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Updates to SimPEG.DCIP

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This commit is contained in:
Rowan Cockett
2016-02-05 15:09:52 -08:00
parent bdfabe620a
commit 7a6d0c9fdd
8 changed files with 255 additions and 269 deletions
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SimPEG/DCIP/BaseDC.py
+178 -180
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@@ -1,7 +1,5 @@
from SimPEG import *
class FieldsDC_CC(Problem.Fields):
knownFields = {'phi_sol':'CC'}
aliasFields = {
@@ -22,7 +20,7 @@ class FieldsDC_CC(Problem.Fields):
# for i, src in enumerate(srcList):
# phi_p = src.phi_p(self.survey.prob)
# if phi_p is not None:
# phi[:,i] += phi_p
# phi[:,i] += phi_p
return phi
def _e(self, phi_sol, srcList):
@@ -30,9 +28,9 @@ class FieldsDC_CC(Problem.Fields):
# for i, src in enumerate(srcList):
# e_p = src.e_p(self.survey.prob)
# if e_p is not None:
# e[:,i] += e_p
# e[:,i] += e_p
return e
def _j(self, phi_sol, srcList):
j = -self._Mfinv*self.survey.prob.Msig*self._cellGrad*phi_sol
@@ -56,7 +54,7 @@ class SrcDipole(Survey.BaseSrc):
super(SrcDipole, self).__init__(rxList, **kwargs)
def eval(self, prob):
# Recompute rhs
# Recompute rhs
# if getattr(self, '_rhsDict', None) is None:
# self._rhsDict = {}
# if mesh not in self._rhsDict:
@@ -191,12 +189,12 @@ class ProblemDC_CC(Problem.BaseProblem):
def fields(self, m):
F = self.fieldsPair(self.mesh, self.survey)
F = self.fieldsPair(self.mesh, self.survey)
self.curModel = m
A = self.A
self.Ainv = self.Solver(A, **self.solverOpts)
RHS = self.getRHS()
Phi = self.Ainv * RHS
Phi = self.Ainv * RHS
Srcs = self.survey.srcList
F[Srcs, 'phi_sol'] = Phi
@@ -302,51 +300,51 @@ def readUBC_DC2DModel(fileName):
Output:
:param SimPEG TensorMesh 2D object
:return
Created on Thu Nov 12 13:14:10 2015
@author: dominiquef
"""
# Open fileand skip header... assume that we know the mesh already
obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
dim = np.array(obsfile[0].split(),dtype=float)
temp = np.array(obsfile[1].split(),dtype=float)
if len(temp) > 1:
model = np.zeros(dim)
for ii in range(len(obsfile)-1):
mm = np.array(obsfile[ii+1].split(),dtype=float)
model[:,ii] = mm
model = model[:,::-1]
else:
if len(obsfile[1:])==1:
mm = np.array(obsfile[1:].split(),dtype=float)
else:
mm = np.array(obsfile[1:],dtype=float)
# Permute the second dimension to flip the order
model = mm.reshape(dim[1],dim[0])
model = model[::-1,:]
model = np.transpose(model, (1, 0))
model = mkvc(model)
return model
def plot_pseudoSection(Tx,Rx,data,z0, stype):
from SimPEG import np, mkvc
from scipy.interpolate import griddata
from matplotlib.colors import LogNorm
@@ -355,265 +353,265 @@ def plot_pseudoSection(Tx,Rx,data,z0, stype):
"""
Read list of 2D tx-rx location and plot a speudo-section of apparent
resistivity.
Assumes flat topo for now...
