|
||||
if flag == 'ind':
|
||||
|
||||
if survey.srcField.rxList[0].rxType =='tmi':
|
||||
G[ii,:] = Ptmi.dot(np.vstack((tx,ty,tz)))*Mxyz
|
||||
|
||||
elif survey.srcField.rxList[0].rxType =='xyz':
|
||||
G[ii,:] = tx*Mxyz
|
||||
G[ii+ndata,:] = ty*Mxyz
|
||||
G[ii+2*ndata,:] = tz*Mxyz
|
||||
|
||||
elif flag == 'full':
|
||||
G[ii,:] = tx
|
||||
G[ii+ndata,:] = ty
|
||||
G[ii+2*ndata,:] = tz
|
||||
|
||||
|
||||
# Display progress
|
||||
count = progress(ii,count,ndata)
|
||||
|
||||
print "Done 100% ...forward operator completed!!\n"
|
||||
|
||||
return G
|
||||
|
||||
class MagneticsDiffSecondary(Problem.BaseProblem):
|
||||
"""
|
||||
Secondary field approach using differential equations!
|
||||
"""
|
||||
|
||||
surveyPair = BaseMag.BaseMagSurvey
|
||||
modelPair = BaseMag.BaseMagMap
|
||||
surveyPair = MAG.BaseMagSurvey
|
||||
modelPair = MAG.BaseMagMap
|
||||
|
||||
def __init__(self, model, mapping=None, **kwargs):
|
||||
Problem.BaseProblem.__init__(self, model, mapping=mapping, **kwargs)
|
||||
@@ -823,9 +1004,9 @@ def dipazm_2_xyz(dip,azm_N):
|
||||
M = np.zeros((nC,3))
|
||||
|
||||
# Modify azimuth from North to Cartesian-X
|
||||
azm_X = (450.- azm_N) % 360.
|
||||
azm_X = (450.- np.asarray(azm_N)) % 360.
|
||||
|
||||
D = np.deg2rad(dip)
|
||||
D = np.deg2rad(np.asarray(dip))
|
||||
I = np.deg2rad(azm_X)
|
||||
|
||||
M[:,0] = np.cos(D) * np.cos(I) ;
|
||||
@@ -926,7 +1107,7 @@ def get_dist_wgt(mesh,rxLoc,actv,R,R0):
|
||||
|
||||
return wr
|
||||
|
||||
def writeUBCobs(filename,B,M,rxLoc,d,wd):
|
||||
def writeUBCobs(filename,survey,d):
|
||||
"""
|
||||
writeUBCobs(filename,B,M,rxLoc,d,wd)
|
||||
|
||||
@@ -934,11 +1115,8 @@ def writeUBCobs(filename,B,M,rxLoc,d,wd):
|
||||
|
||||
INPUT
|
||||
filename : Name of out file including directory
|
||||
B : Inducing field parameters [Inc, Decl, Intensity]
|
||||
M : Magnetization orientation [Inc, Decl, dtype]
|
||||
rxLoc : Observation locations [obsx, obsy, obsz]
|
||||
d : Data vector
|
||||
wd : Uncertainty vector
|
||||
survey
|
||||
flag : dobs | dpred
|
||||
|
||||
OUTPUT
|
||||
Obsfile
|
||||
@@ -948,11 +1126,17 @@ def writeUBCobs(filename,B,M,rxLoc,d,wd):
|
||||
@author: dominiquef
|
||||
"""
|
||||
|
||||
B = survey.srcField.param
|
||||
|
||||
rxLoc = survey.srcField.rxList[0].locs
|
||||
|
||||
wd = survey.std
|
||||
|
||||
data = np.c_[rxLoc , d , wd]
|
||||
|
||||
with file(filename,'w') as fid:
|
||||
fid.write('%6.2f %6.2f %6.2f\n' %(B[0], B[1], B[2]) )
|
||||
fid.write('%6.2f %6.2f %6.2f\n' %(M[0], M[1], 1) )
|
||||
fid.write('%6.2f %6.2f %6.2f\n' %(B[2], B[1], B[0]) )
|
||||
fid.write('%6.2f %6.2f %6.2f\n' %(B[2], B[1], 1) )
|
||||
fid.write('%i\n' %len(d) )
|
||||
np.savetxt(fid, data, fmt='%e',delimiter=' ',newline='\n')
|
||||
