def generate_hom_world_with_inclusion(world_dim: list, incl_start: list,
incl_dim: list):
""" Creates a homogeneous world with inclusion.
Utility function to create a homogeneous world with an inclusion. Region markers are set to 1 for the background
world and 2 for the inclusion.
Parameter:
world_dim: World dimensions as [x,z].
incl_start: Inclusion upper left corner as [x,z].
incl_dim: Inclusion dimension as [x,z].
Returns:
The created world.
"""
# Create geometric objects
world = mt.createWorld(start=[0, 0], end=[world_dim[0], -world_dim[1]])
inclusion = mt.createRectangle(
start=incl_start,
end=[incl_start[0] + incl_dim[0], incl_start[1] - incl_dim[1]],
marker=2,
boundaryMarker=10)
# Merge geometries
geom = mt.mergePLC([world, inclusion])
return geom
def createSynthModel():
"""Return the modelling mesh, the porosity distribution and the
parametric mesh for inversion.
"""
# Create the synthetic model
world = mt.createCircle(boundaryMarker=-1, nSegments=64)
tri = mt.createPolygon([[-0.8, -0], [-0.5, -0.7], [0.7, 0.5]],
isClosed=True, area=0.0015)
c1 = mt.createCircle(radius=0.2, pos=[-0.2, 0.5], nSegments=32,
area=0.0025, marker=3)
c2 = mt.createCircle(radius=0.2, pos=[0.32, -0.3], nSegments=32,
area=0.0025, marker=3)
poly = mt.mergePLC([world, tri, c1, c2])
poly.addRegionMarker([0.0, 0, 0], 1, area=0.0015)
poly.addRegionMarker([-0.9, 0, 0], 2, area=0.0015)
c = mt.createCircle(radius=0.99, nSegments=16, start=np.pi, end=np.pi*3)
[poly.createNode(p.pos(), -99) for p in c.nodes()]
mesh = pg.meshtools.createMesh(poly, q=34.4, smooth=[1, 10])
mesh.scale(1.0/5.0)
mesh.rotate([0., 0., 3.1415/3])
mesh.rotate([0., 0., 3.1415])
petro = pg.solver.parseArgToArray([[1, 0.9], [2, 0.6], [3, 0.3]],
mesh.cellCount(), mesh)
# Create the parametric mesh that only reflect the domain geometry
world = mt.createCircle(boundaryMarker=-1, nSegments=32, area=0.0051)
paraMesh = pg.meshtools.createMesh(world, q=34.0, smooth=[1, 10])
paraMesh.scale(1.0/5.0)
return mesh, paraMesh, petro
def createSynthModel():
"""Return the modeling mesh, the porosity distribution and the
parametric mesh for inversion.
"""
# Create the synthetic model
world = mt.createCircle(boundaryMarker=-1, segments=64)
tri = mt.createPolygon([[-0.8, -0], [-0.5, -0.7], [0.7, 0.5]],
isClosed=True, area=0.0015)
c1 = mt.createCircle(radius=0.2, pos=[-0.2, 0.5], segments=32,
area=0.0025, marker=3)
c2 = mt.createCircle(radius=0.2, pos=[0.32, -0.3], segments=32,
area=0.0025, marker=3)
poly = mt.mergePLC([world, tri, c1, c2])
poly.addRegionMarker([0.0, 0, 0], 1, area=0.0015)
poly.addRegionMarker([-0.9, 0, 0], 2, area=0.0015)
c = mt.createCircle(radius=0.99, segments=16, start=np.pi, end=np.pi*3)
[poly.createNode(p.pos(), -99) for p in c.nodes()]
mesh = pg.meshtools.createMesh(poly, q=34.4, smooth=[1, 10])
mesh.scale(1.0/5.0)
mesh.rotate([0., 0., 3.1415/3])
mesh.rotate([0., 0., 3.1415])
petro = pg.solver.parseArgToArray([[1, 0.9], [2, 0.6], [3, 0.3]],
mesh.cellCount(), mesh)
# Create the parametric mesh that only reflects the domain geometry
world = mt.createCircle(boundaryMarker=-1, segments=32, area=0.0051)
paraMesh = pg.meshtools.createMesh(world, q=34.0, smooth=[1, 10])
paraMesh.scale(1.0/5.0)
return mesh, paraMesh, petro
def get_fwd_mesh():
"""Generate the forward mesh (with embedded anomalies)"""
scheme = get_scheme()
# Mesh generation
world = mt.createWorld(
start=[-55, 0], end=[105, -80], worldMarker=True)
conductive_anomaly = mt.createCircle(
pos=[10, -7], radius=5, marker=2
)
polarizable_anomaly = mt.createCircle(
pos=[40, -7], radius=5, marker=3
)
plc = mt.mergePLC((world, conductive_anomaly, polarizable_anomaly))
# local refinement of mesh near electrodes
for s in scheme.sensors():
plc.createNode(s + [0.0, -0.2])
mesh_coarse = mt.createMesh(plc, quality=33)
mesh = mesh_coarse.createH2()
return mesh
def simulateSynth(model, tMax=5000, satSteps=150, ertSteps=10, area=0.1,
synthPath='synth/'):
"""Create synthetic example."""
