def plotSingleArrayAparentResistivity(self):
if self.singleArray :
survey2D = DCUtils.convertObs_DC3D_to_2D(self.survey, numpy.ones(self.survey.nSrc), 'Xloc')
survey2D.dobs = numpy.hstack(self.survey.dobs)
fig = plt.figure(figsize=(5, 8), num = self.title + ': Apparent resistivity')
ax1 = plt.subplot(2, 1, 1, aspect="equal")
clim = [self.mesh.tunnelParams.log_sigmaRock - 1, self.mesh.tunnelParams.log_sigmaDis]
slice = int(self.coreMesh.nCy / 2)
dat1 = self.coreMesh.plotSlice(((self.givenModelOnCoreMesh)),
ax=ax1, normal='Y', clim=clim, grid=False, ind=slice)
ax1.scatter(self.allSurveyPoints[:, 0], self.allSurveyPoints[:, 2], s=5, c='w')
ax2 = plt.subplot(2, 1, 2, aspect="equal")
dat2 = DCUtils.plot_pseudoSection(
survey2D, ax2, survey_type='dipole-dipole', data_type='appConductivity',
space_type='whole-space', scale="log", data_location=True
)
#plt.gca().set_aspect('equal', adjustable='box')
plt.xlim([self.coreMesh.vectorNx[0], self.coreMesh.vectorNx[-1]])
plt.ylim([-25, 0])
ax2.scatter(self.allSurveyPoints[:, 0], self.allSurveyPoints[:, 2]* (-1), s=5, c='k')
else:
pass
pass
def setUp(self):
url = 'https://storage.googleapis.com/simpeg/tests/dc_utils/'
cloudfiles = [
'dPred_fullspace.txt', 'AB_GIF_fullspace.txt',
'MN_GIF_fullspace.txt', 'AM_GIF_fullspace.txt',
'AN_GIF_fullspace.txt', 'BM_GIF_fullspace.txt',
'BN_GIF_fullspace.txt', 'RhoApp_GIF_fullspace.txt'
]
self.basePath = os.path.expanduser('~/Downloads/TestDCUtilsFullSpace')
self.files = io_utils.download(
[url+f for f in cloudfiles],
folder=self.basePath,
overwrite=True
)
survey_file = os.path.sep.join([self.basePath, 'dPred_fullspace.txt'])
DCsurvey = DCUtils.readUBC_DC3Dobs(survey_file)
DCsurvey = DCsurvey['dc_survey']
self.survey = DCsurvey
def test_apparent_resistivity(self):
# Compute apparent resistivity from survey
rhoapp = DCUtils.apparent_resistivity(
self.survey, dobs=self.survey.dobs,
survey_type='dipole-dipole',
space_type='whole-space', eps=1e-16
)
# Load benchmarks files from UBC-GIF codes
rhoappfile = os.path.sep.join(
[self.basePath, 'RhoApp_GIF_fullspace.txt']
)
rhogif = np.loadtxt(rhoappfile)
# remove value with almost null geometric factor
idx = rhoapp < 1e8
# Assert agreements between the two codes
passed = np.allclose(rhoapp[idx], rhogif[idx])
self.assertTrue(passed)
# Clean up the working directory
shutil.rmtree(self.basePath)
def test_ElecSep(self):
# Compute dipoles distances from survey
elecSepDict = DCUtils.electrode_separations(self.survey)
AM = elecSepDict['AM']
BM = elecSepDict['BM']
AN = elecSepDict['AN']
BN = elecSepDict['BN']
MN = elecSepDict['MN']
AB = elecSepDict['AB']
# Load benchmarks files from UBC-GIF codes
AB_file = os.path.sep.join([self.basePath, 'AB_GIF_fullspace.txt'])
MN_file = os.path.sep.join([self.basePath, 'MN_GIF_fullspace.txt'])
AM_file = os.path.sep.join([self.basePath, 'AM_GIF_fullspace.txt'])
AN_file = os.path.sep.join([self.basePath, 'AN_GIF_fullspace.txt'])
BM_file = os.path.sep.join([self.basePath, 'BM_GIF_fullspace.txt'])
BN_file = os.path.sep.join([self.basePath, 'BN_GIF_fullspace.txt'])
AB_GIF = np.loadtxt(AB_file)
MN_GIF = np.loadtxt(MN_file)
AM_GIF = np.loadtxt(AM_file)
AN_GIF = np.loadtxt(AN_file)
BM_GIF = np.loadtxt(BM_file)
BN_GIF = np.loadtxt(BN_file)
# Assert agreements between the two codes
test_AB = np.allclose(AB_GIF, AB)
test_MN = np.allclose(MN_GIF, MN)
test_AM = np.allclose(AM_GIF, AM)
test_AN = np.allclose(AN_GIF, AN)
test_BM = np.allclose(BM_GIF, BM)
test_BN = np.allclose(BN_GIF, BN)
passed = np.all([test_AB, test_MN, test_AM, test_AN, test_BM, test_BN])
self.assertTrue(passed)
bottomHalf = bottomHalf[0:-1, :]
cylinderPoints = np.vstack([topHalf, bottomHalf])
cylinderPoints = np.vstack([cylinderPoints, topHalf[0, :]])
return cylinderPoints
# Setup a synthetic Dipole-Dipole Survey
# Line 1
xmin, xmax = -15., 15.
