def createERTData(elecs, schemeName='none', **kwargs):
""" Simple data creator for compatibility (advanced version in BERT).
Parameters
----------
sounding : bool [False]
Create a 1D VES Schlumberger configuration.
elecs need to be an array with elecs[0] = mn/2 and elecs[1:] = ab/2.
"""
if kwargs.pop('sounding', False):
data = pg.DataContainerERT()
data.setSensors(pg.cat(-elecs[::-1], elecs))
nElecs = len(elecs)
for i in range(nElecs - 1):
data.createFourPointData(i, i, 2 * nElecs - i - 1, nElecs - 1,
nElecs)
return data
if schemeName != "dd":
import pybert as pb # that's bad!!! TODO: remove pybert deps
return pb.createData(elecs, schemeName, **kwargs)
isClosed = kwargs.pop('closed', False)
data = pg.DataContainerERT()
data.setSensors(elecs)
nElecs = len(elecs)
a = []
b = []
m = []
n = []
eb = 0
for i in range(nElecs):
for j in range(eb + 2, nElecs):
ea = i
eb = ea + 1
em = j
en = em + 1
if isClosed:
en = en % nElecs
if en < nElecs and en != ea:
a.append(ea)
b.append(eb)
m.append(em)
n.append(en)
data.resize(len(a))
data.add('a', a)
data.add('b', b)
data.add('m', m)
data.add('n', n)
data.set('valid', np.ones(len(a)))
return data
def main(inv_par, project_conf, bw_surface, max_dist=1.0):
a = bw_surface._bs_surface.eval(0, 0)
b = bw_surface._bs_surface.eval(1, 0)
c = bw_surface._bs_surface.eval(0, 1)
a[2] = 0
b[2] = 0
c[2] = 0
ab = b - a
ac = c - a
tr = np.array([ab, ac, [0, 0, 1]]).T
inv_tr = np.linalg.inv(tr)
if project_conf.method == GenieMethod.ERT:
data = pg.DataContainerERT("input.dat", removeInvalid=False)
else:
data = pg.DataContainer("input.dat",
sensorTokens='s g',
removeInvalid=False)
for i in range(len(data.sensorPositions())):
pos = data.sensorPosition(i)
pos = np.array([pos[0], pos[1], pos[2]])
pos_l = inv_tr @ (pos - a)
try:
new_pos = bw_surface._bs_surface.eval(pos_l[0], pos_l[1])
except IndexError:
pass
else:
if np.linalg.norm(new_pos - pos) <= max_dist:
data.setSensorPosition(i, new_pos)
data.save("input_snapped.dat")
def mesh_from_brep(brep_file, mesh_file, project_conf, inv_par):
if project_conf.method == GenieMethod.ERT:
data = pg.DataContainerERT("input_snapped.dat", removeInvalid=False)
else:
data = pg.DataContainer("input_snapped.dat",
sensorTokens='s g',
removeInvalid=False)
el_pos = []
for i in range(len(data.sensorPositions())):
pos = data.sensorPosition(i)
pos = np.array([pos[0], pos[1], pos[2]])
el_pos.append(pos)
model = gmsh.GeometryOCC("model_name")
compound = model.import_shapes(brep_file, highestDimOnly=False)
points = [model.point(pos).tags[0] for pos in el_pos]
dist = field.distance_nodes(points)
f_distance = field.threshold(dist,
lower_bound=(inv_par.elementSize_d,
inv_par.elementSize_d),
upper_bound=(inv_par.elementSize_D,
inv_par.elementSize_H))
model.set_mesh_step_field(f_distance)
model.mesh_options.CharacteristicLengthMin = 0.1
model.mesh_options.CharacteristicLengthMax = 100
model.make_mesh([compound])
model.write_mesh(mesh_file, gmsh.MeshFormat.msh2)
def createDataVES(ab2, mn2):
""" Utility one-liner to create a BERT datafile for Schlumberger 1D VES
Parameters
----------
ab2: array
Half distance between current electrodes
mn2: float
Half distance between measurement electrodes
Returns
-------
data : DataContainerERT
"""
data = pg.DataContainerERT()
if type(mn2) is float or type(mn2) is int:
mn2 = [mn2]
count = 0
for mn in mn2:
emID = data.createSensor([-mn, 0.0, 0.0])
enID = data.createSensor([mn, 0.0, 0.0])
for x in ab2:
eaID = data.createSensor([-x, 0.0, 0.0])
ebID = data.createSensor([x, 0.0, 0.0])
data.createFourPointData(count, eaID, ebID, emID, enID)
count += 1
data.fitFillSize()
return data
def restore(self):
"""Read data from json infos"""
if os.path.exists(self._name + '.json'):
# Fricking mpl kills locale setting to system default .. this went
# horrible wrong for german 'decimal_point': ','
pg.checkAndFixLocaleDecimal_point(verbose=False)
try:
with open(self._name + '.json') as file:
self.info = json.load(file)
# if len(self.info['type']) != 1:
# pg.error('only single return caches supported for now.')
#pg._y(pg.pf(self.info))
if self.info['type'] == 'DataContainerERT':
self._value = pg.DataContainerERT(self.info['file'],
removeInvalid=False)
# print(self._value)
elif self.info['type'] == 'RVector':
self._value = pg.Vector()
self._value.load(self.info['file'], format=pg.core.Binary)
elif self.info['type'] == 'Mesh':
pg.tic()
self._value = pg.Mesh()
self._value.loadBinaryV2(self.info['file'] + '.bms')
pg.debug("Restoring cache took:", pg.dur(), "s")
elif self.info['type'] == 'ndarray':
self._value = np.load(self.info['file'] + '.npy',
allow_pickle=True)
elif self.info['type'] == 'Cm05Matrix':
self._value = pg.matrix.Cm05Matrix(self.info['file'])
elif self.info['type'] == 'GeostatisticConstraintsMatrix':
self._value = pg.matrix.GeostatisticConstraintsMatrix(
self.info['file'])
else:
self._value = np.load(self.info['file'] + '.npy',
allow_pickle=True)
if self.value is not None:
self.info['restored'] = self.info['restored'] + 1
self.updateCacheInfo()
pg.info('Cache {3} restored ({1}s x {0}): {2}'.\
format(self.info['restored'],
round(self.info['dur'], 1),
self._name, self.info['codeinfo']))
else:
# default try numpy
pg.warn('Could not restore cache of type {0}.'.format(self.info['type']))
pg.debug("Restoring cache took:", pg.dur(), "s")
except Exception as e:
import traceback
traceback.print_exc(file=sys.stdout)
print(self.info)
pg.error('Cache restoring failed.')
def prepare_old(electrode_groups, measurements):
"""
Prepares data for GIMLI inversion.
:param electrode_groups:
:param measurements:
:return:
"""
el_offset = 0
electrodes = []
a = pd.Series()
b = pd.Series()
m = pd.Series()
n = pd.Series()
i = pd.Series()
u = pd.Series()
err = pd.Series()
rhoa = pd.Series()
for ms in measurements:
if ms.data is None:
continue
d = ms.data["data"]
for e_id in range(ms.el_start, ms.el_stop+1):
e = _find_el(electrode_groups, e_id)
if e is None:
print("chyba")
electrodes.append(e)
a = a.append(d["ca"] + el_offset, ignore_index=True)
b = b.append(d["cb"] + el_offset, ignore_index=True)
m = m.append(d["pa"] + el_offset, ignore_index=True)
n = n.append(d["pb"] + el_offset, ignore_index=True)
i = i.append(d["I"], ignore_index=True)
u = u.append(d["V"], ignore_index=True)
err = err.append(d["std"], ignore_index=True)
rhoa = rhoa.append(d["AppRes"], ignore_index=True)
el_offset += ms.el_stop - ms.el_start + 1
data = pg.DataContainerERT()
for e in electrodes:
data.createSensor([e.x, e.y, e.z])
data.resize(len(a))
data.set('a', a)
data.set('b', b)
data.set('m', m)
data.set('n', n)
data.set('i', i)
data.set('u', u)
data.set('err', err)
data.set('rhoa', rhoa)
data.markValid(data('rhoa') > 0)
return data
def checkData(self, data=None):
"""Return data from container.
THINKABOUT: Data will be changed, or should the manager keep a copy?
