.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/04_probabilistic_modeling/01_thickness_problem_gempy.py"
.. LINE NUMBERS ARE GIVEN BELOW.
.. only:: html
.. note::
:class: sphx-glr-download-link-note
:ref:`Go to the end <sphx_glr_download_examples_04_probabilistic_modeling_01_thickness_problem_gempy.py>`
to download the full example code
.. rst-class:: sphx-glr-example-title
.. _sphx_glr_examples_04_probabilistic_modeling_01_thickness_problem_gempy.py:
2.2 - Including GemPy
=====================
Complex probabilistic model
---------------------------
.. GENERATED FROM PYTHON SOURCE LINES 8-29
.. code-block:: Python
import os
import numpy as np
import matplotlib.pyplot as plt
import torch
import pyro
import pyro.distributions as dist
from pyro.infer import MCMC, NUTS, Predictive
from pyro.infer.autoguide import init_to_mean
import gempy as gp
import gempy_engine
import gempy_viewer as gpv
from gempy_engine.core.backend_tensor import BackendTensor
import arviz as az
from gempy_probability.plot_posterior import default_red, default_blue
from gempy_viewer.modules.plot_2d.drawer_contours_2d import plot_regular_grid_contacts
# sphinx_gallery_thumbnail_number = -1
.. rst-class:: sphx-glr-script-out
.. code-block:: none
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/home/leguark/.virtualenvs/gempy_dependencies/bin/sphinx-build", line 8, in <module>
sys.exit(main())
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 339, in main
return make_main(argv)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 213, in make_main
return make_mode.run_make_mode(argv[1:])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 181, in run_make_mode
return make.run_generic_build(args[0])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 169, in run_generic_build
return build_main(args + opts)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 293, in build_main
app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 272, in __init__
self._init_builder()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 343, in _init_builder
self.events.emit('builder-inited')
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst
) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst
intro, title, (t, mem) = generate_file_rst(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst
output_blocks, time_elapsed = execute_script(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script
execute_code_block(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block
is_last_expr, mem_max = _exec_and_get_memory(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 818, in _exec_and_get_memory
mem_max, _ = gallery_conf["call_memory"](
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory
return 0.0, func()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__
exec(self.code, self.fake_main.__dict__)
File "/home/leguark/vector-geology/examples/04_probabilistic_modeling/01_thickness_problem_gempy.py", line 22, in <module>
import arviz as az
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/__init__.py", line 33, in <module>
from .data import *
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/__init__.py", line 3, in <module>
from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array, pytree_to_dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/base.py", line 13, in <module>
import xarray as xr
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import groupers, testing, tutorial
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/groupers.py", line 17, in <module>
from xarray.coding.cftime_offsets import BaseCFTimeOffset, _new_to_legacy_freq
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftime_offsets.py", line 56, in <module>
from xarray.coding.cftimeindex import CFTimeIndex, _parse_iso8601_with_reso
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftimeindex.py", line 54, in <module>
from xarray.coding.times import (
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/times.py", line 14, in <module>
from xarray.coding.variables import (
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/variables.py", line 13, in <module>
from xarray.core import dtypes, duck_array_ops, indexing
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/core/indexing.py", line 20, in <module>
from xarray.core.types import T_Xarray
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/core/types.py", line 106, in <module>
from cftime import datetime as CFTimeDatetime
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/cftime/__init__.py", line 1, in <module>
from ._cftime import (datetime, real_datetime,
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/home/leguark/.virtualenvs/gempy_dependencies/bin/sphinx-build", line 8, in <module>
sys.exit(main())
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 339, in main
return make_main(argv)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 213, in make_main
return make_mode.run_make_mode(argv[1:])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 181, in run_make_mode
return make.run_generic_build(args[0])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 169, in run_generic_build
return build_main(args + opts)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 293, in build_main
app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 272, in __init__
self._init_builder()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 343, in _init_builder
self.events.emit('builder-inited')
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst
) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst
intro, title, (t, mem) = generate_file_rst(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst
output_blocks, time_elapsed = execute_script(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script
execute_code_block(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block
is_last_expr, mem_max = _exec_and_get_memory(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 818, in _exec_and_get_memory
mem_max, _ = gallery_conf["call_memory"](
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory
return 0.0, func()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__
exec(self.code, self.fake_main.__dict__)
File "/home/leguark/vector-geology/examples/04_probabilistic_modeling/01_thickness_problem_gempy.py", line 22, in <module>
import arviz as az
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/__init__.py", line 33, in <module>
from .data import *
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/__init__.py", line 3, in <module>
from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array, pytree_to_dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/base.py", line 13, in <module>
import xarray as xr
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import groupers, testing, tutorial
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/groupers.py", line 17, in <module>
from xarray.coding.cftime_offsets import BaseCFTimeOffset, _new_to_legacy_freq
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftime_offsets.py", line 56, in <module>
from xarray.coding.cftimeindex import CFTimeIndex, _parse_iso8601_with_reso
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftimeindex.py", line 54, in <module>
from xarray.coding.times import (
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/times.py", line 14, in <module>
from xarray.coding.variables import (
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/variables.py", line 14, in <module>
from xarray.core.variable import Variable
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/core/variable.py", line 20, in <module>
from xarray.core import common, dtypes, duck_array_ops, indexing, nputils, ops, utils
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/core/common.py", line 28, in <module>
import cftime
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/cftime/__init__.py", line 1, in <module>
from ._cftime import (datetime, real_datetime,
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/home/leguark/.virtualenvs/gempy_dependencies/bin/sphinx-build", line 8, in <module>
sys.exit(main())
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 339, in main
return make_main(argv)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 213, in make_main
return make_mode.run_make_mode(argv[1:])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 181, in run_make_mode
return make.run_generic_build(args[0])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 169, in run_generic_build
return build_main(args + opts)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 293, in build_main
app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 272, in __init__
self._init_builder()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 343, in _init_builder
self.events.emit('builder-inited')
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst
) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst
intro, title, (t, mem) = generate_file_rst(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst
output_blocks, time_elapsed = execute_script(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script
execute_code_block(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block
is_last_expr, mem_max = _exec_and_get_memory(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 818, in _exec_and_get_memory
mem_max, _ = gallery_conf["call_memory"](
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory
return 0.0, func()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__
exec(self.code, self.fake_main.__dict__)
File "/home/leguark/vector-geology/examples/04_probabilistic_modeling/01_thickness_problem_gempy.py", line 22, in <module>
import arviz as az
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/__init__.py", line 33, in <module>
from .data import *
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/__init__.py", line 3, in <module>
from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array, pytree_to_dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/base.py", line 13, in <module>
import xarray as xr
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import groupers, testing, tutorial
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/groupers.py", line 17, in <module>
from xarray.coding.cftime_offsets import BaseCFTimeOffset, _new_to_legacy_freq
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftime_offsets.py", line 56, in <module>
from xarray.coding.cftimeindex import CFTimeIndex, _parse_iso8601_with_reso
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftimeindex.py", line 54, in <module>
from xarray.coding.times import (
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/times.py", line 35, in <module>
import cftime
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/cftime/__init__.py", line 1, in <module>
from ._cftime import (datetime, real_datetime,
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/home/leguark/.virtualenvs/gempy_dependencies/bin/sphinx-build", line 8, in <module>
sys.exit(main())
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 339, in main
return make_main(argv)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 213, in make_main
return make_mode.run_make_mode(argv[1:])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 181, in run_make_mode
return make.run_generic_build(args[0])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 169, in run_generic_build
return build_main(args + opts)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 293, in build_main
app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 272, in __init__
self._init_builder()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 343, in _init_builder
self.events.emit('builder-inited')
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst
) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst
intro, title, (t, mem) = generate_file_rst(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst
output_blocks, time_elapsed = execute_script(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script
execute_code_block(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block
is_last_expr, mem_max = _exec_and_get_memory(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 818, in _exec_and_get_memory
mem_max, _ = gallery_conf["call_memory"](
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory
return 0.0, func()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__
exec(self.code, self.fake_main.__dict__)
File "/home/leguark/vector-geology/examples/04_probabilistic_modeling/01_thickness_problem_gempy.py", line 22, in <module>
import arviz as az
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/__init__.py", line 33, in <module>
from .data import *
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/__init__.py", line 3, in <module>
from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array, pytree_to_dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/base.py", line 13, in <module>
import xarray as xr
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import groupers, testing, tutorial
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/groupers.py", line 17, in <module>
from xarray.coding.cftime_offsets import BaseCFTimeOffset, _new_to_legacy_freq
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftime_offsets.py", line 56, in <module>
from xarray.coding.cftimeindex import CFTimeIndex, _parse_iso8601_with_reso
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftimeindex.py", line 64, in <module>
import cftime
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/cftime/__init__.py", line 1, in <module>
from ._cftime import (datetime, real_datetime,
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/home/leguark/.virtualenvs/gempy_dependencies/bin/sphinx-build", line 8, in <module>
sys.exit(main())
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 339, in main
return make_main(argv)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 213, in make_main
return make_mode.run_make_mode(argv[1:])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 181, in run_make_mode
return make.run_generic_build(args[0])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 169, in run_generic_build
return build_main(args + opts)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 293, in build_main
app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 272, in __init__
self._init_builder()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 343, in _init_builder
self.events.emit('builder-inited')
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst
) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst
intro, title, (t, mem) = generate_file_rst(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst
output_blocks, time_elapsed = execute_script(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script
execute_code_block(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block
is_last_expr, mem_max = _exec_and_get_memory(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 818, in _exec_and_get_memory
mem_max, _ = gallery_conf["call_memory"](
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory
return 0.0, func()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__
exec(self.code, self.fake_main.__dict__)
File "/home/leguark/vector-geology/examples/04_probabilistic_modeling/01_thickness_problem_gempy.py", line 22, in <module>
import arviz as az
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/__init__.py", line 33, in <module>
from .data import *
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/__init__.py", line 3, in <module>
from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array, pytree_to_dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/base.py", line 13, in <module>
import xarray as xr
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import groupers, testing, tutorial
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/groupers.py", line 17, in <module>
from xarray.coding.cftime_offsets import BaseCFTimeOffset, _new_to_legacy_freq
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/cftime_offsets.py", line 73, in <module>
import cftime
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/cftime/__init__.py", line 1, in <module>
from ._cftime import (datetime, real_datetime,
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/home/leguark/.virtualenvs/gempy_dependencies/bin/sphinx-build", line 8, in <module>
sys.exit(main())
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 339, in main
return make_main(argv)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 213, in make_main
return make_mode.run_make_mode(argv[1:])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 181, in run_make_mode
return make.run_generic_build(args[0])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 169, in run_generic_build
return build_main(args + opts)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 293, in build_main
app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 272, in __init__
self._init_builder()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 343, in _init_builder
self.events.emit('builder-inited')
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst
) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst
intro, title, (t, mem) = generate_file_rst(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst
output_blocks, time_elapsed = execute_script(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script
execute_code_block(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block
is_last_expr, mem_max = _exec_and_get_memory(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 818, in _exec_and_get_memory
mem_max, _ = gallery_conf["call_memory"](
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory
return 0.0, func()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__
exec(self.code, self.fake_main.__dict__)
File "/home/leguark/vector-geology/examples/04_probabilistic_modeling/01_thickness_problem_gempy.py", line 22, in <module>
import arviz as az
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/__init__.py", line 33, in <module>
from .data import *
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/__init__.py", line 3, in <module>
from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array, pytree_to_dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/base.py", line 13, in <module>
import xarray as xr
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import groupers, testing, tutorial
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/groupers.py", line 20, in <module>
from xarray.core.dataarray import DataArray
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/core/dataarray.py", line 29, in <module>
from xarray.coding.calendar_ops import convert_calendar, interp_calendar
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/coding/calendar_ops.py", line 20, in <module>
import cftime
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/cftime/__init__.py", line 1, in <module>
from ._cftime import (datetime, real_datetime,
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/home/leguark/.virtualenvs/gempy_dependencies/bin/sphinx-build", line 8, in <module>
sys.exit(main())
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 339, in main
return make_main(argv)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 213, in make_main
return make_mode.run_make_mode(argv[1:])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 181, in run_make_mode
return make.run_generic_build(args[0])
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/make_mode.py", line 169, in run_generic_build
return build_main(args + opts)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/cmd/build.py", line 293, in build_main
app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 272, in __init__
self._init_builder()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/application.py", line 343, in _init_builder
self.events.emit('builder-inited')
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx/events.py", line 97, in emit
results.append(listener.handler(self.app, *args))
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 632, in generate_gallery_rst
) = generate_dir_rst(src_dir, target_dir, gallery_conf, seen_backrefs)
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 531, in generate_dir_rst
intro, title, (t, mem) = generate_file_rst(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1203, in generate_file_rst
output_blocks, time_elapsed = execute_script(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 1108, in execute_script
execute_code_block(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 970, in execute_code_block
is_last_expr, mem_max = _exec_and_get_memory(
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 818, in _exec_and_get_memory
mem_max, _ = gallery_conf["call_memory"](
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_gallery.py", line 244, in call_memory
return 0.0, func()
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/sphinx_gallery/gen_rst.py", line 722, in __call__
exec(self.code, self.fake_main.__dict__)
File "/home/leguark/vector-geology/examples/04_probabilistic_modeling/01_thickness_problem_gempy.py", line 22, in <module>
import arviz as az
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/__init__.py", line 33, in <module>
from .data import *
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/__init__.py", line 3, in <module>
from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array, pytree_to_dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/base.py", line 13, in <module>
import xarray as xr
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/__init__.py", line 3, in <module>
from xarray import groupers, testing, tutorial
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/groupers.py", line 20, in <module>
from xarray.core.dataarray import DataArray
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/core/dataarray.py", line 49, in <module>
from xarray.core.dataset import Dataset
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/core/dataset.py", line 131, in <module>
from xarray.plot.accessor import DatasetPlotAccessor
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/plot/__init__.py", line 10, in <module>
from xarray.plot.dataarray_plot import (
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/plot/dataarray_plot.py", line 13, in <module>
from xarray.plot.facetgrid import _easy_facetgrid
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/plot/facetgrid.py", line 13, in <module>
from xarray.plot.utils import (
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/xarray/plot/utils.py", line 30, in <module>
import cftime
File "/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/cftime/__init__.py", line 1, in <module>
from ._cftime import (datetime, real_datetime,
.. GENERATED FROM PYTHON SOURCE LINES 30-31
Config
.. GENERATED FROM PYTHON SOURCE LINES 31-35
.. code-block:: Python
seed = 123456
torch.manual_seed(seed)
pyro.set_rng_seed(seed)
.. GENERATED FROM PYTHON SOURCE LINES 36-37
Set the data path
.. GENERATED FROM PYTHON SOURCE LINES 37-40
.. code-block:: Python
data_path = os.path.abspath('../')
.. GENERATED FROM PYTHON SOURCE LINES 41-42
Define a function for plotting geological settings with wells
.. GENERATED FROM PYTHON SOURCE LINES 42-76
.. code-block:: Python
def plot_geo_setting_well(geo_model, alpha=1., show_lith=True):
"""
This function plots the geological settings along with the well locations.
It uses gempy_viewer to create 2D plots of the model.
"""
# Define well and device locations
device_loc = np.array([[6e3, 0, 3700]])
well_1 = 3.41e3
well_2 = 3.6e3
# Create a 2D plot
p2d = gpv.plot_2d(
geo_model,
show_topography=False,
legend=False,
show=False,
show_lith=show_lith,
kwargs_boundaries={'alpha': alpha}
)
# Add well and device markers to the plot
p2d.axes[0].scatter([3e3], [well_1], marker='^', s=400, c='#71a4b3', zorder=10)
p2d.axes[0].scatter([9e3], [well_2], marker='^', s=400, c='#71a4b3', zorder=10)
p2d.axes[0].scatter(device_loc[:, 0], device_loc[:, 2], marker='x', s=400, c='#DA8886', zorder=10)
# Add vertical lines to represent wells
p2d.axes[0].vlines(3e3, .5e3, well_1, linewidth=4, color='gray')
p2d.axes[0].vlines(9e3, .5e3, well_2, linewidth=4, color='gray')
# Show the plot
p2d.fig.show()
return p2d
.. GENERATED FROM PYTHON SOURCE LINES 77-81
Creating the Geological Model
-----------------------------
Here we create a geological model using GemPy. The model defines the spatial extent,
resolution, and geological information derived from orientations and surface points data.
.. GENERATED FROM PYTHON SOURCE LINES 81-92
.. code-block:: Python
geo_model = gp.create_geomodel(
project_name='Wells',
extent=[0, 12000, -500, 500, 0, 4000],
resolution=[100, 2, 100],
# refinement=1,
importer_helper=gp.data.ImporterHelper(
path_to_orientations=data_path + "/data/2-layers/2-layers_orientations.csv",
path_to_surface_points=data_path + "/data/2-layers/2-layers_surface_points.csv"
)
)
.. GENERATED FROM PYTHON SOURCE LINES 93-97
Configuring the Model
---------------------
We configure the interpolation options for the geological model.
These options determine how the model interpolates between data points.
.. GENERATED FROM PYTHON SOURCE LINES 97-102
.. code-block:: Python
geo_model.interpolation_options.uni_degree = 1
geo_model.interpolation_options.mesh_extraction = False
geo_model.interpolation_options.sigmoid_slope = 1000 # ! Temporary fix to set the hard sigmoid
.. GENERATED FROM PYTHON SOURCE LINES 103-107
Setting up a Custom Grid
------------------------
A custom grid is set for the model, defining specific points in space
where geological formations will be evaluated.
.. GENERATED FROM PYTHON SOURCE LINES 107-114
.. code-block:: Python
x_loc = 6000
y_loc = 0
z_loc = np.linspace(0, 4000, 100)
xyz_coord = np.array([[x_loc, y_loc, z] for z in z_loc])
gp.set_custom_grid(geo_model.grid, xyz_coord=xyz_coord)
.. rst-class:: sphx-glr-script-out
.. code-block:: none
Active grids: GridTypes.NONE|CUSTOM|DENSE
<gempy.core.data.grid_modules.grid_types.CustomGrid object at 0x7f27af42b850>
.. GENERATED FROM PYTHON SOURCE LINES 115-119
Plotting the Initial Geological Setting
---------------------------------------
Before running any probabilistic analysis, we first visualize the initial geological setting.
This step ensures that our model is correctly set up with the initial data.
.. GENERATED FROM PYTHON SOURCE LINES 119-123
.. code-block:: Python
# Plot initial geological settings
plot_geo_setting_well(geo_model=geo_model)
.. image-sg:: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_001.png
:alt: Cell Number: mid Direction: y
:srcset: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_001.png
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
.. code-block:: none
<gempy_viewer.modules.plot_2d.visualization_2d.Plot2D object at 0x7f280b0e6f80>
.. GENERATED FROM PYTHON SOURCE LINES 124-128
Interpolating the Initial Guess
-------------------------------
The model interpolates an initial guess for the geological formations.
This step is crucial to provide a starting point for further probabilistic analysis.
.. GENERATED FROM PYTHON SOURCE LINES 128-135
.. code-block:: Python
gp.compute_model(
gempy_model=geo_model,
engine_config=gp.data.GemPyEngineConfig(backend=gp.data.AvailableBackends.numpy)
)
plot_geo_setting_well(geo_model=geo_model)
.. image-sg:: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_002.png
:alt: Cell Number: mid Direction: y
:srcset: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_002.png
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
.. code-block:: none
Setting Backend To: AvailableBackends.numpy
<gempy_viewer.modules.plot_2d.visualization_2d.Plot2D object at 0x7f27ad1b15a0>
.. GENERATED FROM PYTHON SOURCE LINES 136-141
Probabilistic Geomodeling with Pyro
-----------------------------------
In this section, we introduce a probabilistic approach to geological modeling.
By using Pyro, a probabilistic programming language, we define a model that integrates
geological data with uncertainty quantification.
.. GENERATED FROM PYTHON SOURCE LINES 141-147
.. code-block:: Python
sp_coords_copy = geo_model.interpolation_input_copy.surface_points.sp_coords.copy()
# Change the backend to PyTorch for probabilistic modeling
BackendTensor.change_backend_gempy(engine_backend=gp.data.AvailableBackends.PYTORCH)
.. rst-class:: sphx-glr-script-out
.. code-block:: none
Setting Backend To: AvailableBackends.PYTORCH
.. GENERATED FROM PYTHON SOURCE LINES 148-153
Defining the Probabilistic Model
--------------------------------
The Pyro model represents the probabilistic aspects of the geological model.
It defines a prior distribution for the top layer's location and computes the thickness
of the geological layer as an observed variable.
.. GENERATED FROM PYTHON SOURCE LINES 153-190
.. code-block:: Python
def model(y_obs_list):
"""
This Pyro model represents the probabilistic aspects of the geological model.
It defines a prior distribution for the top layer's location and
computes the thickness of the geological layer as an observed variable.
"""
# Define prior for the top layer's location
prior_mean = sp_coords_copy[0, 2]
mu_top = pyro.sample(
name=r'$\mu_{top}$',
fn=dist.Normal(prior_mean, torch.tensor(0.02, dtype=torch.float64))
)
# Update the model with the new top layer's location
interpolation_input = geo_model.interpolation_input_copy
interpolation_input.surface_points.sp_coords = torch.index_put(
interpolation_input.surface_points.sp_coords,
(torch.tensor([0]), torch.tensor([2])),
mu_top
)
# Compute the geological model
geo_model.solutions = gempy_engine.compute_model(
interpolation_input=interpolation_input,
options=geo_model.interpolation_options,
data_descriptor=geo_model.input_data_descriptor,
geophysics_input=geo_model.geophysics_input,
)
# Compute and observe the thickness of the geological layer
simulated_well = geo_model.solutions.octrees_output[0].last_output_center.custom_grid_values
thickness = simulated_well.sum()
pyro.deterministic(r'$\mu_{thickness}$', thickness.detach())
y_thickness = pyro.sample(r'$y_{thickness}$', dist.Normal(thickness, 50), obs=y_obs_list)
.. GENERATED FROM PYTHON SOURCE LINES 191-195
Running Prior Sampling and Visualization
----------------------------------------
Prior sampling is an essential step in probabilistic modeling.
It helps in understanding the distribution of our prior assumptions before observing any data.
.. GENERATED FROM PYTHON SOURCE LINES 197-198
Prepare observation data
.. GENERATED FROM PYTHON SOURCE LINES 198-200
.. code-block:: Python
y_obs_list = torch.tensor([200, 210, 190])
.. GENERATED FROM PYTHON SOURCE LINES 201-202
Run prior sampling and visualization
.. GENERATED FROM PYTHON SOURCE LINES 202-207
.. code-block:: Python
prior = Predictive(model, num_samples=50)(y_obs_list)
data = az.from_pyro(prior=prior)
az.plot_trace(data.prior)
plt.show()
.. image-sg:: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_003.png
:alt: $\mu_{thickness}$, $\mu_{thickness}$, $\mu_{top}$, $\mu_{top}$, $y_{thickness}$, $y_{thickness}$
:srcset: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_003.png
:class: sphx-glr-single-img
.. GENERATED FROM PYTHON SOURCE LINES 208-213
Sampling from the Posterior using MCMC
--------------------------------------
We use Markov Chain Monte Carlo (MCMC) with the NUTS (No-U-Turn Sampler) algorithm
to sample from the posterior distribution. This gives us an understanding of the
distribution of our model parameters after considering the observed data.
.. GENERATED FROM PYTHON SOURCE LINES 215-216
Run MCMC using NUTS to sample from the posterior
.. GENERATED FROM PYTHON SOURCE LINES 216-233
.. code-block:: Python
# Magic sauce
from gempy_engine.core.backend_tensor import BackendTensor
# import gempy_engine.config
# config.DEFAULT_PYKEOPS = False
BackendTensor._change_backend(
engine_backend=gp.data.AvailableBackends.PYTORCH,
dtype="float64",
pykeops_enabled=False
)
pyro.primitives.enable_validation(is_validate=True)
nuts_kernel = NUTS(model, step_size=0.0085, adapt_step_size=True, target_accept_prob=0.9, max_tree_depth=10, init_strategy=init_to_mean)
mcmc = MCMC(nuts_kernel, num_samples=200, warmup_steps=50)
mcmc.run(y_obs_list)
.. rst-class:: sphx-glr-script-out
.. code-block:: none
Setting Backend To: AvailableBackends.PYTORCH
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.. GENERATED FROM PYTHON SOURCE LINES 234-238
Posterior Predictive Checks
---------------------------
After obtaining the posterior samples, we perform posterior predictive checks.
This step is crucial to evaluate the performance and validity of our probabilistic model.
.. GENERATED FROM PYTHON SOURCE LINES 240-241
Sample from posterior predictive and visualize
.. GENERATED FROM PYTHON SOURCE LINES 241-247
.. code-block:: Python
posterior_samples = mcmc.get_samples()
posterior_predictive = Predictive(model, posterior_samples)(y_obs_list)
data = az.from_pyro(posterior=mcmc, prior=prior, posterior_predictive=posterior_predictive)
az.plot_trace(data)
plt.show()
.. image-sg:: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_004.png
:alt: $\mu_{top}$, $\mu_{top}$
:srcset: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_004.png
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
.. code-block:: none
/home/leguark/.virtualenvs/gempy_dependencies/lib/python3.10/site-packages/arviz/data/io_pyro.py:158: UserWarning: Could not get vectorized trace, log_likelihood group will be omitted. Check your model vectorization or set log_likelihood=False
warnings.warn(
.. GENERATED FROM PYTHON SOURCE LINES 248-253
Density Plot of Posterior Predictive
------------------------------------
A density plot provides a visual representation of the distribution of the
posterior predictive checks. It helps in comparing the prior and posterior distributions
and in assessing the impact of our observed data on the model.
.. GENERATED FROM PYTHON SOURCE LINES 255-256
Plot density of posterior predictive and prior predictive
.. GENERATED FROM PYTHON SOURCE LINES 256-265
.. code-block:: Python
az.plot_density(
data=[data.posterior_predictive, data.prior_predictive],
shade=.9,
var_names=[r'$\mu_{thickness}$'],
data_labels=["Posterior Predictive", "Prior Predictive"],
colors=[default_red, default_blue],
)
plt.show()
.. image-sg:: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_005.png
:alt: $\mu_{thickness}$
:srcset: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_005.png
:class: sphx-glr-single-img
.. GENERATED FROM PYTHON SOURCE LINES 266-267
Plot spagetti
.. GENERATED FROM PYTHON SOURCE LINES 267-290
.. code-block:: Python
p2d = plot_geo_setting_well(geo_model, alpha=0.1, show_lith=False)
for i in range(0,199,5):
gp.modify_surface_points(
geo_model=geo_model,
slice=0,
Z= geo_model.input_transform.apply_inverse(
points=np.array([[0, 0, data.posterior[r'$\mu_{top}$'][0][i].item()]]))[0,2]
)
gp.compute_model(geo_model)
plot_regular_grid_contacts(
gempy_model=geo_model,
ax=p2d.axes[0],
slicer_data=p2d.section_data_list[0].slicer_data,
resolution=geo_model.grid.regular_grid.resolution,
only_faults=False,
kwargs={'alpha': 0.1}
)
p2d.fig.show()
# sphinx_gallery_thumbnail_number = 2
.. image-sg:: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_006.png
:alt: Cell Number: mid Direction: y
:srcset: /examples/04_probabilistic_modeling/images/sphx_glr_01_thickness_problem_gempy_006.png
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
.. code-block:: none
Setting Backend To: AvailableBackends.numpy
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.. rst-class:: sphx-glr-timing
**Total running time of the script:** (0 minutes 56.217 seconds)
.. _sphx_glr_download_examples_04_probabilistic_modeling_01_thickness_problem_gempy.py:
.. only:: html
.. container:: sphx-glr-footer sphx-glr-footer-example
.. container:: sphx-glr-download sphx-glr-download-jupyter
:download:`Download Jupyter notebook: 01_thickness_problem_gempy.ipynb <01_thickness_problem_gempy.ipynb>`
.. container:: sphx-glr-download sphx-glr-download-python
:download:`Download Python source code: 01_thickness_problem_gempy.py <01_thickness_problem_gempy.py>`
.. only:: html
.. rst-class:: sphx-glr-signature
`Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_