if not os.path.exists('synth/'):
os.mkdir(synthPath)
world = mt.createWorld(start=[-20, 0], end=[20, -16], layers=[-2, -8],
worldMarker=False)
for i, b in enumerate(world.boundaries()):
b.setMarker(i + 1)
block = mt.createRectangle(start=[-6, -3.5], end=[6, -6.0], marker=4,
boundaryMarker=11, area=area)
geom = mt.mergePLC([world, block])
geom.save(synthPath + 'synthGeom')
# pg.show(geom, boundaryMarker=1)
paraMesh = pg.meshtools.createMesh(geom, quality=32, area=area,
smooth=[1, 10])
# translate 1 2 3 4 - > 0 1 2 3
mapMarker = np.array([0, 0, 1, 2, 3], 'float')
paraMesh.setCellMarkers(mapMarker[np.array(paraMesh.cellMarkers())])
paraMesh.save(synthPath + 'synth.bms')
fop = HydroGeophysicalModelling(mesh=paraMesh, tMax=tMax,
satSteps=satSteps,
ertSteps=ertSteps,
verbose=1)
# openblas have some problems with to high thread count ..
# we need to dig into
print("ThreadCount:", pg.threadCount())
pg.setThreadCount(4)
print('##### Simulate synthetic data ' + '#'*50)
pg.tic()
rhoaR = fop.response(pg.RVector(model)[paraMesh.cellMarkers()])
pg.toc()
print('#'*100)
# add some noise here
rand = pg.RVector(len(rhoaR))
pg.randn(rand)
rhoaR *= (1.0 + rand * fop.ws.derr.flatten())
fop.ws.rhoaR = rhoaR.reshape(fop.ws.derr.shape)
# fop.ws.mesh.save(synthPath + 'synth.bms')
np.save(synthPath + 'synthK', fop.ws.k)
np.save(synthPath + 'synthVel', fop.ws.vel)
np.save(synthPath + 'synthSat', fop.ws.sat)
fop.ws.scheme.save(synthPath + 'synth.shm', 'a b m n')
np.save(synthPath + 'synthRhoaRatio', fop.ws.rhoaR)
np.save(synthPath + 'synthRhoa', fop.ws.rhoa)
np.save(synthPath + 'synthErr', fop.ws.derr)
def testCBarLevels():
"""
Expectations
------------
axs[0, 0]: show regions with plc
Show needs to deliver the regions with Set3 colormap. Each tick on the
colobar should be in the middle of the related color section.
axs[1, 0]: show regions with mesh
really the same thing as on axs[0, 0] but with mesh.
ax[0, 1]: show mesh with cell data
if nLevs is given i would expect that the colormap then is levelled.
currently that is not the fact. but at least its the full range. labels
need to be at begin/end of each color section.
ax[1, 1]: show mesh with node data
the colorbar range misses parts of its full range. labels need to be
at begin/end of each color section.
"""
# create a geometry
world = mt.createWorld(start=[-10, 0],
end=[10, -16],
layers=[-8],
worldMarker=False)
block = mt.createRectangle(start=[-6, -3.5],
end=[6, -6.0],
marker=4,
boundaryMarker=10,
area=0.1)
circ = mt.createCircle(pos=[0, -11], marker=5, radius=2, boundaryMarker=11)
poly = mt.mergePLC([world, block, circ])
mesh = mt.createMesh(poly, quality=34)
# create random data
rhomap = [[1, 10], [2, 4], [4, 20], [5, 8]]
# map data to cell/node count
cell_data = pg.solver.parseArgToArray(rhomap, mesh.cellCount(), mesh)
node_data = mt.cellDataToNodeData(mesh, cell_data)
# plot everything
fig, axs = pg.plt.subplots(2, 2, figsize=(20, 10))
pg.show(poly, ax=axs[0, 0])
pg.show(mesh, ax=axs[1, 0], markers=True)
pg.show(mesh, cell_data, ax=axs[0, 1], colorBar=True, nLevs=7)
pg.show(mesh, node_data, ax=axs[1, 1], colorBar=True, nLevs=7)
def plot_fwd_model(axes):
"""This function plots the forward model used to generate the data
"""
# Mesh generation
world = mt.createWorld(
start=[-55, 0], end=[105, -80], worldMarker=True)
conductive_anomaly = mt.createCircle(
pos=[10, -7], radius=5, marker=2
)
polarizable_anomaly = mt.createCircle(
pos=[40, -7], radius=5, marker=3
)
plc = mt.mergePLC((world, conductive_anomaly, polarizable_anomaly))
# local refinement of mesh near electrodes
for s in scheme.sensors():
plc.createNode(s + [0.0, -0.2])
mesh_coarse = mt.createMesh(plc, quality=33)
mesh = mesh_coarse.createH2()
rhomap = [
[1, pg.utils.complex.toComplex(100, 0 / 1000)],
# Magnitude: 50 ohm m, Phase: -50 mrad
[2, pg.utils.complex.toComplex(50, 0 / 1000)],
[3, pg.utils.complex.toComplex(100, -50 / 1000)],
]
rho = pg.solver.parseArgToArray(rhomap, mesh.cellCount(), mesh)
pg.show(
mesh,
data=np.log(np.abs(rho)),
ax=axes[0],
label=r"$log_{10}(|\rho|~[\Omega m])$"
)
pg.show(mesh, data=np.abs(rho), ax=axes[1], label=r"$|\rho|~[\Omega m]$")
pg.show(
mesh, data=np.arctan2(np.imag(rho), np.real(rho)) * 1000,
ax=axes[2],
label=r"$\phi$ [mrad]",
cMap='jet_r'
)
fig.tight_layout()
fig.show()
def generate_layered_world_with_inclusion(world_dim: list, layer_heights: list,
incl_start: list, incl_dim: list):
""" Creates a layered world with inclusion.
Utility function to create a layered world with an inclusion. Region markers are starting at 1 and increasing with
depth. The inclusion has the highest marker number.
Parameter:
world_dim: World dimensions as [x,z].
layer_heights: Heights of the single layers.
incl_start: Inclusion upper left corner as [x,z].
incl_dim: Inclusion dimension as [x,z].
Returns:
The created world.