"""
data = data or pg.DataContainerERT(self.data)
if isinstance(data, pg.DataContainer):
if not data.allNonZero('k'):
pg.warn("Data file contains no geometric factors (token='k').")
data['k'] = createGeometricFactors(data, verbose=True)
if self.fop.complex():
if not data.haveData('rhoa'):
pg.critical('Datacontainer have no "rhoa" values.')
if not data.haveData('ip'):
pg.critical('Datacontainer have no "ip" values.')
# pg.warn('check sign of phases')
rhoa = data['rhoa']
phia = -data['ip'] / 1000 # 'ip' is defined for neg mrad.
# we should think about some 'phia' in rad
return pg.utils.squeezeComplex(pg.utils.toComplex(rhoa, phia))
else:
if not data.haveData('rhoa'):
if data.allNonZero('r'):
pg.info("Creating apparent resistivies from "
"impedences rhoa = r * k")
data['rhoa'] = data['r'] * data['k']
elif data.allNonZero('u') and data.allNonZero('i'):
pg.info("Creating apparent resistivies from "
"voltage and currrent rhoa = u/i * k")
data['rhoa'] = data['u'] / data['i'] * data['k']
else:
pg.critical("Datacontainer have neither: "
"apparent resistivies 'rhoa', "
"or impedances 'r', "
"or voltage 'u' along with current 'i'.")
if any(data['rhoa'] < 0) and \
isinstance(self.inv.dataTrans, pg.core.TransLog):
print(pg.find(data['rhoa'] < 0))
print(data['rhoa'][data['rhoa'] < 0])
pg.critical("Found negative apparent resistivities. "
"These can't be processed with logarithmic "
"data transformation. You should consider to "
"filter them out using "
"data.remove(data['rhoa'] < 0).")
return data['rhoa']
return data
def createERTData(elecs, schemeName='none', **kwargs):
""" Simple data creator for compatibility (advanced version in BERT)."""
if schemeName is not "dd":
import pybert as pb # that's bad!!! TODO: remove pybert deps
return pb.createData(elecs, schemeName, **kwargs)
if isinstance(elecs, pg.RVector):
sPos = []
for e in elecs:
sPos.append(pg.RVector3(e, 0., 0.))
elecs = sPos
isClosed = kwargs.pop('closed', False)
data = pg.DataContainerERT()
data.registerSensorIndex('a')
data.registerSensorIndex('b')
data.registerSensorIndex('m')
data.registerSensorIndex('n')
data.setSensorPositions(elecs)
nElecs = len(elecs)
a = []
b = []
m = []
n = []
eb = 0
for i in range(nElecs):
for j in range(eb + 2, nElecs):
ea = i
eb = ea + 1
em = j
en = em + 1
if isClosed:
en = en % nElecs
if en < nElecs and en != ea:
a.append(ea)
b.append(eb)
m.append(em)
n.append(en)
data.resize(len(a))
data.add('a', a)
data.add('b', b)
data.add('m', m)
data.add('n', n)
data.set('valid', np.ones(len(a)))
return data
def test_HashData(self):
d1 = pg.DataContainerERT()
d2 = pg.DataContainerERT()
self.assertEqual(d1.hash(), d2.hash())
d1.createSensor([1.0, 0.0])
d2.createSensor([2.0, 0.0])
self.assertFalse(d1.hash() == d2.hash())
d2.setSensor(0, [1.0, 0.0])
self.assertTrue(d1.hash() == d2.hash())
d1.resize(10)
d2.resize(12)
d1.add('a', pg.Vector(d1.size(), 1.0))
d2.add('a', pg.Vector(d2.size(), 1.0))
self.assertFalse(d1.hash() == d2.hash())
d2.resize(10)
self.assertTrue(d1.hash() == d2.hash())
d2('a')[3] = 2.0
self.assertFalse(d1.hash() == d2.hash())
d2('a')[3] = 1.0
self.assertTrue(d1.hash() == d2.hash())
def createMesh(geom, topo, sfile, Q):
scheme = pg.DataContainerERT()
scheme.setSensorPositions(topo)
srv = pd.read_csv(sfile, sep='\t', header=None)
for i, elec in enumerate("abmn"):
scheme[elec] = srv.values[:, i + 1].astype(np.int) - 1
for p in scheme.sensors():
geom.createNode(p)
geom.createNode(p - [0, 0.1])
mesh = mt.createMesh(geom, quality=Q)
return scheme, mesh
def export_to_pygimli_scheme(self, norrec='nor', timestep=None):
"""Export the data into a pygimili.DataContainerERT object.
For now, do NOT set any sensor positions
Parameters
----------
Returns
-------
"""
logger.info('Exporting to pygimli DataContainer')
logger.info('{} data will be exported'.format(norrec))
if timestep is None:
logger.info('No timestep selection is applied')
else:
logger.info('timestep(s) {} will be used'.format(timestep))
import pygimli as pg
data_container = pg.DataContainerERT()
query = ' '.join((
'norrec == "{}"'.format(norrec),
))
if timestep is not None:
query += ' and timestep=="{}"'.format(timestep)
logger.debug('Query: {}'.format(query))
subdata = self.data.query(query)
assert subdata.shape[0] != 0
data_container['a'] = subdata['a']
data_container['b'] = subdata['b']
data_container['m'] = subdata['m']
data_container['n'] = subdata['n']
data_container['r'] = subdata['r']
if 'k' in subdata.columns:
data_container['k'] = subdata['k']
if 'rho_a' in subdata.columns:
data_container['rhoa'] = subdata['rho_a']
return data_container
def createElectrodes(self,
nElectrodes=24,
electrodeSpacing=1,
sensorList=None):
self.data_ = pg.DataContainerERT()
if sensorList is not None:
for p in sensorList:
if isinstance(p, float):
self.data_.createSensor((p, 0.))
else:
self.data_.createSensor(p)
else:
for i in range(nElectrodes):
self.data_.createSensor(
pg.Pos(float(i) * electrodeSpacing, 0.0))
self.nElectrodes_ = self.data_.sensorCount()
def create_data_containerERT(self, measurements=numpy.array([[0, 1, 2, 3], ]), # Dipole-Dipole
scheme_type="abmn", verbose=False):
"""
creates the scheme from the previous 4 aruco markers detected
Args:
measurements: Dipole-Dipole
scheme_type: assign the type of electrode to the aruco
verbose:
Returns:
"""
scheme = pg.DataContainerERT()
scheme.setSensorPositions(self.electrode)
for i, elec in enumerate(scheme_type):
scheme[elec] = measurements[:, i]
scheme["k"] = ert.createGeometricFactors(scheme, verbose=verbose)
self.scheme = scheme
return self.scheme
def create(self,
nElectrodes=24,
electrodeSpacing=1,
sensorList=None,
**kwargs):
"""
"""
self.createElectrodes(nElectrodes, electrodeSpacing, sensorList)
self.createData(**kwargs)
if self.addInverse_:
out = pg.DataContainerERT(self.data_)
self.setInverse(not self.inverse_)
self.createData(**kwargs)
self.data_.add(out)
self.data_.removeInvalid()
self.data_.sortSensorsIndex()
if kwargs.values():
print("Warning! DataSchemeBase::create has unhandled arguments")
print(kwargs)
return self.data_
def test_Int64Problem(self):
data = pg.DataContainerERT()
pos = np.arange(4, dtype=np.int)
data.createFourPointData(0, pos[0], pos[1], pos[2], pos[3])
pos = np.arange(4, dtype=np.int32)
data.createFourPointData(1, pos[0], pos[1], pos[2], pos[3])
pos = np.arange(4, dtype=np.int64)
data.createFourPointData(2, pos[0], pos[1], pos[2], pos[3])
pos = np.arange(4, dtype=np.float)
data.createFourPointData(3, pos[0], pos[1], pos[2], pos[3])
pos = np.arange(4, dtype=np.float32)
data.createFourPointData(4, pos[0], pos[1], pos[2], pos[3])
pos = np.arange(4, dtype=np.float64)
data.createFourPointData(5, pos[0], pos[1], pos[2], pos[3])
pos = np.arange(4)
data.createFourPointData(6, pos[0], pos[1], pos[2], pos[3])
pos = range(4)
data.addFourPointData(pos[0], pos[1], pos[2], pos[3])
#print(data('a'), data('b'), data('m'), data('n'))
self.assertEqual(sum(data('a')), 8 * 0)
self.assertEqual(sum(data('b')), 8 * 1)
self.assertEqual(sum(data('m')), 8 * 2)
self.assertEqual(sum(data('n')), 8 * 3)
def createData(elecs, schemeName='none', **kwargs):
""" Utility one-liner to create a BERT datafile
Parameters
----------
elecs : int | list[pos] | array(x)
Number of electrodes or electrode positions or x-positions
schemeName : str ['none']
Name of the configuration. If you provide an unknown scheme name, all
known schemes ['wa', 'wb', 'pp', 'pd', 'dd', 'slm', 'hw', 'gr'] listed.
**kwargs :
Arguments that will be forwarded to the scheme generator.
* inverse : bool
interchange AB MN with MN AB
* reciprocity : bool
interchange AB MN with BA NM
* addInverse : bool
add additional inverse measurements
* spacing : float [1]
electrode spacing in meters
* closed : bool
Close the chain. Measure from the end of the array to the first
electrode.
Returns
-------
data : DataContainerERT
Examples
--------
>>> import matplotlib.pyplot as plt
>>> from pygimli.physics import ert
>>>
>>> schemes = ['wa', 'wb', 'pp', 'pd', 'dd', 'slm', 'hw', 'gr']
>>> fig, ax = plt.subplots(3,3)
>>>
>>> for i, schemeName in enumerate(schemes):
... s = ert.createData(elecs=41, schemeName=schemeName)
... k = ert.geometricFactors(s)
... _ = ert.show(s, vals=k, ax=ax.flat[i], label='k - ' + schemeName)
>>>
>>> plt.show()
"""
if kwargs.pop('sounding', False):
data = pg.DataContainerERT()
data.setSensors(pg.cat(-elecs[::-1], elecs))
nElecs = len(elecs)
for i in range(nElecs - 1):
data.createFourPointData(i, i, 2 * nElecs - i - 1, nElecs - 1,
nElecs)
return data
mg = DataSchemeManager()
if schemeName == "none":
pg.error('argument "schemeName" not set. Valid schemeNames are:')
for i in mg.schemes():
print(i, "scheme: " + mg.scheme(i).prefix)
scheme = mg.scheme(schemeName)
scheme.setInverse(kwargs.pop('inverse', False))
scheme.addInverse(kwargs.pop('addInverse', False))
scheme._closed = kwargs.pop('closed', False)
if isinstance(elecs, int):
data = scheme.create(nElectrodes=elecs,
electrodeSpacing=kwargs.pop('spacing', 1),
**kwargs)
elif hasattr(elecs, '__iter__'):
if isinstance(elecs[0], float) or isinstance(elecs[0], int):
data = scheme.create(nElectrodes=len(elecs), **kwargs)
data.setSensors(elecs)
else:
data = scheme.create(sensorList=elecs, **kwargs)
else:
print(elecs)
pg.critical("Can't interpret elecs")
return data
def importRes2dInv(filename, verbose=False, return_header=False):
"""Read res2dinv format
Parameters
----------
filename : str
verbose : bool [False]
return_header : bool [False]
Returns
-------
pg.DataContainerERT and (in case of return_header=True)
header dictionary
Format
------
str - title
float - unit spacing [m]
int - Array Number (1-Wenner, 3-Dipole-dipole atm only)
int - Number of Datapoints
float - x-location given in terms of first electrode
use 1 if mid-point location is given
int - 0 for no IP, use 1 if IP present
str - Phase Angle if IP present
str - mrad if IP present
0,90.0 - if IP present
dataBody
"""
def getNonEmptyRow(i, comment='#'):
s = next(i)
while s[0] is comment:
s = next(i)
return s.split('\r\n')[0]
# def getNonEmptyRow(...)
with open(filename, 'r') as fi:
content = fi.readlines()
it = iter(content)
header = {}
header['name'] = getNonEmptyRow(it, comment=';')
header['spacing'] = float(getNonEmptyRow(it, comment=';'))
typrow = getNonEmptyRow(it, comment=';')
typ = int(typrow.rstrip('\n').rstrip('R').rstrip('L'))
if typ == 11:
# independent electrode positions
header['subtype'] = int(getNonEmptyRow(it, comment=';'))
header['dummy'] = getNonEmptyRow(it, comment=';')
isR = int(getNonEmptyRow(it, comment=';'))
nData = int(getNonEmptyRow(it, comment=';'))
xLoc = float(getNonEmptyRow(it, comment=';'))
hasIP = int(getNonEmptyRow(it, comment=';'))
if hasIP:
header['ipQuantity'] = getNonEmptyRow(it, comment=';')
header['ipUnit'] = getNonEmptyRow(it, comment=';')
header['ipData'] = getNonEmptyRow(it, comment=';')
ipline = header['ipData'].rstrip('\n').rstrip('\r').split(' ')
if len(ipline) > 2: # obviously spectral data?
header['ipNumGates'] = int(ipline[0])
header['ipDelay'] = float(ipline[1])
header['onTime'] = float(ipline[-2])
header['offTime'] = float(ipline[-1])
header['ipDT'] = np.array(ipline[2:-2], dtype=float)
header['ipGateT'] = np.cumsum(np.hstack((header['ipDelay'],
header['ipDT'])))
data = pg.DataContainerERT()
data.resize(nData)
if typ == 9 or typ == 10:
raise Exception("Don't know how to read:" + str(typ))
if typ == 11 or typ == 12 or typ == 13: # mixed array
res = pg.Vector(nData, 0.0)
ip = pg.Vector(nData, 0.0)
specIP = []
for i in range(nData):
vals = getNonEmptyRow(it, comment=';').replace(',', ' ').split()
# row starts with 4
if int(vals[0]) == 4:
eaID = data.createSensor(pg.Pos(float(vals[1]),
float(vals[2])))
ebID = data.createSensor(pg.Pos(float(vals[3]),
float(vals[4])))
emID = data.createSensor(pg.Pos(float(vals[5]),
float(vals[6])))
enID = data.createSensor(pg.Pos(float(vals[7]),
float(vals[8])))
elif int(vals[0]) == 3:
eaID = data.createSensor(pg.Pos(float(vals[1]),
float(vals[2])))
ebID = -1
emID = data.createSensor(pg.Pos(float(vals[3]),
float(vals[4])))
enID = data.createSensor(pg.Pos(float(vals[5]),
float(vals[6])))
elif int(vals[0]) == 2:
eaID = data.createSensor(pg.Pos(float(vals[1]),
float(vals[2])))
ebID = -1
emID = data.createSensor(pg.Pos(float(vals[3]),
float(vals[4])))
enID = -1
else:
raise Exception('dont know how to handle row', vals[0])
res[i] = float(vals[int(vals[0])*2+1])
if hasIP:
# ip[i] = float(vals[int(vals[0])*2+2])
ipCol = int(vals[0])*2+2
ip[i] = float(vals[ipCol])
if 'ipNumGates' in header:
specIP.append(vals[ipCol:])
data.createFourPointData(i, eaID, ebID, emID, enID)
if isR:
data.set('r', res)
else:
data.set('rhoa', res)
if hasIP:
data.set('ip', ip)
if 'ipNumGates' in header:
A = np.array(specIP, dtype=float)
A[A > 1000] = -999
A[A < -1000] = -999
for i in range(header['ipNumGates']):
data.set('ip'+str(i+1), A[:, i])
data.sortSensorsX()
data.sortSensorsIndex()
if return_header:
return data, header
else:
return data
# amount of values per collumn per typ
nntyp = [0, 3, 3, 4, 3, 3, 4, 4, 3, 0, 0, 8, 10]
nn = nntyp[typ] + hasIP
# dataBody = pg.Matrix(nn, nData)
dataBody = np.zeros((nn, nData))
for i in range(nData):
vals = getNonEmptyRow(it, comment=';').replace(',', ' ').split()
dataBody[:, i] = np.array(vals, dtype=float)
# for j in range(nn):
# dataBody[j][i] = float(vals[j])
XX = dataBody[0]
EL = dataBody[1]
SP = pg.Vector(nData, 1.0)
if nn - hasIP == 4:
SP = dataBody[2]
AA = None
BB = None
NN = None
MM = None
if typ == 1: # Wenner
AA = XX - xLoc * EL * 1.5
MM = AA + EL
NN = MM + EL
BB = NN + EL
elif typ == 2: # Pole-Pole
AA = XX - xLoc * EL * 0.5
MM = AA + EL
elif typ == 3: # Dipole-Dipole
AA = XX - xLoc * EL * (SP / 2. + 1.)
BB = AA + EL
MM = BB + SP * EL
NN = MM + EL
pass
elif typ == 3: # Dipole-Dipole
AA = XX - xLoc * EL * (SP / 2. + 1.)
BB = AA + EL
MM = BB + SP * EL
NN = MM + EL
elif typ == 4: # WENNER-BETA
AA = XX - xLoc * EL * 1.5
BB = AA + EL
MM = BB + EL
NN = MM + EL
elif typ == 5: # WENNER-GAMMA
AA = XX - xLoc * EL * 1.5
MM = AA + EL
BB = MM + EL
NN = BB + EL
elif typ == 6: # POLE-DIPOLE
AA = XX - xLoc * SP * EL - (SP - 1.) * (SP < 0.) * EL
MM = AA + SP * EL
NN = MM + pg.sign(SP) * EL
elif typ == 7: # SCHLUMBERGER
AA = XX - xLoc * EL * (SP + 0.5)
MM = AA + SP * EL
NN = MM + EL
BB = NN + SP * EL
else:
raise Exception('Datatype ' + str(typ) + ' not yet suppoted')
for i in range(len(AA)):
if AA is not None:
eaID = data.createSensor(pg.Pos(AA[i], 0.0))
else:
eaID = -1
if BB is not None:
ebID = data.createSensor(pg.Pos(BB[i], 0.0))
else:
ebID = -1
if MM is not None:
emID = data.createSensor(pg.Pos(MM[i], 0.0))
else:
emID = -1
if NN is not None:
enID = data.createSensor(pg.Pos(NN[i], 0.0))
else:
enID = -1
data.createFourPointData(i, eaID, ebID, emID, enID)
data.set('rhoa', dataBody[nn - hasIP - 1])
if hasIP:
data.set('ip', dataBody[nn - 1])
data.sortSensorsX()
if return_header:
return data, header
else:
return data
def prepare(electrode_groups, measurements, mesh_cut_tool_param=None, masked_meas_lines=None):
"""
Prepares data for GIMLI inversion.
:param electrode_groups:
:param measurements:
:return:
"""
#el_offset = 0
electrodes = []
sensor_ids = []
a = pd.Series()
b = pd.Series()
m = pd.Series()
n = pd.Series()
i = pd.Series()
u = pd.Series()
err = pd.Series()
rhoa = pd.Series()
meas_info = MeasurementsInfo()
data = pg.DataContainerERT()
if mesh_cut_tool_param is not None:
base_point, gen_vecs = cut_point_cloud.cut_tool_to_gen_vecs(mesh_cut_tool_param, only_inv=True)
inv_tr_mat = cut_point_cloud.inv_tr(gen_vecs)
for ms in measurements:
if ms.data is None:
continue
d = ms.data["data"]
ind_to_rem = set()
# remove masked lines from measurements
if masked_meas_lines is not None:
if ms.number in masked_meas_lines:
ind_to_rem.update({i for i, b in enumerate(masked_meas_lines[ms.number][:d.shape[0]]) if b})
# remove measurements outside inversion region
if mesh_cut_tool_param is not None:
for j in range(d.shape[0]):
for col in ["ca", "cb", "pa", "pb"]:
e = _find_el(electrode_groups, ms.meas_map[d[col][j]])
nl = cut_point_cloud.tr_to_local(base_point, inv_tr_mat, np.array([e.x, e.y, e.z]))
if not (0 <= nl[0] <= 1 and 0 <= nl[1] <= 1 and 0 <= nl[2] <= 1):
ind_to_rem.add(j)
break
d = d.drop(d.index[list(ind_to_rem)])
meas_map_sensor = {}
for meas_id, e_id in ms.meas_map.items():
# todo: prepsat nejak inteligentneji
if (meas_id not in [v for v in d["ca"]]) and (meas_id not in [v for v in d["cb"]]) and (meas_id not in [v for v in d["pa"]]) and (meas_id not in [v for v in d["pb"]]):
continue
ind = -1
for j, e in enumerate(electrodes):
if e.id == e_id:
ind = j
break
if ind < 0:
e = _find_el(electrode_groups, e_id)
if e is None:
print("chyba")
ind = len(electrodes)
electrodes.append(e)
s_id = data.createSensor([e.x, e.y, e.z])
sensor_ids.append(s_id)
meas_map_sensor[meas_id] = sensor_ids[ind]
a = a.append(pd.Series([meas_map_sensor[v] for v in d["ca"]]), ignore_index=True)
b = b.append(pd.Series([meas_map_sensor[v] for v in d["cb"]]), ignore_index=True)
m = m.append(pd.Series([meas_map_sensor[v] for v in d["pa"]]), ignore_index=True)
n = n.append(pd.Series([meas_map_sensor[v] for v in d["pb"]]), ignore_index=True)
i = i.append(d["I"], ignore_index=True)
u = u.append(d["V"], ignore_index=True)
err = err.append(d["std"], ignore_index=True)
rhoa = rhoa.append(d["AppRes"], ignore_index=True)
#el_offset += len(ms.meas_map)
for j in d.index:
meas_info.items.append(MeasurementInfoItem(measurement_number=ms.number,
ca=d["ca"][j], cb=d["cb"][j], pa=d["pa"][j], pb=d["pb"][j],
I=d["I"][j], V=d["V"][j], AppRes=d["AppRes"][j], std=d["std"][j],
inv_ca=meas_map_sensor[d["ca"][j]], inv_cb=meas_map_sensor[d["cb"][j]], inv_pa=meas_map_sensor[d["pa"][j]], inv_pb=meas_map_sensor[d["pb"][j]]))
data.resize(len(a))
data.set('a', a)
data.set('b', b)
data.set('m', m)
data.set('n', n)
data.set('i', i)
data.set('u', u)
data.set('err', err)
data.set('rhoa', rhoa)
#data.markValid(data('rhoa') > 0)
# zakomentovano kvuli analyse_measurement_dialog.py
return data, meas_info
def prepare_old2(electrode_groups, measurements):
"""
Prepares data for GIMLI inversion.
:param electrode_groups:
:param measurements:
:return:
"""
#el_offset = 0
electrodes = []
a = pd.Series()
b = pd.Series()
m = pd.Series()
n = pd.Series()
i = pd.Series()
u = pd.Series()
err = pd.Series()
rhoa = pd.Series()
for ms in measurements:
if ms.data is None:
continue
d = ms.data["data"]
meas_map_sensor = {}
for meas_id, e_id in ms.meas_map.items():
ind = -1
for j, e in enumerate(electrodes):
if e.id == e_id:
ind = j
break
if ind < 0:
e = _find_el(electrode_groups, e_id)
if e is None:
print("chyba")
ind = len(electrodes)
electrodes.append(e)
meas_map_sensor[meas_id] = ind
a = a.append(pd.Series([meas_map_sensor[v] for v in d["ca"]]), ignore_index=True)
b = b.append(pd.Series([meas_map_sensor[v] for v in d["cb"]]), ignore_index=True)
m = m.append(pd.Series([meas_map_sensor[v] for v in d["pa"]]), ignore_index=True)
n = n.append(pd.Series([meas_map_sensor[v] for v in d["pb"]]), ignore_index=True)
i = i.append(d["I"], ignore_index=True)
u = u.append(d["V"], ignore_index=True)
err = err.append(d["std"], ignore_index=True)
rhoa = rhoa.append(d["AppRes"], ignore_index=True)
#el_offset += len(ms.meas_map)
data = pg.DataContainerERT()
for e in electrodes:
data.createSensor([e.x, e.y, e.z])
data.resize(len(a))
data.set('a', a)
data.set('b', b)
data.set('m', m)
data.set('n', n)
data.set('i', i)
data.set('u', u)
data.set('err', err)
data.set('rhoa', rhoa)
data.markValid(data('rhoa') > 0)
return data
def inv_ert(inversion_conf, project_conf):
inv_par = inversion_conf.inversion_param
cut_par = inversion_conf.mesh_cut_tool_param
remove_old_files()
ret, bw_surface = prepare(cut_par, inv_par, project_conf)
if not ret:
return
#return
# snap electrodes
print()
print_headline("Snapping electrodes")
if inv_par.meshFrom == MeshFrom.SURFACE_CLOUD:
snap_surf.main(inv_par,
project_conf,
bw_surface,
max_dist=inv_par.snapDistance)
else:
snap_electrodes.main(inv_par,
project_conf,
max_dist=inv_par.snapDistance)
#ball_mesh("inv_mesh.msh", "inv_mesh2.msh", [-622342, -1128822, 22], 5.0)
#return
print()
print_headline("Creating inversion mesh")
mesh_from_brep("inv_mesh_tmp.brep", "inv_mesh_tmp.msh2", project_conf,
inv_par)
print()
print_headline("Modify mesh")
modify_mesh("inv_mesh_tmp.msh2", "inv_mesh.msh", cut_par)
#if inv_par.meshFrom == MeshFrom.SURFACE_CLOUD:
print()
print_headline("Snapping electrodes final")
snap_electrodes.main(inv_par,
project_conf,
max_dist=inv_par.snapDistance,
final=True)
print()
print_headline("Inversion")
# res = pb.Resistivity("input.dat")
# res.invert()
# np.savetxt('resistivity.vector', res.resistivity)
# return
# load data file
data = pg.DataContainerERT("input_snapped.dat", removeInvalid=False)
#data = pg.DataContainerERT("ldp2.dat")
#print(data.size())
#print(data("a"))
#print(data.sensorIdx())
#return
# mark all data valid
#data.markValid(data('rhoa') > 0)
#data.markValid(data('rhoa') <= 0)
#data.markValid(data('u') > 0)
# k, rhoa
#inv_par.k_ones = True
if inv_par.k_ones:
data.set("k", np.ones(data.size()))
else:
data.set("k", misc.geometricFactors(data))
#data.set("err", pb.Resistivity.estimateError(data, absoluteUError=0.0001, relativeError=0.03))
#data.set("k", np.ones(data.size()))
#data.set("k", misc.geometricFactors(data))
data.set("rhoa", data("u") / data("i") * data("k"))
tolerance = 1e-12
#data.markValid(np.abs(data('rhoa')) > tolerance)
data.markValid(data('rhoa') > tolerance)
data.markInvalid(data('rhoa') <= tolerance) # udelat poradne
# remove invalid data
oldsize = data.size()
data.removeInvalid()
newsize = data.size()
if newsize < oldsize:
print('Removed ' + str(oldsize - newsize) + ' values.')
if not data.allNonZero('rhoa'):
print("No or partial rhoa values.")
return
# check, compute error
# if data.allNonZero('err'):
# error = data('err')
# else:
# print("estimate data error")
# error = inv_par.relativeError + inv_par.absoluteError / data('rhoa')
error = data('err')
min_err = 0.0005
for i in range(data.size()):
if error[i] < min_err:
error[i] = min_err
# create FOP
fop = pg.core.DCSRMultiElectrodeModelling(verbose=inv_par.verbose)
fop.setThreadCount(psutil.cpu_count(logical=False))
fop.setData(data)
# create Inv
inv = pg.core.RInversion(verbose=inv_par.verbose, dosave=False)
# variables tD, tM are needed to prevent destruct objects
tM = pg.core.RTransLogLU(inv_par.minModel, inv_par.maxModel)
if inv_par.data_log:
tD = pg.core.RTransLog()
inv.setTransData(tD)
inv.setTransModel(tM)
inv.setForwardOperator(fop)
# mesh
mesh_file = "inv_mesh.msh"
#mesh_file = inv_par.meshFile
if mesh_file == "":
depth = inv_par.depth
if depth is None:
depth = pg.core.DCParaDepth(data)
poly = pg.meshtools.createParaMeshPLC(
data.sensorPositions(),
paraDepth=depth,
paraDX=inv_par.paraDX,
paraMaxCellSize=inv_par.maxCellArea,
paraBoundary=2,
boundary=2)
if inv_par.verbose:
print("creating mesh...")
mesh = pg.meshtools.createMesh(poly,
quality=inv_par.quality,
smooth=(1, 10))
else:
mesh = pg.Mesh(pg.load(mesh_file))
mesh.createNeighbourInfos()
if inv_par.verbose:
print(mesh)
sys.stdout.flush() # flush before multithreading
fop.setMesh(mesh)
fop.regionManager().setConstraintType(1)
# print(fop.regionManager().regionCount())
# print(fop.regionManager().paraDomain().cellMarkers())
# pg.show(mesh, data=mesh.cellMarkers())
# print(fop.regionManager().region(1).cellMarkers())
# return
if not inv_par.omitBackground:
if fop.regionManager().regionCount() > 1:
fop.regionManager().region(1).setBackground(True)
if mesh_file == "":
fop.createRefinedForwardMesh(True, False)
else:
fop.createRefinedForwardMesh(inv_par.refineMesh, inv_par.refineP2)
paraDomain = fop.regionManager().paraDomain()
#paraDomain = fop.regionManager().mesh()
inv.setForwardOperator(fop) # necessary?
# in_ball = find_markers_in_ball(paraDomain, [-622342, -1128822, 22], 5.0)
# print(pg.median(data('rhoa')))
# pc = fop.regionManager().parameterCount()
# x = pg.RVector(pc, 10000.0)
# for i, m in enumerate(paraDomain.cellMarkers()):
# if m in in_ball:
# x[i] = 1000.0
# resp = fop.response(x)
# print(resp)
#return
# inversion parameters
inv.setData(data('rhoa'))
#inv.setData(resp)
inv.setRelativeError(error)
#inv.setRelativeError(pg.RVector(data.size(), 0.03))
fop.regionManager().setZWeight(inv_par.zWeight)
inv.setLambda(inv_par.lam)
inv.setOptimizeLambda(inv_par.optimizeLambda)
inv.setMaxIter(inv_par.maxIter)
inv.setRobustData(inv_par.robustData)
inv.setBlockyModel(inv_par.blockyModel)
inv.setRecalcJacobian(inv_par.recalcJacobian)
pc = fop.regionManager().parameterCount()
if inv_par.k_ones:
# hack of gimli hack
v = pg.Vector(
pg.Vector(
pc,
pg.core.median(data('rhoa') * misc.geometricFactors(data))))
v[0] += tolerance * 2
startModel = v
else:
startModel = pg.Vector(pc, pg.core.median(data('rhoa')))
#startModel = pg.RVector(pc, 2000.0)
inv.setModel(startModel)
# Run the inversion
sys.stdout.flush() # flush before multithreading
model = inv.run()
resistivity = model[paraDomain.cellMarkers()]
np.savetxt('resistivity.vector', resistivity)
paraDomain.addData('Resistivity', resistivity)
#paraDomain.addExportData('Resistivity (log10)', np.log10(resistivity))
#paraDomain.addExportData('Coverage', coverageDC(fop, inv, paraDomain))
#paraDomain.exportVTK('resistivity')
# output in local coordinates
if inv_par.local_coord:
base_point, gen_vecs = cut_point_cloud.cut_tool_to_gen_vecs(cut_par)
localparaDomain = pg.Mesh(paraDomain)
localparaDomain.translate(pg.RVector3(-base_point))
localparaDomain.rotate(
pg.RVector3(0, 0, -math.atan2(gen_vecs[0][1], gen_vecs[0][0])))
localparaDomain.exportVTK('resistivity')
else:
paraDomain.exportVTK('resistivity')
# measurements on model
print()
print_headline("Measurements on model")
with open("measurements_info.json") as fd:
meas_info = MeasurementsInfo.deserialize(json.load(fd))
resp = fop.response(resistivity)
# hack of gimli hack
v = pg.Vector(startModel)
v[0] += tolerance * 2
resp_start = fop.response(v)
map = {}
map_start = {}
map_appres_gimli = {}
for i in range(data.size()):
map[(data("a")[i], data("b")[i], data("m")[i], data("n")[i])] = resp[i]
map_start[(data("a")[i], data("b")[i], data("m")[i],
data("n")[i])] = resp_start[i]
map_appres_gimli[(data("a")[i], data("b")[i], data("m")[i],
data("n")[i])] = data('rhoa')[i]
meas_model_info = MeasurementsModelInfo()
with open("measurements_model.txt", "w") as fd:
fd.write(
"meas_number ca cb pa pb I[A] V[V] AppRes[Ohmm] std AppResGimli[Ohmm] AppResModel[Ohmm] ratio AppResStartModel[Ohmm] start_ratio\n"
)
fd.write(
"-------------------------------------------------------------------------------------------------------------------------------------------------\n"
)
for item in meas_info.items:
k = (item.inv_ca, item.inv_cb, item.inv_pa, item.inv_pb)
if k in map:
m_on_m = "{:17.2f} {:17.2f} {:7.2f} {:22.2f} {:7.2f}".format(
map_appres_gimli[k], map[k], map[k] / map_appres_gimli[k],
map_start[k], map_start[k] / map_appres_gimli[k])
meas_model_info.items.append(
MeasurementModelInfoItem(
measurement_number=item.measurement_number,
ca=item.ca,
cb=item.cb,
pa=item.pa,
pb=item.pb,
app_res_model=map[k],
app_res_start_model=map_start[k]))
else:
m_on_m = " not used"
fd.write(
"{:11} {:3} {:3} {:3} {:3} {:8.6f} {:9.6f} {:12.2f} {:6.4f} {}\n"
.format(item.measurement_number, item.ca, item.cb, item.pa,
item.pb, item.I, item.V, item.AppRes, item.std,
m_on_m))
with open("measurements_model_info.json", "w") as fd:
json.dump(meas_model_info.serialize(), fd, indent=4, sort_keys=True)
if inv_par.p3d:
print()
print_headline("Saving p3d")
t = time.time()
save_p3d(paraDomain, model.array(), cut_par, inv_par.p3dStep,
"resistivity", inv_par.local_coord)
print("save_p3d elapsed time: {:0.3f} s".format(time.time() - t))
print()
print("All done.")