ymin, ymax = 0., 0.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey1 = DCUtils.gen_DCIPsurvey(endl,
"dipole-dipole",
dim=mesh.dim,
a=3,
b=3,
n=8)
# Line 2
xmin, xmax = -15., 15.
ymin, ymax = 5., 5.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey2 = DCUtils.gen_DCIPsurvey(endl,
"dipole-dipole",
dim=mesh.dim,
a=3,
b=3,
n=8)
axs.scatter(tx[0, 1], tx[1, 2], c='b', s=75, marker='v')
else:
axs.scatter(tx[0], tx[2], c='r', s=75, marker='v')
#cfm1=get_current_fig_manager().window
#%%
# Add z coordinate to all survey... assume flat
nz = mesh.vectorNz
var = np.c_[np.asarray(srvy_end), np.ones(2).T * nz[-1]]
# Snap the endpoints to the grid. Easier to create 2D section.
indx = Utils.closestPoints(mesh, var)
endl = np.c_[mesh.gridCC[indx, 0], mesh.gridCC[indx, 1], np.ones(2).T * nz[-1]]
survey = StaticUtils.gen_DCIPsurvey(endl, mesh, stype, a, b, n)
#survey = DC.SurveyDC.Survey(srcList)
Tx = StaticUtils.getSrc_locs(survey)
dl_len = np.sqrt(np.sum((endl[0, :] - endl[1, :])**2))
dl_x = (Tx[-1][0] - Tx[0][0]) / dl_len
dl_y = (Tx[-1][1] - Tx[0][1]) / dl_len
azm = np.arctan(dl_y / dl_x)
# Plot stations along line
if stype == 'gradient':
Rx = survey.srcList[0].rxList[0].locs
plt.scatter(Tx[0][0::3], Tx[0][1::3], s=40, c='r')
plt.scatter(np.c_[Rx[0][:, 0], Rx[1][:, 0]],
np.c_[Rx[0][:, 1], Rx[1][:, 1]],
cfm1.activateWindow() plt.sca(ax_prim) # Takes two points from ginput and create survey #gin = plt.ginput(2, timeout = 0) # Add z coordinate to all survey... assume flat nz = mesh.vectorNz var = np.c_[np.asarray(srvy_end), np.ones(2).T * nz[-1]] # Snap the endpoints to the grid. Easier to create 2D section. indx = Utils.closestPoints(mesh, var) endl = np.c_[mesh.gridCC[indx, 0], mesh.gridCC[indx, 1], np.ones(2).T * nz[-1]] survey2D = DCUtils.gen_DCIPsurvey(endl, mesh, stype, a, b, n) Tx = DCUtils.getSrc_locs(survey2D) Rx = survey2D.srcList[0].rxList[0].locs dl_len = np.sqrt(np.sum((endl[0, :] - endl[1, :])**2)) dl_x = (Tx[-1][0] - Tx[0][0]) / dl_len dl_y = (Tx[-1][1] - Tx[0][1]) / dl_len azm = np.arctan(dl_y / dl_x) #%% Create a 2D mesh along axis of Tx end points and keep z-discretization dx = np.min([np.min(mesh.hx), np.min(mesh.hy), dx_in]) ncx = np.ceil(dl_len / dx) + 3 ncz = np.ceil(depth / dx) padx = dx * np.power(1.4, range(1, padc))
# Model:
ln_sigback = -5.
mtrue_2 = ln_sigback * np.ones(mesh_2d.nC)
mtrue_3 = ln_sigback * np.ones(mesh_3d.nC)
# Survey:
# Setup a Dipole-Dipole Survey
xmin, xmax = -20., 20.
ymin, ymax = -9., -9.,
zmin, zmax = mesh_2d.vectorCCy[-1], mesh_2d.vectorCCy[-1]
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey_2 = DCUtils.gen_DCIPsurvey(endl,
"dipole-dipole",
dim=mesh_2d.dim,
a=10,
b=10,
n=1,
d2flag='2D')
# Line 1
xmin, xmax = -20., 20.
ymin, ymax = 0., 0.
zmin, zmax = -9., -9.
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey_3 = DCUtils.gen_DCIPsurvey(endl,
"dipole-dipole",
dim=mesh_3d.dim,
a=10,
b=10,
n=1)
bottomHalf = bottomHalf[0:-1, :]
cylinderPoints = np.vstack([topHalf, bottomHalf])
cylinderPoints = np.vstack([cylinderPoints, topHalf[0, :]])
return cylinderPoints
# Setup a Dipole-Dipole Survey
xmin, xmax = -15., 15.
ymin, ymax = 0., 0.
zmin, zmax = mesh.vectorCCy[-1], mesh.vectorCCy[-1]
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey = DCUtils.gen_DCIPsurvey(endl,
"dipole-dipole",
dim=mesh.dim,
a=1,
b=1,
n=10,
d2flag='2D')
# Setup Problem with exponential mapping and Active cells only in the core mesh
expmap = Maps.ExpMap(mesh)
mapactive = Maps.InjectActiveCells(mesh=mesh,
indActive=actind,
valInactive=-5.)
mapping = expmap * mapactive
problem = DC.Problem3D_CC(mesh, sigmaMap=mapping)
problem.pair(survey)
problem.Solver = Solver
survey.dpred(mtrue[actind])
topHalf = np.vstack([xLoc1, zLoc1]).T
topHalf = topHalf[0:-1, :]
bottomHalf = np.vstack([xLoc2, zLoc2]).T
bottomHalf = bottomHalf[0:-1, :]
cylinderPoints = np.vstack([topHalf, bottomHalf])
cylinderPoints = np.vstack([cylinderPoints, topHalf[0, :]])
return cylinderPoints
# Setup a Dipole-Dipole Survey
xmin, xmax = -15., 15.
ymin, ymax = 0., 0.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey = DCUtils.gen_DCIPsurvey(endl, mesh, "dipole-dipole",
a=1, b=1, n=10, d2flag='2D')
# Setup Problem with exponential mapping and Active cells only in the core mesh
expmap = Maps.ExpMap(mesh)
mapactive = Maps.InjectActiveCells(mesh=mesh, indActive=actind,
valInactive=-5.)
mapping = expmap*mapactive
problem = DC.Problem3D_CC(mesh, sigmaMap=mapping)
problem.pair(survey)
problem.Solver = Solver
survey.dpred(mtrue[actind])
survey.makeSyntheticData(mtrue[actind], std=0.05, force=True)
######################
dsep = '\\' # Forward solver # Number of padding cells to remove from plotting padc = 15 # Plotting parameters xmin, xmax = 10500, 13000 zmin, zmax = -600, 600 vmin, vmax = -4, 2 z = np.linspace(zmin, zmax, 4) x = np.asarray([11000, 11750, 12500]) #%% load obs file 3D dobs = Utils.readUBC_DC3Dobs(home_dir + dsep + obs_file) DCsurvey = dobs['DCsurvey'] srcMat = Utils.getSrc_locs(DCsurvey) # Assign line ID to the survey lineID = Utils.xy_2_lineID(DCsurvey) uniqueID = np.unique(lineID) # Convert 3D locations to 2D survey survey2D = Utils.convertObs_DC3D_to_2D(DCsurvey, lineID, 'Xloc') srcMat = Utils.getSrc_locs(survey2D) #DCdata[src0, src0.rxList[0]]
# Takes two points from ginput and create survey
#if re.match(stype,'gradient'):
#gin = [(423230. , 546440.), (423715. , 546440.)]
#else:
#gin = plt.ginput(2, timeout = 0)
#gin = [(370, 12155), (2000, 12155)]
# Add z coordinate to all survey... assume flat
nz = mesh.vectorNz
var = np.c_[np.asarray(srvy_end),np.ones(2).T*nz[-1]]
# Snap the endpoints to the grid. Easier to create 2D section.
indx = Utils.closestPoints(mesh, var )
endl = np.c_[mesh.gridCC[indx,0],mesh.gridCC[indx,1],np.ones(2).T*nz[-1]]
srcList = StaticUtils.gen_DCIPsurvey(endl, mesh, stype, a, b, n)
survey = DC.SurveyDC.Survey(srcList)
Tx = StaticUtils.getSrc_locs(srcList)
dl_len = np.sqrt( np.sum((endl[0,:] - endl[1,:])**2) )
dl_x = ( Tx[-1][0] - Tx[0][0] ) / dl_len
dl_y = ( Tx[-1][1] - Tx[0][1] ) / dl_len
azm = np.arctan(dl_y/dl_x)
# Plot stations along line
if stype == 'gradient':
plt.scatter(Tx[0][0::3],Tx[0][1::3],s=40,c='r')
plt.scatter(np.c_[Rx[0][:,0],Rx[1][:,0]],np.c_[Rx[0][:,1],Rx[1][:,1]],s=20,c='y')
plt.show()
def test_dipole_dipole(self):
# Setup a dipole-dipole Survey
survey = DCUtils.gen_DCIPsurvey(
self.xyz,
survey_type="dipole-dipole",
dim=self.mesh.dim,
a=self.survey_a,
b=self.survey_b,
n=self.survey_n
)
# Setup Problem with exponential mapping
expmap = Maps.ExpMap(self.mesh)
problem = DC.Problem3D_CC(self.mesh, sigmaMap=expmap)
problem.pair(survey)
problem.Solver = Solver
# Create synthetic data
survey.makeSyntheticData(self.model, std=0., force=True)
survey.eps = 1e-5
# Testing IO
surveyfile = os.path.sep.join(
[self.basePath, '2sph_dipole_dipole.obs']
)
DCUtils.writeUBC_DCobs(
surveyfile,
survey,
dim=3,
format_type='GENERAL'
)
survey = DCUtils.readUBC_DC3Dobs(surveyfile)
survey = survey['dc_survey']
DCUtils.writeUBC_DCobs(
surveyfile,
survey,
dim=3,
format_type='GENERAL'
)
survey = DCUtils.readUBC_DC3Dobs(surveyfile)
survey = survey['dc_survey']
if self.plotIt:
import matplotlib.pyplot as plt
# Test Pseudosections plotting
fig, ax = plt.subplots(1, 1, figsize=(15, 3))
ax = DCUtils.plot_pseudoSection(
survey, ax, survey_type='dipole-dipole',
scale='log', clim=None,
data_type='appResistivity',
pcolorOpts={"cmap": "viridis"},
data_location=True
)
plt.show()
# Test the utils functions electrode_separations,
# source_receiver_midpoints, geometric_factor,
# apparent_resistivity all at once
rhoapp = DCUtils.apparent_resistivity(
survey, survey_type='dipole-dipole',
space_type='half-space', eps=0.
)
rhoA_GIF_file = os.path.sep.join([self.basePath, 'rhoA_GIF_dd.txt'])
rhoA_GIF_dd = np.loadtxt(rhoA_GIF_file)
passed = np.allclose(rhoapp, rhoA_GIF_dd)
self.assertTrue(passed)
def plot_pseudoSection(dc_survey,
ax=None,
survey_type='dipole-dipole',
data_type="appConductivity",
space_type='half-space',
clim=None,
scale="linear",
sameratio=True,
pcolorOpts={},
data_location=False,
dobs=None,
dim=2):
"""
Read list of 2D tx-rx location and plot a speudo-section of apparent
resistivity.
Assumes flat topo for now...
Input:
:param SimPEG.EM.Static.DC.SurveyDC.Survey dc_survey: DC survey object
:param matplotlib.pyplot.axes ax: figure axes on which to plot
:param str survey_type: Either 'dipole-dipole' | 'pole-dipole' |
'dipole-pole' | 'pole-pole'
:param str data_type: Either 'appResistivity' | 'appConductivity' |
'volt' (potential)
:param str space_type: Either 'half-space' (default) or 'whole-space'
:param str scale: Either 'linear' (default) or 'log'
Output:
:return matplotlib.pyplot.figure plot overlayed on image
"""
import pylab as plt
from scipy.interpolate import griddata
# Set depth to 0 for now
z0 = 0.
rho = []
# Use dobs in survey if dobs is None
if dobs is None:
if dc_survey.dobs is None:
raise Exception()
else:
dobs = dc_survey.dobs
rhoApp = DCUtils.apparent_resistivity(dc_survey,
dobs=dobs,
survey_type=survey_type,
space_type=space_type)
midx, midz = DCUtils.source_receiver_midpoints(dc_survey,
survey_type=survey_type,
dim=dim)
if data_type == 'volt':
if scale == "linear":
rho = dobs
elif scale == "log":
rho = np.log10(abs(dobs))
elif data_type == 'appConductivity':
if scale == "linear":
rho = 1. / rhoApp
elif scale == "log":
rho = np.log10(1. / rhoApp)
elif data_type == 'appResistivity':
if scale == "linear":
rho = rhoApp
elif scale == "log":
rho = np.log10(rhoApp)
else:
print()
raise Exception("""data_type must be 'appResistivity' |
'appConductivity' | 'volt' """
" not {}".format(data_type))
# Grid points
grid_x, grid_z = np.meshgrid(
np.linspace(np.min(midx), np.max(midx),
int(2. * (np.abs(np.max(midx) - np.min(midx))) + 1)),
np.linspace(np.min(midz), np.max(midz),
int(2. * (np.abs(np.min(midz) - np.max(midz))) + 1)),
indexing='xy')
grid_x, grid_z = grid_x.T, grid_z.T
grid_rho = griddata(np.c_[midx, midz],
rho.T, (grid_x, grid_z),
method='linear',
rescale=True)
if clim is None:
vmin, vmax = rho.min(), rho.max()
else:
vmin, vmax = clim[0], clim[1]
if ax is None:
fig, ax = plt.subplots(1, 1, figsize=(15, 3))
grid_rho = np.ma.masked_where(np.isnan(grid_rho), grid_rho)
ph = ax.contourf(grid_x[:, 0],
grid_z[0, :],
grid_rho.T,
vmin=vmin,
vmax=vmax,
**pcolorOpts)
ax.set_xlabel('X(m)', fontsize=16)
ax.set_ylabel('n', fontsize=16)
ax.tick_params(labelsize=14)
if scale == "log":
cbar = plt.colorbar(ph,
format="$10^{%.1f}$",
fraction=0.04,
orientation="horizontal")
elif scale == "linear":
cbar = plt.colorbar(ph,
format="%.1f",
fraction=0.04,
orientation="horizontal")
if data_type == 'appConductivity':
cbar.set_label("App.Cond", size=16)
elif data_type == 'appResistivity':
cbar.set_label("Apparent Resistivity (Ohm-m)", size=16)
elif data_type == 'volt':
cbar.set_label("Potential (V)", size=16)
#cmin, cmax = cbar.get_clim()
#ticks = np.linspace(cmin, cmax, 5)
#cbar.set_ticks(ticks)
#cbar.ax.tick_params(labelsize=14)
cbar.set_ticks(ph.levels)
cbar.ax.tick_params(labelsize=16)
# Plot apparent resistivity
if data_location:
ax.plot(midx, midz, 'k.', ms=2, alpha=0.8, label='data locations')
#ax.plot(grid_x, grid_z, 'k.', ms=1, alpha=0.4)
ax.legend(fontsize=14)
if sameratio:
ax.set_aspect('equal', adjustable='box')
return ax, midx, midz, grid_x, grid_z, rho
topHalf = topHalf[0:-1, :]
bottomHalf = np.vstack([xLoc2, zLoc2]).T
bottomHalf = bottomHalf[0:-1, :]
cylinderPoints = np.vstack([topHalf, bottomHalf])
cylinderPoints = np.vstack([cylinderPoints, topHalf[0, :]])
return cylinderPoints
# Setup a synthetic Dipole-Dipole Survey
# Line 1
xmin, xmax = -15., 15.
ymin, ymax = 0., 0.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey1 = DCUtils.gen_DCIPsurvey(endl, "dipole-dipole", dim=mesh.dim,
a=3, b=3, n=8)
# Line 2
xmin, xmax = -15., 15.
ymin, ymax = 5., 5.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey2 = DCUtils.gen_DCIPsurvey(endl, "dipole-dipole", dim=mesh.dim,
a=3, b=3, n=8)
# Line 3
xmin, xmax = -15., 15.
ymin, ymax = -5., -5.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey3 = DCUtils.gen_DCIPsurvey(endl, "dipole-dipole", dim=mesh.dim,
topHalf = topHalf[0:-1, :]
bottomHalf = np.vstack([xLoc2, zLoc2]).T
bottomHalf = bottomHalf[0:-1, :]
cylinderPoints = np.vstack([topHalf, bottomHalf])
cylinderPoints = np.vstack([cylinderPoints, topHalf[0, :]])
return cylinderPoints
# Setup a synthetic Dipole-Dipole Survey
# Line 1
xmin, xmax = -15., 15.
ymin, ymax = 0., 0.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey1 = DCUtils.gen_DCIPsurvey(endl, mesh, "dipole-dipole", a=3, b=3, n=8)
# Line 2
xmin, xmax = -15., 15.
ymin, ymax = 5., 5.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey2 = DCUtils.gen_DCIPsurvey(endl, mesh, "dipole-dipole", a=3, b=3, n=8)
# Line 3
xmin, xmax = -15., 15.
ymin, ymax = -5., -5.
zmin, zmax = 0, 0
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
survey3 = DCUtils.gen_DCIPsurvey(endl, mesh, "dipole-dipole", a=3, b=3, n=8)