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Merge pull request #307 from simpeg/ref/dev

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Ref/dev
This commit is contained in:
Lindsey
2016-05-29 14:50:43 -07:00
parent cf89f5f6a2 406703f1c6
commit 09eb2106ec
9 changed files with 306 additions and 293 deletions
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SimPEG/DCIP/DCIPUtils.py
+157 -196
View File
@@ -1,12 +1,16 @@
from SimPEG import np
from SimPEG import np, Utils
import BaseDC as DC
import BaseDC as IP
import warnings
def getActiveindfromTopo(mesh, topo):
# def genActiveindfromTopo(mesh, topo):
"""
Get active indices from topography
"""
warnings.warn(
"`getActiveindfromTopo` is deprecated and will be removed in future versions. Use `SimPEG.Utils.surface2ind_topo` instead",
FutureWarning)
from scipy.interpolate import NearestNDInterpolator
if mesh.dim==3:
nCxy = mesh.nCx*mesh.nCy
@@ -28,6 +32,9 @@ def gettopoCC(mesh, airind):
"""
Get topography from active indices of mesh.
"""
warnings.warn(
"`gettopoCC` is deprecated and will be removed in future versions. Use `SimPEG.Utils.surface2ind_topo` instead",
FutureWarning)
mesh2D = Mesh.TensorMesh([mesh.hx, mesh.hy], mesh.x0[:2])
zc = mesh.gridCC[:,2]
AIRIND = airind.reshape((mesh.vnC[0]*mesh.vnC[1],mesh.vnC[2]), order='F')
@@ -118,34 +125,27 @@ def readUBC_DC3Dobstopo(filename,mesh,topo,probType="CC"):
def readUBC_DC2DModel(fileName):
"""
Read UBC GIF 2DTensor model and generate 2D Tensor model in simpeg
Read UBC GIF 2DTensor model and generate 2D Tensor model in simpeg
Input:
:param fileName, path to the UBC GIF 2D model file
Output:
:param SimPEG TensorMesh 2D object
:return
Created on Thu Nov 12 13:14:10 2015
@author: dominiquef
:param string fileName: path to the UBC GIF 2D model file
:rtype: TensorMesh
:return: SimPEG TensorMesh 2D object
"""
from SimPEG import np, mkvc
# Open fileand skip header... assume that we know the mesh already
obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
obsfile = np.genfromtxt(fileName, delimiter=' \n', dtype=np.str, comments='!')
dim = np.array(obsfile[0].split(),dtype=float)
dim = np.array(obsfile[0].split(), dtype=float)
temp = np.array(obsfile[1].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)
mm = np.array(obsfile[ii+1].split(), dtype=float)
model[:,ii] = mm
model = model[:,::-1]
@@ -153,10 +153,10 @@ def readUBC_DC2DModel(fileName):
else:
if len(obsfile[1:])==1:
mm = np.array(obsfile[1:].split(),dtype=float)
mm = np.array(obsfile[1:].split(), dtype=float)
else:
mm = np.array(obsfile[1:],dtype=float)
mm = np.array(obsfile[1:], dtype=float)
# Permute the second dimension to flip the order
model = mm.reshape(dim[1],dim[0])
@@ -169,23 +169,19 @@ def readUBC_DC2DModel(fileName):
return model
def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None, cblabel=True, axlabel = True, colorbar = True, contour = None):
def plot_pseudoSection(DCsurvey, axs, surveyType='dipole-dipole', unitType='volt', clim=None, cblabel=True, axlabel = True, colorbar = True, contour = None):
"""
Read list of 2D tx-rx location and plot a speudo-section of apparent
resistivity.
Read list of 2D tx-rx location and plot a speudo-section of apparent
resistivity.
Assumes flat topo for now...
Assumes flat topo for now...