# spatial dimensions and need different boundary conditions (BC).
#
# As there is no current flow through the tanks boundary at all, homogeneous
# (Neumann) BC are defined for the whole boundary.
# Neumann BC are natural (intrinsic) for the finite element simulations.
# \link{tutorial:fem:bc}, so we just need to define a cube geometry including
# region markers.
plc = mt.createCube(size=[0.99, 0.5, 1.0], pos=[0.495, 0.25], boundaryMarker=1)
###############################################################################
# We first read the measuring scheme file and add the electrodes as nodes with
# the marker -99 to the geometry.
filename = pg.getExampleFile("ert/modeltank.shm")
shm = pg.DataContainerERT(filename)
for s in shm.sensors():
plc.createNode(s, marker=-99)
###############################################################################
# There are two small problems to overcome for simulating Neumann bodies.
#
# First, we always need dipole current injection since there can be no current
# flow out of the closed boundaries of our experimental tank.
# (Note that by default single poles are simulated and superpositioned.)
# Therefore we define a reference electrode position inside the PLC, with a
# marker -999, somewhere away from the electrodes.
plc.createNode([0.5, 0.5, -0.5], marker=-999)
def simulate(self, mesh, scheme, res, **kwargs):
"""Simulate an ERT measurement.
Perform the forward task for a given mesh, a resistivity distribution
(per cell), a measurement
scheme and will return data (apparent resistivity) or potential fields.
This function can also operate on complex resistivity models, thereby
computing complex apparent resistivities.
The forward operator itself only calculate potential values
for the given scheme file.
To calculate apparent resistivities, geometric factors (k) are needed.
If there are no values k in the DataContainerERT scheme, then we will
try to calculate them, either analytic or by using a p2-refined
version of the given mesh.
TODO
----
* 2D + Complex + SR
Args
----
mesh : :gimliapi:`GIMLI::Mesh`
2D or 3D Mesh to calculate for.
res : float, array(mesh.cellCount()) | array(N, mesh.cellCount()) | list
Resistivity distribution for the given mesh cells can be:
. float for homogeneous resistivity
. single array of length mesh.cellCount()
. matrix of N resistivity distributions of length mesh.cellCount()
. resistivity map as [[regionMarker0, res0],
[regionMarker0, res1], ...]
scheme : :gimliapi:`GIMLI::DataContainerERT`
Data measurement scheme.
Keyword Args
------------
verbose: bool[False]
Be verbose. Will override class settings.
calcOnly: bool [False]
Use fop.calculate instead of fop.response. Useful if you want
to force the calculation of impedances for homogeneous models.
No noise handling. Solution is put as token 'u' in the returned
DataContainerERT.
noiseLevel: float [0.0]
add normally distributed noise based on
scheme('err') or on noiseLevel if scheme did not contain 'err'
noiseAbs: float [0.0]
Absolute voltage error in V
returnArray: bool [False]
Returns an array of apparent resistivities instead of
a DataContainerERT
returnFields: bool [False]
Returns a matrix of all potential values (per mesh nodes)
for each injection electrodes.
Returns
-------
DataContainerERT | array(N, data.size()) | array(N, data.size()) |
array(N, data.size()):
Data container with resulting apparent resistivity data and
errors (if noiseLevel or noiseAbs is set).
Optional returns a Matrix of rhoa values
(for returnArray==True forces noiseLevel=0).
In case of a complex valued resistivity model, phase values will be
returned in the DataContainerERT (see example below), or as an
additional returned array.
Examples
--------
# TODO: Remove pybert dependencies
# >>> import pybert as pb
# >>> import pygimli as pg
# >>> import pygimli.meshtools as mt
# >>> world = mt.createWorld(start=[-50, 0], end=[50, -50],
# ... layers=[-1, -5], worldMarker=True)
# >>> scheme = pb.createData(
# ... elecs=pg.utils.grange(start=-10, end=10, n=21),
# ... schemeName='dd')
# >>> for pos in scheme.sensorPositions():
# ... _= world.createNode(pos)
# ... _= world.createNode(pos + [0.0, -0.1])
# >>> mesh = mt.createMesh(world, quality=34)
# >>> rhomap = [
# ... [1, 100. + 0j],
# ... [2, 50. + 0j],
# ... [3, 10.+ 0j],
# ... ]
# >>> ert = pb.ERTManager()
# >>> data = ert.simulate(mesh, res=rhomap, scheme=scheme, verbose=True)
# >>> rhoa = data.get('rhoa').array()
# >>> phia = data.get('phia').array()
"""
verbose = kwargs.pop('verbose', self.verbose)
calcOnly = kwargs.pop('calcOnly', False)
returnFields = kwargs.pop("returnFields", False)
returnArray = kwargs.pop('returnArray', False)
noiseLevel = kwargs.pop('noiseLevel', 0.0)
noiseAbs = kwargs.pop('noiseAbs', 1e-4)
seed = kwargs.pop('seed', None)
#segfaults with self.fop (test & fix)
fop = self.createForwardOperator(useBert=self.useBert, sr=self.sr)
fop.data = scheme
fop.setMesh(mesh, ignoreRegionManager=True)
fop.verbose = verbose
rhoa = None
phia = None
isArrayData = False
# parse the given res into mesh-cell-sized array
if isinstance(res, int) or isinstance(res, float):
res = np.ones(mesh.cellCount()) * float(res)
elif isinstance(res, complex):
res = np.ones(mesh.cellCount()) * res
elif hasattr(res[0], '__iter__'): # ndim == 2
if len(res[0]) == 2: # res seems to be a res map
# check if there are markers in the mesh that are not defined in
# the rhomap. better signal here before it results in some error
meshMarkers = list(set(mesh.cellMarkers()))
mapMarkers = [m[0] for m in res]
if any([mark not in mapMarkers for mark in meshMarkers]):
left = [m for m in meshMarkers if m not in mapMarkers]
pg.critical(
"Mesh contains markers without assigned resistivities {}. Please fix given rhomap."