|
||||
@@ -1048,4 +1232,359 @@ def plot_obs_2D(rxLoc,d,wd,varstr):
|
||||
plt.scatter(rxLoc[:,0],rxLoc[:,1], c=d, s=20)
|
||||
plt.title(varstr)
|
||||
plt.gca().set_aspect('equal', adjustable='box')
|
||||
|
||||
|
||||
def readUBCmagObs(obs_file):
|
||||
|
||||
"""
|
||||
Read and write UBC mag file format
|
||||
|
||||
INPUT:
|
||||
:param fileName, path to the UBC obs mag file
|
||||
|
||||
OUTPUT:
|
||||
:param survey
|
||||
:param M, magnetization orentiaton (MI, MD)
|
||||
|
||||
"""
|
||||
|
||||
fid = open(obs_file,'r')
|
||||
|
||||
# First line has the inclination,declination and amplitude of B0
|
||||
line = fid.readline()
|
||||
B = np.array(line.split(),dtype=float)
|
||||
|
||||
# Second line has the magnetization orientation and a flag
|
||||
line = fid.readline()
|
||||
M = np.array(line.split(),dtype=float)
|
||||
|
||||
# Third line has the number of rows
|
||||
line = fid.readline()
|
||||
ndat = np.array(line.split(),dtype=int)
|
||||
|
||||
# Pre-allocate space for obsx, obsy, obsz, data, uncert
|
||||
line = fid.readline()
|
||||
temp = np.array(line.split(),dtype=float)
|
||||
|
||||
d = np.zeros(ndat, dtype=float)
|
||||
wd = np.zeros(ndat, dtype=float)
|
||||
locXYZ = np.zeros( (ndat,3), dtype=float)
|
||||
|
||||
for ii in range(ndat):
|
||||
|
||||
temp = np.array(line.split(),dtype=float)
|
||||
locXYZ[ii,:] = temp[:3]
|
||||
d[ii] = temp[3]
|
||||
wd[ii] = temp[4]
|
||||
line = fid.readline()
|
||||
|
||||
rxLoc = MAG.RxObs(locXYZ)
|
||||
srcField = MAG.SrcField([rxLoc],B[2],B[0],B[1])
|
||||
survey = MAG.LinearSurvey(srcField)
|
||||
survey.dobs = d
|
||||
survey.std = wd
|
||||
return survey
|
||||
|
||||
def read_MAGfwr_inp(input_file):
|
||||
|
||||
"""Read input files for forward modeling MAG data with integral form
|
||||
INPUT:
|
||||
input_file: File name containing the forward parameter
|
||||
|
||||
OUTPUT:
|
||||
mshfile
|
||||
obsfile
|
||||
modfile
|
||||
magfile
|
||||
topofile
|
||||
# All files should be in the working directory, otherwise the path must
|
||||
# be specified.
|
||||
|
||||
Created on Jul 17, 2013
|
||||
|
||||
@author: dominiquef
|
||||
"""
|
||||
|
||||
|
||||
fid = open(input_file,'r')
|
||||
|
||||
line = fid.readline()
|
||||
l_input = line.split('!')
|
||||
mshfile = l_input[0].rstrip()
|
||||
|
||||
line = fid.readline()
|
||||
l_input = line.split('!')
|
||||
obsfile = l_input[0].rstrip()
|
||||
|
||||
line = fid.readline()
|
||||
l_input = line.split('!')
|
||||
modfile = l_input[0].rstrip()
|
||||
|
||||
line = fid.readline()
|
||||
l_input = line.split('!')
|
||||
if l_input=='null':
|
||||
magfile = []
|
||||
|
||||
else:
|
||||
magfile = l_input[0].rstrip()
|
||||
|
||||
|
||||
line = fid.readline()
|
||||
l_input = line.split('!')
|
||||
if l_input=='null':
|
||||
topofile = []
|
||||
|
||||
else:
|
||||
topofile = l_input[0].rstrip()
|
||||
|
||||
return mshfile, obsfile, modfile, magfile, topofile
|
||||
|
||||
def read_MAGinv_inp(input_file):
|
||||
"""Read input files for forward modeling MAG data with integral form
|
||||
INPUT:
|
||||
input_file: File name containing the forward parameter
|
||||
|
||||
OUTPUT:
|
||||
mshfile
|
||||
obsfile
|
||||
topofile
|
||||
start model
|
||||
ref model
|
||||
mag model
|
||||
weightfile
|
||||
chi_target
|
||||
as, ax ,ay, az
|
||||
upper, lower bounds
|
||||
lp, lqx, lqy, lqz
|
||||
|
||||
# All files should be in the working directory, otherwise the path must
|
||||
# be specified.
|
||||
|
||||
Created on Dec 21th, 2015
|
||||
|
||||
@author: dominiquef
|
||||
"""
|
||||
|
||||
|
||||
fid = open(input_file,'r')
|
||||
|
||||
# Line 1
|
||||
line = fid.readline()
|
||||
l_input = line.split('!')
|
||||
mshfile = l_input[0].rstrip()
|
||||
|
||||
# Line 2
|
||||
line = fid.readline()
|
||||
l_input = line.split('!')
|
||||
obsfile = l_input[0].rstrip()
|
||||
|
||||
# Line 3
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
if l_input=='null':
|
||||
topofile = []
|
||||
|
||||
else:
|
||||
topofile = l_input[0].rstrip()
|
||||
|
||||
|
||||
# Line 4
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
if l_input[0]=='VALUE':
|
||||
mstart = float(l_input[1])
|
||||
|
||||
else:
|
||||
mstart = l_input[0].rstrip()
|
||||
|
||||
# Line 5
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
if l_input[0]=='VALUE':
|
||||
mref = float(l_input[1])
|
||||
|
||||
else:
|
||||
mref = l_input[0].rstrip()
|
||||
|
||||
|
||||
# Line 6
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
if l_input=='DEFAULT':
|
||||
magfile = []
|
||||
|
||||
else:
|
||||
magfile = l_input[0].rstrip()
|
||||
|
||||
# Line 7
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
if l_input=='DEFAULT':
|
||||
wgtfile = []
|
||||
|
||||
else:
|
||||
wgtfile = l_input[0].rstrip()
|
||||
|
||||
# Line 8
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
chi = float(l_input[0])
|
||||
|
||||
# Line 9
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
val = np.array(l_input[0:4])
|
||||
alphas = val.astype(np.float)
|
||||
|
||||
# Line 10
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
if l_input[0]=='VALUE':
|
||||
val = np.array(l_input[1:3])
|
||||
bounds = val.astype(np.float)
|
||||
|
||||
else:
|
||||
bounds = l_input[0].rstrip()
|
||||
|
||||
# Line 11
|
||||
line = fid.readline()
|
||||
l_input = re.split('[!\s]',line)
|
||||
if l_input[0]=='VALUE':
|
||||
val = np.array(l_input[1:6])
|
||||
lpnorms = val.astype(np.float)
|
||||
|
||||
else:
|
||||
lpnorms = l_input[0].rstrip()
|
||||
|
||||
return mshfile, obsfile, topofile, mstart, mref, magfile, wgtfile, chi, alphas, bounds, lpnorms
|
||||
|
||||
def read_GOCAD_ts(tsfile):
|
||||
"""Read GOCAD triangulated surface (*.ts) file
|
||||
INPUT:
|
||||
tsfile: Triangulated surface
|
||||
|
||||
OUTPUT:
|
||||
vrts : Array of vertices in XYZ coordinates [n x 3]
|
||||
trgl : Array of index for triangles [m x 3]. The order of the vertices
|
||||
is important and describes the normal
|
||||
n = cross( (P2 - P1 ) , (P3 - P1) )
|
||||
|
||||
|
||||
Created on Jan 13th, 2016
|
||||
|
||||
Author: @fourndo
|
||||
"""
|
||||
|
||||
|
||||
fid = open(tsfile,'r')
|
||||
line = fid.readline()
|
||||
|
||||
# Skip all the lines until the vertices
|
||||
while re.match('TFACE',line)==None:
|
||||
line = fid.readline()
|
||||
|
||||
line = fid.readline()
|
||||
vrtx = []
|
||||
|
||||
# Run down all the vertices and save in array
|
||||
while re.match('VRTX',line):
|
||||
l_input = re.split('[\s*]',line)
|
||||
temp = np.array(l_input[2:5])
|
||||
vrtx.append(temp.astype(np.float))
|
||||
|
||||
# Read next line
|
||||
line = fid.readline()
|
||||
|
||||
vrtx = np.asarray(vrtx)
|
||||
|
||||
# Skip lines to the triangles
|
||||
while re.match('TRGL',line)==None:
|
||||
line = fid.readline()
|
||||
|
||||
# Run down the list of triangles
|
||||
trgl = []
|
||||
|
||||
# Run down all the vertices and save in array
|
||||
while re.match('TRGL',line):
|
||||
l_input = re.split('[\s*]',line)
|
||||
temp = np.array(l_input[1:4])
|
||||
trgl.append(temp.astype(np.int))
|
||||
|
||||
# Read next line
|
||||
line = fid.readline()
|
||||
|
||||
trgl = np.asarray(trgl)
|
||||
|
||||
return vrtx, trgl
|
||||
|
||||
def gocad2vtk(gcFile,mesh,bcflag,inflag):
|
||||
""""
|
||||
Function to read gocad polystructure file and output indexes of mesh with in the structure.