Input:
:param d2D, z0
:switch stype -> Either 'pdp' (pole-dipole) | 'dpdp' (dipole-dipole)
:switch dtype=-> Either 'appr' (app. res) | 'appc' (app. con) | 'volt' (potential)
Output:
:figure scatter plot overlayed on image
Edited Feb 17th, 2016
@author: dominiquef
:param SurveyDC DCsurvey:
:param string surveyType: Either 'pole-dipole' | 'dipole-dipole'
:param string unitType: Either 'appResistivity' | 'appConductivity' | 'volt'
:rtype: matplotlib.plt
:return: figure scatter plot overlayed on image
"""
from SimPEG import np
@@ -218,39 +214,39 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None, cbl
Cmid = (Tx[0][0] + Tx[1][0])/2
Pmid = (Rx[0][:,0] + Rx[1][:,0])/2
# Change output for dtype
if dtype == 'volt':
# Change output for unitType
if unitType == 'volt':
rho = np.hstack([rho,data])
else:
# Compute pant leg of apparent rho
if stype == 'pdp':
if surveyType == 'pole-dipole':
leg = data * 2*np.pi * MA * ( MA + MN ) / MN
elif stype == 'dpdp':
elif surveyType == 'dipole-dipole':
leg = data * 2*np.pi / ( 1/MA - 1/MB - 1/NB + 1/NA )
else:
print """dtype must be 'pdp'(pole-dipole) | 'dpdp' (dipole-dipole) """
print """unitType must be 'pole-dipole' | 'dipole-dipole' """
break
if dtype == 'appc':
if unitType == 'appConductivity':
leg = np.log10(abs(1./leg))
rho = np.hstack([rho,leg])
elif dtype == 'appr':
elif unitType == 'appResistivity':
leg = np.log10(abs(leg))
rho = np.hstack([rho,leg])
else:
print """dtype must be 'appr' | 'appc' | 'volt' """
print """unitType must be 'appResistivity' | 'appConductivity' | 'volt' """
break
midx = np.hstack([midx, ( Cmid + Pmid )/2 ])
@@ -259,7 +255,7 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None, cbl
# Grid points
grid_x, grid_z = np.mgrid[np.min(midx):np.max(midx), np.min(midz):np.max(midz)]
grid_rho = griddata(np.c_[midx,midz], rho.T, (grid_x, grid_z), method='linear')
# Scale the color scheme
if clim == None:
vmin, vmax = rho.min(), rho.max()
@@ -268,36 +264,37 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None, cbl
# Plot data
grid_rho = np.ma.masked_where(np.isnan(grid_rho), grid_rho)
ph = plt.pcolormesh(grid_x[:,0],grid_z[0,:],grid_rho.T, vmin = vmin, vmax = vmax)
plt.gca().tick_params(axis='both', which='major', labelsize=8)
if contour is not None:
plt.contour(grid_x,grid_z,grid_rho,levels = contour,colors = 'r', vmin = vmin, vmax = vmax)
# Add scatter points
axs.scatter(midx,midz,s=10,c=rho.T, vmin = vmin, vmax = vmax)
if colorbar:
if dtype == 'volt':
if unitType == 'volt':
cbar = plt.colorbar(ph, ax = axs, format="%4.1f",fraction=0.04,orientation="horizontal")
else:
else:
cbar = plt.colorbar(ph, ax = axs, format="$10^{%.1f}$",fraction=0.04,orientation="horizontal")
cmin,cmax = cbar.get_clim()
ticks = np.linspace(cmin,cmax,3)
cbar.set_ticks(ticks)
cbar.ax.tick_params(labelsize=10)
if cblabel:
if dtype == 'appc':
cbar.set_label("App.Cond",size=12)
elif dtype == 'appr':
cbar.set_label("App.Res.",size=12)
elif dtype == 'volt':
cbar.set_label("Potential (V)",size=12)
cmin,cmax = cbar.get_clim()
ticks = np.linspace(cmin,cmax,3)
cbar.set_ticks(ticks)
cbar.ax.tick_params(labelsize=10)
if unitType == 'appConductivity':
cbar.set_label("App.Cond",size=12)
elif unitType == 'appResistivity':
cbar.set_label("App.Res.",size=12)
elif unitType == 'volt':
cbar.set_label("Potential (V)",size=12)
if not axlabel:
@@ -310,27 +307,24 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None, cbl
return ph
def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
"""
Load in endpoints and survey specifications to generate Tx, Rx location
stations.
Load in endpoints and survey specifications to generate Tx, Rx location
stations.
Assumes flat topo for now...
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
:param numpy.array endl: input endpoints [[x1, y1] , [x2, y2]]
:param Mesh mesh: SimPEG mesh object
:param string surveyType: 'dipole-dipole' | 'pole-dipole' | 'gradient'
:param float AM_sep: transmitter (A) - receiver (M) seperation
:param float b: receiver dipole seperation
:param float nrx: 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
:rtype: DC.Survey, Src, Rx
:returns: DC survey, Source
Created on Wed December 9th, 2015
@author: dominiquef
!! Require clean up to deal with DCsurvey
!! Require clean up to deal with DCsurvey
"""
from SimPEG import np
@@ -346,17 +340,17 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
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 )
nstn = np.floor( dl_len / AM_sep )
# 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
stn_x = endl[0,0] + np.array(range(int(nstn)))*dl_x*AM_sep
stn_y = endl[0,1] + np.array(range(int(nstn)))*dl_y*AM_sep
# 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]]
N = np.c_[stn_x+AM_sep*dl_x, stn_y+AM_sep*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]
@@ -366,14 +360,14 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
SrcList = []
if stype != 'gradient':
if surveyType != 'gradient':
for ii in range(0, int(nstn)-1):
if stype == 'dpdp':
if surveyType == 'dipole-dipole':
tx = np.c_[M[ii,:],N[ii,:]]
elif stype == 'pdp':
elif surveyType == 'pole-dipole':
tx = np.c_[M[ii,:],M[ii,:]]
# Rx.append(np.c_[M[ii+1:indx,:],N[ii+1:indx,:]])
@@ -382,33 +376,33 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
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])
nstn = np.min([np.floor( (AB - MN_sep) / AM_sep ) , nrx])
# 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
stn_x = N[ii,0] + dl_x*MN_sep + np.array(range(int(nstn)))*dl_x*AM_sep
stn_y = N[ii,1] + dl_y*MN_sep + np.array(range(int(nstn)))*dl_y*AM_sep
# 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]]
P2 = np.c_[stn_x+AM_sep*dl_x, stn_y+AM_sep*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
Rx.append(np.c_[P1,P2])
rxClass = DC.RxDipole(P1, P2)
Tx.append(tx)
if stype == 'dpdp':
if surveyType == 'dipole-dipole':
srcClass = DC.SrcDipole([rxClass], M[ii,:],N[ii,:])
elif stype == 'pdp':
elif surveyType == 'pole-dipole':
srcClass = DC.SrcDipole([rxClass], M[ii,:],M[ii,:])
SrcList.append(srcClass)
elif stype == 'gradient':
elif surveyType == '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
@@ -416,23 +410,23 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
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
min_x = endl[0,0] + dl_x * MN_sep
min_y = endl[0,1] + dl_y * MN_sep
max_x = endl[1,0] - dl_x * b
max_y = endl[1,1] - dl_y * b
max_x = endl[1,0] - dl_x * MN_sep
max_y = endl[1,1] - dl_y * MN_sep
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 )
nstn = np.floor( box_l / AM_sep )
# 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
stn_x = min_x + np.array(range(int(nstn)))*dl_x*AM_sep
stn_y = min_y + np.array(range(int(nstn)))*dl_y*AM_sep
# Define number of cross lines
nlin = int(np.floor( box_w / a ))
nlin = int(np.floor( box_w / AM_sep ))
lind = range(-nlin,nlin+1)
ngrad = nstn * len(lind)
@@ -441,12 +435,12 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
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
lxx = stn_x - lind[ii]*AM_sep*dl_y
lyy = stn_y + lind[ii]*AM_sep*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]]
N = np.c_[ lxx+AM_sep*dl_x, lyy+AM_sep*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
rx[(ii*nstn):((ii+1)*nstn),:] = np.c_[M,N]
@@ -455,44 +449,38 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
srcClass = DC.SrcDipole([rxClass], M[0,:], N[-1,:])
SrcList.append(srcClass)
else:
print """stype must be either 'pdp', 'dpdp' or 'gradient'. """
print """surveyType must be either 'pole-dipole', 'dipole-dipole' or 'gradient'. """
survey = DC.SurveyDC(SrcList)
return survey, Tx, Rx
def writeUBC_DCobs(fileName, DCsurvey, dtype='3D', stype='SURFACE', iptype = 0):
def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
"""
Write UBC GIF DCIP 2D or 3D observation file
Input:
:string fileName -> including path where the file is written out
:DCsurvey DC survey class object
:string dtype -> either '2D' | '3D'
:string stype -> either 'SURFACE' | 'GENERAL'
Output:
:param UBC2D-Data file
:return
Last edit: February 16th, 2016
@author: dominiquef
:param string fileName: including path where the file is written out
:param Survey DCsurvey: DC survey class object
:param string dim: either '2D' | '3D'
:param string surveyType: either 'SURFACE' | 'GENERAL'
:rtype: file
:return: UBC2D-Data file
"""
from SimPEG import mkvc
assert (dtype=='2D') | (dtype=='3D'), "Data must be either '2D' | '3D'"
assert (stype=='SURFACE') | (stype=='GENERAL') | (stype=='SIMPLE'), "Data must be either 'SURFACE' | 'GENERAL' | 'SIMPLE'"
assert (dim=='2D') | (dim=='3D'), "Data must be either '2D' | '3D'"
assert (surveyType=='SURFACE') | (surveyType=='GENERAL') | (surveyType=='SIMPLE'), "Data must be either 'SURFACE' | 'GENERAL' | 'SIMPLE'"
fid = open(fileName,'w')
fid.write('! ' + surveyType + ' FORMAT\n')
if iptype!=0:
fid.write('IPTYPE=%i\n'%iptype)
else:
fid.write('! ' + stype + ' FORMAT\n')
count = 0
for ii in range(DCsurvey.nSrc):
@@ -506,33 +494,33 @@ def writeUBC_DCobs(fileName, DCsurvey, dtype='3D', stype='SURFACE', iptype = 0):
M = rx[0]
N = rx[1]
# Adapt source-receiver location for dtype and stype
if dtype=='2D':
# Adapt source-receiver location for dim and surveyType
if dim=='2D':
if stype == 'SIMPLE':
if surveyType == 'SIMPLE':
#fid.writelines("%e " % ii for ii in mkvc(tx[0,:]))
A = np.repeat(tx[0,0],M.shape[0],axis=0)
B = np.repeat(tx[0,1],M.shape[0],axis=0)
M = M[:,0]
N = N[:,0]
np.savetxt(fid, np.c_[A, B, M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
else:
if stype == 'SURFACE':
if surveyType == 'SURFACE':
fid.writelines("%f " % ii for ii in mkvc(tx[0,:]))
M = M[:,0]
N = N[:,0]
if stype == 'GENERAL':
if surveyType == 'GENERAL':
# Flip sign for z-elevation to depth
tx[2::2,:] = -tx[2::2,:]
fid.writelines("%e " % ii for ii in mkvc(tx[::2,:]))
M = M[:,0::2]
N = N[:,0::2]
@@ -540,31 +528,31 @@ def writeUBC_DCobs(fileName, DCsurvey, dtype='3D', stype='SURFACE', iptype = 0):
# Flip sign for z-elevation to depth
M[:,1::2] = -M[:,1::2]
N[:,1::2] = -N[:,1::2]
fid.write('%i\n'% nD)
np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%f',delimiter=' ',newline='\n')
if dtype=='3D':
if dim=='3D':
if stype == 'SURFACE':
if surveyType == 'SURFACE':
fid.writelines("%e " % ii for ii in mkvc(tx[0:2,:]))
M = M[:,0:2]
N = N[:,0:2]
if stype == 'GENERAL':
if surveyType == 'GENERAL':
fid.writelines("%e " % ii for ii in mkvc(tx[0:3,:]))
fid.write('%i\n'% nD)
np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
fid.write('\n')
count += nD
fid.close()
def convertObs_DC3D_to_2D(DCsurvey,lineID, flag = 'local'):
def convertObs_DC3D_to_2D(DCsurvey, lineID, flag='local'):
"""
Read DC survey and projects the coordinate system
according to the flag = 'Xloc' | 'Yloc' | 'local' (default)
@@ -573,15 +561,9 @@ def convertObs_DC3D_to_2D(DCsurvey,lineID, flag = 'local'):
The Z value is preserved, but Y coordinates zeroed.
Input:
:param survey3D
Output:
:figure survey2D
Edited April 6th, 2016
@author: dominiquef
:param DC.Survey survey3D: 3D simpeg DC survey
:rtype: DC.Survey
:return: survey2D
"""
from SimPEG import np
@@ -666,39 +648,34 @@ def convertObs_DC3D_to_2D(DCsurvey,lineID, flag = 'local'):
DCsurvey2D.std = np.asarray(DCsurvey.std)
return DCsurvey2D
def readUBC_DC3Dobs(fileName, dtype = 'DC'):
def readUBC_DC3Dobs(fileName, rtype = 'DC'):
"""
Read UBC GIF IP 3D observation file and generate survey
Input:
:param fileName, path to the UBC GIF 3D obs file
Output:
:param IPsurvey
:return
@author: dominiquef
:param string fileName:, path to the UBC GIF 3D obs file
:rtype: Survey
:return: DCIPsurvey
"""
zflag = True # Flag for z value provided
# Load file
if dtype == 'IP':
if rtype == 'IP':
obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='IPTYPE')
elif dtype == 'DC':
elif rtype == 'DC':
obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
else:
print "dtype must be 'DC'(default) | 'IP'"
print "rtype must be 'DC'(default) | 'IP'"
# Pre-allocate
srcLists = []
Rx = []
d = []
wd = []
# Countdown for number of obs/tx
count = 0
@@ -717,7 +694,7 @@ def readUBC_DC3Dobs(fileName, dtype = 'DC'):
# Check if z value is provided, if False -> nan
if len(temp)==5:
tx = np.r_[temp[0:2],np.nan,temp[2:4],np.nan]
zflag = False # Pass on the flag to the receiver loc
else:
@@ -729,12 +706,12 @@ def readUBC_DC3Dobs(fileName, dtype = 'DC'):
temp = np.fromstring(obsfile[ii], dtype=float,sep=' ') # Get the string
# Filter out negative IP
# if temp[-2] < 0:
# if temp[-2] < 0:
# count = count -1
# print "Negative!"
#
#
# else:
# If the Z-location is provided, otherwise put nan
if zflag:
@@ -772,17 +749,9 @@ def readUBC_DC2Dobs(fileName):
------- NEEDS TO BE UPDATED ------
Read UBC GIF 2D observation file and generate arrays for tx-rx location
Input:
:param fileName, path to the UBC GIF 2D model file
Output:
:param rx, tx
:return
Created on Thu Nov 12 13:14:10 2015
@author: dominiquef
:param string fileName: path to the UBC GIF 2D model file
:rtype: (DC.Src, DC.Rx, ??, ??)
:return: source_locs, rx_locs, ??, ??
"""
from SimPEG import np
@@ -822,11 +791,9 @@ def readUBC_DC2Dpre(fileName):
Read UBC GIF DCIP 2D observation file and generate arrays for tx-rx location
Input:
:param fileName, path to the UBC GIF 3D obs file
Output:
DCsurvey
:return
:param string fileName: path to the UBC GIF 3D obs file
:rtype: DC.Survey
:return: DCsurvey
Created on Mon March 9th, 2016 << Doug's 70th Birthday !! >>
@@ -888,12 +855,9 @@ def readUBC_DC2DMesh(fileName):
"""
Read UBC GIF 2DTensor mesh and generate 2D Tensor mesh in simpeg
Input:
:param fileName, path to the UBC GIF mesh file
Output:
:param SimPEG TensorMesh 2D object
:return
:param string fileName: path to the UBC GIF mesh file
:rtype: Mesh.TensorMesh
:return: SimPEG TensorMesh 2D object
Created on Thu Nov 12 13:14:10 2015
@@ -959,12 +923,9 @@ def xy_2_lineID(DCsurvey):
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
:param numpy.array DCdict: Vectors of station location
:rtype: numpy.array
:return: LineID Vector of integers
Created on Thu Feb 11, 2015
SimPEG/Examples/DC_Forward_PseudoSection.py
+15 -17
View File
@@ -2,7 +2,7 @@ from SimPEG import Mesh, Utils, np, sp
import SimPEG.DCIP as DC
import time
def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', plotIt=True):
def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', unitType='appConductivity', plotIt=True):
"""
DC Forward Simulation
=====================
@@ -15,14 +15,14 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
loc = Location of spheres [[x1,y1,z1],[x2,y2,z2]]
radi = Radius of spheres [r1,r2]
param = Conductivity of background and two spheres [m0,m1,m2]
stype = survey type "pdp" (pole dipole) or "dpdp" (dipole dipole)
dtype = Data type "appr" (app res) | "appc" (app cond) | "volt" (potential)
surveyType = survey type 'pole-dipole' or 'dipole-dipole'
unitType = Data type "appResistivity" | "appConductivity" | "volt"
Created by @fourndo
"""
assert stype in ['pdp', 'dpdp'], "Source type (stype) must be pdp or dpdp (pole dipole or dipole dipole)"
assert dtype in ['appr', 'appc', 'volt'], "Data type (dtype) must be appr (app res) or appc (app cond) or volt (potential)"
assert surveyType in ['pole-dipole', 'dipole-dipole'], "Source type (surveyType) must be pdp or dpdp (pole dipole or dipole dipole)"
assert unitType in ['appResistivity', 'appConductivity', 'volt'], "Unit type (unitType) must be appResistivity or appConductivity or volt (potential)"
if loc is None:
loc = np.c_[[-50.,0.,-50.],[50.,0.,-50.]]
