"""Timelapse ERT manager class."""
import os.path
from glob import glob
from datetime import datetime, timedelta
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import pygimli as pg
from pygimli.physics import ert
from .processing import combineMultipleData
# move general timelapse stuff to method-independent class
# class Timelapse():
# mask
# chooseTime
# class TimelapseERT(Timelapse)
[docs]
class TimelapseERT():
"""Class for crosshole ERT data manipulation.
Note that this class is to be split into a hierarchy of classes for general
timelapse data management, timelapse ERT and crosshole ERT.
You can load data, filter them data in the temporal or measuring axis, plot
data, run inversion and export data and result files.
"""
[docs]
def __init__(self, filename=None, **kwargs):
"""Initialize class and possibly load data.
Parameters
----------
filename : str
filename to load data, times, RHOA and ERR from
data : DataContainerERT
The data with quadrupoles for all
times : np.array of datetime objects
measuring times
DATA : 2d np.array (data.size(), len(times))
all apparent resistivities
ERR : 2d np.array (data.size(), len(times))
all apparent relative errors
bhmap : array
map electrode numbers to borehole numbers
mesh : array
mesh for inversion
"""
self.data = kwargs.pop("data", None)
self.DATA = kwargs.pop("DATA", [])
self.ERR = kwargs.pop("ERR", [])
self.times = kwargs.pop("times", [])
self.mesh = kwargs.pop("mesh", None)
self.name = "new"
self.models = []
self.responses = []
self.chi2s = []
self.model = None
self.mgr = ert.ERTManager()
self.pd = None
if filename is not None:
if isinstance(filename, str):
self.load(filename, **kwargs)
else:
self.DATA = filename
if np.any(self.DATA):
if isinstance(self.DATA[0], pg.DataContainerERT):
self.data, self.DATA, self.ERR = combineMultipleData(self.DATA)
self.mask()
if "name" in kwargs:
self.name = kwargs["name"]
nt = self.DATA.shape[1]
if len(self.times) != nt: # default: days from now
self.times = datetime.now() + np.arange(nt) * timedelta(days=1)
def __repr__(self): # for print function
"""Return string representation of the class."""
out = ['Timelapse ERT data:', self.data.__str__()]
if np.any(self.DATA):
out.append("{} time steps".format(self.DATA.shape[1]))
if np.any(self.times):
out[-1] += " from " + self.times[0].isoformat(" ", "minutes")
out[-1] += " to " + self.times[-1].isoformat(" ", "minutes")
return "\n".join(out)
[docs]
def load(self, filename):
"""Load or import data (or data files using *)."""
if os.path.isfile(filename):
self.data = ert.load(filename)
if os.path.isfile(filename[:-4]+".rhoa"):
self.DATA = np.loadtxt(filename[:-4]+".rhoa")
if os.path.isfile(filename[:-4]+".err"):
self.ERR = np.loadtxt(filename[:-4]+".err")
if os.path.isfile(filename[:-4]+".times"):
timestr = np.loadtxt(filename[:-4]+".times", dtype=str)
self.times = np.array([datetime.fromisoformat(s) for s in timestr])
elif "*" in filename:
DATA = [ert.load(fname) for fname in glob(filename)]
self.data, self.DATA, self.ERR = combineMultipleData(DATA)
self.name = filename[:-4].replace("*", "All")
[docs]
def saveData(self, filename=None):
"""Save all data as datacontainer, times, rhoa and error arrays."""
filename = filename or self.name
if filename.endswith(".shm"):
filename = filename[:-4]
self.data.save(filename+".shm", "a b m n k")
np.savetxt(filename+".rhoa", self.DATA, fmt="%6.2f")
if np.any(self.ERR):
np.savetxt(filename+".err", self.ERR, fmt="%6.2f")
with open(filename+".times", "w", encoding="utf-8") as fid:
for d in self.times:
fid.write(d.isoformat()+"\n")
self.name = filename
[docs]
def timeIndex(self, t): #
"""Return index of closest timestep in times to t.
Parameters
----------
t : int|str|datetime
datetime object or string
"""
if isinstance(t, str): # convert into datetime
t = datetime.fromisoformat(t) # check others
if isinstance(t, datetime): # detect closest point
return np.argmin(np.abs(self.times-t))
elif isinstance(t, (int, np.int32, np.int64)):
return t
elif hasattr(t, "__iter__"):
return np.array([self.timeIndex(ti) for ti in t], dtype=int)
else:
raise TypeError("Unknown type", type(t))
[docs]
def filter(self, tmin=0, tmax=None, t=None, select=None, kmax=None):
"""Filter data set temporally or data-wise.
Parameters
----------
tmin, tmax : int|str|datetime
minimum and maximum times to keep
t : int|str|datetime
time to remove
select : list[int]
times to select
kmax : float
maximum geometric factor to allow
"""
if np.any(self.DATA):
if select is not None:
ind = self.timeIndex(select)
else:
tmin = self.timeIndex(tmin) # converts dt/str to int
if tmax is None:
tmax = self.DATA.shape[1]
else:
tmax = self.timeIndex(tmax)
ind = np.arange(tmin, tmax)
if t is not None:
ind = np.setxor1d(ind, t)
self.DATA = self.DATA[:, ind]
if np.any(self.ERR):
self.ERR = self.ERR[:, ind]
if np.any(self.times):
self.times = self.times[ind]
if kmax is not None:
ind = np.nonzero(np.abs(self.data["k"]) < kmax)[0]
self.data["valid"] = 0
self.data.markValid(ind)
self.data.removeInvalid()
if np.any(self.DATA):
self.DATA = self.DATA[ind, :]
if np.any(self.ERR):
self.ERR = self.ERR[ind, :]
[docs]
def mask(self, rmin=0.1, rmax=1e6, emax=None):
"""Mask data (i.e. remove them from inversion).
Parameters
----------
rmin, rmax : float
minimum and maximum apparent resistivity
emax : float
maximum error
"""
self.DATA = np.ma.masked_invalid(self.DATA)
self.DATA = np.ma.masked_outside(self.DATA, rmin, rmax)
if emax is not None:
self.DATA.mask = np.bitwise_or(self.DATA.mask, self.ERR > emax)
[docs]
def showData(self, v="rhoa", x="a", y="m", t=None, **kwargs):
"""Show data as pseudosections (single-hole) or cross-plot (crosshole)
Parameters
----------
v : str|array ["rhoa]
array or field to plot
x, y : str|array ["a", "m"]
values to use for x and y axes
t : int|str|datetime
time to choose
kwargs : dict
forwarded to ert.show or showDataContainerAsMatrix
"""
kwargs.setdefault("cMap", "Spectral_r")
if t is not None:
t = self.timeIndex(t)
rhoa = self.DATA[:, t]
v = rhoa.data
v[rhoa.mask] = np.nan
if kwargs.pop("crossplot", "x" in kwargs and "y" in kwargs):
x = kwargs.pop("x", ["a", "b"])
y = kwargs.pop("y", ["m", "n"])
return pg.viewer.mpl.showDataContainerAsMatrix(
self.data, x, y, v, **kwargs)
else:
return self.data.show(v, **kwargs)
[docs]
def showTimeline(self, ax=None, **kwargs):
"""Show data timeline.
Parameters
----------
ax : mpl.Axes|None
matplotlib axes to plot (otherwise new)
a, b, m, n : int
tokens to extract data from
"""
if ax is None:
_, ax = plt.subplots(figsize=[8, 5])
good = np.ones(self.data.size(), dtype=bool)
lab = kwargs.pop("label", "ABMN") + ": "
for k, v in kwargs.items():
good = np.bitwise_and(good, self.data[k] == v)
abmn = [self.data[tok] for tok in "abmn"]
for i in np.nonzero(good)[0]:
lab1 = lab + " ".join([str(tt[i]) for tt in abmn])
ax.semilogy(self.times, self.DATA[i, :], "x-", label=lab1)
ax.grid(True)
ax.legend()
ax.set_xlabel("time")
ax.set_ylabel("resistivity (Ohmm)")
return ax
[docs]
def fitReciprocalErrorModel(self, **kwargs):
"""Fit all data by analysing normal/reciprocal data.
Parameters
----------
show : bool
show temporal behaviour of absolute & relative errors
kwargs passed on to ert.fitReciprocalErrorModel)
nBins : int
number of bins to subdivide data (4 < data.size()//30 < 30)
rel : bool [False]
fit relative instead of absolute errors
Returns
-------
p, a : array
relative (p) and absolute (a) errors for every time step
"""
data = self.data.copy()
p = np.zeros(self.DATA.shape[1])
a = np.zeros_like(p)
show = kwargs.pop("show", False) # avoid show single fits
rel = kwargs.get("rel", True)
for i, rhoa in enumerate(self.DATA.T):
if isinstance(rhoa, np.ma.MaskedArray):
rhoa = rhoa.data
data['rhoa'] = rhoa
try:
pp, aa = ert.fitReciprocalErrorModel(data, **kwargs)
if not rel:
pp, aa = aa, pp
p[i], a[i] = pp, aa
except:
print("Could not get reciprocal model for timestep", i)
if show:
_, ax = plt.subplots(nrows=2, sharex=True)
ax[0].plot(self.times, p*100)
ax[1].plot(self.times, a)
ax[0].set_ylabel("relative error (%)")
ax[1].set_ylabel("absolute error (Ohm)")
ax[0].grid()
ax[1].grid()
return p, a
[docs]
def generateDataPDF(self, **kwargs):
"""Generate a pdf with all data as timesteps in individual pages.
Iterates through times and calls showData into multi-page pdf
"""
kwargs.setdefault("verbose", False)
with PdfPages(self.name+'-data.pdf') as pdf:
fig = plt.figure(figsize=kwargs.pop("figsize", [5, 5]))
for i in range(self.DATA.shape[1]):
ax = fig.subplots()
self.showData(t=i, ax=ax, **kwargs)
ax.set_title(str(i)+": "+ self.times[i].isoformat(" ", "minutes"))
fig.savefig(pdf, format='pdf')
fig.clf()
[docs]
def chooseTime(self, t=None):
"""Return data for specific time.
Parameters
----------
t : int|str|datetime
"""
if not isinstance(t, (int, np.int32, np.int64)):
t = self.timeIndex(t)
rhoa = self.DATA[:, t].copy()
arhoa = np.abs(rhoa.data)
arhoa[rhoa.mask] = np.nanmedian(arhoa)
data = self.data.copy()
data["rhoa"] = arhoa
data.estimateError()
data["err"][rhoa.mask] = 1e8
self.data = data
return data
[docs]
def createMesh(self, **kwargs):
"""Generate inversion mesh."""
self.mesh = ert.createInversionMesh(self.data, **kwargs)
self.mgr.setMesh(mesh=self.mesh)
if kwargs.pop("show", False):
print(self.mesh)
pg.show(self.mesh, markers=True, showMesh=True)
[docs]
def invert(self, t=None, reg=None, regTL=None, **kwargs):
"""Run inversion for a specific timestep or all subsequently.
Parameter
---------
t : int|datetime|str|array
time index, string or datetime object, or array of any of these
reg : dict
regularization options (setRegularization) for all inversions
regTL : dict
regularization options for timesteps inversion only
**kwargs : dict
keyword arguments passed to ERTManager.invert
"""
if t is not None:
t = self.timeIndex(t)
if self.mesh is None:
self.createMesh()
self.mgr.fop.setVerbose(False)
if isinstance(reg, dict):
self.mgr.inv.setRegularization(**reg)
if t is None: # all
t = np.arange(len(self.times))
t = np.atleast_1d(t)
models = []
responses = []
self.chi2s = []
startModel = kwargs.pop("startModel", 100)
creep = kwargs.pop("creep", False)
kwargs.setdefault("isReference", True)
for i, ti in enumerate(np.atleast_1d(t)):
self.mgr.setData(self.chooseTime(ti))
self.model = self.mgr.invert(startModel=startModel, **kwargs)
if i == 0 or creep:
startModel = self.model.copy()
models.append(self.model)
responses.append(self.mgr.inv.response)
self.chi2s.append(self.mgr.inv.chi2())
if i == 0 and isinstance(regTL, dict):
kwargs.update(regTL)
# self.mgr.inv.setRegularization(**regTL)
if len(t) == 1:
self.mgr.showResult()
self.models = np.array(models)
self.responses = np.array(responses)
self.pd = self.mgr.paraDomain
[docs]
def fullInversion(self, scalef=1.0, **kwargs):
"""Full (4D) inversion."""
DATA = [self.chooseTime(ti) for ti in range(len(self.times))]
fop = pg.frameworks.MultiFrameModelling(ert.ERTModelling, scalef=scalef)
fop.setData(DATA)
if self.mesh is None:
self.createMesh()
fop.setMesh(self.mesh)
print(fop.mesh()) # important to call mesh() function once!
dataVec = np.concatenate([data["rhoa"] for data in DATA])
errorVec = np.concatenate([data["err"] for data in DATA])
startModel = fop.createStartModel(dataVec)
inv = pg.Inversion(fop=fop, startModel=startModel, verbose=True)
fop.createConstraints(C=kwargs.pop("C", None))
kwargs.setdefault("maxIter", 10)
kwargs.setdefault("verbose", True)
kwargs.setdefault("startModel", startModel)
model = inv.run(dataVec, errorVec, **kwargs)
self.models = np.reshape(model, [len(DATA), -1])
self.responses = np.reshape(inv.response, [DATA[0].size(), -1])
self.pd = fop.paraDomain
return model
[docs]
def showFit(self, **kwargs):
"""Show data, model response and misfit."""
_, ax = plt.subplots(nrows=3, figsize=(10, 6), sharex=True, sharey=True)
kwargs.setdefault("verbose", False)
_, cb = self.showData(ax=ax[0], **kwargs)
self.showData(self.mgr.inv.response, ax=ax[1],
cMin=cb.vmin, cMax=cb.vmax, **kwargs)
misfit = self.mgr.inv.response / self.data["rhoa"] * 100 - 100
self.showData(misfit, ax=ax[2], cMin=-10,
cMax=10, cMap="bwr", **kwargs)
return ax
[docs]
def showAllModels(self, ncols=2, **kwargs):
"""Show all models as subplots.
Parameters
----------
ncols : int [2]
number of columns
**kwargs : dict
keyword arguments passed to pg.show
"""
nT = self.DATA.shape[1]
showRatio = kwargs.pop("ratio", False)
nrows = int(np.ceil(nT/ncols))
_, ax = plt.subplots(nrows=nrows, ncols=ncols,
figsize=kwargs.pop("figsize", [8, 5]))
ratiokw = kwargs.copy()
kwargs.setdefault("cMin", np.min(self.models))
kwargs.setdefault("cMax", np.max(self.models))
kwargs.setdefault("cMap", "Spectral_r")
kwargs.setdefault("logScale", True)
models = self.models.copy()
if showRatio:
models = self.models / self.models[0]
rmax = np.maximum(np.max(models), 1/np.min(models))
ratiokw["cMax"] = kwargs.pop("rMax", rmax)
ratiokw["cMin"] = 1 / ratiokw["cMax"]
ratiokw["cMap"] = "bwr"
ratiokw["logScale"] = True
for i, model in enumerate(models):
if i == 0 or not showRatio:
pg.show(self.pd, self.models[i], ax=ax.flat[i], **kwargs)
else:
pg.show(self.pd, model, ax=ax.flat[i], **ratiokw)
return ax
[docs]
def generateModelPDF(self, **kwargs):
"""Generate a multi-page pdf with the model results.
Parameters
----------
**kwargs : keyword arguments passed to pg.show()
"""
kwargs.setdefault('label', pg.unit('res'))
kwargs.setdefault('cMap', pg.utils.cMap('res'))
kwargs.setdefault('logScale', True)
with PdfPages(self.name+'-model.pdf') as pdf:
fig = plt.figure(figsize=kwargs.pop("figsize", [8, 5]))
for i, model in enumerate(self.models):
ax = fig.subplots()
pg.show(self.pd, model, ax=ax, **kwargs)
ax.set_title(str(i)+": " + self.times[i].isoformat(" ", "minutes"))
fig.savefig(pdf, format='pdf')
fig.clf()
[docs]
def generateRatioPDF(self, **kwargs):
"""Generate a multi-page pdf with the model results.
Parameters
----------
creep : bool [False]
Use preceding time step as reference (default is baseline)
cMax : float [2]
maximum of color scale
cMax : float [1/cMax]
minimum of color scale
logScale : bool [True]
logarithmic color scale
cMap : str ['bwr']
colormap
"""
kwargs.setdefault('label', 'ratio')
kwargs.setdefault('cMap', 'bwr')
kwargs.setdefault('logScale', True)
kwargs.setdefault("cMax", 2.0)
kwargs.setdefault("cMin", 1/kwargs["cMax"])
basemodel = self.models[0]
creep = kwargs.pop("creep", False)
with PdfPages(self.name+'-ratio.pdf') as pdf:
fig = plt.figure(figsize=kwargs.pop("figsize", [8, 5]))
for i, model in enumerate(self.models[1:]):
ax = fig.subplots()
pg.show(self.pd, model/basemodel, ax=ax, **kwargs)
ax.set_title(str(i)+": " + self.times[i+1].isoformat(" ", "minutes") + "/" +
self.times[i].isoformat(" ", "minutes"))
fig.savefig(pdf, format='pdf')
fig.clf()
if creep:
basemodel = model
[docs]
def exportVTK(self, name=None, oneforall=False):
"""Generate output vtk(s) for postprocessing."""
name = name or self.name
if name.endswith(".vtk"):
name = name[:-4]
vtk = self.pd.copy()
if oneforall:
for i, model in enumerate(self.models):
vtk[f"model{i}"] = model
vtk.exportVTK(name+"_results.vtk")
else:
for i, model in enumerate(self.models):
vtk["resistivity"] = model
vtk.exportVTK(name+f"_result{i}.vtk")
if __name__ == "__main__":
pass