|
||||
|
||||
"""
|
||||
import vtk, vtk.util.numpy_support as npsup
|
||||
|
||||
print "Reading GOCAD ts file..."
|
||||
vrtx, trgl = read_GOCAD_ts(gcFile)
|
||||
# Adjust the index
|
||||
trgl = trgl - 1
|
||||
|
||||
# Make vtk pts
|
||||
ptsvtk = vtk.vtkPoints()
|
||||
ptsvtk.SetData(npsup.numpy_to_vtk(vrtx,deep=1))
|
||||
|
||||
# Make the polygon connection
|
||||
polys = vtk.vtkCellArray()
|
||||
for face in trgl:
|
||||
poly = vtk.vtkPolygon()
|
||||
poly.GetPointIds().SetNumberOfIds(len(face))
|
||||
for nrv, vert in enumerate(face):
|
||||
poly.GetPointIds().SetId(nrv,vert)
|
||||
polys.InsertNextCell(poly)
|
||||
|
||||
# Make the polydata, structure of connections and vrtx
|
||||
polyData = vtk.vtkPolyData()
|
||||
polyData.SetPoints(ptsvtk)
|
||||
polyData.SetPolys(polys)
|
||||
|
||||
# Make implicit func
|
||||
ImpDistFunc = vtk.vtkImplicitPolyDataDistance()
|
||||
ImpDistFunc.SetInput(polyData)
|
||||
|
||||
# Convert the mesh
|
||||
vtkMesh = vtk.vtkRectilinearGrid()
|
||||
vtkMesh.SetDimensions(mesh.nNx,mesh.nNy,mesh.nNz)
|
||||
vtkMesh.SetXCoordinates(npsup.numpy_to_vtk(mesh.vectorNx,deep=1))
|
||||
vtkMesh.SetYCoordinates(npsup.numpy_to_vtk(mesh.vectorNy,deep=1))
|
||||
vtkMesh.SetZCoordinates(npsup.numpy_to_vtk(mesh.vectorNz,deep=1))
|
||||
# Add indexes
|
||||
vtkInd = npsup.numpy_to_vtk(np.arange(mesh.nC),deep=1)
|
||||
vtkInd.SetName('Index')
|
||||
vtkMesh.GetCellData().AddArray(vtkInd)
|
||||
|
||||
extractImpDistRectGridFilt = vtk.vtkExtractGeometry() # Object constructor
|
||||
extractImpDistRectGridFilt.SetImplicitFunction(ImpDistFunc) #
|
||||
extractImpDistRectGridFilt.SetInputData(vtkMesh)
|
||||
|
||||
if bcflag is True:
|
||||
extractImpDistRectGridFilt.ExtractBoundaryCellsOn()
|
||||
|
||||
else:
|
||||
extractImpDistRectGridFilt.ExtractBoundaryCellsOff()
|
||||
|
||||
if inflag is True:
|
||||
extractImpDistRectGridFilt.ExtractInsideOn()
|
||||
|
||||
else:
|
||||
extractImpDistRectGridFilt.ExtractInsideOff()
|
||||
|
||||
print "Extracting indices from grid..."
|
||||
# Executing the pipe
|
||||
extractImpDistRectGridFilt.Update()
|
||||
|
||||
# Get index inside
|
||||
insideGrid = extractImpDistRectGridFilt.GetOutput()
|
||||
insideGrid = npsup.vtk_to_numpy(insideGrid.GetCellData().GetArray('Index'))
|
||||
|
||||
|
||||
# Return the indexes inside
|
||||
return insideGrid
|
||||
File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user