Input:
:param d2D, z0
:switch stype -> Either 'pdp' (pole-dipole) | 'dpdp' (dipole-dipole)
Output:
:figure scatter plot overlayed on image
Created on Mon December 7th, 2015
@author: dominiquef
"""
#d2D = np.asarray(d2D)
midl = []
midz = []
rho = []
for ii in range(len(Tx)):
# Get distances between each poles
rC1P1 = np.abs(Tx[ii][0] - Rx[ii][:,0])
rC1P1 = np.abs(Tx[ii][0] - Rx[ii][:,0])
rC2P1 = np.abs(Tx[ii][1] - Rx[ii][:,0])
rC1P2 = np.abs(Tx[ii][1] - Rx[ii][:,1])
rC2P2 = np.abs(Tx[ii][0] - Rx[ii][:,1])
rP1P2 = np.abs(Rx[ii][:,1] - Rx[ii][:,0])
rP1P2 = np.abs(Rx[ii][:,1] - Rx[ii][:,0])
# Compute apparent resistivity
if re.match(stype,'pdp'):
rho = np.hstack([rho, data[ii] * 2*np.pi * rC1P1 * ( rC1P1 + rP1P2 ) / rP1P2] )
elif re.match(stype,'dpdp'):
rho = np.hstack([rho, data[ii] * 2*np.pi / ( 1/rC1P1 - 1/rC2P1 - 1/rC1P2 + 1/rC2P2 ) ])
Cmid = (Tx[ii][0] + Tx[ii][1])/2
Pmid = (Rx[ii][:,0] + Rx[ii][:,1])/2
midl = np.hstack([midl, ( Cmid + Pmid )/2 ])
midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + z0 ])
# Grid points
grid_x, grid_z = np.mgrid[np.min(midl):np.max(midl), np.min(midz):np.max(midz)]
grid_rho = griddata(np.c_[midl,midz], np.log10(abs(1/rho.T)), (grid_x, grid_z), method='linear')
#plt.subplot(2,1,2)
plt.imshow(grid_rho.T, extent = (np.min(midl),np.max(midl),np.min(midz),np.max(midz)), origin='lower', alpha=0.8)
cbar = plt.colorbar(format = '%.2f',fraction=0.02)
cmin,cmax = cbar.get_clim()
ticks = np.linspace(cmin,cmax,3)
cbar.set_ticks(ticks)
# Plot apparent resistivity
plt.scatter(midl,midz,s=50,c=np.log10(abs(1/rho.T)))
def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
from SimPEG import np
import re
"""
Load in endpoints and survey specifications to generate Tx, Rx location
stations.
Assumes flat topo for now...
Input:
:param endl -> input endpoints [x1, y1, z1, x2, y2, z2]
:object mesh -> SimPEG mesh object
:switch stype -> "dpdp" (dipole-dipole) | "pdp" (pole-dipole) | 'gradient'
: param a, n -> pole seperation, number of rx dipoles per tx
Output:
:param Tx, Rx -> List objects for each tx location
Lines: P1x, P1y, P1z, P2x, P2y, P2z
Created on Wed December 9th, 2015
@author: dominiquef
"""
def xy_2_r(x1,x2,y1,y2):
r = np.sqrt( np.sum((x2 - x1)**2 + (y2 - y1)**2) )
return r
return r
## Evenly distribute electrodes and put on surface
# Mesure survey length and direction
dl_len = xy_2_r(endl[0,0],endl[1,0],endl[0,1],endl[1,1])
dl_x = ( endl[1,0] - endl[0,0] ) / dl_len
dl_y = ( endl[1,1] - endl[0,1] ) / dl_len
nstn = np.floor( dl_len / a )
# Compute discrete pole location along line
stn_x = endl[0,0] + np.array(range(int(nstn)))*dl_x*a
stn_y = endl[0,1] + np.array(range(int(nstn)))*dl_y*a
# Create line of P1 locations
M = np.c_[stn_x, stn_y, np.ones(nstn).T*mesh.vectorNz[-1]]
# Create line of P2 locations
N = np.c_[stn_x+a*dl_x, stn_y+a*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
## Build list of Tx-Rx locations depending on survey type
# Dipole-dipole: Moving tx with [a] spacing -> [AB a MN1 a MN2 ... a MNn]
# Pole-dipole: Moving pole on one end -> [A a MN1 a MN2 ... MNn a B]
Tx = []
Rx = []
if not re.match(stype,'gradient'):
for ii in range(0, int(nstn)-1):
for ii in range(0, int(nstn)-1):
if re.match(stype,'dpdp'):
tx = np.c_[M[ii,:],N[ii,:]]
elif re.match(stype,'pdp'):
tx = np.c_[M[ii,:],M[ii,:]]
#Rx.append(np.c_[M[ii+1:indx,:],N[ii+1:indx,:]])
# Current elctrode seperation
AB = xy_2_r(tx[0,1],endl[1,0],tx[1,1],endl[1,1])
# Number of receivers to fit
nstn = np.min([np.floor( (AB - b) / a ) , n])
# Check if there is enough space, else break the loop
if nstn <= 0:
continue
# Compute discrete pole location along line
stn_x = N[ii,0] + dl_x*b + np.array(range(int(nstn)))*dl_x*a
stn_y = N[ii,1] + dl_y*b + np.array(range(int(nstn)))*dl_y*a
# Create receiver poles
# Create line of P1 locations
P1 = np.c_[stn_x, stn_y, np.ones(nstn).T*mesh.vectorNz[-1]]
# Create line of P2 locations
P2 = np.c_[stn_x+a*dl_x, stn_y+a*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
Rx.append(np.c_[P1,P2])
Tx.append(tx)
Tx.append(tx)
#==============================================================================
# elif re.match(stype,'dpdp'):
#
# for ii in range(0, int(nstn)-2):
#
#
# for ii in range(0, int(nstn)-2):
#
# indx = np.min([ii+n+1,nstn])
# Tx.append(np.c_[M[ii,:],N[ii,:]])
# Rx.append(np.c_[M[ii+2:indx,:],N[ii+2:indx,:]])
#==============================================================================
elif re.match(stype,'gradient'):
# Gradient survey only requires Tx at end of line and creates a square
# grid of receivers at in the middle at a pre-set minimum distance
Tx.append(np.c_[M[0,:],N[-1,:]])
# Get the edge limit of survey area
min_x = endl[0,0] + dl_x * b
min_y = endl[0,1] + dl_y * b
max_x = endl[1,0] - dl_x * b
max_y = endl[1,1] - dl_y * b
box_l = np.sqrt( (min_x - max_x)**2 + (min_y - max_y)**2 )
box_w = box_l/2.
nstn = np.floor( box_l / a )
# Compute discrete pole location along line
stn_x = min_x + np.array(range(int(nstn)))*dl_x*a
stn_y = min_y + np.array(range(int(nstn)))*dl_y*a
# Define number of cross lines
nlin = int(np.floor( box_w / a ))
lind = range(-nlin,nlin+1)
lind = range(-nlin,nlin+1)
ngrad = nstn * len(lind)
rx = np.zeros([ngrad,6])
for ii in range( len(lind) ):
# Move line in perpendicular direction by dipole spacing
lxx = stn_x - lind[ii]*a*dl_y
lyy = stn_y + lind[ii]*a*dl_x
M = np.c_[ lxx, lyy , np.ones(nstn).T*mesh.vectorNz[-1]]
N = np.c_[ lxx+a*dl_x, lyy+a*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
rx[(ii*nstn):((ii+1)*nstn),:] = np.c_[M,N]
Rx.append(rx)
else:
print """stype must be either 'pdp', 'dpdp' or 'gradient'. """
return Tx, Rx
return Tx, Rx
def writeUBC_DCobs(fileName,Tx,Rx,d,wd, dtype):
from SimPEG import np, mkvc
import re
"""
Read UBC GIF DCIP 3D observation file and generate arrays for tx-rx location
Input:
:param fileName, path to the UBC GIF 3D obs file
Output:
:param rx, tx, d, wd
:return
Created on Mon December 7th, 2015
@author: dominiquef
"""
fid = open(fileName,'w')
fid.write('! GENERAL FORMAT\n')
fid.write('! GENERAL FORMAT\n')
for ii in range(len(Tx)):
tx = np.asarray(Tx[ii])
rx = np.asarray(Rx[ii])
nrx = rx.shape[0]
fid.write('\n')
if re.match(dtype,'2D'):
for jj in range(nrx):
fid.writelines("%e " % ii for ii in mkvc(tx))
fid.writelines("%e " % ii for ii in mkvc(rx[jj]))
fid.write('%e %e\n'% (d[ii][jj],wd[ii][jj]))
#np.savetxt(fid, np.c_[ rx ,np.asarray(d[ii]), np.asarray(wd[ii]) ], fmt='%e',delimiter=' ',newline='\n')
#np.savetxt(fid, np.c_[ rx ,np.asarray(d[ii]), np.asarray(wd[ii]) ], fmt='%e',delimiter=' ',newline='\n')
elif re.match(dtype,'3D'):
fid.write('\n')
fid.writelines("%e " % ii for ii in mkvc(tx))
fid.write('%i\n'% nrx)
np.savetxt(fid, np.c_[ rx ,np.asarray(d[ii]), np.asarray(wd[ii]) ], fmt='%e',delimiter=' ',newline='\n')
fid.close()
np.savetxt(fid, np.c_[ rx ,np.asarray(d[ii]), np.asarray(wd[ii]) ], fmt='%e',delimiter=' ',newline='\n')
fid.close()
def convertObs_DC3D_to_2D(Tx,Rx):
from SimPEG import np
import numpy.matlib as npm
"""
@@ -622,35 +620,35 @@ def convertObs_DC3D_to_2D(Tx,Rx):
First transmitter pole is assumed to be at the origin
Assumes flat topo for now...
Input:
:param Tx, Rx
Output:
:figure Tx2d, Rx2d
Created on Mon December 7th, 2015
@author: dominiquef
"""
Tx2d = []
Rx2d = []
for ii in range(len(Tx)):
if ii == 0:
endp = Tx[0][0:2,0]
nrx = Rx[ii].shape[0]
rP1 = np.sqrt( np.sum( ( endp - Tx[ii][0:2,0] )**2 , axis=0))
rP2 = np.sqrt( np.sum( ( endp - Tx[ii][0:2,1] )**2 , axis=0))
rC1 = np.sqrt( np.sum( ( npm.repmat(endp.T,nrx,1) - Rx[ii][:,0:2] )**2 , axis=1))
rC2 = np.sqrt( np.sum( ( npm.repmat(endp.T,nrx,1) - Rx[ii][:,3:5] )**2 , axis=1))
Tx2d.append( np.r_[rP1, rP2] )
Rx2d.append( np.c_[rC1, rC2] )
#np.savetxt(fid, data, fmt='%e',delimiter=' ',newline='\n')
@@ -658,72 +656,72 @@ def convertObs_DC3D_to_2D(Tx,Rx):
return Tx2d, Rx2d
def readUBC_DC3Dobs(fileName):
from SimPEG import np
"""
Read UBC GIF DCIP 3D observation file and generate arrays for tx-rx location
Input:
:param fileName, path to the UBC GIF 3D obs file
Output:
:param rx, tx, d, wd
:return
Created on Mon December 7th, 2015
@author: dominiquef
"""
# Load file
obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
# Pre-allocate
Tx = []
Rx = []
d = []
wd = []
# Countdown for number of obs/tx
count = 0
for ii in range(obsfile.shape[0]):
if not obsfile[ii]:
continue
# First line is transmitter with number of receivers
if count==0:
temp = (np.fromstring(obsfile[ii], dtype=float,sep=' ').T)
count = int(temp[-1])
temp = np.reshape(temp[0:-1],[2,3]).T
Tx.append(temp)
rx = []
continue
temp = np.fromstring(obsfile[ii], dtype=float,sep=' ')
rx.append(temp)
count = count -1
# Reach the end of
rx.append(temp)
count = count -1
# Reach the end of
if count == 0:
temp = np.asarray(rx)
Rx.append(temp[:,0:6])
# Check for data + uncertainties
if temp.shape[1]==8:
d.append(temp[:,6])
wd.append(temp[:,7])
# Check for data only
# Check for data only
elif temp.shape[1]==7:
d.append(temp[:,6])
return Tx, Rx, d, wd
def readUBC_DC2DLoc(fileName):
@@ -738,13 +736,13 @@ def readUBC_DC2DLoc(fileName):
Output:
:param rx, tx
:return
Created on Thu Nov 12 13:14:10 2015
@author: dominiquef
"""
# Open fileand skip header... assume that we know the mesh already
#==============================================================================
# fopen = open(fileName,'r')
@@ -754,32 +752,32 @@ def readUBC_DC2DLoc(fileName):
# Load file
obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
# Check first line and figure out if 2D or 3D file format
line = np.array(obsfile[0].split(),dtype=float)
line = np.array(obsfile[0].split(),dtype=float)
tx_A = []
tx_B = []
rx_M = []
rx_N = []
d = []
wd = []
for ii in range(obsfile.shape[0]):
# If len==3, then simple format where tx-rx is listed on each line
if len(line) == 4:
temp = np.fromstring(obsfile[ii], dtype=float,sep=' ')
tx_A = np.hstack((tx_A,temp[0]))
tx_B = np.hstack((tx_B,temp[1]))
rx_M = np.hstack((rx_M,temp[2]))
rx_N = np.hstack((rx_N,temp[3]))
rx = np.transpose(np.array((rx_M,rx_N)))
rx = np.transpose(np.array((rx_M,rx_N)))
tx = np.transpose(np.array((tx_A,tx_B)))
return tx, rx, d, wd
def readUBC_DC2DMesh(fileName):
@@ -794,59 +792,59 @@ def readUBC_DC2DMesh(fileName):
Output:
:param SimPEG TensorMesh 2D object
:return
Created on Thu Nov 12 13:14:10 2015
@author: dominiquef
"""
# Open file
# Open file
fopen = open(fileName,'r')
# Read down the file and unpack dx vector
def unpackdx(fid,nrows):
for ii in range(nrows):
line = fid.readline()
var = np.array(line.split(),dtype=float)
if ii==0:
x0= var[0]
xvec = np.ones(int(var[2])) * (var[1] - var[0]) / int(var[2])
xend = var[1]
xend = var[1]
else:
xvec = np.hstack((xvec,np.ones(int(var[1])) * (var[0] - xend) / int(var[1])))
xend = var[0]
xend = var[0]
return x0, xvec
#%% Start with dx block
# First line specifies the number of rows for x-cells
line = fopen.readline()
nl = np.array(line.split(),dtype=float)
[x0, dx] = unpackdx(fopen,nl)
[x0, dx] = unpackdx(fopen,nl)
#%% Move down the file until reaching the z-block
line = fopen.readline()
if not line:
line = fopen.readline()
#%% End with dz block
# First line specifies the number of rows for z-cells
line = fopen.readline()
nl = np.array(line.split(),dtype=float)
[z0, dz] = unpackdx(fopen,nl)
[z0, dz] = unpackdx(fopen,nl)
# Flip z0 to be the bottom of the mesh for SimPEG
z0 = z0 - sum(dz)
dz = dz[::-1]
#%% Make the mesh using SimPEG
from SimPEG import Mesh
tensMsh = Mesh.TensorMesh([dx,dz],(x0, z0))
return tensMsh