"""
# Check parameter integrity
if sum(layer_heights) > world_dim[1]:
return None
# Create geometric objects
world = mt.createWorld(start=[0, 0], end=[world_dim[0], -world_dim[1]])
current_depth = 0
layers = []
for i in range(len(layer_heights)):
layer = mt.createRectangle(
start=[0, -current_depth],
end=[world_dim[0], -(current_depth + layer_heights[i])],
marker=i + 1,
boundaryMarker=10)
current_depth += layer_heights[i]
layers.append(layer)
if current_depth != world_dim[1]:
layer = mt.createRectangle(start=[0, -current_depth],
end=[world_dim[0], -world_dim[1]],
marker=i + 2,
boundaryMarker=10)
layers.append(layer)
inclusion = mt.createRectangle(
start=incl_start,
end=[incl_start[0] + incl_dim[0], incl_start[1] - incl_dim[1]],
marker=len(layers) + 1,
boundaryMarker=10)
# Merge geometries
geom = mt.mergePLC([world, inclusion] + layers)
return geom
def create_geometry(position=0, depth=3, radius=4):
elecs = np.linspace(-25, 25, 15) # x coordinate of the electrodes
# Create geometry definition for the modelling domain.
# worldMarker=True indicates the default boundary conditions for the ERT
world = mt.createWorld(start=[-50, 0], end=[50, -50], worldMarker=True)
# Create a circular heterogeneous body
block = mt.createCircle(pos=[position, -depth],
radius=radius,
marker=2,
boundaryMarker=0,
area=5)
# Merge geometry definition into a Piecewise Linear Complex (PLC)
geom = mt.mergePLC([world, block])
fig, ax = plt.subplots(figsize=(10, 6))
pg.show(geom, ax=ax, hold=True)
ax.plot(elecs, np.zeros_like(elecs), "kv")
ax.set_ylim(-20, 0)
return geom
def generate_tiled_world(world_dim: list, tile_size: list):
""" Creates a tiled layered world.
Utility function to create a tiled layered world. Region marker 1 is upper left corner.
Parameter:
world_dim: World dimensions as [x,z].
tile_size: Tile dimensions as [x,z].
Returns:
The created world.
"""
# Create world
world = mt.createWorld(start=[0, 0], end=[world_dim[0], -world_dim[1]])
# Create tile counts
n_tiles_x = int(np.ceil(world_dim[0] / tile_size[0]))
n_tiles_y = int(np.ceil(world_dim[1] / tile_size[1]))
# Create and merge tiles
for j in range(n_tiles_y):
for i in range(n_tiles_x):
x_start = int(i * tile_size[0])
x_end = int((i + 1) * tile_size[0])
y_start = int(-j * tile_size[1])
y_end = int(-(j + 1) * tile_size[1])
if x_end > world_dim[0]:
x_end = world_dim[0]
if y_end < -world_dim[1]:
y_end = -world_dim[1]
marker = 1
if ((-1)**i) * ((-1)**j) < 0:
marker = 2
tile = mt.createRectangle(start=[x_start, y_start],
end=[x_end, y_end],
marker=marker,
boundaryMarker=10)
world = mt.mergePLC([world, tile])
return world
def generate_layered_world(world_dim: list, layer_heights: list):
""" Creates a layered world.
Utility function to create a layered world. Region markers are starting at 1 and increasing with depth.
Parameter:
world_dim: World dimensions as [x,z].
layer_heights: Heights of the single layers.
Returns:
The created world.
"""
# Check parameter integrity
if sum(layer_heights) > world_dim[1]:
return None
# Create geometric objects
world = mt.createWorld(start=[0, 0], end=[world_dim[0], -world_dim[1]])
current_depth = 0
layers = []
for i in range(len(layer_heights)):
layer = mt.createRectangle(
start=[0, -current_depth],
end=[world_dim[0], -(current_depth + layer_heights[i])],
marker=i + 1,
boundaryMarker=10)
current_depth += layer_heights[i]
layers.append(layer)
if current_depth != world_dim[1]:
layer = mt.createRectangle(start=[0, -current_depth],
end=[world_dim[0], -world_dim[1]],
marker=i + 2,
boundaryMarker=10)
layers.append(layer)
# Merge geometries
geom = mt.mergePLC([world] + layers)
return geom
import pygimli as pg
import pygimli.meshtools as mt
# Create geometry definition for the modelling domain
world = mt.createWorld(start=[-20, 0],
end=[20, -16],
layers=[-2, -8],
worldMarker=False)
# Create a heterogeneous block
block = mt.createRectangle(start=[-6, -3.5],
end=[6, -6.0],
marker=4,
boundaryMarker=10,
area=0.1)
# Merge geometrical entities
geom = mt.mergePLC([world, block])
pg.show(geom, boundaryMarker=True, savefig='geometry.pdf')
# Create a mesh from the geometry definition
mesh = mt.createMesh(geom, quality=33, area=0.2, smooth=[1, 10])
pg.show(mesh, savefig='mesh.pdf')
# $\diverg(a\grad T)=0$ with $T(bottom)=1$, $T(top)=0$
T = pg.solver.solveFiniteElements(mesh,
a=[[1, 1.0], [2, 2.0], [3, 3.0], [4, 0.1]],
uB=[[8, 1.0], [4, 0.0]],
verbose=True)
ax, _ = pg.show(mesh,
data=T,
label='Temperature $T$',
rhomap = [[0, 500], [1, 50], [2, 100], [3, 2000]]
#CREACION MODELO GENERAL
background = mt.createWorld(start=[-10, 0], end=[81, -20], area=1, marker=0)
pol0 = mt.createPolygon([[-10, -2.5], [27.5, -2.5], [30, 0], [-10, 0]],
isClosed=True,
marker=1)
pol1 = mt.createPolygon([[-10, -20], [10, -20], [27.5, -2.5], [-10, -2.5]],
isClosed=True,
marker=2)
pol2 = mt.createPolygon([[60, 0], [65, 0], [45, -20], [40, -20]],
isClosed=True,
marker=3)
world = mt.mergePLC([background, pol0, pol1, pol2])
mesh = mt.createMesh(world, quality=33, area=0.1, smooth=[1, 2])
#EXPORTACION DATOS DE RESISTIVIDAD DEL MODELO (VECTOR)
res_model = pg.solver.parseArgToArray(rhomap, mesh.cellCount(), mesh)
pg.show(mesh, res_model)
#INTERPOLACION DATOS MODELO A MESH INVERSION
nan = 99.9
model_vector = []
for pos in grid.cellCenters():
cell = mesh.findCell(pos)
if cell:
def simulateSynth(model,
tMax=5000,
satSteps=150,
ertSteps=10,
area=0.1,
synthPath='synth/'):
"""Create synthetic example."""