.format(left))
res = pg.solver.parseArgToArray(res, mesh.cellCount(), mesh)
else: # probably nData x nCells array
# better check for array data here
isArrayData = True
if isinstance(res[0], np.complex) or isinstance(res, pg.CVector):
pg.info("Complex resistivity values found.")
fop.setComplex(True)
else:
fop.setComplex(False)
if not scheme.allNonZero('k') and not calcOnly:
if verbose:
pg.info('Calculate geometric factors.')
scheme.set('k', fop.calcGeometricFactor(scheme))
ret = pg.DataContainerERT(scheme)
## just be sure that we don't work with artifacts
ret['u'] *= 0.0
ret['i'] *= 0.0
ret['r'] *= 0.0
if isArrayData:
rhoa = np.zeros((len(res), scheme.size()))
for i, r in enumerate(res):
rhoa[i] = fop.response(r)
if verbose:
print(i, "/", len(res), " : ", pg.dur(), "s", "min r:",
min(r), "max r:", max(r), "min r_a:", min(rhoa[i]),
"max r_a:", max(rhoa[i]))
else: # res is single resistivity array
if len(res) == mesh.cellCount():
if calcOnly:
fop.mapERTModel(res, 0)
dMap = pg.core.DataMap()
fop.calculate(dMap)
if fop.complex():
pg.critical('Implement me')
else:
ret["u"] = dMap.data(scheme)
ret["i"] = np.ones(ret.size())
if returnFields:
return pg.Matrix(fop.solution())
return ret
else:
if fop.complex():
res = pg.utils.squeezeComplex(res)
resp = fop.response(res)
if fop.complex():
rhoa, phia = pg.utils.toPolar(resp)
else:
rhoa = resp
else:
print(mesh)
print("res: ", res)
raise BaseException(
"Simulate called with wrong resistivity array.")
if not isArrayData:
ret['rhoa'] = rhoa
if phia is not None:
ret.set('phia', phia)
else:
ret.set('rhoa', rhoa[0])
if phia is not None:
ret.set('phia', phia[0])
if returnFields:
return pg.Matrix(fop.solution())
if noiseLevel > 0: # if errors in data noiseLevel=1 just triggers
if not ret.allNonZero('err'):
# 1A and #100µV
ret.set(
'err',
self.estimateError(ret,
relativeError=noiseLevel,
absoluteUError=noiseAbs,
absoluteCurrent=1))
print("Data error estimate (min:max) ", min(ret('err')), ":",
max(ret('err')))
rhoa *= 1. + pg.randn(ret.size(), seed=seed) * ret('err')
ret.set('rhoa', rhoa)
ipError = None
if phia is not None:
if scheme.allNonZero('iperr'):
ipError = scheme('iperr')
else:
# np.abs(self.data("phia") +TOLERANCE) * 1e-4absoluteError
if noiseLevel > 0.5:
noiseLevel /= 100.
if 'phiErr' in kwargs:
ipError = np.ones(
ret.size()) * kwargs.pop('phiErr') / 1000
else:
ipError = abs(ret["phia"]) * noiseLevel
if verbose:
print("Data IP abs error estimate (min:max) ",
min(ipError), ":", max(ipError))
phia += np.randn(ret.size(), seed=seed) * ipError
ret['iperr'] = ipError
ret['phia'] = phia
# check what needs to be setup and returned
if returnArray:
if phia is not None:
return rhoa, phia
else:
return rhoa
return ret
------------------------
In this example, we illustrate how to visualize the sensitivities of four-point
arrays. You can easily loop over the plotting command to create something like:
https://www.youtube.com/watch?v=lt1qV-2d5Ps
"""
import numpy as np
import matplotlib.pyplot as plt
import pygimli as pg
import pygimli.meshtools as mt
import pygimli.physics.ert as ert
###############################################################################
# We start by creating a ERT data container with three four-point arrays.
scheme = pg.DataContainerERT()
nelecs = 10
pos = np.zeros((nelecs, 2))
pos[:, 0] = np.linspace(5, 25, nelecs)
scheme.setSensorPositions(pos)
measurements = np.array((
[0, 3, 6, 9], # Dipole-Dipole
[0, 9, 3, 6], # Wenner
[0, 9, 4, 5] # Schlumberger
))
for i, elec in enumerate("abmn"):
scheme[elec] = measurements[:,i]
def main():
# read config file
conf_file = "inv.conf"
with open(conf_file, "r") as fd:
conf = json.load(fd)
# res = pb.Resistivity("input.dat")
# res.invert()
# np.savetxt('resistivity.vector', res.resistivity)
# return
# load data file
data = pg.DataContainerERT("input.dat")
# remove invalid data
oldsize = data.size()
data.removeInvalid()
newsize = data.size()
if newsize < oldsize:
print('Removed ' + str(oldsize - newsize) + ' values.')
if not data.allNonZero('rhoa'):
print("No or partial rhoa values.")
return
# check, compute error
if data.allNonZero('err'):
error = data('err')
else:
print("estimate data error")
error = conf["relativeError"] + conf["absoluteError"] / data('rhoa')
# create FOP
fop = pg.DCSRMultiElectrodeModelling(verbose=conf["verbose"])
fop.setThreadCount(psutil.cpu_count(logical=False))
fop.setData(data)
# create Inv
inv = pg.RInversion(verbose=conf["verbose"], dosave=False)
# variables tD, tM are needed to prevent destruct objects
tD = pg.RTransLog()
tM = pg.RTransLogLU()
inv.setTransData(tD)
inv.setTransModel(tM)
inv.setForwardOperator(fop)
# mesh
if conf["meshFile"] == "":
depth = conf["depth"]
if depth is None:
depth = pg.DCParaDepth(data)
poly = pg.meshtools.createParaMeshPLC(
data.sensorPositions(),
paraDepth=depth,
paraDX=conf["paraDX"],
paraMaxCellSize=conf["maxCellArea"],
paraBoundary=2,
boundary=2)
if conf["verbose"]:
print("creating mesh...")
mesh = pg.meshtools.createMesh(poly,
quality=conf["quality"],
smooth=(1, 10))
else:
mesh = pg.Mesh(pg.load(conf["meshFile"]))
mesh.createNeighbourInfos()
if conf["verbose"]:
print(mesh)
sys.stdout.flush() # flush before multithreading
fop.setMesh(mesh)
fop.regionManager().setConstraintType(1)
if not conf["omitBackground"]:
if fop.regionManager().regionCount() > 1:
fop.regionManager().region(1).setBackground(True)
if conf["meshFile"] == "":
fop.createRefinedForwardMesh(True, False)
else:
fop.createRefinedForwardMesh(conf["refineMesh"], conf["refineP2"])
paraDomain = fop.regionManager().paraDomain()
inv.setForwardOperator(fop) # necessary?
# inversion parameters
inv.setData(data('rhoa'))
inv.setRelativeError(error)
fop.regionManager().setZWeight(conf['zWeight'])
inv.setLambda(conf['lam'])
inv.setMaxIter(conf['maxIter'])
inv.setRobustData(conf['robustData'])
inv.setBlockyModel(conf['blockyModel'])
inv.setRecalcJacobian(conf['recalcJacobian'])
pc = fop.regionManager().parameterCount()
startModel = pg.RVector(pc, pg.median(data('rhoa')))
inv.setModel(startModel)
# Run the inversion
sys.stdout.flush() # flush before multithreading
model = inv.run()
resistivity = model(paraDomain.cellMarkers())
np.savetxt('resistivity.vector', resistivity)
print("Done.")
