Cpt conditioning continued by bramvandeneijnden · Pull Request #5 · StemVibrations/RandomFields

bramvandeneijnden · 2024-12-06T09:45:06Z

Complete CPT interpretation module for generating conditioned random fields of elastic properties based on CPT data.

example to be added to documentation

new file: random_fields/generate_conditioned_field.py

modified: random_fields/generate_conditioned_field.py

Changes to be committed: modified: ../README.md new file: Makefile renamed: static/random_field.png -> _static/random_field.png new file: _static/random_field_1.png new file: _static/random_field_2.png new file: _static/random_field_3.png renamed: static/random_field_3D.png -> _static/random_field_3D.png new file: authors.rst new file: conf.py new file: contributions.rst new file: index.rst new file: installation.rst new file: make.bat new file: requirements.txt new file: theory.rst new file: tutorials.rst modified: ../random_fields/generate_conditioned_field.py modified: ../random_fields/generate_field.py modified: ../random_fields/utils.py

Changes committed: new file: _static/conditioned_random_field_3D.png new file: _static/kriging_mean_2D.png new file: _static/kriging_mean_3D.png new file: _static/kriging_std_2D.png new file: _static/kriging_std_3D.png new file: _static/random_field_4.png new file: _static/random_field_5.png modified: index.rst modified: tutorials.rst modified: ../random_fields/utils.py

Changes to be committed: modified: tutorials.rst modified: ../requirements.txt

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

modified: docs/contributions.rst modified: docs/installation.rst modified: random_fields/generate_field.py modified: random_fields/utils.py modified: requirements_dev.txt new file: tests/data/kriging_mean_3D.txt new file: tests/data/kriging_std_3D.txt modified: tests/test_random_field.py

- style changes - update docstrings - extended test modified: docs/contributions.rst modified: random_fields/generate_field.py modified: random_fields/utils.py modified: requirements.txt modified: requirements_dev.txt new file: tests/data/conditioned_rf_3D.txt deleted: tests/data/kriging_mean_3D.txt deleted: tests/data/kriging_std_3D.txt modified: tests/test_random_field.py

modified: requirements_dev.txt

new file: random_fields/geostatistical_cpt_interpretation.py modified: random_fields/geostatistical_cpt_interpretation.py

modified: random_fields/geostatistical_cpt_interpretation.py

modified: random_fields/geostatistical_cpt_interpretation.py modified: requirements.txt modified: requirements_dev.txt new file: tests/data/DelftSchiedam_cpts/CPT000000217393_IMBRO.gef new file: tests/data/DelftSchiedam_cpts/CPT000000217402_IMBRO.gef new file: tests/data/DelftSchiedam_cpts/CPT000000217406_IMBRO.gef new file: tests/data/DelftSchiedam_cpts/CPT000000217408_IMBRO.gef new file: tests/data/DelftSchiedam_cpts/CPT000000217409_IMBRO.gef new file: tests/data/DelftSchiedam_cpts/locatie_levering.kml

modified: random_fields/geostatistical_cpt_interpretation.py modified: setup.cfg

modified: random_fields/geostatistical_cpt_interpretation.py

modified: requirements.txt modified: requirements_dev.txt

modified: random_fields/geostatistical_cpt_interpretation.py modified: requirements.txt modified: requirements_dev.txt modified: setup.cfg deleted: tests/data/DelftSchiedam_cpts/112-074.400-2022-01-CPT-01.gef deleted: tests/data/DelftSchiedam_cpts/112-074.500-2022-01-CPT-01.gef deleted: tests/data/DelftSchiedam_cpts/112-074.600-2022-01-CPT-01.gef deleted: tests/data/DelftSchiedam_cpts/112-074.700-2022-01-CPT-01.gef deleted: tests/data/DelftSchiedam_cpts/112-074.800-2022-01-CPT-01.gef

modified: requirements.txt modified: requirements_dev.txt modified: setup.cfg

EleniSmyrniou · 2024-12-10T12:33:51Z

+import scipy.stats as st
+import logging
+
+from generate_field import RandomFields, ModelName


This does not work please change to random_fields.generate_field

fix package reference to `random_fields`

…nd XML files

…field generation functions

…able figure sizes; update documentation for 2D and 3D random field visualizations.