if not os.path.exists('synth/'):
os.mkdir(synthPath)
world = mt.createWorld(start=[-20, 0],
end=[20, -16],
layers=[-2, -8],
worldMarker=False)
for i, b in enumerate(world.boundaries()):
b.setMarker(i + 1)
block = mt.createRectangle(start=[-6, -3.5],
end=[6, -6.0],
marker=4,
boundaryMarker=11,
area=area)
geom = mt.mergePLC([world, block])
geom.save(synthPath + 'synthGeom')
# pg.show(geom, boundaryMarker=1)
paraMesh = pg.meshtools.createMesh(geom,
quality=32,
area=area,
smooth=[1, 10])
# translate 1 2 3 4 - > 0 1 2 3
mapMarker = np.array([0, 0, 1, 2, 3], 'float')
paraMesh.setCellMarkers(mapMarker[np.array(paraMesh.cellMarkers())])
paraMesh.save(synthPath + 'synth.bms')
fop = HydroGeophysicalModelling(mesh=paraMesh,
tMax=tMax,
satSteps=satSteps,
ertSteps=ertSteps,
verbose=1)
# openblas have some problems with to high thread count ..
# we need to dig into
print("TC", pg.threadCount())
pg.setThreadCount(4)
print('##### Simulate synthetic data ' + '#' * 50)
pg.tic()
rhoaR = fop.response(pg.RVector(model)[paraMesh.cellMarkers()])
pg.toc()
print('#' * 100)
# add some noise here
rand = pg.RVector(len(rhoaR))
pg.randn(rand)
rhoaR *= (1.0 + rand * fop.ws.derr.flatten())
fop.ws.rhoaR = rhoaR.reshape(fop.ws.derr.shape)
# fop.ws.mesh.save(synthPath + 'synth.bms')
np.save(synthPath + 'synthK', fop.ws.k)
np.save(synthPath + 'synthVel', fop.ws.vel)
np.save(synthPath + 'synthSat', fop.ws.sat)
fop.ws.scheme.save(synthPath + 'synth.shm', 'a b m n')
np.save(synthPath + 'synthRhoaRatio', fop.ws.rhoaR)
np.save(synthPath + 'synthRhoa', fop.ws.rhoa)
np.save(synthPath + 'synthErr', fop.ws.derr)
gz_p = solveGravimetry(circ, dRho, pnts, complete=False)
###############################################################################
# Integration for complete 2D mesh after :cite:`WonBev1987`
world = createWorld(start=[-20, 0], end=[20, -10], marker=1)
mesh = createMesh([world, circ])
dRhoC = pg.solver.parseMapToCellArray([[1, 0.0], [2, dRho]], mesh)
gc_m = solveGravimetry(mesh, dRhoC, pnts)
###############################################################################
# Finite Element solution for :math:`u`
world = createWorld(start=[-200, 200], end=[200, -200], marker=1)
# Add some nodes to the measurement points to increase the accuracy a bit
[world.createNode(x_, 0.0, 1) for x_ in x]
plc = mergePLC([world, circ])
mesh = createMesh(plc, quality=34)
mesh = mesh.createP2()
density = pg.solver.parseMapToCellArray([[1, 0.0], [2, dRho]], mesh)
u = pg.solver.solve(mesh, a=1, f=density, uB=[[-2, 0], [-1, 0]])
###############################################################################
# Calculate gradient of gravimetric potential
# :math:`\frac{\partial u}{\partial (x,z)}`
dudz = np.zeros(len(pnts))
for i, p in enumerate(pnts):
c = mesh.findCell(p)
g = c.grad(p, u)
dudz[i] = -g[1] * 4. * np.pi * pg.physics.constants.GmGal # why 4 pi here?
depth = -np.arange(sensor_spacing, bh_length + sensor_spacing, sensor_spacing)