@@ -73,8 +73,8 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
locs = np.c_[mesh.gridCC[indx,0],mesh.gridCC[indx,1],np.ones(2).T*mesh.vectorNz[-1]]
# We will handle the geometry of the survey for you and create all the combination of tx-rx along line
# [Tx, Rx] = DC.gen_DCIPsurvey(locs, mesh, stype, param[0], param[1], param[2])
survey, Tx, Rx = DC.gen_DCIPsurvey(locs, mesh, stype, param[0], param[1], param[2])
# [Tx, Rx] = DC.gen_DCIPsurvey(locs, mesh, surveyType, param[0], param[1], param[2])
survey, Tx, Rx = DC.gen_DCIPsurvey(locs, mesh, surveyType, param[0], param[1], param[2])
# Define some global geometry
dl_len = np.sqrt( np.sum((locs[0,:] - locs[1,:])**2) )
@@ -118,8 +118,8 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
rxloc_N = np.asarray(Rx[ii][:,3:])
# For usual cases "dpdp" or "gradient"
if stype == 'pdp':
# For usual cases 'dipole-dipole' or "gradient"
if surveyType == 'pole-dipole':
# Create an "inifinity" pole
tx = np.squeeze(Tx[ii][:,0:1])
tinf = tx + np.array([dl_x,dl_y,0])*dl_len*2
@@ -157,12 +157,12 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
fig = plt.figure(figsize=(7,7))
ax = plt.subplot(2,1,1, aspect='equal')
# Plot the location of the spheres for reference
circle1=plt.Circle((loc[0,0],loc[2,0]),radi[0],color='w',fill=False, lw=3)
circle2=plt.Circle((loc[0,1],loc[2,1]),radi[1],color='k',fill=False, lw=3)
circle1=plt.Circle((loc[0,0], loc[2,0]), radi[0], color='w', fill=False, lw=3)
circle2=plt.Circle((loc[0,1], loc[2,1]), radi[1], color='k', fill=False, lw=3)
ax.add_artist(circle1)
ax.add_artist(circle2)
dat = mesh.plotSlice(np.log10(model), ax =ax, normal = 'Y',
dat = mesh.plotSlice(np.log10(model), ax = ax, normal = 'Y',
ind = indy,grid=True, clim = np.log10([sig.min(),sig.max()]))
ax.set_title('3-D model')
@@ -188,15 +188,13 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
ax2 = plt.subplot(2,1,2, aspect='equal')
# Plot the location of the spheres for reference
circle1=plt.Circle((loc[0,0],loc[2,0]),radi[0],color='w',fill=False, lw=3)
circle2=plt.Circle((loc[0,1],loc[2,1]),radi[1],color='k',fill=False, lw=3)
circle1=plt.Circle((loc[0,0], loc[2,0]), radi[0], color='w', fill=False, lw=3)
circle2=plt.Circle((loc[0,1], loc[2,1]), radi[1], color='k', fill=False, lw=3)
ax2.add_artist(circle1)
ax2.add_artist(circle2)
# Add the speudo section
dat = DC.plot_pseudoSection(survey2D,ax2,stype=stype, dtype = dtype)
# plt.scatter(Tx2d[0][:],Tx[0][2,:],s=40,c='g', marker='v')
dat = DC.plot_pseudoSection(survey2D, ax2, surveyType=surveyType, unitType=unitType) # plt.scatter(Tx2d[0][:],Tx[0][2,:],s=40,c='g', marker='v')
# plt.scatter(Rx2d[0][:],Rx[0][:,2::3],s=40,c='y')
# plt.plot(np.r_[Tx2d[0][0],Rx2d[-1][-1,-1]],np.ones(2)*mesh.vectorNz[-1], color='k')
ax2.set_title('Apparent Conductivity data')
SimPEG/Examples/Utils_surface2ind_topo.py
+41
View File
@@ -0,0 +1,41 @@
from SimPEG import *
from SimPEG.Utils import surface2ind_topo
def run(plotIt=False, nx = 5, ny = 5):
"""
Here we show how to use :code:`Utils.surface2ind_topo` to identify cells below
a topographic surface.
"""
mesh = Mesh.TensorMesh([nx,ny], x0='CC') # 2D mesh
xtopo = np.linspace(mesh.gridN[:,0].min(), mesh.gridN[:,0].max())
topo = 0.4*np.sin(xtopo*5) # define a topographic surface
Topo = np.hstack([Utils.mkvc(xtopo,2),Utils.mkvc(topo,2)]) #make it an array
indcc = surface2ind_topo(mesh, Topo,'CC')
if plotIt:
from matplotlib.pylab import plt
from scipy.interpolate import interp1d
fig, ax = plt.subplots(1,1,figsize=(6,6))
mesh.plotGrid(ax=ax, nodes=True, centers=True)
ax.plot(xtopo,topo,'k',linewidth=1)
# ax.plot(mesh.vectorNx, interp1d(xtopo,topo)(mesh.vectorNx),'--k',linewidth=3)
ax.plot(mesh.vectorCCx, interp1d(xtopo,topo)(mesh.vectorCCx),'--k',linewidth=3)
aveN2CC = Utils.sdiag(mesh.aveN2CC.T.sum(1))*mesh.aveN2CC.T
a = aveN2CC * indcc
a[a > 0] = 1.
a[a < 0.25] = np.nan
a = a.reshape(mesh.vnN, order='F')
masked_array = np.ma.array(a, mask=np.isnan(a))
ax.pcolor(mesh.vectorNx,mesh.vectorNy,masked_array.T, cmap = plt.cm.gray,alpha=0.2)
plt.show()
if __name__ == '__main__':
run(plotIt=True)
SimPEG/Examples/__init__.py
+2 -1
View File
@@ -20,8 +20,9 @@ import Mesh_QuadTree_HangingNodes
import Mesh_Tensor_Creation
import MT_1D_ForwardAndInversion
import MT_3D_Foward
import Utils_surface2ind_topo
__examples__ = ["DC_Analytic_Dipole", "DC_Forward_PseudoSection", "EM_FDEM_1D_Inversion", "EM_FDEM_Analytic_MagDipoleWholespace", "EM_Schenkel_Morrison_Casing", "EM_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Forward_BasicDirectCurrent", "Inversion_IRLS", "Inversion_Linear", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation", "MT_1D_ForwardAndInversion", "MT_3D_Foward"]
__examples__ = ["DC_Analytic_Dipole", "DC_Forward_PseudoSection", "EM_FDEM_1D_Inversion", "EM_FDEM_Analytic_MagDipoleWholespace", "EM_Schenkel_Morrison_Casing", "EM_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Forward_BasicDirectCurrent", "Inversion_IRLS", "Inversion_Linear", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation", "MT_1D_ForwardAndInversion", "MT_3D_Foward", "Utils_surface2ind_topo"]
##### AUTOIMPORTS #####
SimPEG/Maps.py
-77
View File
@@ -533,83 +533,6 @@ class ActiveCells(InjectActiveCells):
FutureWarning)
InjectActiveCells.__init__(self, mesh, indActive, valInactive, nC)
class InjectActiveCellsTopo(IdentityMap):
"""
Active model parameters. Extend for cells on topography to air cell (only works for tensor mesh)
"""
indActive = None #: Active Cells
valInactive = None #: Values of inactive Cells
nC = None #: Number of cells in the full model
def __init__(self, mesh, indActive, nC=None):
self.mesh = mesh
self.nC = nC or mesh.nC
if indActive.dtype is not bool:
z = np.zeros(self.nC,dtype=bool)
z[indActive] = True
indActive = z
self.indActive = indActive
self.indInactive = np.logical_not(indActive)
inds = np.nonzero(self.indActive)[0]
self.P = sp.csr_matrix((np.ones(inds.size),(inds, range(inds.size))), shape=(self.nC, self.nP))
@property
def shape(self):
return (self.nC, self.nP)
@property
def nP(self):
"""Number of parameters in the model."""
return self.indActive.sum()
def _transform(self, m):
val_temp = np.zeros(self.mesh.nC)
val_temp[self.indActive] = m
valInactive = np.zeros(self.mesh.nC)
#1D
if self.mesh.dim == 1:
z_temp = self.mesh.gridCC
val_temp[~self.indActive] = val_temp[np.argmax(z_temp[self.indActive])]
#2D
elif self.mesh.dim == 2:
act_temp = self.indActive.reshape((self.mesh.nCx, self.mesh.nCy), order = 'F')
val_temp = val_temp.reshape((self.mesh.nCx, self.mesh.nCy), order = 'F')
y_temp = self.mesh.gridCC[:,1].reshape((self.mesh.nCx, self.mesh.nCy), order = 'F')
for i in range(self.mesh.nCx):
act_tempx = act_temp[i,:] == 1
val_temp[i,~act_tempx] = val_temp[i,np.argmax(y_temp[i,act_tempx])]
valInactive[~self.indActive] = Utils.mkvc(val_temp)[~self.indActive]
#3D
elif self.mesh.dim == 3:
act_temp = self.indActive.reshape((self.mesh.nCx*self.mesh.nCy, self.mesh.nCz), order = 'F')
val_temp = val_temp.reshape((self.mesh.nCx*self.mesh.nCy, self.mesh.nCz), order = 'F')
z_temp = self.mesh.gridCC[:,2].reshape((self.mesh.nCx*self.mesh.nCy, self.mesh.nCz), order = 'F')
for i in range(self.mesh.nCx*self.mesh.nCy):
act_tempxy = act_temp[i,:] == 1
val_temp[i,~act_tempxy] = val_temp[i,np.argmax(z_temp[i,act_tempxy])]
valInactive[~self.indActive] = Utils.mkvc(val_temp)[~self.indActive]
self.valInactive = valInactive
return self.P*m + self.valInactive
def inverse(self, D):
return self.P.T*D
def deriv(self, m):
return self.P
class ActiveCellsTopo(InjectActiveCellsTopo):
def __init__(self, mesh, indActive, valInactive, nC=None):
warnings.warn(
"`ActiveCellsTopo` is deprecated and will be removed in future versions. Use `InjectActiveCellsTopo` instead",
FutureWarning)
InjectActiveCellsTopo.__init__(self, mesh, indActive, valInactive, nC)
class Weighting(IdentityMap):
"""
SimPEG/Utils/__init__.py
+1
View File
@@ -7,3 +7,4 @@ from CounterUtils import *
import ModelBuilder
import SolverUtils
from coordutils import *
from modelutils import *
SimPEG/Utils/modelutils.py
+63
View File
@@ -0,0 +1,63 @@
from matutils import mkvc, ndgrid
import numpy as np
def surface2ind_topo(mesh, topo, gridLoc='CC'):
# def genActiveindfromTopo(mesh, topo):
"""
Get active indices from topography
"""
if mesh.dim == 3:
from scipy.interpolate import NearestNDInterpolator
Ftopo = NearestNDInterpolator(topo[:,:2], topo[:,2])
if gridLoc == 'CC':
XY = ndgrid(mesh.vectorCCx, mesh.vectorCCy)
Zcc = mesh.gridCC[:,2].reshape((np.prod(mesh.vnC[:2]), mesh.nCz), order='F')
gridTopo = Ftopo(XY)
actind = [gridTopo[ixy] <= Zcc[ixy,:] for ixy in range(np.prod(mesh.vnC[0]))]
actind = np.hstack(actind)
elif gridLoc == 'N':
XY = ndgrid(mesh.vectorNx, mesh.vectorNy)
gridTopo = Ftopo(XY).reshape(mesh.vnN[:2], order='F')
if mesh._meshType not in ['TENSOR', 'CYL', 'BASETENSOR']:
raise NotImplementedError('Nodal surface2ind_topo not implemented for %s mesh'%mesh._meshType)
Nz = mesh.vectorNz[1:] # TODO: this will only work for tensor meshes
actind = np.array([False]*mesh.nC).reshape(mesh.vnC, order='F')
for ii in range(mesh.nCx):
for jj in range(mesh.nCy):
actind[ii,jj,:] = [np.all(gridTopo[ii:ii+2, jj:jj+2] >= Nz[kk]) for kk in range(len(Nz)) ]
elif mesh.dim == 2:
from scipy.interpolate import interp1d
Ftopo = interp1d(topo[:,0], topo[:,1])
if gridLoc == 'CC':
gridTopo = Ftopo(mesh.gridCC[:,0])
actind = mesh.gridCC[:,1] <= gridTopo
elif gridLoc == 'N':
gridTopo = Ftopo(mesh.vectorNx)
if mesh._meshType not in ['TENSOR', 'CYL', 'BASETENSOR']:
raise NotImplementedError('Nodal surface2ind_topo not implemented for %s mesh'%mesh._meshType)
Ny = mesh.vectorNy[1:] # TODO: this will only work for tensor meshes
actind = np.array([False]*mesh.nC).reshape(mesh.vnC, order='F')
for ii in range(mesh.nCx):
actind[ii,:] = [np.all(gridTopo[ii:ii+2] > Ny[kk]) for kk in range(len(Ny)) ]
else:
raise NotImplementedError('surface2ind_topo not implemented for 1D mesh')
return mkvc(actind)
docs/examples/DC_Forward_PseudoSection.rst
+3 -2
View File
@@ -20,8 +20,9 @@ INPUT:
loc = Location of spheres [[x1,y1,z1],[x2,y2,z2]]
radi = Radius of spheres [r1,r2]
param = Conductivity of background and two spheres [m0,m1,m2]
stype = survey type "pdp" (pole dipole) or "dpdp" (dipole dipole)
dtype = Data type "appr" (app res) | "appc" (app cond) | "volt" (potential)
surveyType = survey type 'pole-dipole' or 'dipole-dipole'
unitType = Data type "appResistivity" | "appConductivity" | "volt"
Created by @fourndo
docs/examples/Utils_surface2ind_topo.rst
+24
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@@ -0,0 +1,24 @@
.. _examples_Utils_surface2ind_topo:
.. --------------------------------- ..
.. ..
.. THIS FILE IS AUTO GENEREATED ..
.. ..
.. SimPEG/Examples/__init__.py ..
.. ..
.. --------------------------------- ..
Here we show how to use :code:`Utils.surface2ind_topo` to identify cells below
a topographic surface.
.. plot::
from SimPEG import Examples
Examples.Utils_surface2ind_topo.run()
.. literalinclude:: ../../SimPEG/Examples/Utils_surface2ind_topo.py
:language: python
:linenos: