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Implement fix, single, background #329

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merged 3 commits into from
Jun 22, 2024
Merged

Implement fix, single, background #329

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a5c3946
Start working on fix/single/background
prisae Jun 21, 2024
f4229de
Make fix,single
prisae Jun 21, 2024
cc8b049
Add background
prisae Jun 22, 2024
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98 changes: 78 additions & 20 deletions emg3d/inversion/pygimli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,17 +84,26 @@ def __init__(self, simulation, markers=None, pgthreads=2):
z=simulation.model.grid.nodes_z,
)

# Set mesh and, if provided, markers.
# Set markers.
if markers is not None:
mesh.setCellMarkers(markers.ravel('F'))
self.markers = markers
else:
self.markes = np.zeros(simulation.model.size, dtype=int)
# Store original properties; required if a region is set to ``background``.
self._model = simulation.model.property_x.copy()
# Store volumes; required if a region is set to ``single``.
self._volumes = simulation.model.grid.cell_volumes.reshape(
self._model.shape, order='F')
# Set mesh.
self.setMesh(mesh)

# Create J, store and set it.
self.J = self.Jacobian(
simulation=self.simulation,
data2pygimli=self.data2pygimli,
data2gimli=self.data2gimli,
data2emg3d=self.data2emg3d,
model2pygimli=self.model2pygimli,
model2gimli=self.model2gimli,
model2emg3d=self.model2emg3d,
)
self.setJacobian(self.J)
Expand All @@ -112,17 +121,16 @@ def response(self, model):
_ = self.simulation.misfit

# Return the responses as pyGIMLi array
return self.data2pygimli(self.simulation.data.synthetic.data)
return self.data2gimli(self.simulation.data.synthetic.data)

def createStartModel(self, dataVals=None):
"""Returns the model from the provided simulation."""
return self.model2pygimli(self.simulation.model.property_x)
return self.model2gimli(self.simulation.model.property_x)

def createJacobian(self, model):
"""Dummy to prevent pyGIMLi from doing it the hard way."""
pass # do nothing

def data2pygimli(self, data):
def data2gimli(self, data):
"""Convert an emg3d data-xarray to a pyGIMLi data array."""
out = data[self.simulation.survey.isfinite]
if np.iscomplexobj(out):
Expand All @@ -141,34 +149,85 @@ def data2emg3d(self, data):
out[self.simulation.survey.isfinite] = data[:ind] + 1j*data[ind:]
return out

def model2pygimli(self, model):
def model2gimli(self, model):
"""Convert an emg3d Model property to a pyGIMLi model array.

This function deals with the regions defined in pyGIMLi.
"""
out = np.empty(model.size)
out[self.mesh().cellMarkers()] = model.ravel('F')

# If the inversion model is smaller than the model, we have to
# take care of the regions.
if len(model) != self.simulation.model.size:

out = np.empty(self.simulation.model.size)
i = 0

for n, v in self.regionProperties().items():
ni = self.markers == n
if v['background'] or v['fix']:
ii = 0
elif v['single']:
ii = 1
out[i] = np.average(model[ni], weights=self._volumes[ni])
else:
ii = np.sum(ni)
out[i:i+ii] = model[ni]
i += ii

out = out[:i]

else:
out = np.empty(model.size)
out[self.mesh().cellMarkers()] = model.ravel('F')

return out

def model2emg3d(self, model):
"""Convert a pyGIMLi model array to an emg3d Model property.

This function deals with the regions defined in pyGIMLi.
"""
out = np.asarray(model[self.mesh().cellMarkers()])
return out.reshape(self.simulation.model.shape, order='F')

# If the inversion model is smaller than the model, we have to
# take care of the regions.
if len(model) != self.simulation.model.size:

out = np.empty(self.simulation.model.shape)
i = 0

for n, v in self.regionProperties().items():
ni = self.markers == n
if v['background']:
ii = 0
out[ni] = self._model[ni]
elif v['fix']:
ii = 0
out[ni] = v['startModel']
elif v['single']:
ii = 1
out[ni] = model[i]
else:
ii = np.sum(ni)
out[ni] = model[i:ii+i]
i += ii

else:
out = np.asarray(model[self.mesh().cellMarkers()]).reshape(
self.simulation.model.shape, order='F')

return out

class Jacobian(pygimli.Matrix):
"""Return Jacobian operator for pyGIMLi(emg3d)."""

def __init__(self, simulation,
data2pygimli, data2emg3d, model2pygimli, model2emg3d):
data2gimli, data2emg3d, model2gimli, model2emg3d):
"""Initiate a new Jacobian instance."""
super().__init__()
self.simulation = simulation
self.data2pygimli = data2pygimli
self.data2gimli = data2gimli
self.data2emg3d = data2emg3d
self.model2pygimli = model2pygimli
self.model2gimli = model2gimli
self.model2emg3d = model2emg3d

def cols(self):
Expand All @@ -182,16 +241,15 @@ def rows(self):
def mult(self, x):
"""Multiply the Jacobian with a vector, Jm."""
jvec = self.simulation.jvec(vector=self.model2emg3d(x))
return self.data2pygimli(jvec)
return self.data2gimli(jvec)

def transMult(self, x):
"""Multiply Jacobian transposed with a vector, Jᵀd = (dJᵀ)ᵀ."""
jtvec = self.simulation.jtvec(self.data2emg3d(x))
return self.model2pygimli(jtvec)
return self.model2gimli(jtvec)

def save(self, *args):
"""There is no save for this pseudo-Jacobian."""
pass


@utils._requires('pygimli')
Expand All @@ -213,12 +271,12 @@ def run(self, dataVals=None, errorVals=None, **kwargs):

# Take data from the survey if not provided.
if dataVals is None:
dataVals = self.fop.data2pygimli(
dataVals = self.fop.data2gimli(
self.fop.simulation.data.observed.data)

# Take the error from the survey if not provided.
if errorVals is None:
std_dev = self.fop.data2pygimli(
std_dev = self.fop.data2gimli(
self.fop.simulation.survey.standard_deviation.data)
errorVals = std_dev / abs(dataVals)

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