sensors = np.zeros((len(depth) * 2, 2)) # two boreholes
sensors[len(depth):, 0] = bh_spacing # x
sensors[:, 1] = np.hstack([depth] * 2) # y
################################################################################
# Traveltime calculations work on unstructured meshes and structured grids. We
# demonstrate this here by simulating the synthetic data on an unstructured mesh
# and inverting it on a simple structured grid.
# Create forward model and mesh
c0 = mt.createCircle(pos=(7.0, -10.0), radius=3, segments=25, marker=1)
c1 = mt.createCircle(pos=(12.0, -18.0), radius=4, segments=25, marker=2)
geom = mt.mergePLC([world, c0, c1])
for sen in sensors:
geom.createNode(sen)
mesh_fwd = mt.createMesh(geom, quality=34, area=.25)
model = np.array([2000., 2300, 1700])[mesh_fwd.cellMarkers()]
pg.show(mesh_fwd, model, label="Velocity (m/s)", nLevs=3, logScale=False)
################################################################################
# Create inversion mesh
refinement = 0.25
x = np.arange(0, bh_spacing + refinement, sensor_spacing * refinement)
y = -np.arange(0.0, bh_length + 3, sensor_spacing * refinement)
mesh = pg.createMesh2D(x, y)
ax, _ = pg.show(mesh, hold=True)
import pybert as pb
from pybert.sip import SIPdata
# Create geometry definition for the modelling domain
world = plc.createWorld(start=[-50, 0],
end=[50, -50],
layers=[-1, -5],
worldMarker=True)
# Create some heterogeneous circle
block = plc.createCircle(pos=[0, -3.],
radius=1,
marker=4,
boundaryMarker=10,
area=0.1)
# Merge geometry definition
geom = plc.mergePLC([world, block])
# create measuring scheme (data container without data)
scheme = pb.createData(elecs=np.linspace(-10, 10, 21), schemeName='dd')
for pos in scheme.sensorPositions(): # put all electrodes (sensors) into geom
geom.createNode(pos, marker=-99) # just a historic convention
geom.createNode(pos + pg.RVector3(0, -0.1)) # refine with 10cm
# pg.show(geom, boundaryMarker=1)
mesh = plc.createMesh(geom)
# pg.show(mesh)
scheme = pb.createData(elecs=np.linspace(-10, 10, 21), schemeName='dd')
# dumm, 1.S 2.S 3.S Body
rhovec = np.array([0, 100.0, 50.0, 10.0, 100]) # ohm m
tauvec = np.array([0, 1e-3, 1e-3, 0.1, 1.0]) # s
mvec = np.array([0.001, 0.01, 0.001, 0.5, 0.5]) # - [0-1]
area=1,
marker=2)
sup2 = mt.createPolygon([[40, 0], [81, 0], [81, -1.5], [38.8, -1.5]],
isClosed=True,
area=1,
marker=4)
sup3 = mt.createPolygon([[30, 0], [40, 0], [39.6, -0.5], [30.4, -0.5]],
isClosed=True,
area=1,
marker=4)
pol = mt.createPolygon([[30, 0], [40, 0], [38, -2.5], [32, -2.5]],
isClosed=True,
area=1,
marker=0)
square = mt.createRectangle(start=[34, -0.5], end=[36, -2.5], area=1, marker=3)
world = mt.mergePLC([background, pol, square, sup, sup2, sup3])
mesh = mt.createMesh(world, quality=33, area=0.1, smooth=[1, 2])
res_model = pg.solver.parseArgToArray(rhomap, mesh.cellCount(), mesh)
#INTERPOLACIÓN MODELO A GRID
nan = 99.9
model_vector_nn = []
for pos in grid.cellCenters():
cell = mesh.findCell(pos)
if cell:
model_vector_nn.append(res_model[cell.id()])
else:
model_vector_nn.append(nan)
world = mt.createWorld(start=[-10, 0],
end=[10, -16],
layers=[-8],
worldMarker=False)
# Create a heterogeneous block
block = mt.createRectangle(start=[-6, -3.5],
end=[6, -6.0],
marker=4,
boundaryMarker=10,
area=0.1)
circ = mt.createCircle(pos=[0, -11], radius=2, boundaryMarker=11, isHole=True)
# Merge geometrical entities
geom = mt.mergePLC([world, block, circ])
mesh = mt.createMesh(geom)
fig, axs = plt.subplots(3, 5)
pg.show(geom, ax=axs[0][0])
axs[0][0].set_title('plc, (default)')
pg.show(geom, fillRegion=False, ax=axs[0][1])
axs[0][1].set_title('plc, fillRegion=False')
pg.show(geom, showBoundary=False, ax=axs[0][2])
axs[0][2].set_title('plc, showBoundary=False')
pg.show(geom, markers=True, ax=axs[0][3])
axs[0][3].set_title('plc, markers=True')
pg.show(mesh, ax=axs[0][4], showBoundary=False)
axs[0][4].set_title('mesh, showBoundary=False')
#creación grid para comparación
grid = pg.createGrid(x=pg.utils.grange(start=0.20, end=0.5, n=500),
y=-pg.utils.grange(0, 0.12, n=250, log=False))
grid2 = pg.createGrid(x=pg.utils.grange(start=0.33, end=0.35, n=500),
y=-pg.utils.grange(0.04, 0.06, n=250, log=False))
square = mt.createRectangle(start=[0.33, -0.04], end=[0.35, -0.06])
#MODELO
rhomap = [[1, 150], [0, 3000]]
background = mt.createWorld(start=[-1, 0], end=[1, -1], area=1, marker=1)
circle = mt.createCircle(pos=[0.34, -0.05], radius=0.01, marker=0)
world = mt.mergePLC([background, circle])
mesh = mt.createMesh(world, quality=33, area=0.1, smooth=[1, 2])
res_model = pg.solver.parseArgToArray(rhomap, mesh.cellCount(), mesh)
#INTERPOLACIÓN MODELO A GRID
nan = 99.9
model_vector_nn = []
for pos in grid.cellCenters():
cell = mesh.findCell(pos)
if cell:
model_vector_nn.append(res_model[cell.id()])
else:
model_vector_nn.append(nan)
pos=[width / 2, width / 2, -depth / 2],
marker=1,
area=75) #, boundaryMarker=0)
for i, b in enumerate(world.boundaries()):
# if worldMarker is True:
if b.norm()[2] == 1.0:
b.setMarker(pg.core.MARKER_BOUND_HOMOGEN_NEUMANN)
else:
b.setMarker(pg.core.MARKER_BOUND_MIXED)
ano = mt.createCube(size=[widthAno, lengthAno, HAno],
pos=[width / 2 + shift / 2, width / 2, depthAno],
marker=4,
area=0.01)
plc = mt.mergePLC([world, ano])
# pg.show(plc)
# pg.show(world)
# plc.exportVTK('plc.vtk')
maxA = np.array(ano.boundaryCenters()).max(axis=0)
minA = np.array(ano.boundaryCenters()).min(axis=0)
#%%
n_sensors_surf = 16 * 16
sensors_surf = np.zeros((n_sensors_surf, 3))
# area = [-10.1,10.1,-10.1,10.1]
area = [
minA[0] - widthAno * 2, maxA[0] + widthAno * 2, minA[0] - widthAno * 2,
import pygimli.meshtools as mt
from pygimli.physics import Refraction
###############################################################################
# We start by creating a three-layered slope (The model is taken from the BSc
# thesis of Constanze Reinken (University of Bonn).
layer1 = mt.createPolygon([[0.0, 137], [117.5, 164], [117.5, 162], [0.0, 135]],
isClosed=True, marker=1, area=1)
layer2 = mt.createPolygon([[0.0, 126], [0.0, 135], [117.5, 162], [117.5, 153]],
isClosed=True, marker=2)
layer3 = mt.createPolygon([[0.0, 110], [0.0, 126], [117.5, 153], [117.5, 110]],
isClosed=True, marker=3)
slope = (164 - 137) / 117.5
geom = mt.mergePLC([layer1, layer2, layer3])
mesh = mt.createMesh(geom, quality=34.3, area=3, smooth=[1, 10])
pg.show(mesh)
###############################################################################
# Next we define geophone positions and a measurement scheme, which consists of
# shot and receiver indices.
numberGeophones = 48
sensors = np.linspace(0., 117.5, numberGeophones)
scheme = pg.physics.traveltime.createRAData(sensors)
# Adapt sensor positions to slope
pos = np.array(scheme.sensorPositions())
for x in pos[:, 0]:
i = np.where(pos[:, 0] == x)
depth = -np.arange(sensor_spacing, bh_length + sensor_spacing, sensor_spacing)
sensors = np.zeros((len(depth) * 2, 2)) # two boreholes
sensors[len(depth):, 0] = bh_spacing # x
sensors[:, 1] = np.hstack([depth] * 2) # y
################################################################################
# Traveltime calculations work on unstructured meshes and structured grids. We
# demonstrate this here by simulating the synthetic data on an unstructured mesh
# and inverting it on a simple structured grid.
# Create forward model and mesh
c0 = mt.createCircle(pos=(7.0, -10.0), radius=3, segments=25, marker=1)
c1 = mt.createCircle(pos=(12.0, -18.0), radius=4, segments=25, marker=2)
geom = mt.mergePLC([world, c0, c1])
for sen in sensors:
geom.createNode(sen)
mesh_fwd = mt.createMesh(geom, quality=34, area=.25)
model = np.array([2000., 2300, 1700])[mesh_fwd.cellMarkers()]
pg.show(mesh_fwd, model, label="Velocity (m/s)", nLevs=3, logScale=False)
################################################################################
# Create inversion mesh
refinement = 0.25
x = np.arange(0, bh_spacing + refinement, sensor_spacing * refinement)
y = -np.arange(0.0, bh_length + 3, sensor_spacing * refinement)
mesh = pg.createMesh2D(x, y)
ax, _ = pg.show(mesh, hold=True)
def generate_dipped_layered_world(world_dim: list, layer_borders: list,
dipping_angle: float):
""" Creates a dipped layered world.
Utility function to create a dipped layered world. Region markers are increasing with depth.
Parameter:
world_dim: World dimensions as [x,z].
layer_borders: List of layer borders at world X = 0.
dipping_angle: Angle at which the layers are dipping. Value describing counter-clockwise angle.
Returns:
The created world.
"""
# Nested function to find the index to add a specific node
def get_insert_index(nodes, node):
i = 0
# Get edge starting index
while (i < len(nodes)) and (nodes[i][3] < node[3]):
i = i + 1
edge_start = i
# Get edge ending index
while (i < len(nodes)) and (nodes[i][3] <= node[3]):
i = i + 1
edge_end = i
# Check for input error
if (node[3] == 0) or (node[3] == 2) or (node[3] == 4) or (node[3]
== 6):
print('Function can only be used for non-default edges (1,3,5,7)')
return -1
# Find index based on specific edge
i = edge_start
if node[3] == 1:
while (i < edge_end) and (node[1] > nodes[i][1]):
i = i + 1
if node[3] == 3:
while (i < edge_end) and (node[2] < nodes[i][2]):
i = i + 1
if node[3] == 5:
while (i < edge_end) and (node[1] < nodes[i][1]):
i = i + 1
if node[3] == 7:
while (i < edge_end) and (node[2] > nodes[i][2]):
i = i + 1
return i
# Nested function to find the connecting node of a given node
def get_connecting_node(nodes_list, node, node_connections_list):
for i in range(len(node_connections_list)):
if node_connections_list[i][0] == nodes_list[node][0]:
for j in range(len(nodes_list)):
if node_connections_list[i][1] == nodes_list[j][0]:
return j
return -1
# Nested function to find the next node on the world border
def get_next_node(nodes_list, current_node):
if current_node >= len(nodes_list) - 1:
return 0
else:
return current_node + 1
# Nested function to create a polygon from a set of nodes
def get_polygon_from_nodes(node_set):
vertices = []
for i in range(len(node_set)):
vertices.append([node_set[i][1], node_set[i][2]])
return vertices
# Correct angle
while dipping_angle > 180:
dipping_angle -= 360
while dipping_angle < -180:
dipping_angle += 360
# Create background world
world = mt.createWorld(start=[0, 0],
end=[world_dim[0], -world_dim[1]],
worldMarker=True)
# Remove layers out of world scope
removed_indices = 0
for i in range(len(layer_borders)):
if (dipping_angle >= 0 and layer_borders[i - removed_indices] > 0) or (
dipping_angle <= 0
and layer_borders[i - removed_indices] < -world_dim[1]):
layer_borders.pop(i - removed_indices)
removed_indices = removed_indices + 1
# Compute layer height difference based on dipping angle
dipping_diff = world_dim[0] * math.tan(dipping_angle / 180 * math.pi)
# Compute nodes on world border (id,x,y,edge)
nodes = [[0, 0, 0, 0], [1, world_dim[0], 0, 2],
[2, world_dim[0], -world_dim[1], 4], [3, 0, -world_dim[1], 6]]
node_connections = []
next_id = 4
for i in range(len(layer_borders)):
# Find starting node
if layer_borders[i] <= 0 and layer_borders[i] >= -world_dim[1]:
# Layer starts at left world border (default case)
start_node = [next_id, 0, layer_borders[i], 7]
else:
if layer_borders[i] > 0:
# Layer starts above world
x = layer_borders[i] * math.tan(
(90 + dipping_angle) * math.pi / 180)
start_node = [next_id, x, 0, 1]
else:
# Layer starts below world
x = -(layer_borders[i] + world_dim[1]) * math.tan(
(90 - dipping_angle) * math.pi / 180)
start_node = [next_id, x, -world_dim[1], 5]
nodes.insert(get_insert_index(nodes, start_node), start_node)
next_id = next_id + 1
# Find ending node
if layer_borders[i] + dipping_diff <= 0 and layer_borders[
i] + dipping_diff >= -world_dim[1]:
# Layer ends at right world border (default case)
end_node = [
next_id, world_dim[0], layer_borders[i] + dipping_diff, 3
]
else:
if layer_borders[i] + dipping_diff > 0:
# Layer ends above world
x = -layer_borders[i] / math.tan(dipping_angle / 180 * math.pi)
end_node = [next_id, x, 0, 1]
else:
# Layer ends below world
x = world_dim[0] - (layer_borders[i] + dipping_diff +
world_dim[1]) / math.tan(
dipping_angle / 180 * math.pi)
end_node = [next_id, x, -world_dim[1], 5]
nodes.insert(get_insert_index(nodes, end_node), end_node)
next_id = next_id + 1
# Save node connections
node_connections.append([start_node[0], end_node[0]])
node_connections.append([end_node[0], start_node[0]])
# Compute polygons from nodes
polygons = []
first_node = 0
edge_to_finish = 4
if dipping_angle < 0:
for i in range(len(nodes)):
if nodes[i][3] == 2:
break
first_node = i
edge_to_finish = 6
while edge_to_finish != -1:
polygon = []
last_node_was_connected = False
has_connected_nodes = False
current_node_index = first_node
polygon.append(nodes[first_node])
while (len(polygon) == 1) or (polygon[len(polygon) - 1] != polygon[0]):
if (last_node_was_connected
== False) and (len(polygon) != 1) and (get_connecting_node(
nodes, current_node_index, node_connections) != -1):
current_node_index = get_connecting_node(
nodes, current_node_index, node_connections)
polygon.append(nodes[current_node_index])
last_node_was_connected = True
has_connected_nodes = True
if nodes[current_node_index][3] == edge_to_finish:
edge_to_finish = -1
continue
current_node_index = get_next_node(nodes, current_node_index)
polygon.append(nodes[current_node_index])
if not has_connected_nodes:
first_node = current_node_index
last_node_was_connected = False
if nodes[current_node_index][3] == edge_to_finish:
edge_to_finish = -1
polygons.append(polygon[:-1])
# Merge geometries
for i in range(len(polygons)):
poly = mt.createPolygon(get_polygon_from_nodes(polygons[i]),
marker=i + 1,
isClosed=True)
world = mt.mergePLC([world, poly])
return world
# In this first part we naively combine objects and assign markers to them,
# expecting two regions of concentric rings with markers 1 and 2. Note how the
# outer ring is assigned the marker 0 in the figure, although we specified
# marker=1 for the larger circle? A marker value of 0 is assigned to a region
# if no region marker is found, indicating that the marker for the outer ring
# was overwritten/ignored by the inner circle, which was added later.
circle_outer = mt.createCircle(pos=[0.0, 0.0], radius=3.0, marker=1)
circle_inner = mt.createCircle(
pos=[0.0, 0.0],
radius=1.0,
# area=.3,
boundaryMarker=0,
marker=2)
plc = mt.mergePLC([circle_outer, circle_inner])
ax, cb = pg.show(plc, markers=True)
###############################################################################
# The solution to this problem is the region marker, which defines the marker
# value of the region that it is placed in. By default all region markers are
# assigned the position (0,0,0), thereby overwriting each other (see black dots
# in figure below). If no region marker is present in a region, a marker value
# of 0 is assigned.
fig = ax.get_figure()
for nr, marker in enumerate(plc.regionMarker()):
print('Position marker number {}:'.format(nr + 1), marker.x(), marker.y(),
marker.z())
ax.scatter(marker.x(), marker.y(), s=(2 - nr) * 30, color='k')
#PARAMETROS MODELADO
noise=0
rhomap= [[0,100],[1,100],[2,200],[3,1000]]
#CREACION MODELO GENERAL
background=mt.createWorld(start=[-10,0],end=[81,-20], area=1,marker=0)
pol0=mt.createPolygon([[-10,-2.5],[81,-2.5],[81,0],[-10,0]], isClosed=True,marker=1)
pol1=mt.createPolygon([[-10,-15],[81,-15],[81,-2.5],[-10,-2.5]], isClosed=True,marker=2)
circle1=mt.createCircle(pos=[25.5,-7.5],radius=2,isClosed=True, marker=3)
circle2=mt.createCircle(pos=[45.5,-7.5],radius=2,isClosed=True, marker=3)
circle3=mt.createCircle(pos=[35.5,-7.5],radius=2,isClosed=True,area=1, marker=3)
world = mt.mergePLC([background,circle1,circle2,pol0,pol1])
mesh= mt.createMesh(world, quality=33, area=0.1,smooth=[1,2])
#EXPORTACION DATOS DE RESISTIVIDAD DEL MODELO (VECTOR)
res_model=pg.solver.parseArgToArray(rhomap, mesh.cellCount(), mesh)
pg.show(mesh,res_model)
#INTERPOLACION DATOS MODELO A MESH INVERSION
nan=99.9
model_vector = []
for pos in grid.cellCenters():
cell = mesh.findCell(pos)
if cell:
# We start by creating a three-layered slope (The model is taken from the BSc
# thesis of Constanze Reinken (University of Bonn).
layer1 = mt.createPolygon([[0.0, 137], [117.5, 164], [117.5, 162], [0.0, 135]],
isClosed=True,
marker=1,
area=1)
layer2 = mt.createPolygon([[0.0, 126], [0.0, 135], [117.5, 162], [117.5, 153]],
isClosed=True,
marker=2)
layer3 = mt.createPolygon([[0.0, 110], [0.0, 126], [117.5, 153], [117.5, 110]],
isClosed=True,
marker=3)
slope = (164 - 137) / 117.5
geom = mt.mergePLC([layer1, layer2, layer3])
mesh = mt.createMesh(geom, quality=34.3, area=3, smooth=[1, 10])
pg.show(mesh)
###############################################################################
# Next we define geophone positions and a measurement scheme, which consists of
# shot and receiver indices.
numberGeophones = 48
sensors = np.linspace(0., 117.5, numberGeophones)
scheme = pg.physics.traveltime.createRAData(sensors)
# Adapt sensor positions to slope
pos = np.array(scheme.sensorPositions())
for x in pos[:, 0]:
i = np.where(pos[:, 0] == x)
if not os.path.exists(path_Data):
os.makedirs(path_Data)
# Create geometry definition for the modelling domain
world = mt.createWorld(start=[-20, 0], end=[20, -16], worldMarker=False)
# Create a heterogeneous block
block = mt.createRectangle(start=[-5, -2.5],
end=[5, -5.0],
marker=4,
boundaryMarker=10,
area=0.1)
# block = mt.createRectangle(start=[-5, -5], end=[5, -7.5],
# marker=4, boundaryMarker=10, area=0.1)
# Merge geometrical entities
# geom = mt.mergePLC([world, block])
geom = mt.mergePLC([world, block])
pg.show(geom, boundaryMarker=True, savefig='geometry.pdf')
# Create a mesh from the geometry definition
mesh = mt.createMesh(geom, quality=32, area=0.2, smooth=[1, 10])
# pg.show(mesh, savefig='mesh.pdf')
rMap = [[1, SoilR], [4, AnoR]]
# Map conductivity value per region to each cell in the given mesh
R = pg.solver.parseMapToCellArray(rMap, mesh)
# Dirichlet conditions for hydraulic potential
# Create survey measurement scheme
# ertScheme = ert.createERTData(pg.utils.grange(-20, 20, dx=1.0),
# -*- coding: utf-8 -*-
"""
Minimal example of using pygimli to simulate the steady heat equation.
"""
import pygimli as pg
import pygimli.meshtools as mt
# Create geometry definition for the modelling domain
world = mt.createWorld(start=[-20, 0], end=[20, -16], layers=[-2, -8],
worldMarker=False)
# Create a heterogeneous block
block = mt.createRectangle(start=[-6, -3.5], end=[6, -6.0],
marker=4, boundaryMarker=10, area=0.1)
# Merge geometrical entities
geom = mt.mergePLC([world, block])
pg.show(geom, boundaryMarker=True, savefig='geometry.pdf')
# Create a mesh from the geometry definition
mesh = mt.createMesh(geom, quality=33, area=0.2, smooth=[1, 10])
pg.show(mesh, savefig='mesh.pdf')
# $\diverg(a\grad T)=0$ with $T(bottom)=1$, $T(top)=0$
T = pg.solver.solveFiniteElements(mesh,
a=[[1, 1.0], [2, 2.0], [3, 3.0], [4, 0.1]],
uB=[[8, 1.0], [4, 0.0]], verbose=True)
ax, _ = pg.show(mesh, data=T, label='Temperature $T$', cmap="hot_r",
showBoundary=True, savefig='T_field.pdf')
#ax, _ = pg.show(mesh, data=T, label='Temperature $T$', cmap="hot_r")
boundary=0,
paraBoundary=2)
if case == 1:
for depth in (5, 15):
start = plc.createNode(mesh.xmin(), -depth, 0.0)
end = plc.createNode(mesh.xmax(), -depth, 0.0)
plc.createEdge(start, end, marker=1)
for sensor in ertData.sensorPositions():
plc.createNode([sensor.x(), sensor.y() - 0.1])
rect = mt.createRectangle([mesh.xmin(), mesh.ymin()],
[mesh.xmax(), mesh.ymax()],
boundaryMarker=0)
geom = mt.mergePLC([plc, rect])
meshRST = mt.createMesh(geom, quality=34, area=1, smooth=[1, 2])
for cell in meshRST.cells():
cell.setMarker(2)
for boundary in meshRST.boundaries():
boundary.setMarker(0)
pg.show(meshRST)
print(meshRST)
# %%
meshRST.save("paraDomain_%d.bms" % case)
meshERT = mt.appendTriangleBoundary(meshRST,
xbound=500,
m = scheme['m']
n = scheme['n']
scheme['m'] = n
scheme['n'] = m
scheme.set('k', [1 for x in range(scheme.size())])
###############################################################################
# Mesh generation
world = mt.createWorld(start=[-55, 0], end=[105, -80], worldMarker=True)
conductive_anomaly = mt.createCircle(pos=[10, -7], radius=5, marker=2)
polarizable_anomaly = mt.createCircle(pos=[40, -7], radius=5, marker=3)
plc = mt.mergePLC((world, conductive_anomaly, polarizable_anomaly))
# local refinement of mesh near electrodes
for s in scheme.sensors():
plc.createNode(s + [0.0, -0.2])
mesh_coarse = mt.createMesh(plc, quality=33)
# additional refinements
mesh = mesh_coarse.createH2()
pg.show(plc, marker=True)
pg.show(plc, markers=True)
pg.show(mesh)
###############################################################################
# Prepare the model parameterization
# We have two markers here: 1: background 2: circle anomaly
# In this first part we naively combine objects and assign markers to them,
# expecting two regions of concentric rings with markers 1 and 2. Note how the
# outer ring is assigned the marker 0 in the figure, although we specified
# marker=1 for the larger circle? A marker value of 0 is assigned to a region
# if no region marker is found, indicating that the marker for the outer ring
# was overwritten/ignored by the inner circle, which was added later.
circle_outer = mt.createCircle(pos=[0.0, 0.0], radius=3.0, marker=1)
circle_inner = mt.createCircle(
pos=[0.0, 0.0],
radius=1.0,
# area=.3,
boundaryMarker=0,
marker=2)
plc = mt.mergePLC([circle_outer, circle_inner])
ax, cb = pg.show(plc, markers=True)
###############################################################################
# The solution to this problem is the region marker, which defines the marker
# value of the region that it is placed in. By default all region markers are
# assigned the position (0,0,0), thereby overwriting each other (see black dots
# in figure below). If no region marker is present in a region, a marker value
# of 0 is assigned.
fig = ax.get_figure()
for nr, marker in enumerate(plc.regionMarker()):
print('Position marker number {}:'.format(nr + 1), marker.x(), marker.y(),
marker.z())
ax.scatter(marker.x(), marker.y(), s=(2 - nr) * 30, color='k')