…le to PNG

…ct spelling of "functionalities"

…oned Random Field on CPT data

…ting.assert_allclose for better precision

…by adding relative tolerance

… pull request branch coverage

…r readability

…stency

… code readability

aronnoordam · 2025-01-15T17:05:05Z

+import random_fields
+
+project = 'RandomFields'
+copyright = '2024, STEM team'


Suggested change

copyright = '2024, STEM team'

copyright = '2025, STEM team'

aronnoordam · 2025-01-15T17:08:54Z

I think we should also test the tutorials, like we do in STEM, but maybe in another PR

aronnoordam · 2025-01-15T19:50:27Z

+            self.trans_model_vs.x_to_z(self.conditioning_data.vs[self.conditional_sample_index]))
+
+        # initiate two independent random field generators for shear wave velocity `vs` and density `rho`
+        self._random_fields_vs = RandomFields(model_name=ModelName.Gaussian,


i would make model_name a class attribute

aronnoordam · 2025-01-15T19:52:16Z

+        self.young_modulus = 2 * GO * (1. + self.poisson_ratio)
+        self.solid_density = rho * (1. - self.porosity) + self.porosity * self.water_density
+
+        for value in self.return_property:


else warning, property does not exist

aronnoordam · 2025-01-15T19:54:22Z

are all these plotting functions overlapping with the plotting functions in the random field classes?

aronnoordam · 2025-01-15T19:55:08Z

+
+@pytest.mark.parametrize("cpt_folder_path, test_file", [("./tests/cpts/gef", "./tests/data/2d_rf_gef.pickle"),
+                                                        ("./tests/cpts/xml", "./tests/data/2d_rf_xml.pickle")])
+def test_2d_random_field(cpt_folder_path, test_file):


missing type hints

aronnoordam · 2025-01-15T19:57:10Z

-    idx_end = data_org.index("currentfile DataString readhexstring pop")
-    data = [val == data_new[header + i] for i, val in enumerate(data_org[header:idx_end])]
-    assert all(data)
+    assert os.path.isfile("random_field.eps")


should this eps file be removed after the test?

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

…lidation checks

bramvandeneijnden and others added 23 commits June 13, 2024 17:07

added first version of conditioned random field generator

8015988

new file: random_fields/generate_conditioned_field.py

corrections, clean-up, efficiency and commenting

dfe8826

modified: random_fields/generate_conditioned_field.py

added sklearn to the requirements

6b54e89

Changes to be committed: modified: tutorials.rst modified: ../requirements.txt

deleted: random_fields/generate_conditioned_field.py

78643d3

modified: setup.cfg

5fadc51

modified: setup.cfg (sklearn --> scikit-learn)

04170dd

Update docs/installation.rst

3b9df07

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

Update random_fields/generate_field.py

72e157b

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

modified: requirements.txt

f76e0f0

modified: requirements_dev.txt

Introduction of geostatistical interpretation of CPTs

fadddba

new file: random_fields/geostatistical_cpt_interpretation.py modified: random_fields/geostatistical_cpt_interpretation.py

TODO: update dependencies...

ecfd3e4

modified: random_fields/geostatistical_cpt_interpretation.py

added function to export conditioning data for visualisation

837f49b

modified: random_fields/geostatistical_cpt_interpretation.py

modified: random_fields/geostatistical_cpt_interpretation.py

0ccabe9

added dependencies scikit-learn and d-geolib-plus

ae546bb

modified: random_fields/geostatistical_cpt_interpretation.py modified: setup.cfg

minor fix

5bc2477

modified: random_fields/geostatistical_cpt_interpretation.py

set numpy version from ==1.24 to >= 1.24

59eebfc

modified: requirements.txt modified: requirements_dev.txt

scipy requirements weakened

13f246a

modified: requirements.txt modified: requirements_dev.txt modified: setup.cfg

bramvandeneijnden requested review from aronnoordam and brunozc as code owners December 6, 2024 09:45

EleniSmyrniou reviewed Dec 10, 2024

View reviewed changes

bramvandeneijnden and others added 4 commits December 10, 2024 13:42

Update geostatistical_cpt_interpretation.py

be3acd2

fix package reference to `random_fields`

updated authors.rst

d1a77a0

Correct GitHub username casing in documentation configuration

ec7bc72

Update dependency versions in requirements and setup configuration

bb76a5c

brunozc added 21 commits January 13, 2025 19:47

Add unit tests for conditional 2D random field generation using GEF a…

93dd70c

…nd XML files

Downgrade scipy version to 1.13.1 in requirements files

cc45031

Refactor code for improved readability and maintainability in random …

f19560f

…field generation functions

fixed test for linux

c94a6d3

Fix file path for 3D random field test on Windows and remove skip marker

ea2eb6a

Add Read the Docs configuration file for documentation build

6d04569

Enhance plotting functions to support conditional points and customiz…

6439e69

…able figure sizes; update documentation for 2D and 3D random field visualizations.

fixed style

268d135

Update 3D random field test to use pickle format and change output fi…

e224365

…le to PNG

Rename "STEM team" to "Random Fields team" in documentation and corre…

290abe0

…ct spelling of "functionalities"

Update tutorial to reflect 2D/3D conditioned Random Field on CPT data

60b7837

Update tutorial heading to use "and" for clarity in 2D and 3D conditi…

ecc4d98

…oned Random Field on CPT data

fixed bug in test

2833dbc

Update output file format in 3D random field test from PNG to EPS

c4a686f

Add tests for ElasticityFieldsFromCpt and RandomFieldProperties

50b54ca

Refactor assertions in 3D conditioned random field test to use np.tes…

963cf01

…ting.assert_allclose for better precision

Increase precision of assertions in 3D conditioned random field test …

e7247be

…by adding relative tolerance

Update GitHub Actions workflow to allow manual triggering and broaden…

caa7cd6

… pull request branch coverage

Fix formatting in tutorial_4.rst by adding missing newlines for bette…

8d5e1d3

…r readability

Improve mathematical notation in tutorial_4.rst for clarity and consi…

69fe1a3

…stency

Refactor ElasticityFieldsFromCpt class to improve variable naming and…

1f6152a

… code readability

aronnoordam reviewed Jan 15, 2025

View reviewed changes

brunozc and others added 8 commits January 15, 2025 21:02

Update docs/tutorial_4.rst

580569b

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

Update docs/conf.py

1753666

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

Update docs/tutorial_4.rst

829600e

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

Update random_fields/generate_field.py

1461715

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

Update random_fields/generate_field.py

cc0faad

Co-authored-by: aronnoordam <51492202+aronnoordam@users.noreply.github.com>

Enhance calibration method to accept three boolean indices and add va…

9d1dc3d

…lidation checks

Merge branch 'main' into CPT_conditioning_continued

83cbce7

update: refine dependencies and remove redundant entries in setup.cfg

33b2815

Navigation Menu

Uh oh!

Cpt conditioning continued - #5

Cpt conditioning continued#5
bramvandeneijnden wants to merge 63 commits into
mainfrom
CPT_conditioning_continued

bramvandeneijnden commented Dec 6, 2024

Uh oh!

EleniSmyrniou Dec 10, 2024

Uh oh!

bramvandeneijnden Dec 10, 2024

Uh oh!

Uh oh!

aronnoordam Jan 15, 2025

Uh oh!

aronnoordam Jan 15, 2025

Uh oh!

Uh oh!

Uh oh!

aronnoordam Jan 15, 2025

Uh oh!

aronnoordam Jan 15, 2025

Uh oh!

aronnoordam Jan 15, 2025

Uh oh!

aronnoordam Jan 15, 2025

Uh oh!

aronnoordam Jan 15, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Uh oh!

Conversation

bramvandeneijnden commented Dec 6, 2024

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants