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Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip/dev

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This commit is contained in:
Rowan Cockett
2016-02-16 13:01:48 -08:00
parent 1d06b768e2 cb9e820eb3
commit 6ccfa71dd7
1 changed files with 332 additions and 77 deletions
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SimPEG/DCIP/DCIPUtils.py
+332 -77
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@@ -109,8 +109,7 @@ def readUBC_DC3Dobstopo(filename,mesh,topo,probType="CC"):
DATA = np.vstack(DATA)
survey.dobs = np.vstack(DATA)[:,-2]
# DCdata = Survey.Data(surveytest, surveytest.dobs)
# DCdata[src0, src0.rxList[0]]
return {'DCsurvey':survey, 'airind':airind, 'topoCC':topoCC, 'SRC':SRC}
def readUBC_DC2DModel(fileName):
@@ -168,7 +167,7 @@ def readUBC_DC2DModel(fileName):
return model
def plot_pseudoSection(Tx,Rx,data,z0, stype):
def plot_pseudoSection(DCsurvey,lineID,ID, stype):
from SimPEG import np, mkvc
from scipy.interpolate import griddata
@@ -194,48 +193,110 @@ def plot_pseudoSection(Tx,Rx,data,z0, stype):
"""
#d2D = np.asarray(d2D)
z0 = 0.
for jj in range(len(ID)):
midl = []
midz = []
rho = []
indx = np.where(lineID==ID[jj])[0]
for ii in range(len(Tx)):
# Get distances between each poles
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])
midx_l = []
midz_l = []
midx_r = []
midz_r = []
rho_l = []
rho_r = []
# Compute apparent resistivity
if re.match(stype,'pdp'):
rho = np.hstack([rho, data[ii] * 2*np.pi * rC1P1 * ( rC1P1 + rP1P2 ) / rP1P2] )
for ii in range(len(indx)):
elif re.match(stype,'dpdp'):
rho = np.hstack([rho, data[ii] * 2*np.pi / ( 1/rC1P1 - 1/rC2P1 - 1/rC1P2 + 1/rC2P2 ) ])
Tx = DCsurvey.srcList[indx[ii]].loc
Rx = DCsurvey.srcList[indx[ii]].rxList[0].locs
data = DCsurvey.dobs[indx[ii]]
# Get distances between each poles
rC1P1 = np.abs(Tx[0][0,0] - Rx[0][:,0])
rC2P1 = np.abs(Tx[1][0,0] - Rx[0][:,0])
rC1P2 = np.abs(Tx[1][0,0] - Rx[1][:,0])
rC2P2 = np.abs(Tx[0][0,0] - Rx[1][:,0])
rP1P2 = np.abs(Rx[1][:,0] - Rx[0][:,0])
Cmid = (Tx[ii][0] + Tx[ii][1])/2
Pmid = (Rx[ii][:,0] + Rx[ii][:,1])/2
# Create mid-point location
Cmid = (Tx[0][0,0] + Tx[1][0,0])/2
Pmid = (Rx[0][:,0] + Rx[1][:,0])/2
midl = np.hstack([midl, ( Cmid + Pmid )/2 ])
midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + z0 ])
# Seperate left/right tx-rx configurations
ileft = Pmid < Cmid
iright = Pmid >= Cmid
# Compute apparent resistivity
if re.match(stype,'pdp'):
rho = data * 2*np.pi * rC1P1 * ( rC1P1 + rP1P2 ) / rP1P2
rho = np.log10(abs(1/rho))
elif re.match(stype,'dpdp'):
rho = data * 2*np.pi / ( 1/rC1P1 - 1/rC2P1 - 1/rC1P2 + 1/rC2P2 )
if np.any(ileft):
midx_l = np.hstack([midx_l, ( Cmid + Pmid[ileft] )/2 ])
midz_l = np.hstack([midz_l, -np.abs(Cmid-Pmid[ileft])/2 + z0 ])
rho_l = np.hstack([rho_l,rho[ileft]])
if np.any(iright):
midx_r = np.hstack([midx_r, ( Cmid + Pmid[iright] )/2 ])
midz_r = np.hstack([midz_r, -np.abs(Cmid-Pmid[iright])/2 + z0 ])
rho_r = np.hstack([rho_r,rho[iright]])
#plt.figure(figsize=(10, 4))
if np.any(midx_l):
ax1 = plt.subplot(1,2,1)
# Grid points
grid_x, grid_z = np.mgrid[np.min(midx_l):np.max(midx_l), np.min(midz_l):np.max(midz_l)]
grid_rho = griddata(np.c_[midx_l,midz_l], rho_l.T, (grid_x, grid_z), method='linear')
# 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.imshow(grid_rho.T, extent = (np.min(midx_l),np.max(midx_l),np.min(midz_l),np.max(midz_l)), origin='lower', alpha=0.8, vmin = np.min(np.r_[rho_l,rho_r]), vmax = np.max(np.r_[rho_l,rho_r]))
cbar = plt.colorbar(format = '%.2f',fraction=0.02,orientation="horizontal")
cbar.set_label('App Cond (S/m)',verticalalignment='bottom',labelpad=-25.)
cmin,cmax = cbar.get_clim()
ticks = np.linspace(cmin,cmax,3)
cbar.set_ticks(ticks)
# Plot apparent resistivity
plt.scatter(midx_l,midz_l,s=50,c=rho_l.T)
ax1.set_ylabel('Pseudo-Z (m)')
ax1.xaxis.tick_top()
ax1.set_xlabel('X (m)')
ax1.xaxis.set_label_position('top')
if np.any(midx_r):
ax2 = plt.subplot(1,2,2)
# Grid points
grid_x, grid_z = np.mgrid[np.min(midx_r):np.max(midx_r), np.min(midz_r):np.max(midz_r)]
grid_rho = griddata(np.c_[midx_r,midz_r], rho_r.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)))
plt.imshow(grid_rho.T, extent = (np.min(midx_r),np.max(midx_r),np.min(midz_r),np.max(midz_r)), origin='lower', alpha=0.8, vmin = np.min(np.r_[rho_l,rho_r]), vmax = np.max(np.r_[rho_l,rho_r]))
cbar = plt.colorbar(format = '%.2f',fraction=0.02,orientation="horizontal")
cbar.set_label('App Cond (S/m)',verticalalignment='bottom',labelpad=-25.)
cmin,cmax = cbar.get_clim()
ticks = np.linspace(cmin,cmax,3)
cbar.set_ticks(ticks)
# Plot apparent resistivity
plt.scatter(midx_r,midz_r,s=50,c=rho_r.T)
ax2.set_yticklabels([])
ax2.xaxis.tick_top()
ax2.set_xlabel('X (m)')
ax2.xaxis.set_label_position('top')
return ax1, ax2
def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
from SimPEG import np
@@ -435,13 +496,14 @@ def writeUBC_DCobs(fileName,Tx,Rx,d,wd, dtype):
fid.close()
def convertObs_DC3D_to_2D(Tx,Rx):
def convertObs_DC3D_to_2D(DCsurvey,lineID):
from SimPEG import np
import numpy.matlib as npm
"""
Read list of 3D Tx Rx location and change coordinate system to distance
along line assuming all data is acquired along line
Read DC survey and data and change
coordinate system to distance along line assuming
all data is acquired along line.
First transmitter pole is assumed to be at the origin
Assumes flat topo for now...
@@ -458,31 +520,74 @@ def convertObs_DC3D_to_2D(Tx,Rx):
"""
def stn_id(v0,v1,r):
"""
Compute station ID along line
"""
dl = int(v0.dot(v1)) * r
return dl
Tx2d = []
Rx2d = []
srcLists = []
for ii in range(len(Tx)):
srcMat = getSrc_locs(DCsurvey)
if ii == 0:
endp = Tx[0][0:2,0]
uniqueID = np.unique(lineID)
for jj in range(len(uniqueID)):
nrx = Rx[ii].shape[0]
indx = np.where(lineID==uniqueID[jj])[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))
# Find origin of survey
r = 1e+8 # Initialize to some large number
Tx = srcMat[indx]
Tx2d.append( np.r_[rP1, rP2] )
Rx2d.append( np.c_[rC1, rC2] )
#np.savetxt(fid, data, fmt='%e',delimiter=' ',newline='\n')
x0 = Tx[0][0,0:2] # Define station zero along line
vecTx, r1 = r_unit(x0,Tx[-1][1,0:2])
return Tx2d, Rx2d
for ii in range(len(indx)):
Rx = DCsurvey.srcList[indx[ii]].rxList[0].locs
nrx = Rx[0].shape[0]
vec, r = r_unit(x0,Tx[ii][0,0:2])
rP1 = stn_id(vecTx,vec,r)
vec, r = r_unit(x0,Tx[ii][1,0:2])
rP2 = stn_id(vecTx,vec,r)
rC1 = np.zeros(nrx)
rC2 = np.zeros(nrx)
for kk in range(nrx):
vec, r = r_unit(x0,Rx[0][kk,0:2])
rC1[kk] = stn_id(vecTx,vec,r)
vec, r = r_unit(x0,Rx[1][kk,0:2])
rC2[kk] = stn_id(vecTx,vec,r)
#rC1 = np.sqrt( np.sum( ( npm.repmat(endp.T,nrx,1) - Rx[0][:,0:2] )**2 , axis=1))
#rC2 = np.sqrt( np.sum( ( npm.repmat(endp.T,nrx,1) - Rx[1][:,0:2] )**2 , axis=1))
Rx = DC.RxDipole(np.c_[rC1,np.zeros(nrx),Rx[0][:,2]],np.c_[rC2,np.zeros(nrx),Rx[1][:,2]])
#np.savetxt(fid, data, fmt='%e',delimiter=' ',newline='\n')
srcLists.append( DC.SrcDipole( [Rx], np.c_[rP1,0,Tx[ii][0,2]],np.c_[rP2,0,Tx[ii][1,2]] ) )
srvy2D = DC.SurveyDC(srcLists)
srvy2D.dobs = np.asarray(DCsurvey.dobs)
srvy2D.std = np.asarray(DCsurvey.std)
return srvy2D
def readUBC_DC3Dobs(fileName):
from SimPEG import np
"""
Read UBC GIF DCIP 3D observation file and generate arrays for tx-rx location
@@ -501,53 +606,70 @@ def readUBC_DC3Dobs(fileName):
# Load file
obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
# Pre-allocate
Tx = []
srcLists = []
Rx = []
d = []
wd = []
zflag = True # Flag for z value provided
# 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)
# Check if z value is provided, if False -> nan
if len(temp)==5:
tx = np.r_[temp[0:2],np.nan,temp[0:2],np.nan]
zflag = False
else:
tx = temp[:-1]
rx = []
continue
temp = np.fromstring(obsfile[ii], dtype=float,sep=' ')
if zflag:
rx.append(temp[:-2])
# Check if there is data with the location
if len(temp)==8:
d.append(temp[-2])
wd.append(temp[-1])
rx.append(temp)
else:
rx.append(np.r_[temp[0:2],np.nan,temp[0:2],np.nan] )
# Check if there is data with the location
if len(temp)==6:
d.append(temp[-2])
wd.append(temp[-1])
count = count -1
# Reach the end of
count = count -1
# Reach the end of transmitter block
if count == 0:
temp = np.asarray(rx)
Rx.append(temp[:,0:6])
rx = np.asarray(rx)
Rx = DC.RxDipole(rx[:,:3],rx[:,3:])
srcLists.append( DC.SrcDipole( [Rx], tx[:3],tx[3:]) )
survey = DC.SurveyDC(srcLists)
survey.dobs = np.asarray(d)
survey.std = np.asarray(wd)
# DCdata[src0, src0.rxList[0]]
# Check for data + uncertainties
if temp.shape[1]==8:
d.append(temp[:,6])
wd.append(temp[:,7])
# Check for data only
elif temp.shape[1]==7:
d.append(temp[:,6])
return Tx, Rx, d, wd
return {'DCsurvey':survey}
def readUBC_DC2DLoc(fileName):
@@ -673,3 +795,136 @@ def readUBC_DC2DMesh(fileName):
from SimPEG import Mesh
tensMsh = Mesh.TensorMesh([dx,dz],(x0, z0))
return tensMsh
def xy_2_lineID(DCsurvey):
"""
Read DC survey class and append line ID.
Assumes that the locations are listed in the order
they were collected. May need to generalize for random
point locations, but will be more expensive
Input:
:param DCdict Vectors of station location
Output:
:param LineID Vector of integers
:return
Created on Thu Feb 11, 2015
@author: dominiquef
"""
# Compute unit vector between two points
nstn = DCsurvey.nSrc
# Pre-allocate space
lineID = np.zeros(nstn)
linenum = 0
indx = 0
for ii in range(nstn):
if ii == 0:
A = DCsurvey.srcList[ii].loc[0]
B = DCsurvey.srcList[ii].loc[1]
xout = np.mean([A[0:2],B[0:2]], axis = 0)
xy0 = A[:2]
xym = xout
# Deal with replicate pole location
if np.all(xy0==xym):
xym[0] = xym[0] + 1e-3
continue
A = DCsurvey.srcList[ii].loc[0]
B = DCsurvey.srcList[ii].loc[1]
xin = np.mean([A[0:2],B[0:2]], axis = 0)
# Compute vector between neighbours
vec1, r1 = r_unit(xout,xin)
# Compute vector between current stn and mid-point
vec2, r2 = r_unit(xym,xin)
# Compute vector between current stn and start line
vec3, r3 = r_unit(xy0,xin)
# Compute vector between mid-point and start line
vec4, r4 = r_unit(xym,xy0)
# Compute dot product
ang1 = np.abs(vec1.dot(vec2))
ang2 = np.abs(vec3.dot(vec4))
# If the angles are smaller then 45d, than next point is on a new line
if ((ang1 < np.cos(np.pi/4.)) | (ang2 < np.cos(np.pi/4.))) & (np.all(np.r_[r1,r2,r3,r4] > 0)):
# Re-initiate start and mid-point location
xy0 = A[:2]
xym = xin
# Deal with replicate pole location
if np.all(xy0==xym):
xym[0] = xym[0] + 1e-3
linenum += 1
indx = ii
else:
xym = np.mean([xy0,xin], axis = 0)
lineID[ii] = linenum
xout = xin
return lineID
def r_unit(p1,p2):
"""
r_unit(x,y) : Function computes the unit vector
between two points with coordinates p1(x1,y1) and p2(x2,y2)
"""
assert len(p1)==len(p2), 'locs must be the same shape.'
dx = []
for ii in range(len(p1)):
dx.append((p2[ii] - p1[ii]))
# Compute length of vector
r = np.linalg.norm(np.asarray(dx))
if r!=0:
vec = dx/r
else:
vec = np.zeros(len(p1))
return vec, r
def getSrc_locs(DCsurvey):
"""
"""
srcMat = np.zeros((DCsurvey.nSrc,2,3))
for ii in range(DCsurvey.nSrc):
srcMat[ii][:,:] = np.asarray(DCsurvey.srcList[ii].loc)
return srcMat