maxIter = 15
############
# Poro to rock content (inversion parameter)
fr_min = 1 - poro_max
fr_max = 1 - poro_min
# Load meshes and data
mesh = pg.load("mesh.bms")
true = np.load("true_model.npz")
sensors = np.load("sensors.npy", allow_pickle=True)
veltrue, rhotrue, fatrue, fitrue, fwtrue = true["vel"], true["rho"], true[
"fa"], true["fi"], true["fw"]
ertScheme = pg.DataContainerERT("erttrue.dat")
meshRST = pg.load("paraDomain_%d.bms" % case)
meshERT = pg.load("meshERT_%d.bms" % case)
if fix_poro:
frtrue = np.load("true_model.npz")["fr"]
phi = []
for cell in meshRST.cells():
idx = mesh.findCell(cell.center()).id()
phi.append(1 - frtrue[idx])
phi = np.array(phi)
fr_min = 0
fr_max = 1
else:
phi = poro
if case == 2:
case = 2
constrained = True
mesh = pg.load("mesh_2.bms")
paraDomain = pg.load("paraDomain_2.bms")
else:
case = 1
constrained = False
mesh = pg.load("mesh_1.bms")
paraDomain = pg.load("paraDomain_1.bms")
pg.boxprint("Calculating case %s" % case)
# Load meshes and data
ertScheme = pg.DataContainerERT("ert_filtered.data")
fr_min = 0.1
fr_max = 0.9
phi = np.ones(paraDomain.cellCount()) * poro
# Setup managers and equip with meshes
ert = ERTManager()
ert.setMesh(mesh)
ert.setData(ertScheme)
ert.fop.createRefinedForwardMesh()
ttData = pg.DataContainer("rst_filtered.data", "s g")
rst = Refraction()
rst.setMesh(paraDomain)
rst.setData(ttData)
def main(inv_par, project_conf, max_dist=1.0, final=False):
if inv_par.meshFrom == MeshFrom.GALLERY_CLOUD:
mesh_file = "gallery_mesh.msh"
offset = np.array([
project_conf.point_cloud_origin_x,
project_conf.point_cloud_origin_y,
project_conf.point_cloud_origin_z
])
elif inv_par.meshFrom == MeshFrom.SURFACE_CLOUD:
mesh_file = "inv_mesh_tmp.msh2"
offset = np.array([0.0, 0.0, 0.0])
else:
mesh_file = "../../gallery_mesh.msh"
offset = np.array([
project_conf.gallery_mesh_origin_x,
project_conf.gallery_mesh_origin_y,
project_conf.gallery_mesh_origin_z
])
if final:
mesh_file = "inv_mesh_tmp.msh2"
offset = np.array([0.0, 0.0, 0.0])
mesh = GmshIO(mesh_file)
#mesh.elements = {id: data for id, data in mesh.elements.items() if id not in [714, 2095]}
tree = bih.BIH()
boxes = []
mesh.elements2 = {}
i = 0
for data in mesh.elements.values():
type_, tags, nodeIDs = data
if type_ != 2:
continue
# a = np.array(mesh.nodes[nodeIDs[0]]) + np.array([-622000.0, -1128000.0, 0.0])
# b = np.array(mesh.nodes[nodeIDs[1]]) + np.array([-622000.0, -1128000.0, 0.0])
# c = np.array(mesh.nodes[nodeIDs[2]]) + np.array([-622000.0, -1128000.0, 0.0])
# a = np.array(mesh.nodes[nodeIDs[0]])
# b = np.array(mesh.nodes[nodeIDs[1]])
# c = np.array(mesh.nodes[nodeIDs[2]])
a = np.array(mesh.nodes[nodeIDs[0]]) + offset
b = np.array(mesh.nodes[nodeIDs[1]]) + offset
c = np.array(mesh.nodes[nodeIDs[2]]) + offset
boxes.append(bih.AABB([a, b, c]))
mesh.elements2[i] = data
i += 1
tree.add_boxes(boxes)
tree.construct()
# electrodes = []
# with open("electrodes_small.xyz") as fd:
# for i, line in enumerate(fd):
# s = line.split()
# if len(s) >= 3:
# el = np.array([float(s[0]), float(s[1]), float(s[2])])
# electrodes.append(el)
#
# t = time.time()
# snapped_electrodes = [snap_electrode(el, mesh, tree) for el in electrodes]
# print("elapsed time = {:.3f} s".format(time.time() - t))
#
# with open("electrodes_small_snapped2.xyz", "w") as fd:
# for el in snapped_electrodes:
# fd.write("{} {} {}\n".format(el[0], el[1], el[2]))
if project_conf.method == GenieMethod.ERT:
data = pg.DataContainerERT("input.dat", removeInvalid=False)
else:
data = pg.DataContainer("input.dat",
sensorTokens='s g',
removeInvalid=False)
for i in range(len(data.sensorPositions())):
pos = data.sensorPosition(i)
pos = np.array([pos[0], pos[1], pos[2]])
new_pos = snap_electrode(pos, mesh, tree, max_dist, offset)
data.setSensorPosition(i, new_pos)
data.save("input_snapped.dat")
import numpy as np
import pygimli as pg
import pygimli.meshtools as mt
from fpinv import FourPhaseModel, NN_interpolate
from pygimli.physics import Refraction, ERTManager
from settings import *
#need ertData, rstData, a mesh and phi to be given
ertData = pg.DataContainerERT("ert_filtered.data")
print(ertData)
mesh = pg.load("mesh_1.bms")
paraDomain = pg.load("paraDomain_1.bms")
depth = mesh.ymax() - mesh.ymin()
ert = ERTManager()
resinv = ert.invert(ertData,
mesh=mesh,
lam=60,
zWeight=zWeight,
maxIter=maxIter)
print("ERT chi:", ert.inv.chi2())
print("ERT rms:", ert.inv.relrms())
np.savetxt("res_conventional.dat", resinv)
#############
ttData = pg.DataContainer("rst_filtered.data", "s g")
rst = Refraction(ttData)
# INVERSION
def showERTData(data, vals=None, **kwargs):
"""Plot ERT data as pseudosection matrix (position over separation).
Creates figure, axis and draw a pseudosection.
Parameters
----------
data : :gimliapi:`BERT::DataContainerERT`
**kwargs :
* axes : matplotlib.axes
Axes to plot into. Default is None and a new figure and
axes are created.
* vals : Array[nData]
Values to be plotted. Default is data('rhoa').
"""
var = kwargs.pop('var', 0)
if var > 0:
import pybert as pb
pg._g(kwargs)
return pb.showData(data, vals, var=var, **kwargs)
# remove ax keyword global
ax = kwargs.pop('ax', None)
if ax is None:
fig = pg.plt.figure()
ax = None
axTopo = None
if 'showTopo' in kwargs:
ax = fig.add_subplot(1, 1, 1)
# axs = fig.subplots(2, 1, sharex=True)
# # Remove horizontal space between axes
# fig.subplots_adjust(hspace=0)
# ax = axs[1]
# axTopo = axs[0]
else:
ax = fig.add_subplot(1, 1, 1)
pg.checkAndFixLocaleDecimal_point(verbose=False)
if vals is None:
vals = 'rhoa'
if isinstance(vals, str):
if data.haveData(vals):
vals = data(vals)
else:
pg.critical('field not in data container: ', vals)
kwargs['cMap'] = kwargs.pop('cMap', pg.utils.cMap('rhoa'))
kwargs['label'] = kwargs.pop('label', pg.utils.unit('rhoa'))
kwargs['logScale'] = kwargs.pop('logScale', min(vals) > 0.0)
try:
ax, cbar = drawERTData(ax, data, vals=vals, **kwargs)
except:
pg.warning('Something gone wrong while drawing data. '
'Try fallback with equidistant electrodes.')
d = pg.DataContainerERT(data)
sc = data.sensorCount()
d.setSensors(list(zip(range(sc), np.zeros(sc))))
ax, cbar = drawERTData(ax, d, vals=vals, **kwargs)
# TODO here cbar handling like pg.show
if 'xlabel' in kwargs:
ax.set_xlabel(kwargs['xlabel'])
if 'ylabel' in kwargs:
ax.set_ylabel(kwargs['ylabel'])
if 'showTopo' in kwargs:
# if axTopo is not None:
print(ax.get_position())
axTopo = pg.plt.axes([ax.get_position().x0,
ax.get_position().y0,
ax.get_position().x0+0.2,
ax.get_position().y0+0.2])
x = pg.x(data)
x *= (ax.get_xlim()[1] - ax.get_xlim()[0]) / (max(x)-min(x))
x += ax.get_xlim()[0]
axTopo.plot(x, pg.z(data), '-o', markersize=4)
axTopo.set_ylim(min(pg.z(data)), max(pg.z(data)))
axTopo.set_aspect(1)
# ax.set_aspect('equal')
# plt.pause(0.1)
pg.viewer.mpl.updateAxes(ax)
return ax, cbar
meshERT = pg.load("meshERT_2.bms")
for cell in meshRST.cells():
NN = mesh.findCell(cell.center())
cell.setMarker(mesh.cellMarkers()[NN.id()])
for cell in meshERT.cells():
NN = mesh.findCell(cell.center())
if NN:
cell.setMarker(mesh.cellMarkers()[NN.id()])
else:
cell.setMarker(len(np.unique(mesh.cellMarkers()))) # triangle boundary
# create scheme files
sensors = np.load("sensors.npy", allow_pickle=True)
shmERT = pg.DataContainerERT("erttrue.dat")
shmSRT = createRAData(sensors)
Fsyn = np.loadtxt("syn_model.dat")
# %% compute forward response and jacobians
jacERT, jacSRT = jacobian4PM(meshERT, meshRST, shmERT, shmSRT, Fsyn)
jacJoint = np.vstack((jacSRT, jacERT))
print(jacERT.shape, jacSRT.shape, jacJoint.shape)
jacJoint.dump("jacJoint.npz")
pg.tic("Calculating JTJ")
JTJ = jacJoint.T.dot(jacJoint)
pg.toc()
MCM = np.linalg.inv(JTJ)
MCM.dump("MCM.npz")
# plt.matshow(MCM)
