diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index e70de0e0..ac67de34 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -6,7 +6,7 @@ body: - type: markdown attributes: value: | - ## Bug Report + ## 🐛 Bug Report Thanks for submitting a bug report to map2loop! Please use this template to report a bug. Please provide as much detail as possible to help us reproduce and fix the issue efficiently. @@ -16,6 +16,8 @@ body: label: Version description: What version of map2loop and LoopProjectFile are you running? You can find this information by running `import map2loop` and `map2loop.__version__` in your python terminal or jupyter notebook. placeholder: "Enter map2loop and LoopProjectFile versions" + validations: + required: true - type: textarea id: bug_description @@ -33,25 +35,7 @@ body: description: "Provide a minimal reproducible example with the code necessary to reproduce the bug. For more guidance, visit: [How to create a minimal complete reproducible example](https://forum.access-hive.org.au/t/how-to-create-a-minimal-complete-reproducible-example/843)" placeholder: "Enter the steps to reproduce the bug" validations: - required: true - - - type: textarea - id: expected_behavior - attributes: - label: "Expected Behavior" - description: "Describe what you expected to happen." - placeholder: "Enter the expected behavior" - validations: - required: true - - - type: textarea - id: actual_behavior - attributes: - label: "Actual Behavior" - description: "Describe what actually happened when you encountered the bug." - placeholder: "Enter the actual behavior" - validations: - required: true + required: false - type: textarea id: additional_context @@ -69,18 +53,7 @@ body: description: "Specify the environment in which the bug occurred (e.g., operating system, browser, application version)." placeholder: "Enter the environment details" validations: - required: true + required: false + - - type: checkboxes - id: severity - attributes: - label: "Severity" - description: "Select the severity level of the bug." - options: - - label: "Low" - - label: "Medium" - - label: "High" - - label: "Critical" - validations: - required: true diff --git a/.github/ISSUE_TEMPLATE/documentation_request.yml b/.github/ISSUE_TEMPLATE/documentation_request.yml index 9d2ce617..253d9219 100644 --- a/.github/ISSUE_TEMPLATE/documentation_request.yml +++ b/.github/ISSUE_TEMPLATE/documentation_request.yml @@ -6,8 +6,7 @@ body: - type: markdown attributes: value: | - ## Documentation Request - + ## 📓 Documentation Request Please use this template to suggest an improvement or addition to map2loop documentation. Provide as much detail as possible to help us understand and implement your request efficiently @@ -18,13 +17,4 @@ body: description: "Describe the documentation you would like to see. Include details on why it is needed and how it should be structured." placeholder: "Enter a detailed description of the documentation" validations: - required: true - - - type: textarea - id: additional_context - attributes: - label: "Additional Context" - description: "Any other context or information that may be helpful." - placeholder: "Enter any additional context" - validations: - required: false + required: true \ No newline at end of file diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index 5d2d409a..f8fedbdc 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -6,8 +6,7 @@ body: - type: markdown attributes: value: | - ## Feature Request - + ## 🚀 Feature Request Please use this template to submit your feature request. Provide as much detail as possible to help us understand and implement your request efficiently. - type: checkboxes @@ -29,50 +28,12 @@ body: validations: required: true - - type: textarea - id: current_situation - attributes: - label: "Current Situation" - description: "Describe the current situation and how the absence of this feature affects you." - placeholder: "Explain the current situation and its drawbacks" - validations: - required: true - - type: textarea id: version attributes: label: Version description: What version of map2loop and LoopProjectFile are you running that doesn't have this feature? You can find this information by running `import map2loop` and `map2loop.__version__` in your python terminal or jupyter notebook. placeholder: "Enter map2loop and LoopProjectFile versions" - - - type: textarea - id: proposed_solution - attributes: - label: "Proposed Solution" - description: "Describe how you envision the feature working. Include any specific requirements or details" - placeholder: "Explain how the feature should work" validations: required: true - - type: input - id: additional_context - attributes: - label: "Additional Context" - description: "Provide any other context or information that may be helpful in understanding the feature request." - placeholder: "Enter any additional context" - validations: - required: false - - - type: checkboxes - id: affected_areas - attributes: - label: "Affected Areas" - description: "Select the areas of the project that this feature request impacts." - options: - - label: "input data" - - label: "project creation" - - label: "samplers" - - label: "sorters" - - label: "stratigraphic column" - - label: "data types" - - label: "Other" diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml index ba6b949b..871f7252 100644 --- a/.github/ISSUE_TEMPLATE/question.yml +++ b/.github/ISSUE_TEMPLATE/question.yml @@ -6,8 +6,7 @@ body: - type: markdown attributes: value: | - ## Question - + ## 💬 Question Please use this template to ask a question about applying map2loop to your data. Provide as much detail as possible to help us understand and answer your question efficiently. @@ -29,11 +28,11 @@ body: validations: required: false - - type: input + - type: textarea id: additional_context attributes: label: "Additional Context" description: "Provide any other context or information that may be helpful in answering your question." placeholder: "Enter any additional context" validations: - required: false + required: false \ No newline at end of file diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml deleted file mode 100644 index a5d5b47b..00000000 --- a/.github/workflows/CD.yml +++ /dev/null @@ -1,271 +0,0 @@ -# for this workflow to work, need to release LPF=1.0.5, map2model=1.0.1, use json instead of hjson - -name: release-please - -on: [push, pull_request] - -permissions: - contents: write - pull-requests: write - -jobs: - linting: - name: Linting - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install black ruff - - name: Autoformat with black - run: | - black . - - name: Lint with ruff - run: | - ruff check . --fix - - name: Check for local changes - run: | - if [ -n "$(git status --porcelain)" ]; then - git config --global user.name "github-actions[bot]" - git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" - git add . - git commit -m "style: style fixes by ruff and autoformatting by black" - fi - - uses: stefanzweifel/git-auto-commit-action@v5 - with: - commit_message: "style: style fixes by ruff and autoformatting by black" - - pypi-build-sdist: - name: Build SDist - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Build SDist - run: | - pip install build - python -m build - - - uses: actions/upload-artifact@v4 - with: - name: map2loop-dist - path: dist/*.tar.gz - compression-level: 0 - - pypi-test-sdist: - name: Test sdist - needs: pypi-build-sdist - runs-on: ubuntu-latest - steps: - - name: Install GDAL - run: | - sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable - sudo apt-get update - sudo apt-get install -y libgdal-dev gdal-bin - - - name: Download sdist from artifacts - uses: actions/download-artifact@v4 - with: - name: map2loop-dist - path: dist - - - name: Build Map2Loop from sdist and install test dependencies - shell: bash - run: | - pip install --upgrade pip - pip install numpy==1.26.4 - pip install geopandas shapely networkx owslib map2model loopprojectfile beartype gdal==3.8.4 hjson pytest scikit-learn - pip install --no-cache dist/*.tar.gz - pip list - - pypi-build-wheels: - needs: pypi-test-sdist - name: Build Wheels - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - os: - - ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: 3.x - - - name: Build Wheels - run: | - pip install build - python -m build --wheel - - - uses: actions/upload-artifact@v4 - with: - name: map2loop-wheels-${{ matrix.os }} - path: dist/*.whl - compression-level: 0 - - pypi-test-wheels: - name: Test wheels on ${{ matrix.os }} - needs: pypi-build-wheels - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - os: - - ubuntu-latest - include: - - os: "ubuntu-latest" - artifact: map2loop-wheels-ubuntu-latest - - steps: - - name: Checkout - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v5 - - - name: Install GDAL - Linux - if: runner.os == 'Linux' - run: | - sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable - sudo apt-get update - sudo apt-get install -y libgdal-dev gdal-bin - - - name: Upgrade pip - run: | - python -m pip install --upgrade pip - - - name: Download wheels from artifacts - uses: actions/download-artifact@v4 - with: - name: ${{ matrix.artifact }} - path: dist - - - name: Install dependencies and Map2Loop wheel - shell: bash - run: | - pip install --upgrade pip - pip install numpy==1.26.4 - pip install -r dependencies.txt - pip install --no-cache --pre --no-index --find-links dist map2loop - pip list - - - name: Testing - shell: bash -l {0} - run: | - pytest - - conda-build: - name: Conda Build and Deploy ${{ matrix.os }} - Python Version-${{ matrix.python-version }} - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - os: - - ubuntu-latest - # - macos-latest # currently not supported because needs libgcc>= 14 and not available for macos-latest (version available is 4.x.x) - - windows-latest - python-version: ["3.9", "3.10", "3.11", "3.12"] - steps: - - uses: actions/checkout@v4 - - uses: conda-incubator/setup-miniconda@v3 - with: - miniforge-version: latest - activate-environment: anaconda-client-env. - - - name: Installing dependencies - shell: bash -l {0} - run: | - conda install -c conda-forge conda-build anaconda-client conda-verify -y - conda install -c loop3d -c conda-forge --file dependencies.txt -y - conda install pytest -y - - - name: Building and install - shell: bash -l {0} - run: | - pip install . - - - name: Testing - shell: bash -l {0} - run: | - pytest - - - name: Conda Build - env: - ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }} - path: ~/conda_pkgs_dir - shell: bash -l {0} - run: | - conda build -c anaconda -c conda-forge -c loop3d --output-folder conda conda --python ${{ matrix.python-version }} - - - name: upload artifacts - uses: actions/upload-artifact@v4 - with: - name: map2loop-conda-${{ matrix.os }}-${{ matrix.python-version }} - path: conda - - # release-please: - # needs: [pypi-test-wheels, conda-build] - # runs-on: ubuntu-latest - # if: github.ref == 'refs/heads/master' - # steps: - # - uses: actions/checkout@v4 - # - uses: googleapis/release-please-action@v4 - # id: release - # with: - # release-type: "python" - # config-file: "release-please-config.json" - # manifest-file: ".release-please-manifest.json" - # outputs: - # release_created: ${{ steps.release.outputs.release_created }} - # #if a release is created then run the deploy scripts for github.io, conda, pypi and docker - - conda-upload: - needs: [conda-build] - runs-on: ${{matrix.os}} - strategy: - fail-fast: false - matrix: - os: - - ubuntu-latest - # - macos-latest - - windows-latest - python-version: ["3.9", "3.10", "3.11", "3.12"] - # if: ${{ needs.release-please.outputs.release_created }} - steps: - - uses: actions/download-artifact@v4 - with: - name: map2loop-conda-${{ matrix.os }}-${{ matrix.python-version }} - path: conda - - uses: conda-incubator/setup-miniconda@v3 - - name: upload all files to conda-forge - shell: bash -l {0} - env: - ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }} - with: - skip-existing: true - verbose: true - run: | - conda install -c anaconda anaconda-client -y - anaconda upload --label main conda/*/*.tar.bz2 - - pypi-upload: - needs: [pypi-test-wheels] - runs-on: - - ubuntu-latest - # if: ${{ needs.release-please.outputs.release_created }} - permissions: - # IMPORTANT: this permission is mandatory for trusted publishing - id-token: write - steps: - - uses: actions/download-artifact@v4 - with: - name: map2loop-dist - path: dist/ - - uses: pypa/gh-action-pypi-publish@release/v1 - with: - skip-existing: true - verbose: true diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml new file mode 100644 index 00000000..1a9949f1 --- /dev/null +++ b/.github/workflows/conda.yml @@ -0,0 +1,38 @@ +name: Build conda packages + +on: + workflow_dispatch: + +jobs: + build_wheels: + name: Build wheels on + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: ${{ fromJSON(vars.BUILD_OS)}} + python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}} + steps: + - uses: conda-incubator/setup-miniconda@v3 + with: + auto-update-conda: true + python-version: ${{ matrix.python-version }} + + - uses: actions/checkout@v4 + - name: update submodules + run: | + git submodule update --init --recursive + - name: Conda build + env: + ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }} + shell: bash -l {0} + run: | + conda install -c conda-forge conda-build scikit-build-core numpy anaconda-client conda-libmamba-solver -y + conda build -c conda-forge -c loop3d --output-folder conda conda --python ${{matrix.python-version}} + anaconda upload --label main conda/*/*.tar.bz2 + + - name: upload artifacts + uses: actions/upload-artifact@v4 + with: + name: conda-build-${{matrix.os}}-${{ matrix.python-version }} + path: conda \ No newline at end of file diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 0c1ca3bc..a7c722a3 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -3,13 +3,14 @@ name: Build and Deploy Documentation on: workflow_dispatch: - - jobs: documentation-test: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v4 + with: + ref: ${{ github.ref }} + - run: | cp CHANGELOG.md docs/source/CHANGELOG.md docker build . -t=docs -f docs/Dockerfile @@ -19,8 +20,9 @@ jobs: with: name: docs path: docs/build/html + documentation-deploy: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04 if: GitHub.ref == 'refs/heads/master' steps: - uses: actions/checkout@v4 diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml new file mode 100644 index 00000000..a7ea3a0c --- /dev/null +++ b/.github/workflows/linting_and_testing.yml @@ -0,0 +1,48 @@ +name: Linting and Testing + +on: + [push] + +jobs: + linting: + name: Linting + runs-on: ubuntu-24.04 + steps: + - uses: actions/checkout@v4 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install black ruff + ruff check . --fix + + - uses: stefanzweifel/git-auto-commit-action@v5 + with: + commit_message: "style: style fixes by ruff and autoformatting by black" + + testing: + name: Testing + runs-on: ubuntu-24.04 + steps: + - uses: actions/checkout@v4 + - name: Install GDAL + run: | + sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable + sudo apt-get update + sudo apt-get install -y libgdal-dev gdal-bin + + - name: Install dependencies + run: | + conda update -n base -c defaults conda -y + conda install -n base conda-libmamba-solver -c conda-forge -y + conda install -c conda-forge gdal -y + conda install -c conda-forge -c loop3d --file dependencies.txt -y + conda install pytest -y + + - name: Install map2loop + run: | + python -m pip install . + + - name: Run tests + run: | + pytest + diff --git a/.github/workflows/publish_conda.yml b/.github/workflows/publish_conda.yml new file mode 100644 index 00000000..89ab5c00 --- /dev/null +++ b/.github/workflows/publish_conda.yml @@ -0,0 +1,40 @@ +on: + push: + branches: + - master + workflow_dispatch: + +jobs: + release-please: + runs-on: ubuntu-24.04 + steps: + - uses: GoogleCloudPlatform/release-please-action@v4 + id: release + with: + release-type: python + package-name: map2loop + - name: Debug release_created output + run: | + echo "Release created: ${{ steps.release.outputs.release_created }}" + outputs: + release_created: ${{ steps.release.outputs.release_created }} + + pypi: + runs-on: ubuntu-24.04 + needs: release-please + if: ${{ needs.release-please.outputs.release_created }} + steps: + - name: Trigger build for pypi and upload + run: | + curl -X POST \ + -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \ + -H "Accept: application/vnd.github.v3+json" \ + https://api.github.com/repos/Loop3d/map2loop/actions/workflows/pypi.yml/dispatches \ + -d '{"ref":"master"}' + - name: Trigger build for conda and upload + run: | + curl -X POST \ + -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \ + -H "Accept: application/vnd.github.v3+json" \ + https://api.github.com/repos/Loop3d/map2loop/actions/workflows/conda.yml/dispatches \ + -d '{"ref":"master"}' diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml new file mode 100644 index 00000000..50e8d505 --- /dev/null +++ b/.github/workflows/pypi.yml @@ -0,0 +1,43 @@ +name: Deploy to PYPI + +on: + workflow_dispatch: +jobs: + + sdist: + name: Build sdist + runs-on: ubuntu-24.04 + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install build + - name: Build sdist + run: python -m build --sdist + - uses: actions/upload-artifact@v4 + with: + name: dist + path: ./dist/*.tar.gz + + publish: + name: Publish wheels to pypi + runs-on: ubuntu-24.04 + permissions: + # IMPORTANT: this permission is mandatory for trusted publishing + id-token: write + needs: sdist + steps: + - uses: actions/download-artifact@v4 + with: + name: dist + path: dist + - name: copy to wheelhouse + run: | + # cp -r wheelhouse/*/*.whl dist + - uses: pypa/gh-action-pypi-publish@release/v1 + with: + skip-existing: true + verbose: true + packages-dir: dist/ \ No newline at end of file diff --git a/MANIFEST.in b/MANIFEST.in index fee2a8aa..67577e81 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1,8 @@ +include LICENSE +include README.md + include map2loop/_datasets/clut_files/*.csv -include map2loop/_datasets/config_files/*.json \ No newline at end of file +include map2loop/_datasets/config_files/*.json +include map2loop/_datasets/geodata_files/hamersley/* + +recursive-include tests *.py \ No newline at end of file diff --git a/README.md b/README.md index f99a3985..144bc856 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,11 @@ -# Map2Loop 3.0 +![GitHub Release](https://img.shields.io/github/v/release/loop3d/map2loop) +![License](https://img.shields.io/github/license/loop3d/map2loop) +![PyPI - Downloads](https://img.shields.io/pypi/dm/map2loop?label=pip%20downloads) +![Conda Downloads](https://img.shields.io/conda/dn/loop3d/map2loop?label=Conda%20downloads) +[![Testing](https://github.com/Loop3D/map2loop/actions/workflows/linting_and_testing.yml/badge.svg)](https://github.com/Loop3D/map2loop/actions/workflows/linting_and_testing.yml) +[![Build and Deploy Documentation](https://github.com/Loop3D/map2loop/actions/workflows/documentation.yml/badge.svg)](https://github.com/Loop3D/map2loop/actions/workflows/documentation.yml) + +# Map2Loop 3.1 Generate 3D geological model inputs from geological maps — a high-level implementation and extension of the original map2loop code developed by Prof. Mark Jessell at UWA. To see an example interactive model built with map2loop and LoopStructural, follow this link: @@ -23,12 +30,20 @@ conda config --add channels conda-forge ### Run -To just use map2loop, issue the following +To just use map2loop, issue the following. * ```bash -conda install -c conda-forge -c loop3d map2loop -y +git clone https://github.com/Loop3D/map2loop.git + +cd map2loop + +conda install -c loop3d --file dependencies.txt + +pip install . ``` +

* We're actively working towards a better approach - stay tuned!

+ ### Documentation If you can call it that, is available here diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml index cbfd2b0e..d7d85008 100644 --- a/conda/conda_build_config.yaml +++ b/conda/conda_build_config.yaml @@ -1,4 +1,5 @@ python: + - 3.8 - 3.9 - 3.10 - 3.11 diff --git a/conda/meta.yaml b/conda/meta.yaml index b7571e6b..54bf081c 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -1,6 +1,5 @@ {% set name = "map2loop" %} - package: name: "{{ name|lower }}" version: "{{ environ.get('GIT_DESCRIBE_TAG', '') }}" @@ -8,15 +7,20 @@ package: source: git_url: https://github.com/Loop3D/map2loop + build: number: 0 - script: "{{ PYTHON }} -m pip install ." + script: "{{ PYTHON }} -m pip install . --no-deps" requirements: host: - pip - python run: + - loopprojectfile ==0.2.2 + - gdal + - map2model + - beartype - python - numpy - pandas @@ -25,12 +29,6 @@ requirements: - tqdm - networkx - owslib - - hjson - - loopprojectfile=0.1.3 - - map2model - - beartype - - gdal=3.8.4 - about: @@ -43,3 +41,7 @@ about: extra: recipe-maintainers: - lachlangrose + +channels: + - loop3d + - conda-forge \ No newline at end of file diff --git a/dependencies.txt b/dependencies.txt index 4681f3de..57a2f246 100644 --- a/dependencies.txt +++ b/dependencies.txt @@ -1,3 +1,4 @@ + numpy scipy geopandas @@ -5,9 +6,7 @@ shapely networkx owslib map2model -loopprojectfile==0.1.3 +loopprojectfile==0.2.2 beartype -gdal==3.8.4 -hjson pytest -scikit-learn +scikit-learn \ No newline at end of file diff --git a/docs/Dockerfile b/docs/Dockerfile index 2cc8b312..37c8cc89 100644 --- a/docs/Dockerfile +++ b/docs/Dockerfile @@ -12,8 +12,8 @@ RUN apt-get update -qq && \ libgl1\ libtinfo5\ libtiff6\ - libgl1-mesa-glx - + libgl1-mesa-glx\ + libarchive13 COPY . /map2loop @@ -23,7 +23,8 @@ COPY dependencies.txt dependencies.txt COPY dependencies.txt dependenciesdocs.txt RUN cat ./docs/requirements.txt >> dependenciesdocs.txt -RUN conda install -c conda-forge -c loop3d --file dependencies.txt -y +RUN conda install -c conda-forge -c loop3d --file dependenciesdocs.txt -y +RUN conda install gdal -y RUN pip install . diff --git a/docs/docker-compose.yml b/docs/docker-compose.yml index 2481428b..3ec795a5 100644 --- a/docs/docker-compose.yml +++ b/docs/docker-compose.yml @@ -1,5 +1,3 @@ -version: "3" - services: map2loop: build: @@ -9,4 +7,5 @@ services: - ../:/map2loop - ../../LoopStructural:/LoopStructural tty: true + # command: sh map2loop/docs/build_docs.sh \ No newline at end of file diff --git a/docs/requirements.txt b/docs/requirements.txt index 24754e30..8c10ee6e 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,8 +1,7 @@ -# all on conda forge sphinx sphinx-gallery pydata-sphinx-theme myst-parser sphinxcontrib-bibtex -conda-forge::poppler +poppler LoopStructural \ No newline at end of file diff --git a/docs/source/_static/m2l_code_template.ipynb b/docs/source/_static/m2l_code_template.ipynb index 66e4a773..f305f370 100644 --- a/docs/source/_static/m2l_code_template.ipynb +++ b/docs/source/_static/m2l_code_template.ipynb @@ -46,7 +46,7 @@ "from map2loop.m2l_enums import VerboseLevel\n", "from map2loop.m2l_enums import Datatype\n", "from map2loop.sampler import SamplerSpacing, SamplerDecimator\n", - "from map2loop.sorter import SorterUseHint, SorterUseNetworkX, SorterAgeBased, SorterAlpha\n", + "from map2loop.sorter import SorterAlpha\n", "import time" ] }, diff --git a/docs/source/conf.py b/docs/source/conf.py index e5edd5e6..6175247f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -13,7 +13,7 @@ import os import sys -sys.path.insert(0, os.path.abspath(".")) +sys.path.insert(0, os.path.abspath("../../")) # -- Project information ----------------------------------------------------- diff --git a/map2loop/__init__.py b/map2loop/__init__.py index 01a56aaa..17428522 100644 --- a/map2loop/__init__.py +++ b/map2loop/__init__.py @@ -1,5 +1,5 @@ - import logging + loggers = {} ch = logging.StreamHandler() formatter = logging.Formatter("%(levelname)s: %(asctime)s: %(filename)s:%(lineno)d -- %(message)s") @@ -7,3 +7,113 @@ ch.setLevel(logging.WARNING) from .project import Project from .version import __version__ + +import warnings # TODO: convert warnings to logging +from packaging import ( + version as pkg_version, +) # used instead of importlib.version because adheres to PEP 440 using pkg_version.parse +import pathlib +import re +from importlib.metadata import version as get_installed_version, PackageNotFoundError + + +class DependencyChecker: + ''' + A class to check installation and version compatibility of each package in dependencies.txt + + Attributes: + package_name (str): Name of the package + dependency_file (str): path to dependencies.txt + required_version (str or None): required version of the package as in dependencies.txt + installed_version (str or None): installed version of the package in the current environment + ''' + + def __init__(self, package_name, dependency_file="dependencies.txt"): + self.package_name = package_name + self.dependency_file = pathlib.Path(__file__).parent.parent / dependency_file + self.required_version = self.get_required_version() + self.installed_version = self.get_installed_version() + + def get_required_version(self): + ''' + Get the required package version for each package from dependencies.txt; + + Returns: + str or None: The required version of the package (if specified), otherwise None. + ''' + try: + with self.dependency_file.open("r") as file: + for line in file: + if line.startswith(f"{self.package_name}=="): + match = re.match(rf"^{self.package_name}==([\d\.]+)", line.strip()) + if match: + return match.group(1) + elif line.strip() == self.package_name: + return None + print(f"{self.package_name} version not found in {self.dependency_file}.") + except FileNotFoundError: + warnings.warn( + f"{self.dependency_file} not found. Unable to check {self.package_name} version compatibility.", + UserWarning, + ) + return None + + def get_installed_version(self): + ''' + Get the installed version of the package. + + Returns: + str: The installed version of the package. + ''' + try: + # Use importlib.metadata to get the installed version of the package + return get_installed_version(self.package_name) + except PackageNotFoundError: + raise ImportError( + f"{self.package_name} is not installed. Please install {self.package_name}." + ) + + def check_version(self): + ''' + Checks if the installed version of the package matches the required version in the dependencies.txt file. + ''' + if self.required_version is None: + if self.installed_version is None: + raise ImportError( + f"{self.package_name} is not installed. Please install {self.package_name} before using map2loop." + ) + else: + if self.installed_version is None or pkg_version.parse( + self.installed_version + ) != pkg_version.parse(self.required_version): + raise ImportError( + f"Installed version of {self.package_name}=={self.installed_version} does not match required version=={self.required_version}. " + f"Please install the correct version of {self.package_name}." + ) + + +def check_all_dependencies(dependency_file="dependencies.txt"): + dependencies_path = pathlib.Path(__file__).parent.parent / dependency_file + try: + with dependencies_path.open("r") as file: + for line in file: + line = line.strip() + if line.startswith("gdal"): + continue + if line: + if "==" in line: + package_name, _ = line.split("==") + else: + package_name = line + + checker = DependencyChecker(package_name, dependency_file=dependency_file) + checker.check_version() + except FileNotFoundError: + warnings.warn( + f"{dependency_file} not found. No dependencies checked for map2loop.", + UserWarning + ) + + +# Run check for all dependencies listed in dependencies.txt +check_all_dependencies() diff --git a/map2loop/_datasets/config_files/NSW.json b/map2loop/_datasets/config_files/NSW.json index 9261fc2d..88675381 100644 --- a/map2loop/_datasets/config_files/NSW.json +++ b/map2loop/_datasets/config_files/NSW.json @@ -24,7 +24,7 @@ "intrusive_text": "intrusive", "volcanic_text": "volcanic", "objectid_column": "ID", - "ignore_codes": ["cover"]}, + "ignore_lithology_codes": ["cover"]}, "fault": { "structtype_column": "boundaryty", "fault_text": "Fault", @@ -36,7 +36,7 @@ "dipestimate_column": "faultdipan", "dipestimate_text": "Moderate,Listric,Steep,Vertical", "name_column": "name", - "objectid_column": "unique_id" + "objectid_column": "unique_id", }, "fold": { "structtype_column": "codedescpt", diff --git a/map2loop/_datasets/config_files/QLD.json b/map2loop/_datasets/config_files/QLD.json index 7d93454e..d4a3b35e 100644 --- a/map2loop/_datasets/config_files/QLD.json +++ b/map2loop/_datasets/config_files/QLD.json @@ -24,7 +24,7 @@ "intrusive_text": "Y", "volcanic_text": "VOLCANIC", "objectid_column": "ID", - "ignore_codes": ["cover"] + "ignore_lithology_codes": ["cover"] }, "fault": { "structtype_column": "type", diff --git a/map2loop/_datasets/config_files/SA.json b/map2loop/_datasets/config_files/SA.json index f32022f4..daf2806e 100644 --- a/map2loop/_datasets/config_files/SA.json +++ b/map2loop/_datasets/config_files/SA.json @@ -24,7 +24,7 @@ "intrusive_text": "intrusive", "volcanic_text": "volc", "objectid_column": "ID", - "ignore_codes": ["cover"] + "ignore_lithology_codes": ["cover"] }, "fault": { "structtype_column": "descriptio", diff --git a/map2loop/_datasets/config_files/TAS.json b/map2loop/_datasets/config_files/TAS.json index a25adf23..d795f8d2 100644 --- a/map2loop/_datasets/config_files/TAS.json +++ b/map2loop/_datasets/config_files/TAS.json @@ -24,7 +24,7 @@ "intrusive_text": "granit", "volcanic_text": "volc", "objectid_column": "ID", - "ignore_codes": ["cover"] + "ignore_lithology_codes": ["cover"] }, "fault": { "structtype_column": "TYPE", diff --git a/map2loop/_datasets/config_files/VIC.json b/map2loop/_datasets/config_files/VIC.json index 16bb899f..b2762530 100644 --- a/map2loop/_datasets/config_files/VIC.json +++ b/map2loop/_datasets/config_files/VIC.json @@ -24,7 +24,7 @@ "intrusive_text": "intrusion", "volcanic_text": "volc", "objectid_column": "ID", - "ignore_codes": ["cover"] + "ignore_lithology_codes": ["cover"] }, "fault": { "structtype_column": "featuretyp", diff --git a/map2loop/_datasets/config_files/WA.json b/map2loop/_datasets/config_files/WA.json index 8b884fa4..4c722dc8 100644 --- a/map2loop/_datasets/config_files/WA.json +++ b/map2loop/_datasets/config_files/WA.json @@ -23,7 +23,7 @@ "intrusive_text": "intrusive", "volcanic_text": "volcanic", "objectid_column": "ID", - "ignore_codes": ["cover"] + "ignore_lithology_codes": ["cover"] }, "fault": { "structtype_column": "feature", diff --git a/map2loop/_datasets/geodata_files/hamersley/dtm_rp.tif b/map2loop/_datasets/geodata_files/hamersley/dtm_rp.tif new file mode 100644 index 00000000..a9ba843e Binary files /dev/null and b/map2loop/_datasets/geodata_files/hamersley/dtm_rp.tif differ diff --git a/map2loop/_datasets/geodata_files/hamersley/faults.geojson b/map2loop/_datasets/geodata_files/hamersley/faults.geojson new file mode 100644 index 00000000..bfc9d5dd --- /dev/null +++ b/map2loop/_datasets/geodata_files/hamersley/faults.geojson @@ -0,0 +1,42 @@ +{ +"type": "FeatureCollection", +"name": "faults", +"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:EPSG::28350" } }, +"features": [ +{ "type": "Feature", "properties": { "gml_id": "linear_500k.7344", "objectid": "7344", "feature": "Fault or shear zone, major", "type": "exposed", "fname": "None", "code": null, "dip": "90", "dip_est": "-999", "dip_dir": "45", "plunge": "0", "plunge_est": null, "plunge_dir": null, 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390.0, "index_righ": 49, "gml_id": "geol_500k.4685", "objectid": "4685", "x": 552075.5921, "y": 7487793.536, "strike": 300 }, "geometry": { "type": "Point", "coordinates": [ 552075.592163110035472, 7487793.536227280274034 ] } }, +{ "type": "Feature", "properties": { "dip": 52, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 181.0, "index_righ": 25, "gml_id": "geol_500k.14340", "objectid": "14341", "x": 521796.7218, "y": 7509376.561, "strike": 91 }, "geometry": { "type": "Point", "coordinates": [ 521796.721859230019618, 7509376.56236276961863 ] } }, +{ "type": "Feature", "properties": { "dip": 64, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 420.0, "index_righ": 44, "gml_id": "geol_500k.7875", "objectid": "7876", "x": 553087.8922, "y": 7484583.491, "strike": 330 }, "geometry": { "type": "Point", "coordinates": [ 553087.892269309959374, 7484583.492152259685099 ] } }, +{ "type": "Feature", "properties": { "dip": 33, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 219.0, "index_righ": 32, "gml_id": "geol_500k.5501", "objectid": "5501", "x": 544671.5774, "y": 7513917.04, "strike": 129 }, "geometry": { "type": "Point", "coordinates": [ 544671.577467399998568, 7513917.040575330145657 ] } }, +{ "type": "Feature", "properties": { "dip": 60, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 385.0, "index_righ": 31, "gml_id": "geol_500k.16188", "objectid": "16190", "x": 539933.7822, "y": 7483374.355, "strike": 295 }, "geometry": { "type": "Point", "coordinates": [ 539933.782225199975073, 7483374.356403660029173 ] } }, +{ "type": "Feature", "properties": { "dip": 60, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 171.0, "index_righ": 57, "gml_id": "geol_500k.6148", "objectid": "6148", "x": 521993.3993, "y": 7508834.989, "strike": 81 }, "geometry": { "type": "Point", "coordinates": [ 521993.399334150017239, 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"geometry": { "type": "Point", "coordinates": [ 553113.250977969961241, 7484612.185831510461867 ] } }, +{ "type": "Feature", "properties": { "dip": 26, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 405.0, "index_righ": 32, "gml_id": "geol_500k.5501", "objectid": "5501", "x": 544512.13, "y": 7514096.827, "strike": 315 }, "geometry": { "type": "Point", "coordinates": [ 544512.13000452995766, 7514096.828844400122762 ] } }, +{ "type": "Feature", "properties": { "dip": 24, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 230.0, "index_righ": 32, "gml_id": "geol_500k.5501", "objectid": "5501", "x": 529219.0531, "y": 7512991.483, "strike": 140 }, "geometry": { "type": "Point", "coordinates": [ 529219.053161659976467, 7512991.483141110278666 ] } }, +{ "type": "Feature", "properties": { "dip": 58, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 368.0, "index_righ": 58, "gml_id": "geol_500k.16190", "objectid": "16192", "x": 534077.0355, "y": 7482256.828, "strike": 278 }, "geometry": { "type": "Point", "coordinates": [ 534077.035659849992953, 7482256.829784540459514 ] } }, +{ "type": "Feature", "properties": { "dip": 54, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 200.0, "index_righ": 25, "gml_id": "geol_500k.14340", "objectid": "14341", "x": 536789.5709, "y": 7516217.953, "strike": 110 }, "geometry": { "type": "Point", "coordinates": [ 536789.57090088003315, 7516217.954258319921792 ] } }, +{ "type": "Feature", "properties": { "dip": 10, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 190.0, "index_righ": 50, "gml_id": "geol_500k.8420", "objectid": "8421", "x": 560770.7347, "y": 7497966.202, "strike": 100 }, "geometry": { "type": "Point", "coordinates": [ 560770.734732890035957, 7497966.203075700439513 ] } }, +{ "type": "Feature", "properties": { "dip": 24, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 181.0, "index_righ": 25, "gml_id": "geol_500k.14340", "objectid": "14341", "x": 537020.134, "y": 7516172.571, "strike": 91 }, "geometry": { "type": "Point", "coordinates": [ 537020.134009359986521, 7516172.571558499708772 ] } }, +{ "type": "Feature", "properties": { "dip": 50, "feature": "Bedding, showing strike and dip", "structypei": "BEIN", "azimuth2": 185.0, "index_righ": 49, "gml_id": "geol_500k.4685", "objectid": "4685", "x": 559881.968, "y": 7490671.207, "strike": 95 }, "geometry": { "type": "Point", "coordinates": [ 559881.968048759968951, 7490671.208677380345762 ] } } +] +} diff --git a/map2loop/_datasets/geodata_files/load_map2loop_data.py b/map2loop/_datasets/geodata_files/load_map2loop_data.py new file mode 100644 index 00000000..d625af9b --- /dev/null +++ b/map2loop/_datasets/geodata_files/load_map2loop_data.py @@ -0,0 +1,45 @@ +import geopandas +from importlib.resources import files +from osgeo import gdal +gdal.UseExceptions() + +def load_hamersley_geology(): + """ + Loads Hamersley geology data from a shapefile + + Args: + path (str): + The path to the shapefile + + Returns: + geopandas.GeoDataFrame: The geology data + """ + stream = files("map2loop._datasets.geodata_files.hamersley").joinpath("geology.geojson") + return geopandas.read_file(stream) + + +def load_hamersley_structure(): + """ + Loads Hamersley structure data from a shapefile + + Args: + path (str): + The path to the shapefile + + Returns: + geopandas.GeoDataFrame: The structure data + """ + + path = files("map2loop._datasets.geodata_files.hamersley").joinpath("structure.geojson") + return geopandas.read_file(path) + + +def load_hamersley_dtm(): + """ + Load DTM data from a raster file + + Returns: + gdal.Dataset: The DTM data + """ + path = files("map2loop._datasets.geodata_files.hamersley").joinpath("dtm_rp.tif") + return gdal.Open(path) diff --git a/map2loop/config.py b/map2loop/config.py index 92bd7725..48d017d3 100644 --- a/map2loop/config.py +++ b/map2loop/config.py @@ -1,5 +1,6 @@ +import urllib.error import beartype -import hjson +import json import urllib import time import pathlib @@ -9,6 +10,7 @@ logger = getLogger(__name__) + class Config: """ A data structure containing column name mappings for files and keywords @@ -50,7 +52,7 @@ def __init__(self): "intrusive_text": "intrusive", "volcanic_text": "volcanic", "objectid_column": "ID", - "ignore_codes": ["cover"], + "ignore_lithology_codes": ["cover"], } self.fault_config = { "structtype_column": "FEATURE", @@ -64,6 +66,8 @@ def __init__(self): "dipestimate_text": "'NORTH_EAST','NORTH',,'NOT ACCESSED'", "name_column": "NAME", "objectid_column": "ID", + "minimum_fault_length": -1.0, # negative -1 means not set + "ignore_fault_codes": [None], } self.fold_config = { "structtype_column": "FEATURE", @@ -89,146 +93,180 @@ def to_dict(self): } @beartype.beartype - def update_from_dictionary(self, dictionary: dict, lower: bool = False): + def update_from_dictionary(self, dictionary: dict, lower: bool = True): """ Update the config dictionary from a provided dict Args: dictionary (dict): The dictionary to update from """ + # make sure dictionary doesn't contain legacy keys + self.check_for_legacy_keys(dictionary) + + # make sure it has the minimum requirements + self.validate_config_dictionary(dictionary) + if "structure" in dictionary: self.structure_config.update(dictionary["structure"]) for key in dictionary["structure"].keys(): if key not in self.structure_config: - logger.warning(f"Config dictionary structure segment contained {key} which is not used") + logger.warning( + f"Config dictionary structure segment contained {key} which is not used" + ) dictionary.pop("structure") + if "geology" in dictionary: self.geology_config.update(dictionary["geology"]) for key in dictionary["geology"].keys(): if key not in self.geology_config: - logger.warning(f"Config dictionary geology segment contained {key} which is not used") + logger.warning( + f"Config dictionary geology segment contained {key} which is not used" + ) dictionary.pop("geology") if "fault" in dictionary: self.fault_config.update(dictionary["fault"]) for key in dictionary["fault"].keys(): if key not in self.fault_config: - logger.warning(f"Config dictionary fault segment contained {key} which is not used") + logger.warning( + f"Config dictionary fault segment contained {key} which is not used" + ) dictionary.pop("fault") if "fold" in dictionary: self.fold_config.update(dictionary["fold"]) for key in dictionary["fold"].keys(): if key not in self.fold_config: - logger.warning(f"Config dictionary fold segment contained {key} which is not used") + logger.warning( + f"Config dictionary fold segment contained {key} which is not used" + ) dictionary.pop("fold") if len(dictionary): logger.warning(f"Unused keys from config format {list(dictionary.keys())}") - @beartype.beartype - def update_from_legacy_file(self, file_map: dict, lower: bool = False): - """ - Update the config dictionary from the provided old version dictionary - - Args: - file_map (dict): The old version dictionary to update from - """ - - code_mapping = { - "otype": (self.structure_config, "orientation_type"), - "dd": (self.structure_config, "dipdir_column"), - "d": (self.structure_config, "dip_column"), - "sf": (self.structure_config, "description_column"), - "bedding": (self.structure_config, "bedding_text"), - "bo": (self.structure_config, "overturned_column"), - "btype": (self.structure_config, "overturned_text"), - "gi": (self.structure_config, "objectid_column"), - "c": (self.geology_config, "unitname_column"), - "u": (self.geology_config, "alt_unitname_column"), - "g": (self.geology_config, "group_column"), - "g2": (self.geology_config, "supergroup_column"), - "ds": (self.geology_config, "description_column"), - "min": (self.geology_config, "minage_column"), - "max": (self.geology_config, "maxage_column"), - "r1": (self.geology_config, "rocktype_column"), - "r2": (self.geology_config, "alt_rocktype_column"), - "sill": (self.geology_config, "sill_text"), - "intrusive": (self.geology_config, "intrusive_text"), - "volcanic": (self.geology_config, "volcanic_text"), - "f": (self.fault_config, "structtype_column"), - "fault": (self.fault_config, "fault_text"), - "fdipnull": (self.fault_config, "dip_null_value"), - "fdipdip_flag": (self.fault_config, "dipdir_flag"), - "fdipdir": (self.fault_config, "dipdir_column"), - "fdip": (self.fault_config, "dip_column"), - "fdipest": (self.fault_config, "dipestimate_column"), - "fdipest_vals": (self.fault_config, "dipestimate_text"), - "n": (self.fault_config, "name_column"), - "ff": (self.fold_config, "structtype_column"), - "fold": (self.fold_config, "fold_text"), - "t": (self.fold_config, "description_column"), - "syn": (self.fold_config, "synform_text"), - } - for code in code_mapping: - if code in file_map: - if lower is True: - file_map[code] = str(file_map[code]).lower() - code_mapping[code][0][code_mapping[code][1]] = file_map[code] - file_map.pop(code) - - if "o" in file_map: - self.structure_config["objectid_column"] = file_map["o"] - self.fault_config["objectid_column"] = file_map["o"] - self.fold_config["objectid_column"] = file_map["o"] - file_map.pop("o") - - if len(file_map) > 0: - logger.warning(f"Unused keys from legacy format {list(file_map.keys())}") @beartype.beartype def update_from_file( - self, filename: Union[pathlib.Path, str], legacy_format: bool = False, lower: bool = False + self, filename: Union[pathlib.Path, str], lower: bool = False ): """ Update the config dictionary from the provided json filename or url Args: - filename (str): Filename or URL of the JSON config file - legacy_format (bool, optional): Whether the JSON is an old version. Defaults to False. + filename (Union[pathlib.Path, str]): Filename or URL of the JSON config file + lower (bool, optional): convert keys to lowercase. Defaults to False. """ - if legacy_format: - func = self.update_from_legacy_file - else: - func = self.update_from_dictionary + func = self.update_from_dictionary try: filename = str(filename) + # if url, open the url if filename.startswith("http") or filename.startswith("ftp"): - try_count = 10 + try_count = 5 success = False - while try_count >= 0 and not success: + # try 5 times to access the URL + while try_count > 0 and not success: try: with urllib.request.urlopen(filename) as url_data: - data = hjson.load(url_data) + data = json.load(url_data) func(data, lower) success = True - except Exception as e: - # Catch a failed online access or file load, re-attempt - # a few times before throwing further + + # case 1. handle url error + except urllib.error.URLError as e: + # wait 0.25 seconds before trying again time.sleep(0.25) - try_count = try_count - 1 - if try_count < 0: - raise e + # decrease the number of tries by 1 + try_count -= 1 + # if no more tries left, raise the error + if try_count <= 0: + raise urllib.error.URLError( + f"Failed to access URL after multiple attempts: {filename}" + ) from e + + # case 2. handle json error + except json.JSONDecodeError as e: + raise json.JSONDecodeError( + f"Error decoding JSON data from URL: {filename}" + ) from e else: - with open(filename) as url_data: - data = hjson.load(url_data) - func(data, lower) + try: + with open(filename) as file_data: + data = json.load(file_data) + func(data, lower) + except FileNotFoundError as e: + err_string = f"The specified config file does not exist ({filename}).\n" + err_string += ( + "Please check the file exists and is accessible, then try again.\n" + ) + raise FileNotFoundError(err_string) from e + except json.JSONDecodeError as e: + raise json.JSONDecodeError( + f"Error decoding JSON data from file: {filename}" + ) from e + + except FileNotFoundError: + raise + except Exception: err_string = f"There is a problem parsing the config file ({filename}).\n" if filename.startswith("http"): err_string += "Please check the file is accessible online and then\n" else: err_string += "Please check the file exists and is accessible then\n" - if not legacy_format: - err_string += "Also check if this is a legacy config file and add clut_file_legacy=True to the Project function\n" err_string += "Check the contents for mismatched quotes or brackets!" raise Exception(err_string) + + @beartype.beartype + def validate_config_dictionary(self, config_dict: dict) -> None: + """ + Validate the structure and keys of the configuration dictionary. + + Args: + config_dict (dict): The config dictionary to validate. + + Raises: + ValueError: If the dictionary does not meet the minimum requirements for ma2p2loop. + """ + required_keys = { + "structure": {"dipdir_column", "dip_column"}, + "geology": {"unitname_column", "alt_unitname_column"}, + } + + for section, keys in required_keys.items(): + if section not in config_dict: + logger.error(f"Missing required section '{section}' in config dictionary.") + raise ValueError(f"Missing required section '{section}' in config dictionary.") + + for key in keys: + if key not in config_dict[section]: + logger.error( + f"Missing required key '{key}' for '{section}' section of the config dictionary." + ) + raise ValueError( + f"Missing required key '{key}' for '{section}' section of the config dictionary." + ) + + @beartype.beartype + def check_for_legacy_keys(self, config_dict: dict) -> None: + + legacy_keys = { + "otype", "dd", "d", "sf", "bedding", "bo", "btype", "gi", "c", "u", + "g", "g2", "ds", "min", "max", "r1", "r2", "sill", "intrusive", "volcanic", + "f", "fdipnull", "fdipdip_flag", "fdipdir", "fdip", "fdipest", + "fdipest_vals", "n", "ff", "t", "syn" + } + + # Recursively search for keys in the dictionary + def check_keys(d: dict, parent_key=""): + for key, value in d.items(): + if key in legacy_keys: + logger.error( + f"Legacy key found in config - '{key}' at '{parent_key + key}'. Please use the new config format. Use map2loop.utils.update_from_legacy_file to convert between the formats if needed" + ) + raise ValueError( + f"Legacy key found in config - '{key}' at '{parent_key + key}'. Please use the new config format. Use map2loop.utils.update_from_legacy_file to convert between the formats if needed" + ) + if isinstance(value, dict): + check_keys(value, parent_key=f"{parent_key}{key}.") + + check_keys(config_dict) \ No newline at end of file diff --git a/map2loop/deformation_history.py b/map2loop/deformation_history.py index 9bde5420..1bf47a61 100644 --- a/map2loop/deformation_history.py +++ b/map2loop/deformation_history.py @@ -4,18 +4,20 @@ import geopandas import math +from .utils import calculate_minimum_fault_length + + from .logging import getLogger logger = getLogger(__name__) + class DeformationHistory: """ A class containing all the fault and fold summaries and relationships Attributes ---------- - minimum_fault_length_to_export: float - The cutoff for ignoring faults. Any fault shorter than this is not exported history: list The time ordered list of deformation events faultColumns: numpy.dtype @@ -29,14 +31,14 @@ class DeformationHistory: """ - def __init__(self): + def __init__(self, project): """ The initialiser for the deformation history. All attributes are defaulted """ - self.minimum_fault_length_to_export = 500.0 self.history = [] self.fault_fault_relationships = [] - + self.project = project + # Create empty fault and fold dataframes self.faultColumns = numpy.dtype( [ @@ -66,7 +68,7 @@ def __init__(self): ) self.faults = pandas.DataFrame(numpy.empty(0, dtype=self.faultColumns)) # self.faults = self.faults.set_index("name") - + self.foldColumns = numpy.dtype( [ ("eventId", int), @@ -84,27 +86,9 @@ def __init__(self): ) self.folds = pandas.DataFrame(numpy.empty(0, dtype=self.foldColumns)) # self.folds = self.folds.set_index("name") - - def set_minimum_fault_length(self, length): - """ - Sets the minimum fault length to export - - Args: - length (float or int): - The fault length cutoff - """ - logger.info(f"Setting minimum fault length to {length}") - self.minimum_fault_length_to_export = length - - def get_minimum_fault_length(self): - """ - Getter for the fault length cutoff - - Returns: - float: The fault length cutoff - """ - return self.minimum_fault_length_to_export - + + + def findfault(self, id): """ Find the fault in the summary based on its eventId @@ -278,7 +262,8 @@ def summarise_data(self, fault_observations: pandas.DataFrame): self.faults.at[index, "centreX"] = numpy.mean(observations["X"]) self.faults.at[index, "centreY"] = numpy.mean(observations["Y"]) self.faults.at[index, "centreZ"] = numpy.mean(observations["Z"]) - + + def get_faults_for_export(self): """ Get the faults for export (removes any fault that is shorter than the cutoff) @@ -286,8 +271,12 @@ def get_faults_for_export(self): Returns: pandas.DataFrame: The filtered fault summary """ - logger.info("Getting faults for export") - return self.faults[self.faults["length"] >= self.minimum_fault_length_to_export].copy() + # if no minimum fault length is set, calculate it + if self.project.get_minimum_fault_length() < 0: + self.project.set_minimum_fault_length( calculate_minimum_fault_length( + bbox=self.project.bounding_box, area_percentage=0.05 + )) + return self.faults[self.faults["length"] >= self.project.get_minimum_fault_length()].copy() @beartype.beartype def get_fault_relationships_with_ids(self, fault_fault_relationships: pandas.DataFrame): @@ -301,11 +290,9 @@ def get_fault_relationships_with_ids(self, fault_fault_relationships: pandas.Dat pandas.DataFrame: The fault_relationships with the correct eventIds """ logger.info("Getting fault relationships with eventIds") + faultIds = self.get_faults_for_export()[["eventId", "name"]].copy() rel = fault_fault_relationships.copy() - rel['Fault1'] = rel['Fault1'].astype(str) - rel['Fault2'] = rel['Fault2'].astype(str) - faultIds['eventId'] = faultIds['eventId'].astype(str) rel = rel.merge(faultIds, left_on="Fault1", right_on="eventId") rel.rename(columns={"eventId": "eventId1"}, inplace=True) rel.drop(columns=["name"], inplace=True) diff --git a/map2loop/fault_orientation.py b/map2loop/fault_orientation.py index 3a3ef9db..33c790b5 100644 --- a/map2loop/fault_orientation.py +++ b/map2loop/fault_orientation.py @@ -8,6 +8,8 @@ from .logging import getLogger logger = getLogger(__name__) + + class FaultOrientation(ABC): """ Base Class of Fault Orientation assigner to force structure of FaultOrientation @@ -85,7 +87,7 @@ def calculate( logger.info("Assigning fault orientations to fault traces from nearest orientation") orientations = fault_orientations.copy() logger.info(f'There are {len(orientations)} fault orientations to assign') - + orientations["ID"] = -1 for i in orientations.index: diff --git a/map2loop/interpolators.py b/map2loop/interpolators.py index 4cd9a681..9648348e 100644 --- a/map2loop/interpolators.py +++ b/map2loop/interpolators.py @@ -1,17 +1,18 @@ from abc import ABC, abstractmethod from typing import Any, Union -import logging -from .utils import strike_dip_vector, generate_grid - import beartype import numpy from numpy import ndarray from scipy.interpolate import Rbf, LinearNDInterpolator from sklearn.cluster import DBSCAN - import pandas +from .utils import strike_dip_vector, generate_grid + +from .logging import getLogger +logger = getLogger(__name__) + class Interpolator(ABC): """ Base Class of Interpolator used to force structure of Interpolator @@ -345,10 +346,12 @@ def setup_interpolation(self, structure_data: pandas.DataFrame): # Check if there are any clusters with more than one point (indicating collocated points) collocated_clusters = structure_data['cluster'].value_counts() collocated_clusters = collocated_clusters[collocated_clusters > 1] - + if not collocated_clusters.empty: # Log a warning if collocated points are detected - logging.warning(f"Detected {len(collocated_clusters)} collocated point clusters. Aggregating these points.") + logger.warning( + f"Detected {len(collocated_clusters)} collocated point clusters. Aggregating these points.\n " + ) # Aggregate data for collocated points by taking the mean of X, Y, DIP, and DIPDIR within each cluster aggregated_data = ( diff --git a/map2loop/logging.py b/map2loop/logging.py index 486de019..2daaa0c2 100644 --- a/map2loop/logging.py +++ b/map2loop/logging.py @@ -1,5 +1,7 @@ import logging import map2loop + + def get_levels(): """dict for converting to logger levels from string @@ -16,7 +18,8 @@ def get_levels(): "debug": logging.DEBUG, } -def getLogger(name:str): + +def getLogger(name: str): """Get a logger object with a specific name @@ -32,13 +35,17 @@ def getLogger(name:str): """ if name in map2loop.loggers: return map2loop.loggers[name] - logger = logging.getLogger(name) + logger = logging.getLogger(name) logger.addHandler(map2loop.ch) logger.propagate = False map2loop.loggers[name] = logger return logger + + logger = getLogger(__name__) -def set_level(level:str): + + +def set_level(level: str): """Set the level of the logging object @@ -54,4 +61,4 @@ def set_level(level:str): for name in map2loop.loggers: logger = logging.getLogger(name) logger.setLevel(level) - logger.info(f"Logging level set to {level}") \ No newline at end of file + logger.info(f"Logging level set to {level}") diff --git a/map2loop/map2model_wrapper.py b/map2loop/map2model_wrapper.py index 9b272d1e..08738e60 100644 --- a/map2loop/map2model_wrapper.py +++ b/map2loop/map2model_wrapper.py @@ -1,8 +1,14 @@ +# internal imports +from .m2l_enums import VerboseLevel + +# external imports import map2model import pandas import numpy +import geopandas as gpd +import pandas as pd +import numpy as np import os -from .m2l_enums import VerboseLevel import re from .logging import getLogger @@ -30,7 +36,9 @@ class Map2ModelWrapper: A selection that defines how much console logging is output """ - def __init__(self, map_data, verbose_level: VerboseLevel = VerboseLevel.NONE): + def __init__( + self, map_data, mode: str = 'geopandas', verbose_level: VerboseLevel = VerboseLevel.NONE + ): """ The initialiser for the map2model wrapper @@ -40,13 +48,41 @@ def __init__(self, map_data, verbose_level: VerboseLevel = VerboseLevel.NONE): verbose_level (VerboseLevel, optional): How much console output is sent. Defaults to VerboseLevel.ALL. """ - logger + self.mode = mode self.sorted_units = None - self.fault_fault_relationships = None - self.unit_fault_relationships = None - self.unit_unit_relationships = None + self._fault_fault_relationships = None + self._unit_fault_relationships = None + self._unit_unit_relationships = None self.map_data = map_data self.verbose_level = verbose_level + self.buffer_radius = 500 + + @property + def fault_fault_relationships(self): + if self._fault_fault_relationships is None: + if self.mode == 'geopandas': + self._calculate_fault_fault_relationships() + else: + self.run() + return self._fault_fault_relationships + + @property + def unit_fault_relationships(self): + if self._unit_fault_relationships is None: + if self.mode == 'geopandas': + self._calculate_fault_unit_relationships() + else: + self.run() + return self._unit_fault_relationships + + @property + def unit_unit_relationships(self): + if self._unit_unit_relationships is None: + if self.mode == 'geopandas': + self._calculate_unit_unit_relationships() + else: + self.run() + return self._unit_unit_relationships def reset(self): """ @@ -65,8 +101,11 @@ def get_sorted_units(self): Returns: list: The map2model stratigraphic column estimate """ - if self.sorted_units is None: - self.run() + if self.mode == 'geopandas': + raise NotImplementedError("This method is not implemented") + else: + if self.sorted_units is None: + self.run() return self.sorted_units def get_fault_fault_relationships(self): @@ -76,8 +115,7 @@ def get_fault_fault_relationships(self): Returns: pandas.DataFrame: The fault fault relationships """ - if self.fault_fault_relationships is None: - self.run() + return self.fault_fault_relationships def get_unit_fault_relationships(self): @@ -87,8 +125,7 @@ def get_unit_fault_relationships(self): Returns: pandas.DataFrame: The unit fault relationships """ - if self.unit_fault_relationships is None: - self.run() + return self.unit_fault_relationships def get_unit_unit_relationships(self): @@ -98,10 +135,62 @@ def get_unit_unit_relationships(self): Returns: pandas.DataFrame: The unit unit relationships """ - if self.unit_unit_relationships is None: - self.run() + return self.unit_unit_relationships + def _calculate_fault_fault_relationships(self): + + faults = self.map_data.FAULT.copy() + # reset index so that we can index the adjacency matrix with the index + faults.reset_index(inplace=True) + buffers = faults.buffer(self.buffer_radius) + # create the adjacency matrix + intersection = gpd.sjoin( + gpd.GeoDataFrame(geometry=buffers), gpd.GeoDataFrame(geometry=faults["geometry"]) + ) + intersection["index_left"] = intersection.index + intersection.reset_index(inplace=True) + + adjacency_matrix = np.zeros((faults.shape[0], faults.shape[0]), dtype=bool) + adjacency_matrix[ + intersection.loc[:, "index_left"], intersection.loc[:, "index_right"] + ] = True + f1, f2 = np.where(np.tril(adjacency_matrix, k=-1)) + df = pd.DataFrame( + {'Fault1': faults.loc[f1, 'ID'].to_list(), 'Fault2': faults.loc[f2, 'ID'].to_list()} + ) + df['Angle'] = 60 # make it big to prevent LS from making splays + df['Type'] = 'T' + self._fault_fault_relationships = df + + def _calculate_fault_unit_relationships(self): + """Calculate unit/fault relationships using geopandas sjoin. + This will return + """ + units = self.map_data.GEOLOGY["UNITNAME"].unique() + faults = self.map_data.FAULT.copy().reset_index().drop(columns=['index']) + adjacency_matrix = np.zeros((len(units), faults.shape[0]), dtype=bool) + for i, u in enumerate(units): + unit = self.map_data.GEOLOGY[self.map_data.GEOLOGY["UNITNAME"] == u] + intersection = gpd.sjoin( + gpd.GeoDataFrame(geometry=faults["geometry"]), + gpd.GeoDataFrame(geometry=unit["geometry"]), + ) + intersection["index_left"] = intersection.index + intersection.reset_index(inplace=True) + adjacency_matrix[i, intersection.loc[:, "index_left"]] = True + u, f = np.where(adjacency_matrix) + df = pd.DataFrame({"Unit": units[u].tolist(), "Fault": faults.loc[f, "ID"].to_list()}) + self._unit_fault_relationships = df + + def _calculate_unit_unit_relationships(self): + if self.map_data.contacts is None: + self.map_data.extract_all_contacts() + self._unit_unit_relationships = self.map_data.contacts.copy().drop( + columns=['length', 'geometry'] + ) + return self._unit_unit_relationships + def run(self, verbose_level: VerboseLevel = None): """ The main execute function that prepares, runs and parse the output of the map2model process @@ -110,71 +199,69 @@ def run(self, verbose_level: VerboseLevel = None): verbose_level (VerboseLevel, optional): How much console output is sent. Defaults to None (which uses the wrapper attribute). """ - if verbose_level is None: - verbose_level = self.verbose_level - logger.info("Exporting map data for map2model") - self.map_data.export_wkt_format_files() - logger.info("Running map2model...") - - map2model_code_map = { - "o": "ID", # FIELD_COORDINATES - "f": "FEATURE", # FIELD_FAULT_ID - "u": "CODE", # FIELD_POLYGON_LEVEL1_NAME - "g": "GROUP", # FIELD_POLYGON_LEVEL2_NAME - "min": "MIN_AGE", # FIELD_POLYGON_MIN_AGE - "max": "MAX_AGE", # FIELD_POLYGON_MAX_AGE - "c": "UNITNAME", # FIELD_POLYGON_CODE - "ds": "DESCRIPTION", # FIELD_POLYGON_DESCRIPTION - "r1": "ROCKTYPE1", # FIELD_POLYGON_ROCKTYPE1 - "r2": "ROCKTYPE2", # FIELD_POLYGON_ROCKTYPE2 - "msc": "", # FIELD_SITE_CODE - "mst": "", # FIELD_SITE_TYPE - "mscm": "", # FIELD_SITE_COMMO - "fold": self.map_data.config.fold_config["fold_text"], # FAULT_AXIAL_FEATURE_NAME - "sill": self.map_data.config.geology_config["sill_text"], # SILL_STRING - "intrusive": self.map_data.config.geology_config["intrusive_text"], # IGNEOUS_STRING - "volcanic": self.map_data.config.geology_config["volcanic_text"], # VOLCANIC_STRING - "deposit_dist": 100, # deposit_dist - } - logger.info(f"map2model params: {map2model_code_map}") - # TODO: Simplify. Note: this is external so have to match fix to map2model module - logger.info(os.path.join(self.map_data.tmp_path, "map2model_data")) - logger.info(os.path.join(self.map_data.tmp_path, "map2model_data", "geology_wkt.csv")) - logger.info(os.path.join(self.map_data.tmp_path, "map2model_data", "faults_wkt.csv")) - logger.info(self.map_data.get_bounding_box()) - logger.info(map2model_code_map) - logger.info(verbose_level == VerboseLevel.NONE) - - run_log = map2model.run( - os.path.join(self.map_data.tmp_path, "map2model_data"), - os.path.join(self.map_data.tmp_path, "map2model_data", "geology_wkt.csv"), - os.path.join(self.map_data.tmp_path, "map2model_data", "faults_wkt.csv"), - "", - self.map_data.get_bounding_box(), - map2model_code_map, - verbose_level == VerboseLevel.NONE, - "None", - ) - logger.info("Parsing map2model output") - logger.info(run_log) - - logger.info("map2model complete") + if self.mode == 'geopandas': - # Parse units sorted - units_sorted = pandas.read_csv( - os.path.join(self.map_data.tmp_path, "map2model_data", "units_sorted.txt"), - header=None, - sep=' ', - ) - if units_sorted.shape == 0: - self.sorted_units = [] + self.get_fault_fault_relationships() + self.get_unit_fault_relationships() + self.get_unit_unit_relationships() + return else: - self.sorted_units = list(units_sorted[5]) + if verbose_level is None: + verbose_level = self.verbose_level + logger.info("Exporting map data for map2model") + self.map_data.export_wkt_format_files() + logger.info("Running map2model...") + + map2model_code_map = { + "o": "ID", # FIELD_COORDINATES + "f": "FEATURE", # FIELD_FAULT_ID + "u": "CODE", # FIELD_POLYGON_LEVEL1_NAME + "g": "GROUP", # FIELD_POLYGON_LEVEL2_NAME + "min": "MIN_AGE", # FIELD_POLYGON_MIN_AGE + "max": "MAX_AGE", # FIELD_POLYGON_MAX_AGE + "c": "UNITNAME", # FIELD_POLYGON_CODE + "ds": "DESCRIPTION", # FIELD_POLYGON_DESCRIPTION + "r1": "ROCKTYPE1", # FIELD_POLYGON_ROCKTYPE1 + "r2": "ROCKTYPE2", # FIELD_POLYGON_ROCKTYPE2 + "msc": "", # FIELD_SITE_CODE + "mst": "", # FIELD_SITE_TYPE + "mscm": "", # FIELD_SITE_COMMO + "fold": self.map_data.config.fold_config["fold_text"], # FAULT_AXIAL_FEATURE_NAME + "sill": self.map_data.config.geology_config["sill_text"], # SILL_STRING + "intrusive": self.map_data.config.geology_config[ + "intrusive_text" + ], # IGNEOUS_STRING + "volcanic": self.map_data.config.geology_config["volcanic_text"], # VOLCANIC_STRING + "deposit_dist": 100, # deposit_dist + } + logger.info(f"map2model params: {map2model_code_map}") + # TODO: Simplify. Note: this is external so have to match fix to map2model module + logger.info(os.path.join(self.map_data.map2model_tmp_path, "map2model_data")) + logger.info( + os.path.join(self.map_data.map2model_tmp_path, "map2model_data", "geology_wkt.csv") + ) + logger.info( + os.path.join(self.map_data.map2model_tmp_path, "map2model_data", "faults_wkt.csv") + ) + logger.info(self.map_data.get_bounding_box()) + logger.info(map2model_code_map) + logger.info(verbose_level == VerboseLevel.NONE) + + run_log = map2model.run( + os.path.join(self.map_data.map2model_tmp_path), + os.path.join(self.map_data.map2model_tmp_path, "geology_wkt.csv"), + os.path.join(self.map_data.map2model_tmp_path, "faults_wkt.csv"), + "", + self.map_data.get_bounding_box(), + map2model_code_map, + verbose_level == VerboseLevel.NONE, + "None", + ) # Parse fault intersections out = [] fault_fault_intersection_filename = os.path.join( - self.map_data.tmp_path, "map2model_data", "fault-fault-intersection.txt" + self.map_data.map2model_tmp_path, 'fault-fault-intersection.txt' ) logger.info(f"Reading fault-fault intersections from {fault_fault_intersection_filename}") if ( @@ -186,6 +273,7 @@ def run(self, verbose_level: VerboseLevel = None): df[1] = [re.findall("\(.*?\)", i) for i in df[1]] # Valid escape for regex df[0] = list(df[0].str.replace("^[0-9]*, ", "", regex=True)) df[0] = list(df[0].str.replace(", ", "", regex=False)) + # df[0] = "Fault_" + df[0] #removed 7/10/24 as it seems to break the merge in relations = df[1] for j in range(len(relations)): @@ -194,61 +282,111 @@ def run(self, verbose_level: VerboseLevel = None): for _, row in df.iterrows(): for i in numpy.arange(len(row[1])): + out += [[row[0], row[1][i][0], row[1][i][1], float(row[1][i][2])]] else: logger.warning( f"Fault-fault intersections file {fault_fault_intersection_filename} not found" ) + logger.info("Parsing map2model output") + logger.info(run_log) - df_out = pandas.DataFrame(columns=["Fault1", "Fault2", "Type", "Angle"], data=out) - logger.info('Fault intersections') - logger.info(df_out.to_string()) - self.fault_fault_relationships = df_out + logger.info("map2model complete") - # Parse unit fault relationships - out = [] - unit_fault_intersection_filename = os.path.join( - self.map_data.tmp_path, "map2model_data", "unit-fault-intersection.txt" - ) - if ( - os.path.isfile(unit_fault_intersection_filename) - and os.path.getsize(unit_fault_intersection_filename) > 0 - ): - df = pandas.read_csv(unit_fault_intersection_filename, header=None, sep='{') - df[1] = list(df[1].str.replace("}", "", regex=False)) - df[1] = df[1].astype(str).str.split(", ") - df[0] = list(df[0].str.replace("^[0-9]*, ", "", regex=True)) - df[0] = list(df[0].str.replace(", ", "", regex=False)) + # Parse units sorted + units_sorted = pandas.read_csv( + os.path.join(self.map_data.map2model_tmp_path, "units_sorted.txt"), + header=None, + sep=' ', + ) + if units_sorted.shape == 0: + self.sorted_units = [] + else: + self.sorted_units = list(units_sorted[5]) - for _, row in df.iterrows(): - for i in numpy.arange(len(row[1])): - out += [[row[0], "Fault_" + row[1][i]]] + # Parse fault intersections + out = [] + fault_fault_intersection_filename = os.path.join( + self.map_data.map2model_tmp_path, "fault-fault-intersection.txt" + ) + logger.info( + f"Reading fault-fault intersections from {fault_fault_intersection_filename}" + ) + if ( + os.path.isfile(fault_fault_intersection_filename) + and os.path.getsize(fault_fault_intersection_filename) > 0 + ): + df = pandas.read_csv(fault_fault_intersection_filename, delimiter="{", header=None) + df[1] = list(df[1].str.replace("}", "", regex=False)) + df[1] = [re.findall("\(.*?\)", i) for i in df[1]] # Valid escape for regex + df[0] = list(df[0].str.replace("^[0-9]*, ", "", regex=True)) + df[0] = list(df[0].str.replace(", ", "", regex=False)) + # df[0] = "Fault_" + df[0] #removed 7/10/24 as it seems to break the merge in + relations = df[1] + for j in range(len(relations)): + relations[j] = [i.strip("()").replace(" ", "").split(",") for i in relations[j]] + df[1] = relations - df_out = pandas.DataFrame(columns=["Unit", "Fault"], data=out) - self.unit_fault_relationships = df_out + for _, row in df.iterrows(): + for i in numpy.arange(len(row[1])): + out += [[row[0], row[1][i][0], row[1][i][1], float(row[1][i][2])]] - # Parse unit unit relationships - units = [] - links = [] - graph_filename = os.path.join( - self.map_data.tmp_path, "map2model_data", "graph_all_None.gml.txt" - ) - if os.path.isfile(graph_filename) and os.path.getsize(graph_filename) > 0: - with open( - os.path.join(self.map_data.tmp_path, "map2model_data", "graph_all_None.gml.txt") - ) as file: - contents = file.read() - segments = contents.split("\n\n") - for line in segments[0].split("\n"): - units += [line.split(" ")] - for line in segments[1].split("\n")[:-1]: - links += [line.split(" ")] - - df = pandas.DataFrame(columns=["index", "unit"], data=units) - df.set_index("index", inplace=True) - out = [] - for row in links: - out += [[int(row[0]), df["unit"][row[0]], int(row[1]), df["unit"][row[1]]]] - df_out = pandas.DataFrame(columns=["Index1", "UnitName1", "Index2", "UnitName2"], data=out) - self.unit_unit_relationships = df_out + else: + logger.warning( + f"Fault-fault intersections file {fault_fault_intersection_filename} not found" + ) + + df_out = pandas.DataFrame(columns=["Fault1", "Fault2", "Type", "Angle"], data=out) + logger.info('Fault intersections') + logger.info(df_out.to_string()) + self.fault_fault_relationships = df_out + + # Parse unit fault relationships + out = [] + unit_fault_intersection_filename = os.path.join( + self.map_data.map2model_tmp_path, "unit-fault-intersection.txt" + ) + if ( + os.path.isfile(unit_fault_intersection_filename) + and os.path.getsize(unit_fault_intersection_filename) > 0 + ): + df = pandas.read_csv(unit_fault_intersection_filename, header=None, sep='{') + df[1] = list(df[1].str.replace("}", "", regex=False)) + df[1] = df[1].astype(str).str.split(", ") + df[0] = list(df[0].str.replace("^[0-9]*, ", "", regex=True)) + df[0] = list(df[0].str.replace(", ", "", regex=False)) + + for _, row in df.iterrows(): + for i in numpy.arange(len(row[1])): + out += [[row[0], "Fault_" + row[1][i]]] + + df_out = pandas.DataFrame(columns=["Unit", "Fault"], data=out) + self.unit_fault_relationships = df_out + + # Parse unit unit relationships + units = [] + links = [] + graph_filename = os.path.join( + self.map_data.map2model_tmp_path, "graph_all_None.gml.txt" + ) + if os.path.isfile(graph_filename) and os.path.getsize(graph_filename) > 0: + with open( + os.path.join(self.map_data.map2model_tmp_path, "graph_all_None.gml.txt") + ) as file: + contents = file.read() + segments = contents.split("\n\n") + for line in segments[0].split("\n"): + units += [line.split(" ")] + for line in segments[1].split("\n")[:-1]: + links += [line.split(" ")] + + df = pandas.DataFrame(columns=["index", "unit"], data=units) + df.set_index("index", inplace=True) + out = [] + for row in links: + out += [[int(row[0]), df["unit"][row[0]], int(row[1]), df["unit"][row[1]]]] + df_out = pandas.DataFrame( + columns=["Index1", "UnitName1", "Index2", "UnitName2"], data=out + ) + self.unit_unit_relationships = df_out diff --git a/map2loop/mapdata.py b/map2loop/mapdata.py index 4eaff69d..4ef0be89 100644 --- a/map2loop/mapdata.py +++ b/map2loop/mapdata.py @@ -2,7 +2,7 @@ from .m2l_enums import Datatype, Datastate, VerboseLevel from .config import Config from .aus_state_urls import AustraliaStateUrls -from .utils import generate_random_hex_colors +from .utils import generate_random_hex_colors, calculate_minimum_fault_length # external imports import geopandas @@ -11,6 +11,7 @@ import pathlib import shapely from osgeo import gdal, osr +gdal.UseExceptions() from owslib.wcs import WebCoverageService import urllib from gzip import GzipFile @@ -19,11 +20,12 @@ import os from io import BytesIO from typing import Union +import tempfile from .logging import getLogger +logger = getLogger(__name__) -logger = getLogger(__name__) class MapData: @@ -58,21 +60,17 @@ class MapData: The filename of the json config file colour_filename: str The filename of the csv colour table file (columns are unit name and colour in #000000 form) - tmp_path: str - The path to the directory holding the temporary files verbose_level: m2l_enums.VerboseLevel A selection that defines how much console logging is output config: Config A link to the config structure which is defined in config.py """ - def __init__(self, tmp_path: str = "", verbose_level: VerboseLevel = VerboseLevel.ALL): + def __init__(self, verbose_level: VerboseLevel = VerboseLevel.ALL): """ The initialiser for the map data Args: - tmp_path (str, optional): - The directory for storing temporary files. Defaults to "". verbose_level (VerboseLevel, optional): How much console output is sent. Defaults to VerboseLevel.ALL. """ @@ -82,7 +80,6 @@ def __init__(self, tmp_path: str = "", verbose_level: VerboseLevel = VerboseLeve self.basal_contacts = None self.sampled_contacts = None self.filenames = [None] * len(Datatype) - # self.output_filenames = [None] * len(Datatype) self.dirtyflags = [True] * len(Datatype) self.data_states = [Datastate.UNNAMED] * len(Datatype) self.working_projection = None @@ -91,11 +88,19 @@ def __init__(self, tmp_path: str = "", verbose_level: VerboseLevel = VerboseLeve self.bounding_box_str = None self.config_filename = None self.colour_filename = None - self.tmp_path = tmp_path self.verbose_level = verbose_level - self.config = Config() + @property + @beartype.beartype + def minimum_fault_length(self) -> Union[int,float]: + return self.config.fault_config["minimum_fault_length"] + + @minimum_fault_length.setter + @beartype.beartype + def minimum_fault_length(self, length: float): + self.config.fault_config["minimum_fault_length"] = length + def set_working_projection(self, projection): """ Set the working projection for the map data @@ -106,18 +111,18 @@ def set_working_projection(self, projection): """ if issubclass(type(projection), int): - projection = "EPSG:" + str(projection) + projection = f"EPSG:{str(projection)}" self.working_projection = projection elif issubclass(type(projection), str): self.working_projection = projection else: - print( + logger.warning( f"Warning: Unknown projection set {projection}. Leaving all map data in original projection\n" ) if self.bounding_box is not None: self.recreate_bounding_box_str() - logger.info("Setting working projection to {self.working_projection}") - + logger.info(f"Setting working projection to {self.working_projection}") + def get_working_projection(self): """ Get the working projection @@ -251,7 +256,7 @@ def get_filename(self, datatype: Datatype): @beartype.beartype def set_config_filename( - self, filename: Union[pathlib.Path, str], legacy_format: bool = False, lower: bool = False + self, filename: Union[pathlib.Path, str], lower: bool = False ): """ Set the config filename and update the config structure @@ -259,12 +264,13 @@ def set_config_filename( Args: filename (str): The filename of the config file - legacy_format (bool, optional): - Whether the file is in m2lv2 form. Defaults to False. + lower (bool, optional): + Flag to convert the config file to lowercase. Defaults to False. """ logger.info('Setting config filename to {filename}') - self.config_filename = filename - self.config.update_from_file(filename, legacy_format=legacy_format, lower=lower) + + self.config.update_from_file(filename, lower=lower) + logger.info(f"Config is: {self.config.to_dict()}") def get_config_filename(self): @@ -298,28 +304,66 @@ def get_colour_filename(self): return self.colour_filename @beartype.beartype - def set_ignore_codes(self, codes: list): + def set_ignore_lithology_codes(self, codes: list): """ - Set the codes to ignore in the geology shapefile + Set the lithology codes (names) to be ignored in the geology shapefile. + + This method updates the `ignore_lithology_codes` entry in the geology configuration + and marks the geology data as "clipped" to indicate that certain lithologies have been + excluded. Additionally, it sets a dirty flag for the geology data to signal that it + requires reprocessing. Args: codes (list): - The list of codes to ignore + A list of lithology names to ignore in the geology shapefile. These + entries will be excluded from further processing. """ - logger.info(f'Setting ignore codes to {codes}') - self.config.geology_config["ignore_codes"] = codes + self.config.geology_config["ignore_lithology_codes"] = codes self.data_states[Datatype.GEOLOGY] = Datastate.CLIPPED self.dirtyflags[Datatype.GEOLOGY] = True @beartype.beartype - def get_ignore_codes(self) -> list: + def get_ignore_lithology_codes(self) -> list: """ - Get the list of codes to ignore + Retrieve the list of lithology names to be ignored in the geology shapefile. + + This method fetches the current list of lithology names or codes from the geology + configuration that have been marked for exclusion during processing. Returns: - list: The list of strings to ignore + list: A list of lithology names currently set to be ignored in the + geology shapefile. + """ + return self.config.geology_config["ignore_lithology_codes"] + + @beartype.beartype + def set_ignore_fault_codes(self, codes: list): + """ + Set the list of fault codes to be ignored during processing. + + This method updates the `ignore_fault_codes` entry in the fault configuration and + marks the fault data as "clipped" to indicate that it has been filtered. Additionally, + it sets a dirty flag for the fault data to signal that it requires reprocessing. + + Args: + codes (list): A list of fault codes to ignore during further processing. """ - return self.config.geology_config["ignore_codes"] + self.config.fault_config["ignore_fault_codes"] = codes + self.data_states[Datatype.FAULT] = Datastate.CLIPPED + self.dirtyflags[Datatype.FAULT] = True + + @beartype.beartype + def get_ignore_fault_codes(self) -> list: + """ + Retrieve the list of fault codes that are set to be ignored. + + This method fetches the current list of fault codes from the fault configuration + that have been marked for exclusion during processing. + + Returns: + list: A list of fault codes that are currently marked for exclusion. + """ + return self.config.fault_config["ignore_fault_codes"] @beartype.beartype def set_filenames_from_australian_state(self, state: str): @@ -357,7 +401,7 @@ def set_filenames_from_australian_state(self, state: str): else: self.set_config_filename( - AustraliaStateUrls.aus_config_urls[state], legacy_format=False, lower=lower + AustraliaStateUrls.aus_config_urls[state], lower=lower ) self.set_colour_filename(AustraliaStateUrls.aus_clut_urls[state]) else: @@ -376,7 +420,7 @@ def check_filename(self, datatype: Datatype) -> bool: bool: true if the filename is set, false otherwise """ if self.filenames[datatype] is None or self.filenames[datatype] == "": - print(f"Warning: Filename for {str(datatype)} is not set") + logger.warning(f"Warning: Filename for {str(datatype)} is not set") return False return True @@ -499,17 +543,8 @@ def open_http_query(url: str): else: return response except urllib.URLError: - logger.error(f"Failed to open url {url}") return None - @beartype.beartype - def __check_and_create_tmp_path(self): - """ - Create the temporary files directory if it is not valid - """ - if not os.path.isdir(self.tmp_path): - os.mkdir(self.tmp_path) - @beartype.beartype def __retrieve_tif(self, filename: str): """ @@ -522,7 +557,6 @@ def __retrieve_tif(self, filename: str): Returns: _type_: The open geotiff in a gdal handler """ - self.__check_and_create_tmp_path() # For gdal debugging use exceptions gdal.UseExceptions() @@ -532,7 +566,7 @@ def __retrieve_tif(self, filename: str): ) if filename.lower() == "aus" or filename.lower() == "au": - logger.info('Using geoscience australia DEM') + logger.info('Using Geoscience Australia DEM') url = "http://services.ga.gov.au/gis/services/DEM_SRTM_1Second_over_Bathymetry_Topography/MapServer/WCSServer?" wcs = WebCoverageService(url, version="1.0.0") @@ -543,12 +577,14 @@ def __retrieve_tif(self, filename: str): # This is stupid that gdal cannot read a byte stream and has to have a # file on the local system to open or otherwise create a gdal file # from scratch with Create + import pathlib - tmp_file = os.path.join(self.tmp_path, "StupidGDALLocalFile.tif") + tmp_file = pathlib.Path(tempfile.mkdtemp()) / pathlib.Path("temp.tif") with open(tmp_file, "wb") as fh: fh.write(coverage.read()) - tif = gdal.Open(tmp_file) + + tif = gdal.Open(str(tmp_file)) elif filename == "hawaii": logger.info('Using Hawaii DEM') @@ -590,11 +626,7 @@ def __retrieve_tif(self, filename: str): tif = gdal.Open(mmap_name) else: logger.info(f'Opening local file {filename}') - tif = gdal.Open(filename, gdal.GA_ReadOnly) - # except Exception: - # print( - # f"Failed to open geoTIFF file from '{filename}'\n" - # ) + tif = gdal.Open(str(filename), gdal.GA_ReadOnly) return tif @beartype.beartype @@ -685,12 +717,14 @@ def parse_fault_orientations(self) -> tuple: self.raw_data[Datatype.FAULT_ORIENTATION] is None or type(self.raw_data[Datatype.FAULT_ORIENTATION]) is not geopandas.GeoDataFrame ): + logger.warning("Fault orientation shapefile is not loaded or valid") return (True, "Fault orientation shapefile is not loaded or valid") # Create new geodataframe fault_orientations = geopandas.GeoDataFrame( self.raw_data[Datatype.FAULT_ORIENTATION]["geometry"] ) + config = self.config.fault_config # Parse dip direction and dip columns @@ -744,10 +778,11 @@ def parse_structure_map(self) -> tuple: self.raw_data[Datatype.STRUCTURE] is None or type(self.raw_data[Datatype.STRUCTURE]) is not geopandas.GeoDataFrame ): + logger.warning("Structure map is not loaded or valid") return (True, "Structure map is not loaded or valid") if len(self.raw_data[Datatype.STRUCTURE]) < 2: - print( + logger.warning( "Stucture map does not enough orientations to complete calculations (need at least 2), projection may be inconsistent" ) @@ -815,6 +850,7 @@ def parse_geology_map(self) -> tuple: self.raw_data[Datatype.GEOLOGY] is None or type(self.raw_data[Datatype.GEOLOGY]) is not geopandas.GeoDataFrame ): + logger.warning("Geology map is not loaded or valid") return (True, "Geology map is not loaded or valid") # Create new geodataframe @@ -829,6 +865,7 @@ def parse_geology_map(self) -> tuple: else: msg = f"Geology map does not contain unitname_column {config['unitname_column']}" print(msg) + logger.warning(msg) return (True, msg) if config["alt_unitname_column"] in self.raw_data[Datatype.GEOLOGY]: geology["CODE"] = self.raw_data[Datatype.GEOLOGY][config["alt_unitname_column"]].astype( @@ -839,6 +876,7 @@ def parse_geology_map(self) -> tuple: f"Geology map does not contain alt_unitname_column {config['alt_unitname_column']}" ) print(msg) + logger.warning(msg) return (True, msg) # Parse group and supergroup columns @@ -921,7 +959,7 @@ def parse_geology_map(self) -> tuple: geology["SUPERGROUP"] = geology["SUPERGROUP"].str.replace("[ -/?]", "_", regex=True) # Mask out ignored unit_names/codes (ie. for cover) - for code in self.config.geology_config["ignore_codes"]: + for code in self.config.geology_config["ignore_lithology_codes"]: geology = geology[~geology["CODE"].astype(str).str.contains(code)] geology = geology[~geology["UNITNAME"].astype(str).str.contains(code)] @@ -931,10 +969,18 @@ def parse_geology_map(self) -> tuple: self.data[Datatype.GEOLOGY] = geology return (False, "") + @beartype.beartype + def get_minimum_fault_length(self) -> Union[float, int, None]: + """ + Get the minimum fault length + """ + + return self.minimum_fault_length + @beartype.beartype def parse_fault_map(self) -> tuple: """ - Parse the fault shapefile data into a consistent format + Parse the fault shapefile data into a consistent format. Returns: tuple: A tuple of (bool: success/fail, str: failure message) @@ -944,12 +990,25 @@ def parse_fault_map(self) -> tuple: self.raw_data[Datatype.FAULT] is None or type(self.raw_data[Datatype.FAULT]) is not geopandas.GeoDataFrame ): + logger.warning("Fault map is not loaded or valid") return (True, "Fault map is not loaded or valid") - # Create new geodataframe + # Create a new geodataframe faults = geopandas.GeoDataFrame(self.raw_data[Datatype.FAULT]["geometry"]) + + # Get fault configuration config = self.config.fault_config + # update minimum fault length either with the value from the config or calculate it + if self.minimum_fault_length < 0: + logger.info("Calculating minimum fault length") + self.minimum_fault_length = calculate_minimum_fault_length( + bbox=self.bounding_box, area_percentage=0.05 + ) + + # crop + faults = faults.loc[faults.geometry.length >= self.minimum_fault_length] + if config["structtype_column"] in self.raw_data[Datatype.FAULT]: faults["FEATURE"] = self.raw_data[Datatype.FAULT][config["structtype_column"]] faults = faults[faults["FEATURE"].astype(str).str.contains(config["fault_text"])] @@ -957,12 +1016,36 @@ def parse_fault_map(self) -> tuple: if len(faults) < len(self.raw_data[Datatype.GEOLOGY]) and len(faults) == 0: msg = f"Fault map reduced to 0 faults as structtype_column ({config['structtype_column']}) does not contains as row with fault_text \"{config['fault_text']}\"" print(msg) + logger.warning(msg) if config["name_column"] in self.raw_data[Datatype.FAULT]: faults["NAME"] = self.raw_data[Datatype.FAULT][config["name_column"]].astype(str) else: faults["NAME"] = "Fault_" + faults.index.astype(str) + # crop by the ignore fault codes + ignore_codes = config["ignore_fault_codes"] + + # Find the intersection of ignore_codes and the 'NAME' column values + existing_codes = set(ignore_codes).intersection(set(faults["NAME"].values)) + + # Find the codes that do not exist in the DataFrame + non_existing_codes = set(ignore_codes) - existing_codes + + # Issue a warning if there are any non-existing codes + if non_existing_codes: + logger.info(f"Warning: {non_existing_codes} set to fault ignore codes are not in the provided data. Skipping") + + # Filter the DataFrame to remove rows where 'NAME' is in the existing_codes + if existing_codes: + faults = faults[~faults["NAME"].isin(existing_codes)] + logger.info(f"The following codes were found and removed: {existing_codes}") + else: + logger.info("None of the fault ignore codes exist in the original fault data.") + pass + + + # parse dip column if config["dip_column"] in self.raw_data[Datatype.FAULT]: faults["DIP"] = self.raw_data[Datatype.FAULT][config["dip_column"]].astype( numpy.float64 @@ -1039,8 +1122,8 @@ def parse_fault_map(self) -> tuple: axis=1, ) faults["NAME"] = faults["NAME"].str.replace(" -/?", "_", regex=True) - self.data[Datatype.FAULT] = faults + return (False, "") @beartype.beartype @@ -1072,6 +1155,7 @@ def parse_fold_map(self) -> tuple: if self.verbose_level > VerboseLevel.NONE: if len(folds) < len(self.raw_data[Datatype.GEOLOGY]) and len(folds) == 0: msg = f"Fold map reduced to 0 folds as structtype_column ({config['structtype_column']}) does not contains any row with fold_text \"{config['fold_text']}\"" + logger.warning(msg) print(msg) if config["foldname_column"] in self.raw_data[Datatype.FOLD]: @@ -1113,19 +1197,19 @@ def set_working_projection_on_map_data(self, datatype: Datatype): elif type(self.raw_data[datatype]) is geopandas.GeoDataFrame: if self.data_states[datatype] >= Datastate.LOADED: if self.raw_data[datatype].crs is None: - print( + logger.info( f"No projection on original map data, assigning to working_projection {self.working_projection}" ) self.raw_data[datatype].crs = self.working_projection else: self.raw_data[datatype].to_crs(crs=self.working_projection, inplace=True) else: - print( + logger.warning( f"Type of {datatype.name} map not a GeoDataFrame so cannot change map crs projection" ) @beartype.beartype - def save_all_map_data(self, output_dir: str, extension: str = ".csv"): + def save_all_map_data(self, output_dir: pathlib.Path, extension: str = ".csv"): """ Save all the map data to file @@ -1139,12 +1223,14 @@ def save_all_map_data(self, output_dir: str, extension: str = ".csv"): self.save_raw_map_data(output_dir, i, extension) @beartype.beartype - def save_raw_map_data(self, output_dir: str, datatype: Datatype, extension: str = ".shp.zip"): + def save_raw_map_data( + self, output_dir: pathlib.Path, datatype: Datatype, extension: str = ".shp.zip" + ): """ Save the map data from datatype to file Args: - output_dir (str): + output_dir (pathlib.Path): The directory to save to datatype (Datatype): The datatype of the geopanda to save @@ -1152,15 +1238,21 @@ def save_raw_map_data(self, output_dir: str, datatype: Datatype, extension: str The extension to use for the data. Defaults to ".csv". """ try: - filename = os.path.join(output_dir, datatype.name + extension) + filename = pathlib.Path(output_dir) / f"{datatype.name}{extension}" + raw_data = self.raw_data[datatype] + + if raw_data is None: + logger.info(f"No data available for {datatype.name}. Skipping saving to file {filename}.") + return + if extension == ".csv": - # TODO: Add geopandas to pandas converter and then write csv - # self.raw_data[datatype].write_csv(filename) - print("GeoDataFrame to CSV conversion not implimented") + raw_data.to_csv(filename, index=False) # Save as CSV else: self.raw_data[datatype].to_file(filename) - except Exception: - print(f"Failed to save {datatype.name} to file named {filename}\n") + + except Exception as e: + logger.error(f"Failed to save {datatype.name} to file named {filename}\nError: {str(e)}") + print(f"Failed to save {datatype.name} to file named {filename}\nError: {str(e)}") @beartype.beartype def get_raw_map_data(self, datatype: Datatype): @@ -1211,6 +1303,7 @@ def update_filename_with_bounding_box(self, filename: str): str: The modified filename """ if filename is None: + logger.error(f"Filename {filename} is invalid") raise ValueError(f"Filename {filename} is invalid") return filename.replace("{BBOX_STR}", self.bounding_box_str) @@ -1231,6 +1324,7 @@ def update_filename_with_projection(self, filename: str): str: The modified filename """ if filename is None: + logger.error(f"Filename {filename} is invalid") raise ValueError(f"Filename {filename} is invalid") return filename.replace("{PROJ_STR}", self.working_projection) @@ -1242,7 +1336,7 @@ def calculate_bounding_box_and_projection(self): dict, str: The bounding box and projection of the geology shapefile """ if self.filenames[Datatype.GEOLOGY] is None: - print( + logger.info( "Could not open geology file as none set, no bounding box or projection available" ) return None, None @@ -1259,7 +1353,7 @@ def calculate_bounding_box_and_projection(self): "maxy": bounds[3], }, geology_data.crs except Exception: - print( + logger.error( f"Could not open geology file {temp_geology_filename} so no bounding box or projection found" ) return None, None @@ -1272,16 +1366,14 @@ def export_wkt_format_files(self): """ # TODO: - Move away from tab seperators entirely (topology and map2model) - self.__check_and_create_tmp_path() - if not os.path.isdir(os.path.join(self.tmp_path, "map2model_data")): - os.mkdir(os.path.join(self.tmp_path, "map2model_data")) + self.map2model_tmp_path = pathlib.Path(tempfile.mkdtemp()) # Check geology data status and export to a WKT format file self.load_map_data(Datatype.GEOLOGY) if type(self.data[Datatype.GEOLOGY]) is not geopandas.GeoDataFrame: - print("Cannot export geology data as it is not a GeoDataFrame") + logger.warning("Cannot export geology data as it is not a GeoDataFrame") elif self.data_states[Datatype.GEOLOGY] != Datastate.COMPLETE: - print( + logger.warning( f"Cannot export geology data as it only loaded to {self.data_states[Datatype.GEOLOGY].name} status" ) else: @@ -1308,26 +1400,22 @@ def export_wkt_format_files(self): geology["ROCKTYPE1"] = geology["ROCKTYPE1"].replace("", "None") geology["ROCKTYPE2"] = geology["ROCKTYPE2"].replace("", "None") geology.to_csv( - os.path.join(self.tmp_path, "map2model_data", "geology_wkt.csv"), - sep="\t", - index=False, + pathlib.Path(self.map2model_tmp_path) / "geology_wkt.csv", sep="\t", index=False ) # Check faults data status and export to a WKT format file self.load_map_data(Datatype.FAULT) if type(self.data[Datatype.FAULT]) is not geopandas.GeoDataFrame: - print("Cannot export fault data as it is not a GeoDataFrame") + logger.warning("Cannot export fault data as it is not a GeoDataFrame") elif self.data_states[Datatype.FAULT] != Datastate.COMPLETE: - print( + logger.warning( f"Cannot export fault data as it only loaded to {self.data_states[Datatype.FAULT].name} status" ) else: faults = self.get_map_data(Datatype.FAULT).copy() faults.rename(columns={"geometry": "WKT"}, inplace=True) faults.to_csv( - os.path.join(self.tmp_path, "map2model_data", "faults_wkt.csv"), - sep="\t", - index=False, + pathlib.Path(self.map2model_tmp_path) / "faults_wkt.csv", sep="\t", index=False ) @beartype.beartype @@ -1348,7 +1436,7 @@ def get_value_from_raster(self, datatype: Datatype, x, y): """ data = self.get_map_data(datatype) if data is None: - print(f"Cannot get value from {datatype.name} data as data is not loaded") + logger.warning(f"Cannot get value from {datatype.name} data as data is not loaded") return None inv_geotransform = gdal.InvGeoTransform(data.GetGeoTransform()) @@ -1408,7 +1496,7 @@ def get_value_from_raster_df(self, datatype: Datatype, df: pandas.DataFrame): return df data = self.get_map_data(datatype) if data is None: - print("Cannot get value from data as data is not loaded") + logger.warning("Cannot get value from data as data is not loaded") return None inv_geotransform = gdal.InvGeoTransform(data.GetGeoTransform()) @@ -1425,7 +1513,7 @@ def extract_all_contacts(self, save_contacts=True): """ Extract the contacts between units in the geology GeoDataFrame """ - # print('extracting contacts') + logger.info("Extracting contacts") geology = self.get_map_data(Datatype.GEOLOGY).copy() geology = geology.dissolve(by="UNITNAME", as_index=False) # Remove intrusions @@ -1472,21 +1560,59 @@ def extract_basal_contacts(self, stratigraphic_column: list, save_contacts=True) stratigraphic_column (list): The stratigraphic column to use """ + logger.info("Extracting basal contacts") + units = stratigraphic_column basal_contacts = self.contacts.copy() + + # check if the units in the strati colum are in the geology dataset, so that basal contacts can be built + # if not, stop the project + if any(unit not in units for unit in basal_contacts["UNITNAME_1"].unique()): + missing_units = ( + basal_contacts[~basal_contacts["UNITNAME_1"].isin(units)]["UNITNAME_1"] + .unique() + .tolist() + ) + logger.error( + "There are units in the Geology dataset, but not in the stratigraphic column: " + + ", ".join(missing_units) + + ". Please readjust the stratigraphic column if this is a user defined column." + ) + raise ValueError( + "There are units in stratigraphic column, but not in the Geology dataset: " + + ", ".join(missing_units) + + ". Please readjust the stratigraphic column if this is a user defined column." + ) + + # apply minimum lithological id between the two units basal_contacts["ID"] = basal_contacts.apply( lambda row: min(units.index(row["UNITNAME_1"]), units.index(row["UNITNAME_2"])), axis=1 ) + # match the name of the unit with the minimum id basal_contacts["basal_unit"] = basal_contacts.apply(lambda row: units[row["ID"]], axis=1) - basal_contacts["distance"] = basal_contacts.apply( + # how many units apart are the two units? + basal_contacts["stratigraphic_distance"] = basal_contacts.apply( lambda row: abs(units.index(row["UNITNAME_1"]) - units.index(row["UNITNAME_2"])), axis=1 ) + # if the units are more than 1 unit apart, the contact is abnormal (meaning that there is one (or more) unit(s) missing in between the two) basal_contacts["type"] = basal_contacts.apply( - lambda row: "ABNORMAL" if abs(row["distance"]) > 1 else "BASAL", axis=1 + lambda row: "ABNORMAL" if abs(row["stratigraphic_distance"]) > 1 else "BASAL", axis=1 ) + basal_contacts = basal_contacts[["ID", "basal_unit", "type", "geometry"]] + + # added code to make sure that multi-line that touch each other are snapped and merged. + # necessary for the reconstruction based on featureId + basal_contacts["geometry"] = [ + shapely.line_merge(shapely.snap(geo, geo, 1)) for geo in basal_contacts["geometry"] + ] + if save_contacts: - self.basal_contacts = basal_contacts + # keep abnormal contacts as all_basal_contacts + self.all_basal_contacts = basal_contacts + # remove the abnormal contacts from basal contacts + self.basal_contacts = basal_contacts[basal_contacts["type"] == "BASAL"] + return basal_contacts @beartype.beartype @@ -1512,17 +1638,17 @@ def colour_units( try: colour_lookup = pandas.read_csv(self.colour_filename, sep=",") except FileNotFoundError: - print( + logger.info( f"Colour Lookup file {self.colour_filename} not found. Assigning random colors to units" ) self.colour_filename = None if self.colour_filename is None: - print("No colour configuration file found. Assigning random colors to units") + logger.info("\nNo colour configuration file found. Assigning random colors to units") missing_colour_n = len(stratigraphic_units["colour"]) - stratigraphic_units.loc[stratigraphic_units["colour"].isna(), "colour"] = ( - generate_random_hex_colors(missing_colour_n) - ) + stratigraphic_units.loc[ + stratigraphic_units["colour"].isna(), "colour" + ] = generate_random_hex_colors(missing_colour_n) colour_lookup["colour"] = colour_lookup["colour"].str.upper() # if there are duplicates in the clut file, drop. @@ -1536,12 +1662,12 @@ def colour_units( suffixes=("_old", ""), how="left", ) - stratigraphic_units.loc[stratigraphic_units["colour"].isna(), "colour"] = ( - generate_random_hex_colors(int(stratigraphic_units["colour"].isna().sum())) - ) + stratigraphic_units.loc[ + stratigraphic_units["colour"].isna(), "colour" + ] = generate_random_hex_colors(int(stratigraphic_units["colour"].isna().sum())) stratigraphic_units.drop(columns=["UNITNAME", "colour_old"], inplace=True) else: - print( + logger.warning( f"Colour Lookup file {self.colour_filename} does not contain 'UNITNAME' or 'colour' field" ) return stratigraphic_units diff --git a/map2loop/project.py b/map2loop/project.py index 75fb8efe..84aa0eea 100644 --- a/map2loop/project.py +++ b/map2loop/project.py @@ -4,7 +4,7 @@ from .m2l_enums import VerboseLevel, ErrorState, Datatype from .mapdata import MapData from .sampler import Sampler, SamplerDecimator, SamplerSpacing -from .thickness_calculator import ThicknessCalculator, ThicknessCalculatorAlpha +from .thickness_calculator import InterpolatedStructure, ThicknessCalculator from .throw_calculator import ThrowCalculator, ThrowCalculatorAlpha from .fault_orientation import FaultOrientation from .sorter import Sorter, SorterAgeBased, SorterAlpha, SorterUseNetworkX, SorterUseHint @@ -14,10 +14,11 @@ # external imports import LoopProjectFile as LPF -from typing import Union from osgeo import gdal +gdal.UseExceptions() import geopandas import beartype +from beartype.typing import Union, List import pathlib import numpy import pandas @@ -28,6 +29,7 @@ logger = getLogger(__name__) + class Project(object): """ The main entry point into using map2loop @@ -40,8 +42,6 @@ class Project(object): A list of samplers used to extract point samples from polyonal or line segments. Indexed by m2l_enum.Dataype sorter: Sorter The sorting algorithm to use for calculating the stratigraphic column - thickness_calculator: ThicknessCalulator - The algorithm to use for making unit thickness estimations loop_filename: str The name of the loop project file used in this project map_data: MapData @@ -71,7 +71,6 @@ def __init__( config_filename: Union[pathlib.Path, str] = "", config_dictionary: dict = {}, clut_filename: Union[pathlib.Path, str] = "", - clut_file_legacy: bool = False, save_pre_checked_map_data: bool = False, loop_project_filename: str = "", overwrite_loopprojectfile: bool = False, @@ -109,8 +108,6 @@ def __init__( A dictionary version of the configuration file. Defaults to {}. clut_filename (str, optional): The filename of the colour look up table to use. Defaults to "". - clut_file_legacy (bool, optional): - A flag to indicate if the clut file is in the legacy format. Defaults to False. save_pre_checked_map_data (bool, optional): A flag to save all map data to file before use. Defaults to False. loop_project_filename (str, optional): @@ -127,24 +124,28 @@ def __init__( self.verbose_level = verbose_level self.samplers = [SamplerDecimator()] * len(Datatype) self.set_default_samplers() + self.bounding_box = bounding_box self.sorter = SorterUseHint() - self.thickness_calculator = ThicknessCalculatorAlpha() + self.thickness_calculator = [InterpolatedStructure()] self.throw_calculator = ThrowCalculatorAlpha() self.fault_orientation = FaultOrientationNearest() - self.loop_filename = loop_project_filename - self.overwrite_lpf = overwrite_loopprojectfile - - self.map_data = MapData(tmp_path=tmp_path, verbose_level=verbose_level) + self.map_data = MapData(verbose_level=verbose_level) self.map2model = Map2ModelWrapper(self.map_data) self.stratigraphic_column = StratigraphicColumn() - self.deformation_history = DeformationHistory() - + self.deformation_history = DeformationHistory(project=self) + self.loop_filename = loop_project_filename + self.overwrite_lpf = overwrite_loopprojectfile + self.active_thickness = None + + # initialise the dataframes to store data in self.fault_orientations = pandas.DataFrame( columns=["ID", "DIPDIR", "DIP", "X", "Y", "Z", "featureId"] ) self.fault_samples = pandas.DataFrame(columns=["ID", "X", "Y", "Z", "featureId"]) self.fold_samples = pandas.DataFrame(columns=["ID", "X", "Y", "Z", "featureId"]) self.geology_samples = pandas.DataFrame(columns=["ID", "X", "Y", "Z", "featureId"]) + + # Check for alternate config filenames in kwargs if "metadata_filename" in kwargs and config_filename == "": config_filename = kwargs["metadata_filename"] @@ -162,7 +163,6 @@ def __init__( raise TypeError(f"Invalid type for working_projection {type(working_projection)}") # Sanity check bounding box - if issubclass(type(bounding_box), dict) or issubclass(type(bounding_box), tuple): if len(bounding_box) == 4 or len(bounding_box) == 6: self.map_data.set_bounding_box(bounding_box) @@ -180,7 +180,7 @@ def __init__( # Assign filenames if use_australian_state_data != "": # Sanity check on state string - if use_australian_state_data in ["WA", "SA", "QLD", "NSW", "TAS", "VIC", "ACT", "NT"]: + if use_australian_state_data in {"WA", "SA", "QLD", "NSW", "TAS", "VIC", "ACT", "NT"}: self.map_data.set_filenames_from_australian_state(use_australian_state_data) else: logger.error( @@ -189,6 +189,7 @@ def __init__( raise ValueError( f"Australian state {use_australian_state_data} not in state url database" ) + # set the data filenames if geology_filename != "": self.map_data.set_filename(Datatype.GEOLOGY, geology_filename) if structure_filename != "": @@ -201,50 +202,73 @@ def __init__( self.map_data.set_filename(Datatype.DTM, dtm_filename) if fault_orientation_filename != "": self.map_data.set_filename(Datatype.FAULT_ORIENTATION, fault_orientation_filename) + if config_filename != "": - if clut_file_legacy: - logger.warning("DEPRECATION: Legacy files are deprecated and their use will be removed in v3.2") + self.map_data.set_config_filename(config_filename) - self.map_data.set_config_filename(config_filename, legacy_format=clut_file_legacy) if config_dictionary != {}: self.map_data.config.update_from_dictionary(config_dictionary) + if clut_filename != "": self.map_data.set_colour_filename(clut_filename) + + # Load all data (both shape and raster) self.map_data.load_all_map_data() # If flag to save out data is check do so + tmp_path = pathlib.Path(tmp_path) + if save_pre_checked_map_data: + # check if the path exists, and if not, create + if not tmp_path.exists(): + tmp_path.mkdir() self.map_data.save_all_map_data(tmp_path) # Populate the stratigraphic column and deformation history from map data self.stratigraphic_column.populate(self.map_data.get_map_data(Datatype.GEOLOGY)) self.deformation_history.populate(self.map_data.get_map_data(Datatype.FAULT)) - # Set default minimum fault length to 5% of the longest bounding box dimension - bounding_box = self.map_data.get_bounding_box() - largest_dimension = max( - bounding_box["maxx"] - bounding_box["minx"], bounding_box["maxy"] - bounding_box["miny"] - ) - self.deformation_history.set_minimum_fault_length(largest_dimension * 0.05) - if len(kwargs): logger.warning(f"Unused keyword arguments: {kwargs}") # Getters and Setters @beartype.beartype - def set_ignore_codes(self, codes: list): + def set_ignore_lithology_codes(self, codes: list): """ - Set the ignore codes (a list of unit names to ignore in the geology shapefile) + Set the lithology unit names to be ignored in the geology shapefile. + + This method sets the lithology codes that should be excluded from the geology shapefile + and triggers the re-population of the stratigraphic column using the updated data + from the geological map, ensuring the excluded lithologies are not considered. Args: - codes (list): The list of strings to ignore + codes (list): + A list of strings representing the lithology unit names to be ignored + in the geological shapefile. """ - self.map_data.set_ignore_codes(codes) + self.map_data.set_ignore_lithology_codes(codes) # Re-populate the units in the column with the new set of ignored geographical units self.stratigraphic_column.populate(self.map_data.get_map_data(Datatype.GEOLOGY)) + @beartype.beartype + def set_ignore_fault_codes(self, codes: list): + """ + Set the fault names to be ignored in the fault map. + + This method sets the fault codes to be ignored from the fault map and triggers + re-parsing of the fault map to exclude the ignored faults during subsequent processing. + + Args: + codes (list): + A list of strings representing the fault unit names to be ignored + in the fault map. + """ + self.map_data.set_ignore_fault_codes(codes) + # Re-populate the units in the column with the new set of ignored geographical units + self.map_data.parse_fault_map() # remove the ignored faults + @beartype.beartype def set_sorter(self, sorter: Sorter): """ @@ -266,27 +290,6 @@ def get_sorter(self): """ return self.sorter.sorter_label - @beartype.beartype - def set_thickness_calculator(self, thickness_calculator: ThicknessCalculator): - """ - Set the thickness calculator that estimates unit thickness of all units - - Args: - thickness_calculator (ThicknessCalculator): - The calculator to use. Must be of base class ThicknessCalculator - """ - logger.info(f"Setting thickness calculator to {thickness_calculator.thickness_calculator_label}") - self.thickness_calculator = thickness_calculator - - def get_thickness_calculator(self): - """ - Get the name of the thickness calculator being used - - Returns: - str: The name of the thickness calculator used - """ - return self.thickness_calculator.thickness_calculator_label - @beartype.beartype def set_fault_orientation(self, fault_orientation: FaultOrientation): """ @@ -351,6 +354,21 @@ def set_sampler(self, datatype: Datatype, sampler: Sampler): sampler (Sampler): The sampler to use """ + allowed_samplers = { + Datatype.STRUCTURE: SamplerDecimator, + Datatype.GEOLOGY: SamplerSpacing, + Datatype.FAULT: SamplerSpacing, + Datatype.FOLD: SamplerSpacing, + Datatype.DTM: SamplerSpacing, + } + + # Check for wrong sampler + if datatype in allowed_samplers: + allowed_sampler_type = allowed_samplers[datatype] + if not isinstance(sampler, allowed_sampler_type): + raise ValueError( + f"Got wrong argument for this datatype: {type(sampler).__name__}, please use {allowed_sampler_type.__name__} instead" + ) ## does the enum print the number or the label? logger.info(f"Setting sampler for {datatype} to {sampler.sampler_label}") self.samplers[datatype] = sampler @@ -369,7 +387,7 @@ def get_sampler(self, datatype: Datatype): return self.samplers[datatype].sampler_label @beartype.beartype - def set_minimum_fault_length(self, length: float): + def set_minimum_fault_length(self, length: Union[float, int]): """ Set the cutoff length for faults to ignore @@ -377,8 +395,9 @@ def set_minimum_fault_length(self, length: float): length (float): The cutoff length """ - logger.info(f"Setting minimum fault length to {length}") - self.deformation_history.set_minimum_fault_length(length) + logger.info(f"Setting minimum fault length to {length}") + self.map_data.config.fault_config['minimum_fault_length'] = length + self.map_data.parse_fault_map() @beartype.beartype def get_minimum_fault_length(self) -> float: @@ -388,18 +407,51 @@ def get_minimum_fault_length(self) -> float: Returns: float: The cutoff length """ - return self.deformation_history.get_minimum_fault_length() + return float(self.map_data.config.fault_config['minimum_fault_length']) + + @beartype.beartype + def set_active_thickness(self, thickness_calculator: ThicknessCalculator): + """ + Sets the active_thickness attribute based on the provided thickness_calculator. + Args: + thickness_calculator (object or str): The thickness calculator object or its label. + If an object is provided, it should have a 'thickness_calculator_label' attribute. + Returns: + None + Raises: + ValueError: If the thickness calculator label cannot be determined. + """ + + try: + label = thickness_calculator.thickness_calculator_label + except AttributeError: + raise ValueError("The provided thickness calculator object does not have a 'thickness_calculator_label' attribute.") + self.active_thickness = label + + @beartype.beartype + def get_active_thickness(self) -> str: + """ + Retrieves the active_thickness attribute. + Returns: + str: The label of the active thickness calculator. + """ + return self.active_thickness + # Processing functions def sample_map_data(self): """ Use the samplers to extract points along polylines or unit boundaries """ - logger.info(f"Sampling geology map data using {self.samplers[Datatype.GEOLOGY].sampler_label}") + logger.info( + f"Sampling geology map data using {self.samplers[Datatype.GEOLOGY].sampler_label}" + ) self.geology_samples = self.samplers[Datatype.GEOLOGY].sample( self.map_data.get_map_data(Datatype.GEOLOGY), self.map_data ) - logger.info(f"Sampling structure map data using {self.samplers[Datatype.STRUCTURE].sampler_label}") + logger.info( + f"Sampling structure map data using {self.samplers[Datatype.STRUCTURE].sampler_label}" + ) self.structure_samples = self.samplers[Datatype.STRUCTURE].sample( self.map_data.get_map_data(Datatype.STRUCTURE), self.map_data ) @@ -418,9 +470,12 @@ def extract_geology_contacts(self): """ # Use stratigraphic column to determine basal contacts self.map_data.extract_basal_contacts(self.stratigraphic_column.column) + + # sample the contacts self.map_data.sampled_contacts = self.samplers[Datatype.GEOLOGY].sample( self.map_data.basal_contacts ) + self.map_data.get_value_from_raster_df(Datatype.DTM, self.map_data.sampled_contacts) def calculate_stratigraphic_order(self, take_best=False): @@ -429,13 +484,14 @@ def calculate_stratigraphic_order(self, take_best=False): """ if take_best: sorters = [SorterUseHint(), SorterAgeBased(), SorterAlpha(), SorterUseNetworkX()] - logger.info(f"Calculating best stratigraphic column from {[sorter.sorter_label for sorter in sorters]}") + logger.info( + f"Calculating best stratigraphic column from {[sorter.sorter_label for sorter in sorters]}" + ) columns = [ sorter.sort( self.stratigraphic_column.stratigraphicUnits, self.map2model.get_unit_unit_relationships(), - self.map2model.get_sorted_units(), self.map_data.contacts, self.map_data, ) @@ -466,24 +522,130 @@ def calculate_stratigraphic_order(self, take_best=False): self.stratigraphic_column.column = self.sorter.sort( self.stratigraphic_column.stratigraphicUnits, self.map2model.get_unit_unit_relationships(), - self.map2model.get_sorted_units(), self.map_data.contacts, self.map_data, ) + @beartype.beartype + def set_thickness_calculator( + self, thickness_calculator: Union['ThicknessCalculator', List['ThicknessCalculator']] + ) -> None: + """ + Sets the thickness_calculator attribute for the object. + + If a single instance of ThicknessCalculator is passed, it wraps it in a list. + If a list of ThicknessCalculator instances is passed, it validates that all elements + are instances of ThicknessCalculator before setting the attribute. + + Args: + thickness_calculator (ThicknessCalculator or list of ThicknessCalculator): + An instance or a list of ThicknessCalculator objects. + + Raises: + TypeError: If the provided thickness_calculator is not an instance of + ThicknessCalculator or a list of such instances. + """ + if isinstance(thickness_calculator, ThicknessCalculator): + thickness_calculator = [thickness_calculator] + + # Now check if thickness_calculator is a list of valid instances + if not isinstance(thickness_calculator, list) or not all( + isinstance(tc, ThicknessCalculator) for tc in thickness_calculator + ): + raise TypeError( + "All items must be instances of ThicknessCalculator or a single ThicknessCalculator instance." + ) + + # Finally, set the calculators + self.thickness_calculator = thickness_calculator + + def get_thickness_calculator(self) -> List[str]: + """ + Retrieves the thickness_calculator_label from the thickness_calculator attribute. + + This method checks if the thickness_calculator attribute is a list or a single object: + - If it's a list of ThicknessCalculator objects, it returns a list of their labels. + - If it's a single ThicknessCalculator object, it returns the label as a single-item list. + - If neither, it raises a TypeError. + + Returns: + list: A list of thickness_calculator_label(s) from the ThicknessCalculator object(s). + + Raises: + TypeError: If thickness_calculator is neither a list of objects nor a single object + with a 'thickness_calculator_label' attribute. + """ + + if isinstance(self.thickness_calculator, list): + # If it's a list, return labels from all items + return [ + calculator.thickness_calculator_label for calculator in self.thickness_calculator + ] + elif hasattr(self.thickness_calculator, 'thickness_calculator_label'): + # If it's a single object, return the label as a list + return [self.thickness_calculator.thickness_calculator_label] + else: + raise TypeError( + "self.thickness_calculator must be either a list of objects or a single object with a thickness_calculator_label attribute" + ) + def calculate_unit_thicknesses(self): """ - Use the stratigraphic column, and fault and contact data to estimate unit thicknesses + Calculates the unit thickness statistics (mean, median, standard deviation) for each stratigraphic unit + in the stratigraphic column using the provided thickness calculators. + + For each calculator in the `thickness_calculator` list: + - Computes the thickness statistics using the `compute()` method of each calculator. + - Repeats the computed results to match the number of rows in the stratigraphic units. + - Appends these results as new columns to the `stratigraphicUnits` dataframe. + + The new columns added for each calculator will be named in the format: + - {calculator_label}_mean + - {calculator_label}_median + - {calculator_label}_stddev + + Additionally, stores the labels of the calculators in the `thickness_calculator_labels` attribute. + + Returns: + None + + Raises: + None """ - logger.info(f"Calculating unit thicknesses using {self.thickness_calculator.thickness_calculator_label}") - self.stratigraphic_column.stratigraphicUnits = self.thickness_calculator.compute( - self.stratigraphic_column.stratigraphicUnits, - self.stratigraphic_column.column, - self.map_data.basal_contacts, - self.structure_samples, - self.map_data, - ) + labels = [] + + for calculator in self.thickness_calculator: + + result = calculator.compute( + self.stratigraphic_column.stratigraphicUnits, + self.stratigraphic_column.column, + self.map_data.basal_contacts, + self.structure_samples, + self.map_data, + )[['ThicknessMean', 'ThicknessMedian', 'ThicknessStdDev']].to_numpy() + + label = calculator.thickness_calculator_label + labels.append(label) + + # Repeat the results for the number of rows in stratigraphicUnits + num_rows = self.stratigraphic_column.stratigraphicUnits.shape[0] + repeated_result = numpy.tile(result, (num_rows // result.shape[0], 1)) + + # Append the repeated results to the lists + mean_col_name = f"{label}_mean" + median_col_name = f"{label}_median" + stddev_col_name = f"{label}_stddev" + + # Attach the results as new columns to the stratigraphic column dataframe + self.stratigraphic_column.stratigraphicUnits[mean_col_name] = repeated_result[:, 0] + self.stratigraphic_column.stratigraphicUnits[median_col_name] = repeated_result[:, 1] + self.stratigraphic_column.stratigraphicUnits[stddev_col_name] = repeated_result[:, 2] + + self.thickness_calculator_labels = labels + if self.active_thickness is None: + self.active_thickness = labels[0] + def calculate_fault_orientations(self): if self.map_data.get_map_data(Datatype.FAULT_ORIENTATION) is not None: logger.info(f"Calculating fault orientations using {self.fault_orientation.label}") @@ -494,7 +656,10 @@ def calculate_fault_orientations(self): ) self.map_data.get_value_from_raster_df(Datatype.DTM, self.fault_orientations) else: - logger.warning("No fault orientation data found, skipping fault orientation calculation") + logger.warning( + "No fault orientation data found, skipping fault orientation calculation" + ) + def apply_colour_to_units(self): """ Apply the clut file to the units in the stratigraphic column @@ -523,8 +688,7 @@ def summarise_fault_data(self): self.map_data.basal_contacts, self.map_data, ) - logger.info(f'There are {self.deformation_history.faults.shape[0]} faults in the dataset') - + logger.info(f'There are {self.deformation_history.faults.shape[0]} faults in the dataset') def run_all(self, user_defined_stratigraphic_column=None, take_best=False): """ @@ -544,12 +708,12 @@ def run_all(self, user_defined_stratigraphic_column=None, take_best=False): # Calculate the stratigraphic column if issubclass(type(user_defined_stratigraphic_column), list): self.stratigraphic_column.column = user_defined_stratigraphic_column - self.map2model.run() # if we use a user defined stratigraphic column, we still need to calculate the results of map2model + self.map2model.run() # if we use a user defined stratigraphic column, we still need to calculate the results of map2model else: if user_defined_stratigraphic_column is not None: logger.warning( f"user_defined_stratigraphic_column is not of type list and is {type(user_defined_stratigraphic_column)}. Attempting to calculate column" - ) #why not try casting to a list? + ) # why not try casting to a list? self.calculate_stratigraphic_order(take_best) self.sort_stratigraphic_column() @@ -584,7 +748,7 @@ def save_into_projectfile(self): file_exists = False logger.info(f"\nExisting file '{self.loop_filename}' was successfully deleted.") except Exception as e: - logger.errow(f"\nFailed to delete existing file '{self.loop_filename}': {e}") + logger.error(f"\nFailed to delete existing file '{self.loop_filename}': {e}") raise e else: logger.error( @@ -648,6 +812,9 @@ def save_into_projectfile(self): stratigraphic_data = numpy.zeros( len(self.stratigraphic_column.stratigraphicUnits), LPF.stratigraphicLayerType ) + stratigraphic_thicknesses = numpy.zeros( + len(self.stratigraphic_column.stratigraphicUnits), LPF.stratigraphicThicknessType) + stratigraphic_data["layerId"] = self.stratigraphic_column.stratigraphicUnits["layerId"] stratigraphic_data["minAge"] = self.stratigraphic_column.stratigraphicUnits["minAge"] stratigraphic_data["maxAge"] = self.stratigraphic_column.stratigraphicUnits["maxAge"] @@ -655,16 +822,20 @@ def save_into_projectfile(self): stratigraphic_data["group"] = self.stratigraphic_column.stratigraphicUnits["group"] stratigraphic_data["enabled"] = 1 - stratigraphic_data["ThicknessMean"] = self.stratigraphic_column.stratigraphicUnits[ - 'ThicknessMean' - ] - stratigraphic_data['ThicknessMedian'] = self.stratigraphic_column.stratigraphicUnits[ - 'ThicknessMedian' - ] - stratigraphic_data["ThicknessStdDev"] = self.stratigraphic_column.stratigraphicUnits[ - 'ThicknessStdDev' - ] - + stratigraphic_thicknesses['name']= self.stratigraphic_column.stratigraphicUnits["name"] + + # store all of the thickness estimates in a separate table + for i, label in enumerate(self.thickness_calculator_labels): + stratigraphic_thicknesses[f'thickness{i+1}_mean'] = self.stratigraphic_column.stratigraphicUnits.get(f'{label}_mean',0) + stratigraphic_thicknesses[f'thickness{i+1}_median'] = self.stratigraphic_column.stratigraphicUnits.get(f'{label}_median',0) + stratigraphic_thicknesses[f'thickness{i+1}_stddev'] = self.stratigraphic_column.stratigraphicUnits.get(f'{label}_stddev',0) + + # store the active thickness calculator as the default thickness + stratigraphic_data["ThicknessMean"] = self.stratigraphic_column.stratigraphicUnits.get(f'{self.active_thickness}_mean',0) + stratigraphic_data["ThicknessMedian"] = self.stratigraphic_column.stratigraphicUnits.get(f'{self.active_thickness}_median',0) + stratigraphic_data["ThicknessStdDev"] = self.stratigraphic_column.stratigraphicUnits.get(f'{self.active_thickness}_stddev',0) + + # Assign colours to startigraphic data stratigraphic_data["colour1Red"] = [ int(a[1:3], 16) for a in self.stratigraphic_column.stratigraphicUnits["colour"] ] @@ -682,7 +853,28 @@ def save_into_projectfile(self): stratigraphic_data["colour2Blue"] = [ int(a * 0.95) for a in stratigraphic_data["colour1Blue"] ] - LPF.Set(self.loop_filename, "stratigraphicLog", data=stratigraphic_data) + + n_thick_calcs = len(self.thickness_calculator_labels) + # get thickness calculator labels, and fill up with None if empty values up to 5 placeholders + while len(self.thickness_calculator_labels) < 5: + self.thickness_calculator_labels.append("None") + + headers = 'name;'+';'.join([f'{l}_mean;{l}_median;{l}_stddev' for l in self.thickness_calculator_labels[:5]]) + headers = headers.split(';') # split into list + + # save into LPF + LPF.Set( + self.loop_filename, + "stratigraphicLog", + data=stratigraphic_data, + verbose=False, + ) + LPF.Set(self.loop_filename, + "stratigraphicThicknesses", + data=stratigraphic_thicknesses, + headers=headers, + ncols=1+3*n_thick_calcs, # index and mean, median, stddev for each thickness calculator + verbose=False) # Save contacts contacts_data = numpy.zeros(len(self.map_data.sampled_contacts), LPF.contactObservationType) @@ -706,9 +898,9 @@ def save_into_projectfile(self): faults_obs_data["dipDir"][0 : len(self.fault_samples)] = numpy.nan faults_obs_data["dip"][0 : len(self.fault_samples)] = numpy.nan faults_obs_data["posOnly"][0 : len(self.fault_samples)] = 1 - faults_obs_data["displacement"] = ( - 100 # self.fault_samples["DISPLACEMENT"] #TODO remove note needed - ) + faults_obs_data[ + "displacement" + ] = 100 # self.fault_samples["DISPLACEMENT"] #TODO remove note needed faults_obs_data["eventId"][len(self.fault_samples) :] = self.fault_orientations["ID"] faults_obs_data["easting"][len(self.fault_samples) :] = self.fault_orientations["X"] @@ -771,7 +963,7 @@ def save_into_projectfile(self): relationships["angle"] = ff_relationships["Angle"] relationships["type"] = LPF.EventRelationshipType.FAULT_FAULT_ABUT logger.info("Adding fault relationships to projectfile") - logger.info(f"Fault relationships: {relationships}") + logger.info(f"Fault relationships: {relationships}") LPF.Set(self.loop_filename, "eventRelationships", data=relationships) @beartype.beartype diff --git a/map2loop/sampler.py b/map2loop/sampler.py index d369fea5..01600566 100644 --- a/map2loop/sampler.py +++ b/map2loop/sampler.py @@ -166,15 +166,8 @@ def sample( if target.within(t2_polygon): # df2['featureId'] = str(j) - if "ID" in spatial_data.columns: - df2["ID"] = row["ID"] - else: - df2["ID"] = 0 - - if len(df) == 0: - df = df2 - else: - df = pandas.concat([df, df2]) + df2["ID"] = row["ID"] if "ID" in spatial_data.columns else 0 + df = df2 if len(df) == 0 else pandas.concat([df, df2]) df.reset_index(drop=True, inplace=True) return df diff --git a/map2loop/sorter.py b/map2loop/sorter.py index 72d69d58..da4dab76 100644 --- a/map2loop/sorter.py +++ b/map2loop/sorter.py @@ -40,7 +40,6 @@ def sort( self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, - stratigraphic_order_hint: list, contacts: pandas.DataFrame, map_data: MapData, ) -> list: @@ -50,7 +49,6 @@ def sort( Args: units (pandas.DataFrame): the data frame to sort (columns must contain ["layerId", "name", "minAge", "maxAge", "group"]) units_relationships (pandas.DataFrame): the relationships between units (columns must contain ["Index1", "Unitname1", "Index2", "Unitname2"]) - stratigraphic_order_hint (list): a list of unit names to be used as a hint to sorting the units contacts (pandas.DataFrame): unit contacts with length of the contacts in metres map_data (map2loop.MapData): a catchall so that access to all map data is available @@ -60,45 +58,6 @@ def sort( pass -class SorterUseHint(Sorter): - """ - Sorter class which only returns the hint (no algorithm for sorting is done in this class) - """ - - def __init__(self): - """ - Initialiser for use hint sorter - """ - self.sorter_label = "SorterUseHint" - - @beartype.beartype - def sort( - self, - units: pandas.DataFrame, - unit_relationships: pandas.DataFrame, - stratigraphic_order_hint: list, - contacts: pandas.DataFrame, - map_data: MapData, - ) -> list: - """ - Execute sorter method takes unit data, relationships and a hint and returns the sorted unit names based on this algorithm. - In this case it purely returns the hint list - - Args: - units (pandas.DataFrame): the data frame to sort - units_relationships (pandas.DataFrame): the relationships between units - stratigraphic_order_hint (list): a list of unit names to use as a hint to sorting the units - contacts (pandas.DataFrame): unit contacts with length of the contacts in metres - map_data (map2loop.MapData): a catchall so that access to all map data is available - - Returns: - list: the sorted unit names - """ - logger.info('Stratigraphic order calculated using provided hint') - logger.info(','.join(stratigraphic_order_hint)) - return stratigraphic_order_hint - - class SorterUseNetworkX(Sorter): """ Sorter class which returns a sorted list of units based on the unit relationships using a topological graph sorting algorithm @@ -115,7 +74,6 @@ def sort( self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, - stratigraphic_order_hint: list, contacts: pandas.DataFrame, map_data: MapData, ) -> list: @@ -125,24 +83,21 @@ def sort( Args: units (pandas.DataFrame): the data frame to sort units_relationships (pandas.DataFrame): the relationships between units - stratigraphic_order_hint (list): a list of unit names to use as a hint to sorting the units contacts (pandas.DataFrame): unit contacts with length of the contacts in metres map_data (map2loop.MapData): a catchall so that access to all map data is available Returns: list: the sorted unit names """ - try: - import networkx as nx - except Exception: - logger.error("Cannot import networkx module, defaulting to SorterUseHint") - return stratigraphic_order_hint + import networkx as nx graph = nx.DiGraph() + name_to_index = {} for row in units.iterrows(): graph.add_node(int(row[1]["layerId"]), name=row[1]["name"]) + name_to_index[row[1]["name"]] = int(row[1]["layerId"]) for row in unit_relationships.iterrows(): - graph.add_edge(row[1]["Index1"], row[1]["Index2"]) + graph.add_edge(name_to_index[row[1]["UNITNAME_1"]], name_to_index[row[1]["UNITNAME_2"]]) cycles = list(nx.simple_cycles(graph)) for i in range(0, len(cycles)): @@ -161,6 +116,14 @@ def sort( return order +class SorterUseHint(SorterUseNetworkX): + def __init__(self): + logger.info( + "SorterUseHint is deprecated in v3.2. Use SorterUseNetworkX instead" + ) + super().__init__() + + class SorterAgeBased(Sorter): """ Sorter class which returns a sorted list of units based on the min and max ages of the units @@ -176,7 +139,6 @@ def sort( self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, - stratigraphic_order_hint: list, contacts: pandas.DataFrame, map_data: MapData, ) -> list: @@ -196,7 +158,7 @@ def sort( logger.info("Calling age based sorter") sorted_units = units.copy() if "minAge" in units.columns and "maxAge" in units.columns: - print(sorted_units["minAge"], sorted_units["maxAge"]) + # print(sorted_units["minAge"], sorted_units["maxAge"]) sorted_units["meanAge"] = sorted_units.apply( lambda row: (row["minAge"] + row["maxAge"]) / 2.0, axis=1 ) @@ -229,7 +191,6 @@ def sort( self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, - stratigraphic_order_hint: list, contacts: pandas.DataFrame, map_data: MapData, ) -> list: @@ -246,11 +207,7 @@ def sort( Returns: list: the sorted unit names """ - try: - import networkx as nx - except Exception: - logger.warning("Cannot import networkx module, defaulting to SorterUseHint") - return stratigraphic_order_hint + import networkx as nx contacts = contacts.sort_values(by="length", ascending=False)[ ["UNITNAME_1", "UNITNAME_2", "length"] @@ -322,7 +279,6 @@ def sort( self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, - stratigraphic_order_hint: list, contacts: pandas.DataFrame, map_data: MapData, ) -> list: @@ -339,12 +295,8 @@ def sort( Returns: list: the sorted unit names """ - try: - import networkx as nx - import networkx.algorithms.approximation as nx_app - except Exception: - logger.warning("Cannot import networkx module, defaulting to SorterUseHint") - return stratigraphic_order_hint + import networkx as nx + import networkx.algorithms.approximation as nx_app sorted_contacts = contacts.sort_values(by="length", ascending=False) self.graph = nx.Graph() @@ -409,7 +361,6 @@ def sort( self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, - stratigraphic_order_hint: list, contacts: pandas.DataFrame, map_data: MapData, ) -> list: @@ -426,14 +377,10 @@ def sort( Returns: list: the sorted unit names """ - try: - import networkx as nx - import networkx.algorithms.approximation as nx_app - from shapely.geometry import LineString, Point - from map2loop.m2l_enums import Datatype - except Exception: - logger.warning("Cannot import networkx module, defaulting to SorterUseHint") - return stratigraphic_order_hint + import networkx as nx + import networkx.algorithms.approximation as nx_app + from shapely.geometry import LineString, Point + from map2loop.m2l_enums import Datatype geol = map_data.get_map_data(Datatype.GEOLOGY).copy() geol = geol.drop(geol.index[np.logical_or(geol["INTRUSIVE"], geol["SILL"])]) diff --git a/map2loop/stratigraphic_column.py b/map2loop/stratigraphic_column.py index 016088c8..8fa6eedf 100644 --- a/map2loop/stratigraphic_column.py +++ b/map2loop/stratigraphic_column.py @@ -40,13 +40,7 @@ def __init__(self): ("maxAge", float), ("group", str), ("supergroup", str), - ("ThicknessMean", float), - ("ThicknessMedian", float), - ("ThicknessStdDev", float), ("colour", str), - # ("indexInGroup", int), - # ("groupNum", int), - # ("numInGroup", int), ] ) self.stratigraphicUnits = pandas.DataFrame( @@ -61,7 +55,6 @@ def __init__(self): ("minAge", float), ("maxAge", float), ("group", str), - ("ThicknessMedian", float), ("colour", str), ] ) @@ -164,7 +157,6 @@ def populate(self, geology_map_data: geopandas.GeoDataFrame): self.stratigraphicUnits["maxAge"] = geology_data["MAX_AGE"] self.stratigraphicUnits["group"] = geology_data["GROUP"] self.stratigraphicUnits["supergroup"] = geology_data["SUPERGROUP"] - self.stratigraphicUnits["ThicknessMedian"] = -1.0 self.stratigraphicUnits["colour"] = "#000000" # self.stratigraphicUnits["indexInGroup"] = -1 @@ -190,5 +182,5 @@ def sort_from_relationship_list(self, relationshipList: list): The order of the units by name """ sorter = dict(zip(relationshipList, range(len(relationshipList)))) - self.stratigraphicUnits["Order"] = self.stratigraphicUnits["name"].map(sorter) - self.stratigraphicUnits.sort_values(["Order"], inplace=True) + self.stratigraphicUnits["stratigraphic_Order"] = self.stratigraphicUnits["name"].map(sorter) + self.stratigraphicUnits.sort_values(["stratigraphic_Order"], inplace=True) diff --git a/map2loop/thickness_calculator.py b/map2loop/thickness_calculator.py index 376d1f82..eb8a2a67 100644 --- a/map2loop/thickness_calculator.py +++ b/map2loop/thickness_calculator.py @@ -1,5 +1,4 @@ # internal imports -import scipy.interpolate from .utils import ( create_points, rebuild_sampled_basal_contacts, @@ -11,14 +10,17 @@ from .interpolators import DipDipDirectionInterpolator from .mapdata import MapData +from .logging import getLogger +logger = getLogger(__name__) + # external imports from abc import ABC, abstractmethod +import scipy.interpolate import beartype import numpy import scipy import pandas import geopandas -from statistics import mean import shapely import math @@ -31,11 +33,12 @@ class ThicknessCalculator(ABC): ABC (ABC): Derived from Abstract Base Class """ - def __init__(self): + def __init__(self, max_line_length: float = None): """ Initialiser of for ThicknessCalculator """ self.thickness_calculator_label = "ThicknessCalculatorBaseClass" + self.max_line_length = max_line_length def type(self): """ @@ -75,9 +78,24 @@ def compute( If the thickness is not calculated for a given unit, the assigned thickness is -1. For the bottom and top units of the stratigraphic sequence, the assigned thickness is -1. """ - pass + if len(stratigraphic_order) < 3: + logger.warning( + f"Cannot make any thickness calculations with only {len(stratigraphic_order)} units" + ) + return units + def _check_thickness_percentage_calculations(self, thicknesses: pandas.DataFrame): + units_with_no_thickness = len(thicknesses[thicknesses['ThicknessMean'] == -1]) + total_units = len(thicknesses) + + if total_units > 0 and (units_with_no_thickness / total_units) >= 0.75: + logger.warning( + f"More than {int(0.75 * 100)}% of units ({units_with_no_thickness}/{total_units}) " + f"have a calculated thickness of -1. This may indicate that {self.thickness_calculator_label} " + f"is not suitable for this dataset." + ) + class ThicknessCalculatorAlpha(ThicknessCalculator): """ ThicknessCalculator class which estimates unit thickness based on units, basal_contacts and stratigraphic order @@ -117,36 +135,45 @@ def compute( no_distance = -1.0 basal_contacts = basal_contacts[basal_contacts["type"] == "BASAL"] thicknesses = units.copy() - # Set default value + + # Set default values + thicknesses["ThicknessMean"] = no_distance thicknesses["ThicknessMedian"] = no_distance + thicknesses["ThicknessStdDev"] = no_distance + basal_unit_list = basal_contacts["basal_unit"].to_list() + sampled_basal_contacts = rebuild_sampled_basal_contacts( + basal_contacts=basal_contacts, sampled_contacts=map_data.sampled_contacts + ) + if len(stratigraphic_order) < 3: - print( - f"Cannot make any thickness calculations with only {len(stratigraphic_order)} units" + logger.warning( + f"ThicknessCalculatorAlpha: Cannot make any thickness calculations with only {len(stratigraphic_order)} units" ) return thicknesses + for i in range(1, len(stratigraphic_order) - 1): # Compare basal contacts of adjacent units if ( stratigraphic_order[i] in basal_unit_list and stratigraphic_order[i + 1] in basal_unit_list ): - contact1 = basal_contacts[basal_contacts["basal_unit"] == stratigraphic_order[i]][ - "geometry" - ].to_list()[0] - contact2 = basal_contacts[ - basal_contacts["basal_unit"] == stratigraphic_order[i + 1] + contact1 = sampled_basal_contacts[ + sampled_basal_contacts["basal_unit"] == stratigraphic_order[i] + ]["geometry"].to_list()[0] + contact2 = sampled_basal_contacts[ + sampled_basal_contacts["basal_unit"] == stratigraphic_order[i + 1] ]["geometry"].to_list()[0] if contact1 is not None and contact2 is not None: distance = contact1.distance(contact2) else: - print( - f"Cannot calculate thickness between {stratigraphic_order[i]} and {stratigraphic_order[i + 1]}" + logger.warning( + f"ThicknessCalculatorAlpha: Cannot calculate thickness between {stratigraphic_order[i]} and {stratigraphic_order[i + 1]} \n" ) distance = no_distance else: - print( - f"Cannot calculate thickness between {stratigraphic_order[i]} and {stratigraphic_order[i + 1]}" + logger.warning( + f"ThicknessCalculatorAlpha: Cannot calculate thickness between {stratigraphic_order[i]} and {stratigraphic_order[i + 1]} \n" ) distance = no_distance @@ -154,24 +181,14 @@ def compute( # Maximum thickness is the horizontal distance between the minimum of these distances # Find row in unit_dataframe corresponding to unit and replace thickness value if it is -1 or larger than distance idx = thicknesses.index[thicknesses["name"] == stratigraphic_order[i]].tolist()[0] - if thicknesses.loc[idx, "ThicknessMedian"] == -1: + if thicknesses.loc[idx, "ThicknessMean"] == -1: val = distance else: - val = min(distance, thicknesses.at[idx, "ThicknessMedian"]) - thicknesses.loc[idx, "ThicknessMedian"] = val - - # If no thickness calculations can be made with current stratigraphic column set all units - # to a uniform thickness value - if len(thicknesses[thicknesses["ThicknessMedian"] > 0]) < 1: - thicknesses["ThicknessMedian"] = 100.0 - mean_thickness = mean(thicknesses[thicknesses["ThicknessMedian"] > 0]["ThicknessMedian"]) - - # For any unit thickness that still hasn't been calculated (i.e. at -1) set to - # the mean thickness of the other units - thicknesses["ThicknessMedian"] = thicknesses.apply( - lambda row: mean_thickness if row["ThicknessMedian"] == -1 else row["ThicknessMedian"], - axis=1, - ) + val = min(distance, thicknesses.at[idx, "ThicknessMean"]) + thicknesses.loc[idx, "ThicknessMean"] = val + + self._check_thickness_percentage_calculations(thicknesses) + return thicknesses @@ -189,12 +206,14 @@ class InterpolatedStructure(ThicknessCalculator): -> pandas.DataFrame: Calculates a thickness map for the overall map area. """ - def __init__(self): + def __init__(self, max_line_length: float = None): """ Initialiser for interpolated structure version of the thickness calculator """ + super().__init__(max_line_length) self.thickness_calculator_label = "InterpolatedStructure" - self.lines = [] + self.lines = None + @beartype.beartype def compute( @@ -238,7 +257,7 @@ def compute( thicknesses["ThicknessMedian"] = -1.0 thicknesses['ThicknessMean'] = -1.0 # thicknesses["ThicknessStdDev"] is the standard deviation of the thickness of the unit - thicknesses["ThicknessStdDev"] = 0 + thicknesses["ThicknessStdDev"] = -1.0 thicknesses['ThicknessStdDev'] = thicknesses['ThicknessStdDev'].astype('float64') basal_unit_list = basal_contacts["basal_unit"].to_list() # increase buffer around basal contacts to ensure that the points are included as intersections @@ -261,8 +280,10 @@ def compute( contacts = contacts.sjoin(basal_contacts, how="inner", predicate="intersects") contacts = contacts[["X", "Y", "Z", "geometry", "basal_unit"]].copy() bounding_box = map_data.get_bounding_box() + # Interpolate the dip of the contacts interpolator = DipDipDirectionInterpolator(data_type="dip") + # Interpolate the dip of the contacts dip = interpolator(bounding_box, structure_data, interpolator=scipy.interpolate.Rbf) # create a GeoDataFrame of the interpolated orientations interpolated_orientations = geopandas.GeoDataFrame() @@ -291,13 +312,11 @@ def compute( interpolated_orientations = interpolated_orientations[ ["geometry", "dip", "UNITNAME"] ].copy() - - if len(stratigraphic_order) < 3: - print( - f"Cannot make any thickness calculations with only {len(stratigraphic_order)} units" - ) - return thicknesses - + + _lines = [] + _dips = [] + _location_tracking = [] + for i in range(0, len(stratigraphic_order) - 1): if ( stratigraphic_order[i] in basal_unit_list @@ -319,11 +338,18 @@ def compute( dip = interpolated_orientations.loc[ interpolated_orientations["UNITNAME"] == stratigraphic_order[i], "dip" ].to_numpy() + _thickness = [] + for _, row in basal_contact.iterrows(): # find the shortest line between the basal contact points and top contact points short_line = shapely.shortest_line(row.geometry, top_contact_geometry) - self.lines.append(short_line) + _lines.append(short_line[0]) + + # check if the short line is + if self.max_line_length is not None and short_line.length > self.max_line_length: + continue + # extract the end points of the shortest line p1 = numpy.zeros(3) p1[0] = numpy.asarray(short_line[0].coords[0][0]) @@ -336,18 +362,27 @@ def compute( p2[1] = numpy.asarray(short_line[0].coords[-1][1]) # get the elevation Z of the end point p2 p2[2] = map_data.get_value_from_raster(Datatype.DTM, p2[0], p2[1]) - # get the elevation Z of the end point p2 - p2[2] = map_data.get_value_from_raster(Datatype.DTM, p2[0], p2[1]) # calculate the length of the shortest line line_length = scipy.spatial.distance.euclidean(p1, p2) # find the indices of the points that are within 5% of the length of the shortest line indices = shapely.dwithin(short_line, interp_points, line_length * 0.25) # get the dip of the points that are within - # 10% of the length of the shortest line _dip = numpy.deg2rad(dip[indices]) - # get the end points of the shortest line - # calculate the true thickness t = L . sin dip + _dips.append(_dip) + # calculate the true thickness t = L * sin(dip) thickness = line_length * numpy.sin(_dip) + + # add location tracking + location_tracking = pandas.DataFrame( + { + "p1_x": [p1[0]], "p1_y": [p1[1]], "p1_z": [p1[2]], + "p2_x": [p2[0]], "p2_y": [p2[1]], "p2_z": [p2[2]], + "thickness": [thickness], + "unit": [stratigraphic_order[i]] + } + ) + _location_tracking.append(location_tracking) + # Average thickness along the shortest line if all(numpy.isnan(thickness)): pass @@ -369,13 +404,25 @@ def compute( thicknesses.loc[idx, "ThicknessStdDev"] = std_dev else: - print( - f"Cannot calculate thickness between {stratigraphic_order[i]} and {stratigraphic_order[i + 1]}" + logger.warning( + f"Thickness Calculator InterpolatedStructure: Cannot calculate thickness between {stratigraphic_order[i]} and {stratigraphic_order[i + 1]}\n" ) - + + # Combine all location_tracking DataFrames into a single DataFrame + combined_location_tracking = pandas.concat(_location_tracking, ignore_index=True) + + # Save the combined DataFrame as an attribute of the class + self.location_tracking = combined_location_tracking + + # Create GeoDataFrame for lines + self.lines = geopandas.GeoDataFrame(geometry=_lines, crs=basal_contacts.crs) + self.lines['dip'] = _dips + + # Check thickness calculation + self._check_thickness_percentage_calculations(thicknesses) + return thicknesses - class StructuralPoint(ThicknessCalculator): ''' This class is a subclass of the ThicknessCalculator abstract base class. It implements the thickness calculation using a deterministic workflow based on stratigraphic measurements. @@ -390,10 +437,12 @@ class StructuralPoint(ThicknessCalculator): ''' - def __init__(self): + def __init__(self, max_line_length: float = None): + super().__init__(max_line_length) self.thickness_calculator_label = "StructuralPoint" - self.line_length = 10000 self.strike_allowance = 30 + self.lines = None + @beartype.beartype def compute( @@ -454,13 +503,14 @@ def compute( ) # add unitname to the sampled structures sampled_structures['unit_name'] = geopandas.sjoin(sampled_structures, geology)['UNITNAME'] - - # remove nans from sampled structures + + # remove nans from sampled structures # this happens when there are strati measurements within intrusions. If intrusions are removed from the geology map, unit_name will then return a nan - print(f"skipping row(s) {sampled_structures[sampled_structures['unit_name'].isnull()].index.to_numpy()} in sampled structures dataset, as they do not spatially coincide with a valid geology polygon \n") + logger.info( + f"skipping row(s) {sampled_structures[sampled_structures['unit_name'].isnull()].index.to_numpy()} in sampled structures dataset, as they do not spatially coincide with a valid geology polygon \n" + ) sampled_structures = sampled_structures.dropna(subset=['unit_name']) - - + # rebuild basal contacts lines based on sampled dataset sampled_basal_contacts = rebuild_sampled_basal_contacts( basal_contacts, map_data.sampled_contacts @@ -473,6 +523,8 @@ def compute( # create empty lists to store thicknesses and lithologies thicknesses = [] lis = [] + _lines = [] + _dip = [] # loop over each sampled structural measurement for s in range(0, len(sampled_structures)): @@ -490,18 +542,23 @@ def compute( # check if litho_in is in geology # for a special case when the litho_in is not in the geology - if len(geology[geology['UNITNAME'] == litho_in]) == 0: - print(f"There are structural measurements in unit - {litho_in} - that are not in the geology shapefile. Skipping this structural measurement") + if len(geology[geology['UNITNAME'] == litho_in]) == 0: + logger.info( + f"There are structural measurements in unit - {litho_in} - that are not in the geology shapefile. Skipping this structural measurement" + ) continue - else: + else: # make a subset of the geology polygon & find neighbour units GEO_SUB = geology[geology['UNITNAME'] == litho_in]['geometry'].values[0] neighbor_list = list( basal_contacts[GEO_SUB.intersects(basal_contacts.geometry)]['basal_unit'] ) + # draw orthogonal line to the strike (default value 10Km), and clip it by the bounding box of the lithology - B = calculate_endpoints(measurement_pt, strike, self.line_length, bbox_poly) + if self.max_line_length is None: + self.max_line_length = 10000 + B = calculate_endpoints(measurement_pt, strike, self.max_line_length, bbox_poly) b = geopandas.GeoDataFrame({'geometry': [B]}).set_crs(basal_contacts.crs) # find all intersections @@ -573,14 +630,28 @@ def compute( if not (b_s[0] < strike1 < b_s[1] and b_s[0] < strike2 < b_s[1]): continue + #build the debug info + line = shapely.geometry.LineString([int_pt1, int_pt2]) + _lines.append(line) + _dip.append(measurement['DIP']) + # find the lenght of the segment L = math.sqrt(((int_pt1.x - int_pt2.x) ** 2) + ((int_pt1.y - int_pt2.y) ** 2)) + + # if length is higher than max_line_length, skip + if self.max_line_length is not None and L > self.max_line_length: + continue + # calculate thickness thickness = L * math.sin(math.radians(measurement['DIP'])) thicknesses.append(thickness) lis.append(litho_in) - + + # create the debug gdf + self.lines = geopandas.GeoDataFrame(geometry=_lines, crs=basal_contacts.crs) + self.lines["DIP"] = _dip + # create a DataFrame of the thicknesses median and standard deviation by lithology result = pandas.DataFrame({'unit': lis, 'thickness': thicknesses}) result = result.groupby('unit')['thickness'].agg(['median', 'mean', 'std']).reset_index() @@ -588,10 +659,10 @@ def compute( output_units = units.copy() # remove the old thickness column - output_units['ThicknessMedian'] = numpy.empty((len(output_units))) - output_units['ThicknessMean'] = numpy.empty((len(output_units))) - output_units['ThicknessStdDev'] = numpy.empty((len(output_units))) - + output_units['ThicknessMedian'] = numpy.full(len(output_units), numpy.nan) + output_units['ThicknessMean'] = numpy.full(len(output_units), numpy.nan) + output_units['ThicknessStdDev'] = numpy.full(len(output_units), numpy.nan) + # find which units have no thickness calculated names_not_in_result = units[~units['name'].isin(result['unit'])]['name'].to_list() # assign the thicknesses to the each unit @@ -600,6 +671,12 @@ def compute( output_units.loc[idx, 'ThicknessMedian'] = unit['median'] output_units.loc[idx, 'ThicknessMean'] = unit['mean'] output_units.loc[idx, 'ThicknessStdDev'] = unit['std'] + + output_units["ThicknessMean"] = output_units["ThicknessMean"].fillna(-1) + output_units["ThicknessMedian"] = output_units["ThicknessMedian"].fillna(-1) + output_units["ThicknessStdDev"] = output_units["ThicknessStdDev"].fillna(-1) + + # handle the units that have no thickness for unit in names_not_in_result: # if no thickness has been calculated for the unit @@ -611,12 +688,12 @@ def compute( ): idx = stratigraphic_order.index(unit) # throw warning to user - print( - 'It was not possible to calculate thickness between unit ', + logger.warning( + 'Thickness Calculator StructuralPoint: Cannot calculate thickness between', unit, "and ", stratigraphic_order[idx + 1], - 'Assigning thickness of -1', + "\n", ) # assign -1 as thickness output_units.loc[output_units["name"] == unit, "ThicknessMedian"] = -1 @@ -624,9 +701,11 @@ def compute( output_units.loc[output_units["name"] == unit, "ThicknessStdDev"] = -1 # if top//bottom unit assign -1 - if unit == stratigraphic_order[-1] or unit == stratigraphic_order[0]: + if unit in [stratigraphic_order[-1], stratigraphic_order[0]]: output_units.loc[output_units["name"] == unit, "ThicknessMedian"] = -1 output_units.loc[output_units["name"] == unit, "ThicknessMean"] = -1 output_units.loc[output_units["name"] == unit, "ThicknessStdDev"] = -1 + self._check_thickness_percentage_calculations(output_units) + return output_units diff --git a/map2loop/utils.py b/map2loop/utils.py index e54554f8..00e8fa57 100644 --- a/map2loop/utils.py +++ b/map2loop/utils.py @@ -3,8 +3,13 @@ import shapely import geopandas import beartype -from typing import Union, Optional +from beartype.typing import Union, Optional, Dict import pandas +import re +import json + +from .logging import getLogger +logger = getLogger(__name__) @beartype.beartype @@ -261,7 +266,7 @@ def rebuild_sampled_basal_contacts( crs=basal_contacts.crs, ) - basal_contacts['geometry'] = basal_contacts.buffer(1) + basal_contacts.loc[:, 'geometry'] = basal_contacts.buffer(1) sampled_basal_contacts = sampled_geology.sjoin( basal_contacts, how='left', predicate='intersects' ).dropna() @@ -371,3 +376,155 @@ def hex_to_rgb(hex_color: str) -> tuple: raise ValueError("Invalid hex color code. Contains non-hexadecimal characters.") from e return (r, g, b, alpha) + + +@beartype.beartype +def calculate_minimum_fault_length( + bbox: dict[str, int | float], area_percentage: float +) -> float: + + """ + Calculate the minimum fault length based on the map bounding box and a given area percentage. + + Args: + bbox (dict): A dictionary with keys 'minx', 'miny', 'maxx', 'maxy' representing the bounding box in meters. + area_percentage (float): The percentage of the bounding box area to use for calculating the threshold length. + + Returns: + float: The calculated minimum fault length as the square root of the threshold area. + """ + + # Calculate the width and height of the bounding box in meters + width = bbox['maxx'] - bbox['minx'] + height = bbox['maxy'] - bbox['miny'] + + # Calculate the total bounding box area + bbox_area = width * height + + # Calculate the threshold area based on the given percentage + threshold_area = area_percentage * bbox_area + + # Return the square root of the threshold area as the minimum fault length + return threshold_area**0.5 + + +def preprocess_hjson_to_json(hjson_content): + # Remove comments + hjson_content = re.sub(r'#.*', '', hjson_content) + hjson_content = re.sub(r'//.*', '', hjson_content) + # Replace single quotes with double quotes + hjson_content = re.sub(r"(? dict: + try: + # Read the file + with open(file_path, "r", encoding="utf-8") as file: + hjson_content = file.read() + if not hjson_content.strip(): + raise ValueError("The HJSON file is empty.") + # Preprocess HJSON to JSON + preprocessed_content = preprocess_hjson_to_json(hjson_content) + # Parse JSON + return json.loads(preprocessed_content) + except FileNotFoundError as e: + raise FileNotFoundError(f"HJSON file not found: {file_path}") from e + except json.JSONDecodeError as e: + raise ValueError(f"Failed to decode preprocessed HJSON as JSON: {e}") from e + +@beartype.beartype +def update_from_legacy_file( + filename: str, + json_save_path: Optional[str] = None, + lower: bool = False +) -> Optional[Dict[str, Dict]]: + """ + Update the config dictionary from the provided old version dictionary + Args: + filename (str): the path to the legacy file + json_save_path (str, optional): the path to save the updated json file. Defaults to None. + lower (bool, optional): whether to convert all strings to lowercase. Defaults to False. + + Returns: + Dict[Dict]: the updated config dictionary + + Example: + from map2loop.utils import update_from_legacy_file + update_from_legacy_file(filename=r"./source_data/example.hjson") + """ + # only import config if needed + from .config import Config + file_map = Config() + + code_mapping = { + "otype": (file_map.structure_config, "orientation_type"), + "dd": (file_map.structure_config, "dipdir_column"), + "d": (file_map.structure_config, "dip_column"), + "sf": (file_map.structure_config, "description_column"), + "bedding": (file_map.structure_config, "bedding_text"), + "bo": (file_map.structure_config, "overturned_column"), + "btype": (file_map.structure_config, "overturned_text"), + "gi": (file_map.structure_config, "objectid_column"), + "c": (file_map.geology_config, "unitname_column"), + "u": (file_map.geology_config, "alt_unitname_column"), + "g": (file_map.geology_config, "group_column"), + "g2": (file_map.geology_config, "supergroup_column"), + "ds": (file_map.geology_config, "description_column"), + "min": (file_map.geology_config, "minage_column"), + "max": (file_map.geology_config, "maxage_column"), + "r1": (file_map.geology_config, "rocktype_column"), + "r2": (file_map.geology_config, "alt_rocktype_column"), + "sill": (file_map.geology_config, "sill_text"), + "intrusive": (file_map.geology_config, "intrusive_text"), + "volcanic": (file_map.geology_config, "volcanic_text"), + "f": (file_map.fault_config, "structtype_column"), + "fault": (file_map.fault_config, "fault_text"), + "fdipnull": (file_map.fault_config, "dip_null_value"), + "fdipdip_flag": (file_map.fault_config, "dipdir_flag"), + "fdipdir": (file_map.fault_config, "dipdir_column"), + "fdip": (file_map.fault_config, "dip_column"), + "fdipest": (file_map.fault_config, "dipestimate_column"), + "fdipest_vals": (file_map.fault_config, "dipestimate_text"), + "n": (file_map.fault_config, "name_column"), + "ff": (file_map.fold_config, "structtype_column"), + "fold": (file_map.fold_config, "fold_text"), + "t": (file_map.fold_config, "description_column"), + "syn": (file_map.fold_config, "synform_text"), + } + # try and ready the file: + try: + parsed_data = read_hjson_with_json(filename) + except Exception as e: + logger.error(f"Error reading file {filename}: {e}") + return + #map the keys + file_map = file_map.to_dict() + for legacy_key, new_mapping in code_mapping.items(): + if legacy_key in parsed_data: + section, new_key = new_mapping + value = parsed_data[legacy_key] + if lower and isinstance(value, str): + value = value.lower() + section[new_key] = value + + if "o" in parsed_data: + object_id_value = parsed_data["o"] + if lower and isinstance(object_id_value, str): + object_id_value = object_id_value.lower() + file_map['structure']["objectid_column"] = object_id_value + file_map['geology']["objectid_column"] = object_id_value + file_map['fold']["objectid_column"] = object_id_value + + if json_save_path is not None: + with open(json_save_path, "w") as f: + json.dump(parsed_data, f, indent=4) + + return file_map \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 411d846a..c5d1b68a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,15 +32,14 @@ Documentation = 'https://Loop3d.org/map2loop/' "Source Code" = 'https://github.com/Loop3D/map2loop' [tool.setuptools.dynamic] -dependencies = {file = ["dependencies.txt"]} -version = { attr = 'map2loop.version.__version__' } +dependencies = { file = ["dependencies.txt"]} +version = { attr = "map2loop.version.__version__" } [tool.setuptools.packages.find] include = ['map2loop', 'map2loop.*'] - [tool.black] line-length = 100 skip-string-normalization = true diff --git a/setup.py b/setup.py index 56ce64c1..7cea5025 100644 --- a/setup.py +++ b/setup.py @@ -1,13 +1,28 @@ """See pyproject.toml for project metadata.""" -from setuptools import setup import os +from setuptools import setup package_root = os.path.abspath(os.path.dirname(__file__)) +# Get the version from the version.py file version = {} with open(os.path.join(package_root, "map2loop/version.py")) as fp: exec(fp.read(), version) version = version["__version__"] -setup() +# Read dependencies from dependencies.txt +requirements_file = os.path.join(package_root, "dependencies.txt") +with open(requirements_file, 'r') as f: + install_requires = [line.strip() for line in f if line.strip()] + +setup( + name="map2loop", + install_requires=install_requires, + version=version, + license="MIT", + package_data={ + # Include test files: + '': ['tests/*.py'], + }, +) \ No newline at end of file diff --git a/tests/mapdata/test_mapdata_dipdir.py b/tests/mapdata/test_mapdata_dipdir.py index 68f45b47..cc156253 100644 --- a/tests/mapdata/test_mapdata_dipdir.py +++ b/tests/mapdata/test_mapdata_dipdir.py @@ -5,9 +5,10 @@ import pytest import geopandas import shapely -from map2loop.mapdata import MapData +from map2loop.mapdata import MapData from map2loop.m2l_enums import Datatype + def test_if_m2l_returns_all_sampled_structures_with_DIPDIR_lower_than_360(): # call the class @@ -15,27 +16,27 @@ def test_if_m2l_returns_all_sampled_structures_with_DIPDIR_lower_than_360(): # add config definition md.config.structure_config = { - "dipdir_column": "DIPDIR", - "dip_column": "DIP", - "description_column": "DESCRIPTION", - "bedding_text": "Bedding", - "objectid_column": "ID", - "overturned_column": "facing", - "overturned_text": "DOWN", - "orientation_type": "strike" - } + "dipdir_column": "DIPDIR", + "dip_column": "DIP", + "description_column": "DESCRIPTION", + "bedding_text": "Bedding", + "objectid_column": "ID", + "overturned_column": "facing", + "overturned_text": "DOWN", + "orientation_type": "strike", + } # create mock data data = { - 'geometry': [shapely.Point(1, 1), shapely.Point(2, 2), shapely.Point(3, 3),], - 'DIPDIR': [45.0, 370.0, 420.0], + 'geometry': [shapely.Point(1, 1), shapely.Point(2, 2), shapely.Point(3, 3)], + 'DIPDIR': [45.0, 370.0, 420.0], 'DIP': [30.0, 60.0, 50], 'OVERTURNED': ["False", "True", "True"], 'DESCRIPTION': ["Bedding", "Bedding", "Bedidng"], - 'ID': [1, 2, 3] + 'ID': [1, 2, 3], } - #build geodataframe to hold the data + # build geodataframe to hold the data data = geopandas.GeoDataFrame(data) # set it as the raw_data @@ -49,6 +50,9 @@ def test_if_m2l_returns_all_sampled_structures_with_DIPDIR_lower_than_360(): pytest.fail(f"parse_structure_map raised an exception: {e}") # check if all values below 360 - assert md.data[Datatype.STRUCTURE]['DIPDIR'].all() < 360, "MapData.STRUCTURE is producing DIPDIRs > 360 degrees" - -# + assert ( + md.data[Datatype.STRUCTURE]['DIPDIR'].all() < 360 + ), "MapData.STRUCTURE is producing DIPDIRs > 360 degrees" + + +# diff --git a/tests/mapdata/test_minimum_fault_length.py b/tests/mapdata/test_minimum_fault_length.py new file mode 100644 index 00000000..ce78bcc1 --- /dev/null +++ b/tests/mapdata/test_minimum_fault_length.py @@ -0,0 +1,124 @@ +import pytest +import geopandas as gpd +import shapely +import numpy + +from map2loop.mapdata import MapData +from map2loop.m2l_enums import VerboseLevel, Datatype + + +@pytest.fixture +def setup_map_data(): + # Create a mock MapData object with verbose level set to ALL + map_data = MapData(verbose_level=VerboseLevel.ALL) + + # Simulate config with no minimum_fault_length set + map_data.config.fault_config['minimum_fault_length'] = -1.0 + + return map_data + + +# for cases when there is no minimum_fault_length set in the config by user - does it update from map? +def test_update_minimum_fault_length_from_faults(setup_map_data): + map_data = setup_map_data + + # Define a test bounding box (in meters) + bounding_box = { + "minx": 0, + "miny": 0, + "maxx": 10000, # width = 10,000 meters + "maxy": 10000, # height = 10,000 meters + } + + # Set the bounding box in the map data + map_data.set_bounding_box(bounding_box) + + # update config + map_data.config.fault_config['name_column'] = 'NAME' + map_data.config.fault_config['dip_column'] = 'DIP' + + # Define a dummy fault GeoDataFrame with faults of varying lengths + faults = gpd.GeoDataFrame( + { + 'geometry': [ + shapely.geometry.LineString( + [(0, 0), (50, 50)] + ), # Fault 1 (small, length ~70.7 meters) + shapely.geometry.LineString( + [(0, 0), (3000, 3000)] + ), # Fault 2 (length ~4242 meters) + shapely.geometry.LineString( + [(0, 0), (7000, 7000)] + ), # Fault 3 (length ~9899 meters) + ], + 'NAME': ['Fault_1', 'Fault_2', 'Fault_3'], + 'DIP': [60, 45, 30], + } + ) + + faults.crs = "EPSG: 7850" + + # get the cropped fault dataset from parse_fault_map + map_data.raw_data[Datatype.FAULT] = faults + map_data.parse_fault_map() + cropped_faults = map_data.data[Datatype.FAULT] + + # calculate 5% length of the bounding box area + expected_minimum_fault_length = numpy.sqrt( + 0.05 + * (bounding_box['maxx'] - bounding_box['minx']) + * (bounding_box['maxy'] - bounding_box['miny']) + ) + + # Verify that the minimum_fault_length was calculated correctly + assert map_data.minimum_fault_length == pytest.approx(expected_minimum_fault_length, rel=1e-3) + + # There should only be two faults remaining (the second and third ones) + assert len(cropped_faults) == 2 + + # Ensure that the remaining faults are the correct ones + remaining_lengths = cropped_faults.geometry.length + assert all(remaining_lengths >= expected_minimum_fault_length) + assert cropped_faults.geometry.equals( + faults.iloc[1:]['geometry'] + ) # Faults 2 and 3 geometries should be the same in the faults raw and faults cropped + + +# are faults with length less than minimum_fault_length removed from the dataset? +def test_cropping_faults_by_minimum_fault_length(setup_map_data): + map_data = setup_map_data + + # Set minimum_fault_length in the config to 10 + map_data.config.fault_config['minimum_fault_length'] = 10.0 + + map_data.config.fault_config['name_column'] = 'NAME' + map_data.config.fault_config['dip_column'] = 'DIP' + + # Create a mock faults dataset with lengths < 10 and > 10 + faults = gpd.GeoDataFrame( + { + 'geometry': [ + shapely.geometry.LineString([(0, 0), (2, 2)]), # Length ~2.83 (should be cropped) + shapely.geometry.LineString([(0, 0), (5, 5)]), # Length ~7.07 (should be cropped) + shapely.geometry.LineString([(0, 0), (10, 10)]), # Length ~14.14 (should remain) + ], + 'NAME': ['Fault_1', 'Fault_2', 'Fault_3'], + 'DIP': [60, 45, 30], + 'DIPDIR': [90, 120, 150], + } + ) + + # Set the raw data in the map_data object to simulate loaded fault data + map_data.raw_data[Datatype.FAULT] = faults + map_data.parse_fault_map() + cropped_faults = map_data.data[Datatype.FAULT] + + # Assert that only 1 fault remains (the one with length ~14.14) + assert ( + len(cropped_faults) == 1 + ), f"Expected only 1 fault remaining after cropping, but found {len(cropped_faults)}" + + # Optionally, check that the remaining fault has the correct geometry (the long one) + assert cropped_faults.iloc[0].geometry.length == pytest.approx( + 14.14, 0.01 + ), f"Expected remaining fault length to be 14.14, but got {cropped_faults.iloc[0].geometry.length}" diff --git a/tests/mapdata/test_set_get_recreate_bounding_box.py b/tests/mapdata/test_set_get_recreate_bounding_box.py new file mode 100644 index 00000000..5a6e9368 --- /dev/null +++ b/tests/mapdata/test_set_get_recreate_bounding_box.py @@ -0,0 +1,104 @@ +import pytest +from map2loop.mapdata import MapData +import geopandas +import shapely + + +@pytest.fixture +def md(): + return MapData() + + +def test_set_bounding_box_with_tuple(md): + bounding_box = (0, 10, 0, 10) + md.set_bounding_box(bounding_box) + + assert md.bounding_box == { + "minx": 0, + "maxx": 10, + "miny": 0, + "maxy": 10, + "top": 0, + "base": 2000, + }, "MapData.set_bounding_box() not working as expected" + + +def test_set_bounding_box_with_dict(md): + bounding_box = {"minx": 0, "maxx": 10, "miny": 0, "maxy": 10, "top": 5, "base": 15} + md.set_bounding_box(bounding_box) + + assert md.bounding_box == bounding_box, "MapData.set_bounding_box() not working as expected" + + +def test_bounding_box_keys(md): + bounding_box = (0, 10, 0, 10) + md.set_bounding_box(bounding_box) + + for key in ["minx", "maxx", "miny", "maxy", "top", "base"]: + assert key in md.bounding_box, f"MapData.bounding_box missing key: {key}" + + +def test_bounding_box_polygon(md): + bounding_box = (0, 10, 0, 10) + md.set_bounding_box(bounding_box) + + minx, miny, maxx, maxy = 0, 0, 10, 10 + lat_point_list = [miny, miny, maxy, maxy, miny] + lon_point_list = [minx, maxx, maxx, minx, minx] + expected_polygon = geopandas.GeoDataFrame( + index=[0], + crs=md.working_projection, + geometry=[shapely.Polygon(zip(lon_point_list, lat_point_list))], + ) + + assert md.bounding_box_polygon.equals( + expected_polygon + ), "MapData.bounding_box_polygon not returning the correct GeoDataFrame" + + +def test_get_bounding_box_as_dict(md): + bounding_box = {"minx": 0, "maxx": 10, "miny": 0, "maxy": 10, "top": 5, "base": 15} + md.set_bounding_box(bounding_box) + result = md.get_bounding_box() + + assert ( + result == bounding_box + ), "MapData.get_bounding_box() not returning the correct bounding box" + + +def test_get_bounding_box_as_polygon(md): + bounding_box = (0, 10, 0, 10) + md.set_bounding_box(bounding_box) + result = md.get_bounding_box(polygon=True) + + assert isinstance( + result, geopandas.GeoDataFrame + ), "MapData.get_bounding_box(polygon=True) not returning a GeoDataFrame" + assert result.equals( + md.bounding_box_polygon + ), "MapData.get_bounding_box(polygon=True) not returning the correct GeoDataFrame" + + +def test_recreate_bounding_box_str(md): + bounding_box = (0, 10, 0, 10) + md.set_working_projection("EPSG:4326") + md.set_bounding_box(bounding_box) + md.recreate_bounding_box_str() + + expected_str = "0,0,10,10,EPSG:4326" + assert ( + md.bounding_box_str == expected_str + ), "MapData.recreate_bounding_box_str() not working as expected" + + +def test_set_bounding_box_with_missing_keys(md): + bounding_box = { + "minx": 0, + "maxx": 10, + "miny": 0 + # Missing "maxy", "top", "base" + } + with pytest.raises(KeyError): + md.set_bounding_box( + bounding_box + ), "MapData.set_bounding_box accepting wrong argument, but should raise KeyError" diff --git a/tests/mapdata/test_set_get_working_projection.py b/tests/mapdata/test_set_get_working_projection.py new file mode 100644 index 00000000..a0c937cb --- /dev/null +++ b/tests/mapdata/test_set_get_working_projection.py @@ -0,0 +1,43 @@ +import pytest +from map2loop.mapdata import MapData + + +@pytest.mark.parametrize( + "projection, expected_projection, bounding_box, expected_warning", + [ + (4326, "EPSG:4326", None, None), # happy path with int projection + ("EPSG:3857", "EPSG:3857", None, None), # happy path with str projection + (9999, "EPSG:9999", None, None), # edge case with high int projection + ("EPSG:9999", "EPSG:9999", None, None), # edge case with high str projection + (None, None, None, True), # error case with None + ([], None, None, True), # error case with list + ({}, None, None, True), # error case with dict + ], + ids=[ + "int_projection", + "str_projection", + "high_int_projection", + "high_str_projection", + "none_projection", + "list_projection", + "dict_projection", + ], +) +def test_set_working_projection(projection, expected_projection, bounding_box, expected_warning): + # Set up MapData object + map_data = MapData() + map_data.bounding_box = bounding_box + + # Call the method + map_data.set_working_projection(projection) + + # Assert the working projection is correctly set + assert map_data.working_projection == expected_projection, ( + f"Expected working_projection to be {expected_projection}, but got {map_data.working_projection}" + ) + + # Check for the presence of warnings via side effects (if applicable) + if expected_warning: + assert map_data.working_projection is None, ( + "Expected working_projection to remain None when an invalid projection is provided" + ) diff --git a/tests/project/test_ignore_codes_setters_getters.py b/tests/project/test_ignore_codes_setters_getters.py new file mode 100644 index 00000000..4cebdba7 --- /dev/null +++ b/tests/project/test_ignore_codes_setters_getters.py @@ -0,0 +1,70 @@ +import pathlib +from map2loop.project import Project +from map2loop.m2l_enums import Datatype +import map2loop + + +# Sample test function for lithology and fault ignore codes +def test_set_get_ignore_codes(): + # Set up a sample bounding box and other required data + bbox_3d = { + "minx": 515687.31005864, + "miny": 7493446.76593407, + "maxx": 562666.860106543, + "maxy": 7521273.57407786, + "base": -3200, + "top": 3000, + } + + # Set up the config dictionary + config_dictionary = { + "structure": {"dipdir_column": "azimuth2", "dip_column": "dip"}, + "geology": {"unitname_column": "unitname", "alt_unitname_column": "code"}, + } + + project = Project( + working_projection='EPSG:28350', + bounding_box=bbox_3d, + geology_filename=str( + pathlib.Path(map2loop.__file__).parent + / pathlib.Path('_datasets/geodata_files/hamersley/geology.geojson') + ), + fault_filename=str( + pathlib.Path(map2loop.__file__).parent + / pathlib.Path('_datasets/geodata_files/hamersley/faults.geojson') + ), + dtm_filename=str( + pathlib.Path(map2loop.__file__).parent + / pathlib.Path('_datasets/geodata_files/hamersley/dtm_rp.tif') + ), + config_dictionary=config_dictionary, + ) + + # Define test ignore codes for lithology and faults + lithology_codes = ["cover", "Fortescue_Group", "A_FO_od"] + fault_codes = ['Fault_9', "NotAFault"] + + # Test Lithology ignore codes + project.set_ignore_lithology_codes(lithology_codes) + assert ( + project.map_data.get_ignore_lithology_codes() == lithology_codes + ), "Lithology ignore codes mismatch" + + # Test Fault ignore codes + project.set_ignore_fault_codes(fault_codes) + assert project.map_data.get_ignore_fault_codes() == fault_codes, "Fault ignore codes mismatch" + + project.map_data.parse_fault_map() + # check if the skipped fault has been removed now: + assert not project.map_data.get_map_data(Datatype.FAULT)['NAME'].str.contains('Fault_9').any() + + project.map_data.parse_geology_map() + # check if the skipped lithology has been removed now: + assert ( + not project.map_data.get_map_data(Datatype.GEOLOGY)['UNITNAME'] + .str.contains('Fortescue_Group') + .any() + ) + assert ( + not project.map_data.get_map_data(Datatype.GEOLOGY)['UNITNAME'].str.contains('cover').any() + ) diff --git a/tests/project/test_plot_hamersley.py b/tests/project/test_plot_hamersley.py index 027d285a..07393f27 100644 --- a/tests/project/test_plot_hamersley.py +++ b/tests/project/test_plot_hamersley.py @@ -1,15 +1,12 @@ -### This file tests the overall behavior of project.py. Runs from LoopServer. - -#internal imports +import pytest from map2loop.project import Project from map2loop.m2l_enums import VerboseLevel - -#external imports -import pytest +from unittest.mock import patch from pyproj.exceptions import CRSError -import os import requests +import os +# Define constants for common parameters bbox_3d = { "minx": 515687.31005864, "miny": 7493446.76593407, @@ -18,86 +15,83 @@ "base": -3200, "top": 3000, } - loop_project_filename = "wa_output.loop3d" - -def remove_LPF(): - lpf_exists = os.path.exists(loop_project_filename) - if lpf_exists: - os.remove(loop_project_filename) +# create a project function +def create_project(state_data="WA", projection="EPSG:28350"): + return Project( + use_australian_state_data=state_data, + working_projection=projection, + bounding_box=bbox_3d, + verbose_level=VerboseLevel.NONE, + loop_project_filename=loop_project_filename, + overwrite_loopprojectfile=True, + ) +# is the project running? def test_project_execution(): + + proj = create_project() try: - proj = Project( - use_australian_state_data="WA", - working_projection="EPSG:28350", - bounding_box=bbox_3d, - clut_file_legacy=False, - verbose_level=VerboseLevel.NONE, - loop_project_filename=loop_project_filename, - overwrite_loopprojectfile=True, - ) + proj.run_all(take_best=True) + # if there's a timeout: except requests.exceptions.ReadTimeout: - pytest.skip("Connection to the server timed out, skipping test") - - proj.run_all(take_best=True) - assert proj is not None, "Plot Hamersley Basin failed to execute" - - assert os.path.exists(loop_project_filename), f"Expected file {loop_project_filename} was not created" - - -################################################################### -## test if wrong crs will throw a crs error - + print("Timeout occurred, skipping the test.") # Debugging line + pytest.skip( + "Skipping the project test from server data due to timeout while attempting to run proj.run_all" + ) -def test_expect_crs_error(): - with pytest.raises(CRSError): - Project( - use_australian_state_data="WA", - working_projection="NittyGrittyCRS", - bounding_box=bbox_3d, - clut_file_legacy=False, - verbose_level=VerboseLevel.NONE, - loop_project_filename=loop_project_filename, - overwrite_loopprojectfile=True, + # if no timeout: + # is there a project? + assert proj is not None, "Plot Hamersley Basin failed to execute" + # is there a LPF? + assert os.path.exists( + loop_project_filename + ), f"Expected file {loop_project_filename} was not created" + + +# Is the test_project_execution working - ie, is the test skipped on timeout? +def test_timeout_handling(): + # Mock `openURL` in `owslib.util` to raise a ReadTimeout directly + with patch("owslib.util.openURL"): + # Run `test_project_execution` and check if the skip occurs + result = pytest.main( + ["-q", "--tb=short", "--disable-warnings", "-k", "test_project_execution"] ) - print("CRSError was raised as expected.") + assert ( + result.value == pytest.ExitCode.OK + ), "The test was not skipped as expected on timeout." -################################################################### -## test if wrong state throws an error +# does the project fail when the CRS is invalid? +def test_expect_crs_error(): + try: + with pytest.raises(CRSError): + create_project(projection="InvalidCRS") + print("CRSError was raised as expected.") + except requests.exceptions.ReadTimeout: + print("Timeout occurred, skipping test_expect_crs_error.") + pytest.skip("Skipping test_expect_crs_error due to a timeout.") +# does the project fail when the Aus state name is invalid? def test_expect_state_error(): - - with pytest.raises(ValueError): - Project( - use_australian_state_data="NittyGrittyState", - working_projection="EPSG:28350", - bounding_box=bbox_3d, - clut_file_legacy=False, - verbose_level=VerboseLevel.NONE, - loop_project_filename=loop_project_filename, - overwrite_loopprojectfile=True, - ) - - print("ValueError was raised as expected.") + try: + with pytest.raises(ValueError): + create_project(state_data="InvalidState") + print("ValueError was raised as expected.") + except requests.exceptions.ReadTimeout: + print("Timeout occurred, skipping test_expect_state_error.") + pytest.skip("Skipping test_expect_state_error due to a timeout.") -################################################################### -# test if it catches wrong config file +# does the project fail when a config file is invalid? def test_expect_config_error(): - with pytest.raises(Exception): - Project( - use_australian_state_data="WA", - working_projection="EPSG:28350", - bounding_box=bbox_3d, - clut_file_legacy=False, - config_filename='NittyGrittyConfig.csv', - verbose_level=VerboseLevel.NONE, - loop_project_filename=loop_project_filename, - overwrite_loopprojectfile=True, - ) - print("FileNotFoundError//Exception by catchall in project.py was raised as expected.") + try: + with pytest.raises(Exception): + create_project(config_file='InvalidConfig.csv') + print("FileNotFoundError//Exception by catchall in project.py was raised as expected.") + except requests.exceptions.ReadTimeout: + print("Timeout occurred, skipping test_expect_config_error.") + pytest.skip("Skipping test_expect_config_error due to a timeout.") diff --git a/tests/project/test_thickness_calculations.py b/tests/project/test_thickness_calculations.py new file mode 100644 index 00000000..9cf5464d --- /dev/null +++ b/tests/project/test_thickness_calculations.py @@ -0,0 +1,1749 @@ +# imports +import pandas +import geopandas +import numpy + +from map2loop._datasets.geodata_files import load_map2loop_data +from map2loop.thickness_calculator import InterpolatedStructure, StructuralPoint +from map2loop import Project + + +# 1. self.stratigraphic_column.stratigraphicUnits, +st_units = pandas.DataFrame( + { + 'Unnamed: 0': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], + 'layerId': [7, 0, 10, 8, 1, 5, 9, 4, 3, 2, 6], + 'name': [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + ], + 'minAge': [0.0] * 11, + 'maxAge': [100000.0] * 11, + 'group': [None] * 11, + 'supergroup': [None] * 11, + 'stratigraphic_Order': list(range(11)), + 'colour': [ + '#5d7e60', + '#387866', + '#628304', + '#a2f290', + '#0c2562', + '#5fb3c5', + '#f48b70', + '#1932e2', + '#106e8a', + '#d0d47c', + '#e7f2f3', + ], + } +) + +# 2. self.stratigraphic_column.column +st_column = [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + 'Fortescue_Group', +] + +# 3. map_data.basal_contacts +basal_c = [ + {'ID': 0, 'basal_unit': 'Turee_Creek_Group', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Boolgeeda_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Brockman_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Weeli_Wolli_Formation', 'type': 'BASAL'}, + {'ID': 4, 'basal_unit': 'Jeerinah_Formation', 'type': 'BASAL'}, + {'ID': 5, 'basal_unit': 'Bunjinah_Formation', 'type': 'BASAL'}, + {'ID': 6, 'basal_unit': 'Marra_Mamba_Iron_Formation', 'type': 'BASAL'}, + {'ID': 7, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'ABNORMAL'}, + {'ID': 8, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'ABNORMAL'}, + {'ID': 9, 'basal_unit': 'Wittenoom_Formation', 'type': 'BASAL'}, + {'ID': 10, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'BASAL'}, + {'ID': 11, 'basal_unit': 'Woongarra_Rhyolite', 'type': 'BASAL'}, +] +bc_geoms = geopandas.GeoSeries.from_wkt( + [ + 'MULTILINESTRING 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20, 10, 5, 50], + 'OVERTURNED': [False] * 11, + 'BEDDING': [False] * 11, + 'X': [ + 548279.320612, + 548249.155883, + 546137.857561, + 543754.180680, + 520512.912720, + 528512.912720, + 529512.912720, + 530512.912720, + 531512.912720, + 532512.912720, + 533512.912720, + ], + 'Y': [ + 7.493304e06, + 7.493512e06, + 7.494607e06, + 7.504599e06, + 7.497506e06, + 7.497806e06, + 7.498506e06, + 7.499506e06, + 7.500506e06, + 7.501506e06, + 7.502506e06, + ], + 'Z': [543.0, 543.0, 532.0, 559.0, 503.0, 553.0, 563.0, 573.0, 583.0, 593.0, 603.0], + 'layerID': [3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2], + } +) + +# geology +geology_map_data = load_map2loop_data.load_hamersley_geology() + + +# DTM +dtm = load_map2loop_data.load_hamersley_dtm() + +# sampled contacts + +IDS = [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 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'1', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', + '4', + '5', + '5', + '5', + '5', + '5', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', +] + +s_c = pandas.DataFrame({'X': X, 'Y': Y, 'Z': Z, 'featureId': featureid}) + +############################################ +##### test calculate_unit_thicknesses ###### +############################################ + +import map2loop +import pathlib + + +def test_calculate_unit_thicknesses(): + + units = st_units + stratigraphic_order = st_column + structure_data = structures + + # units, stratigraphic_order, basal_contacts, structure_data, map_data = sample_data + config_dictionary = { + "structure": {"dipdir_column": "azimuth2", "dip_column": "dip"}, + "geology": {"unitname_column": "unitname", "alt_unitname_column": "code"}, + } + bbox_3d = { + "minx": 515687.31005864, + "miny": 7493446.76593407, + "maxx": 562666.860106543, + "maxy": 7521273.57407786, + "base": -3200, + "top": 3000, + } + project = Project( + working_projection='EPSG:28350', + bounding_box=bbox_3d, + geology_filename=str( + pathlib.Path(map2loop.__file__).parent + / pathlib.Path('_datasets/geodata_files/hamersley/geology.geojson') + ), + structure_filename=str( + pathlib.Path(map2loop.__file__).parent + / pathlib.Path('_datasets/geodata_files/hamersley/structures.geojson') + ), + dtm_filename=str( + pathlib.Path(map2loop.__file__).parent + / pathlib.Path('_datasets/geodata_files/hamersley/dtm_rp.tif') + ), + config_dictionary=config_dictionary, + ) + + project.structure_samples = structure_data + project.map_data.basal_contacts = bc_gdf + + # Create sample map data + + project.map_data.sampled_contacts = s_c + + # Inject the sample data into the project's stratigraphic column + project.stratigraphic_column.stratigraphicUnits = units + project.stratigraphic_column.column = stratigraphic_order + + ## test if set/get is working for thickness calculator + + assert project.get_thickness_calculator() == [ + 'InterpolatedStructure' + ], "Default for thickness calculator not set" ## default is InterpolatedStructure + + # check set + + project.set_thickness_calculator([StructuralPoint(), InterpolatedStructure()]) + assert project.get_thickness_calculator() == [ + 'StructuralPoint', + 'InterpolatedStructure', + ], "Setter method for thickness calculator not working" ## default is InterpolatedStructure + + # Run the calculate_unit_thicknesses + project.calculate_unit_thicknesses() + + # # Check if all thicknesses have been calculated + columns_to_check = [ + 'StructuralPoint_mean', + 'StructuralPoint_median', + 'StructuralPoint_stddev', + 'InterpolatedStructure_mean', + 'InterpolatedStructure_median', + 'InterpolatedStructure_stddev', + ] + + for column in columns_to_check: + # have all thicknesses been calculated + assert ( + column in project.stratigraphic_column.stratigraphicUnits.columns + ), f"project::calculate_unit_thicknesses: column {column} not in thickness results" + # is the result a number + assert ( + project.stratigraphic_column.stratigraphicUnits[column].dtype == numpy.float64 + ), f"project::calculate_unit_thicknesses: column {column} is not of type numpy.float64" + # should not contain nans + assert ( + not project.stratigraphic_column.stratigraphicUnits[column].isna().any() + ), f"project::calculate_unit_thicknesses: column {column} contains NaNs" + + # have all the units been calculated + assert ( + 'name' in project.stratigraphic_column.stratigraphicUnits.columns + ), 'project::calculate_unit_thicknesses: unitname not in result' + assert all( + name in project.stratigraphic_column.stratigraphicUnits['name'].values + for name in st_units['name'].values + ), 'project::calculate_unit_thicknesses: units missing in results' diff --git a/tests/thickness/InterpolatedStructure/test_interpolated_structure.py b/tests/thickness/InterpolatedStructure/test_interpolated_structure.py index 79971443..9bc28431 100644 --- a/tests/thickness/InterpolatedStructure/test_interpolated_structure.py +++ b/tests/thickness/InterpolatedStructure/test_interpolated_structure.py @@ -1,298 +1,1734 @@ -# This test runs on a portion of the dataset in https://github.com/Loop3D/m2l3_examples/tree/main/Laurent2016_V2_variable_thicknesses (only for lithologies E, F, and G) -# structures are confined to litho_F, and the test confirms if the StructuralPoint thickness is calculated, for all lithologies, if the thickness is correct for F (~90 m), and top/bottom units are assigned -1 -# this creates a temp folder in Appdata to store the data to run the proj, checks the thickness, and then deletes the temp folder -# this was done to avoid overflow of file creation in the tests folder - -### This file tests the function InterpolatedStructure thickness calculator +import pandas +import geopandas +import numpy -import pytest -import pandas as pd -import numpy as np +from map2loop.mapdata import MapData from map2loop.thickness_calculator import InterpolatedStructure -from map2loop.project import Project -from osgeo import gdal, osr -import os -import shapely -import geopandas -import tempfile -import pathlib -from map2loop.sampler import SamplerSpacing, SamplerDecimator +from map2loop._datasets.geodata_files.load_map2loop_data import ( + load_hamersley_geology, + load_hamersley_dtm, +) from map2loop.m2l_enums import Datatype -import map2loop - - -def create_raster(output_path, bbox, epsg, pixel_size, value=100): - minx, miny, maxx, maxy = bbox - cols = int((maxx - minx) / pixel_size) - rows = int((maxy - miny) / pixel_size) - driver = gdal.GetDriverByName('GTiff') - out_raster = driver.Create(output_path, cols, rows, 1, gdal.GDT_Byte) - out_raster.SetGeoTransform([minx, pixel_size, 0, maxy, 0, -pixel_size]) - srs = osr.SpatialReference() - srs.ImportFromEPSG(epsg) - out_raster.SetProjection(srs.ExportToWkt()) - out_band = out_raster.GetRasterBand(1) - out_band.Fill(value) - out_band.FlushCache() - out_raster = None +########################################################################## +### Define the test data for ThicknessCalculator InterpolatedStructure ### +########################################################################## -geology = [ +# Sample stratigraphic units data +st_units = pandas.DataFrame( { - 'UNITNAME': 'Litho_E', - 'geometry': 'POLYGON ((9795.91836734694 9931.26849738919, 9860.73785898637 9795.91836734694, 9935.33621028978 9591.836734693878, 9950.618354641661 9387.755102040817, 10000 9210.342095822705, 10000 8757.661313426739, 9957.613263811385 8571.428571428572, 9795.91836734694 8453.228230379065, 9591.836734693878 8459.27180076132, 9387.755102040817 8424.58063242387, 9183.673469387755 8396.186050103635, 8979.591836734695 8375.328219666773, 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row in geology: - row['geometry'] = shapely.wkt.loads(row['geometry']) - -geology = geopandas.GeoDataFrame(geology, crs='epsg:7854') + 'Unnamed: 0': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], + 'layerId': [7, 0, 10, 8, 1, 5, 9, 4, 3, 2, 6], + 'name': [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + ], + 'minAge': [0.0] * 11, + 'maxAge': [100000.0] * 11, + 'group': [None] * 11, + 'supergroup': [None] * 11, + 'ThicknessMean_ThicknessCalculatorAlpha': [0.0] * 11, + 'ThicknessMedian_ThicknessCalculatorAlpha': [0.0] * 11, + 'ThicknessStdDev_ThicknessCalculatorAlpha': [0.0] * 11, + 'stratigraphic_Order': list(range(11)), + 'colour': [ + '#5d7e60', + '#387866', + '#628304', + '#a2f290', + '#0c2562', + '#5fb3c5', + '#f48b70', + '#1932e2', + '#106e8a', + '#d0d47c', + '#e7f2f3', + ], + } +) -# build structures file -structures = [ - { - 'x': 2775.287768202244933, - 'y': 4330.15, - 'strike2': 45.00, - 'dip_2': 45.70, - 'id': 147.00, - 'sf': 's0', - }, - { - 'x': 3529.794754080061011, - 'y': 3091.192011237949828, - 'strike2': 288.50, - 'dip_2': 41.70, - 'id': 204.00, - 'sf': 's0', - }, - { - 'x': 7928.315269200518742, - 'y': 7234.561058065713951, - 'strike2': 48.80, - 'dip_2': 41.10, - 'id': 229.00, - 'sf': 's0', - }, - { - 'x': 8003.966104268994968, - 'y': 7421.634268009857806, - 'strike2': 48.80, - 'dip_2': 41.10, - 'id': 235.00, - 'sf': 's0', - }, - { - 'x': 6881.165236574942355, - 'y': 1213.128646564158771, - 'strike2': 299.10, - 'dip_2': 44.70, - 'id': 252.00, - 'sf': 's0', - }, - { - 'x': 3674.015651128655009, - 'y': 5266.677487068354822, - 'strike2': 41.20, - 'dip_2': 40.10, - 'id': 347.00, - 'sf': 's0', - }, - { - 'x': 3970.895076049027921, - 'y': 2944.223069901633608, - 'strike2': 273.00, - 'dip_2': 46.00, - 'id': 408.00, - 'sf': 's0', - }, +st_column = [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + 'Fortescue_Group', ] -for row in structures: - row['geometry'] = shapely.Point(row['x'], row['y']) - del row['x'], row['y'] - -structures = geopandas.GeoDataFrame(structures, crs='epsg:7854') - -faults = geopandas.GeoDataFrame(columns=['geometry'], crs='epsg:7854') - -f_path = tempfile.mkdtemp() -bounding_box = {"minx": 0, "miny": 0, "maxx": 10000, "maxy": 10000, "base": 0, "top": -5000} - -create_raster( - os.path.join(f_path, "DEM.tif"), - (bounding_box['minx'], bounding_box['miny'], bounding_box['maxx'], bounding_box['maxy']), - 7854, - 1000, +# 3. map_data.basal_contacts +basal_c = [ + {'ID': 0, 'basal_unit': 'Turee_Creek_Group', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Boolgeeda_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Brockman_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Weeli_Wolli_Formation', 'type': 'BASAL'}, + {'ID': 4, 'basal_unit': 'Jeerinah_Formation', 'type': 'BASAL'}, + {'ID': 5, 'basal_unit': 'Bunjinah_Formation', 'type': 'BASAL'}, + {'ID': 6, 'basal_unit': 'Marra_Mamba_Iron_Formation', 'type': 'BASAL'}, + {'ID': 7, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'ABNORMAL'}, + {'ID': 8, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'ABNORMAL'}, + {'ID': 9, 'basal_unit': 'Wittenoom_Formation', 'type': 'BASAL'}, + {'ID': 10, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'BASAL'}, + {'ID': 11, 'basal_unit': 'Woongarra_Rhyolite', 'type': 'BASAL'}, +] +bc_geoms = geopandas.GeoSeries.from_wkt( + [ + 'MULTILINESTRING ((520000.0000000000000000 7506463.0589317083358765, 520000.0000000000000000 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545353.0321352999890223 7492201.1703274799510837, 544926.6382374600507319 7492066.6692933803424239, 544724.7222984499530867 7491977.1600893298164010, 544410.5210711299441755 7491797.6681312201544642, 544324.8354344329563901 7491754.6016815919429064, 544324.1489822026342154 7491755.3286254471167922))', + 'MULTILINESTRING ((530271.9887491008266807 7504023.8181659672409296, 530272.8096558250254020 7504022.9626687979325652, 529716.5596407300326973 7503911.6010149903595448, 529213.5023450599983335 7503780.5819101296365261, 528797.9000049700262025 7503627.0802137600257993, 527507.3776305499486625 7503343.0594466198235750, 526960.5505161000182852 7503255.5484263198450208, 526610.5993896899744868 7503255.5402162401005626, 526129.4297748099779710 7503146.0497182803228498, 525298.2094937399961054 7503146.0410827100276947, 524313.9806665199575946 7502993.0200903099030256, 522979.7296735499985516 7502796.0099626500159502, 521973.5802435199730098 7502730.4904361795634031, 520967.4508550300379284 7502533.4807597603648901, 520000.0000000000000000 7502409.3710406739264727, 520000.0000000000000000 7502410.3792356532067060), (520000.0000000000000000 7507850.7456019073724747, 520000.0000000000000000 7507851.7444353895261884, 520459.1205355499987490 7507962.4997558500617743, 521252.5692508600186557 7508095.0084923598915339, 522046.0097163000609726 7508306.5182301895692945, 522495.6195994799491018 7508412.0197906903922558, 523447.7511029100278392 7508491.5316420802846551, 524135.4115040699834935 7508571.0508861597627401, 524796.6501091100508347 7508809.0602384395897388, 525537.1616826100507751 7508888.5604379596188664, 526304.1784057499608025 7509047.0794246401637793, 527150.5723233999451622 7509258.6008259104564786, 527891.1703374399803579 7509549.6305759903043509, 528759.1812102999538183 7509752.1486169397830963, 529408.9095765600213781 7509934.6589543297886848, 529609.4298291478771716 7510000.0000000000000000, 529610.4290333546232432 7510000.0000000000000000), (538922.8089907000539824 7510000.0000000000000000, 538923.8080818294547498 7510000.0000000000000000, 538972.1599029799690470 7509914.6897562900558114, 539114.2378285899758339 7509528.6699069095775485, 539134.5507683800533414 7509041.6695242598652840, 539012.7302670100471005 7508493.1818856503814459, 538586.3296623999485746 7507965.1697401199489832, 538180.2115608500316739 7507599.6715208096429706, 537631.9808313100365922 7507214.1684171101078391, 537428.9305590899894014 7507011.1716584600508213, 537002.5204438799992204 7506686.1613326398655772, 536616.7715214400086552 7506544.1692011002451181, 535743.6882477200124413 7506361.1594366002827883, 534931.5578075499506667 7506158.1588880904018879, 534038.1795864100567997 7505813.1479306500405073, 533489.9179332499625161 7505488.1394624896347523, 533022.9010144800413400 7505082.1303953798487782, 532495.0114416599972174 7504737.1207175096496940, 531906.1711659600259736 7504513.6188210602849722, 530728.5093100100057200 7504046.6094597103074193, 530502.3308432935737073 7503928.6902586026117206, 530501.6387504261219874 7503929.4114401936531067), (549037.6348608708940446 7490000.0000000000000000, 549036.4332247237907723 7490000.0000000000000000, 549043.9079029599670321 7490011.2185191400349140, 549204.8611184799810871 7490100.2200202103704214, 549687.5501057700021192 7490279.2203355301171541, 550000.0000000000000000 7490413.2414639443159103, 550000.0000000000000000 7490412.1533525427803397))', + ] ) +bc_gdf = geopandas.GeoDataFrame(basal_c, geometry=bc_geoms, crs='EPSG:28350') -geology.to_file(os.path.join(f_path, "geology.shp")) -structures.to_file(os.path.join(f_path, "structures.shp")) -faults.to_file(os.path.join(f_path, "faults.shp")) -loop_project_filename = os.path.join(f_path, "local_source.loop3d") - -config = { - "structure": { - "orientation_type": "strike", - "dipdir_column": "strike2", - "dip_column": "dip_2", - "description_column": "DESCRIPTION", - "bedding_text": "Bed", - "overturned_column": "structypei", - "overturned_text": "BEOI", - "objectid_column": "objectid", - "desciption_column": "feature", - }, - "geology": { - "unitname_column": "UNITNAME", - "alt_unitname_column": "UNITNAME", - "group_column": "GROUP", - "supergroup_column": "supersuite", - "description_column": "descriptn", - "minage_column": "min_age_ma", - "maxage_column": "max_age_ma", - "rocktype_column": "rocktype1", - "alt_rocktype_column": "rocktype2", - "sill_text": "sill", - "intrusive_text": "intrusive", - "volcanic_text": "volcanic", - "objectid_column": "ID", - "ignore_codes": ["cover"], - }, - "fault": { - "structtype_column": "feature", - "fault_text": "Fault", - "dip_null_value": "0", - "dipdir_flag": "num", - "dipdir_column": "dip_dir", - "dip_column": "dip", - "orientation_type": "dip direction", - "dipestimate_column": "dip_est", - "dipestimate_text": "gentle,moderate,steep", - "name_column": "name", - "objectid_column": "objectid", - }, - "fold": { - "structtype_column": "feature", - "fold_text": "Fold axial trace", - "description_column": "type", - "synform_text": "syncline", - "foldname_column": "NAME", - "objectid_column": "objectid", - }, -} - -module_path = os.path.dirname(map2loop.__file__).replace("__init__.py", "") +structures = pandas.DataFrame( + { + 'ID': [0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20], + 'DIPDIR': [190.0, 190.0, 0.0, 330.0, 165.0, 150.0, 180.0, 210.0, 240.0, 270.0, 300.0], + 'DIP': [55, 55, 15, 15, 0, 45, 30, 20, 10, 5, 50], + 'OVERTURNED': [False] * 11, + 'BEDDING': [False] * 11, + 'X': [ + 548279.320612, + 548249.155883, + 546137.857561, + 543754.180680, + 520512.912720, + 528512.912720, + 529512.912720, + 530512.912720, + 531512.912720, + 532512.912720, + 533512.912720, + ], + 'Y': [ + 7.493304e06, + 7.493512e06, + 7.494607e06, + 7.504599e06, + 7.497506e06, + 7.497806e06, + 7.498506e06, + 7.499506e06, + 7.500506e06, + 7.501506e06, + 7.502506e06, + ], + 'Z': [543.0, 543.0, 532.0, 559.0, 503.0, 553.0, 563.0, 573.0, 583.0, 593.0, 603.0], + 'layerID': [3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2], + } +) +# sampled contacts -@pytest.fixture -def project(): - proj = Project( - geology_filename=os.path.join(f_path, "geology.shp"), - fault_filename=os.path.join(f_path, "faults.shp"), - fold_filename=os.path.join(f_path, "faults.shp"), - structure_filename=os.path.join(f_path, "structures.shp"), - dtm_filename=os.path.join(f_path, 'DEM.tif'), - clut_filename=pathlib.Path(module_path) - / pathlib.Path('_datasets') - / pathlib.Path('clut_files') - / pathlib.Path('WA_clut.csv'), - config_dictionary=config, - clut_file_legacy=False, - working_projection="EPSG:7854", - bounding_box=bounding_box, - loop_project_filename=loop_project_filename, - overwrite_loopprojectfile=True, - ) +IDS = [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 4, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 3, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 8, + 9, + 9, + 9, + 9, + 9, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 7, + 5, + 5, + 5, + 5, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 5, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, + 2, +] +X = [ + 520000.0, + 520992.6699257682, + 521984.6869456721, + 522969.6388939231, + 523954.5908421741, + 524942.1013152138, + 525930.4850180566, + 526908.535657469, + 527891.805258285, + 528880.6323520339, + 529855.6352847969, + 530832.075832642, + 531813.1634102948, + 532804.1384816798, + 533019.2882480841, + 532243.2409444518, + 531376.1445685071, + 530480.68269627, + 529612.3980015446, + 528734.9447395488, + 527783.6457775467, + 526804.9871671252, + 525809.8226356399, + 524816.1487769039, + 523829.21986169985, + 522842.8215091018, + 521858.22077695775, + 520000.0, + 520979.22944531543, + 521963.40533887857, + 522941.7587850634, + 523934.147302897, + 524925.392627546, + 525924.0314485825, + 526915.8477737093, + 527895.0821625991, + 528872.0657047849, + 529800.4947308041, + 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'2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', + '4', + '5', + '5', + '5', + '5', + '5', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', +] - proj.set_thickness_calculator(InterpolatedStructure()) +s_c = pandas.DataFrame({'X': X, 'Y': Y, 'Z': Z, 'featureId': featureid}) - column = ['Litho_G', 'Litho_F', 'Litho_E'] - proj.set_sampler(Datatype.GEOLOGY, SamplerSpacing(100.0)) - proj.set_sampler(Datatype.STRUCTURE, SamplerDecimator(0)) - proj.run_all(user_defined_stratigraphic_column=column) +################################## +### TEST InterpolatedStructure ### +################################## - return proj +geology = load_hamersley_geology() +geology.rename(columns={'unitname': 'UNITNAME', 'code': 'CODE'}, inplace=True) -@pytest.fixture -def interpolated_structure_thickness(): - return InterpolatedStructure() +def check_thickness_values(result, column, description): + for order, position in [ + (max(st_units['stratigraphic_Order']), 'bottom'), + (min(st_units['stratigraphic_Order']), 'top'), + ]: + assert ( + result[result['stratigraphic_Order'] == order][column].values == -1 + ), f"InterpolatedStructure: {position} unit not assigned as -1 ({description})" -@pytest.fixture -def units(project): - return project.stratigraphic_column.stratigraphicUnits +def test_calculate_thickness_InterpolatedStructure(): + # Run the calculation + thickness_calculator = InterpolatedStructure() + md = MapData() + md.sampled_contacts = s_c + md.raw_data[Datatype.GEOLOGY] = geology + md.load_map_data(Datatype.GEOLOGY) + md.check_map(Datatype.GEOLOGY) + md.parse_geology_map() -@pytest.fixture -def stratigraphic_order(project): - return project.stratigraphic_column.column + md.raw_data[Datatype.DTM] = load_hamersley_dtm() + md.data[Datatype.DTM] = md.get_raw_map_data(Datatype.DTM) + md.bounding_box = { + "minx": 515687.31005864, + "miny": 7493446.76593407, + "maxx": 562666.860106543, + "maxy": 7521273.57407786, + "base": -3200, + "top": 3000, + } -@pytest.fixture -def basal_contacts(project): - return project.map_data.basal_contacts + result = thickness_calculator.compute( + units=st_units, + stratigraphic_order=st_column, + basal_contacts=bc_gdf, + structure_data=structures, + map_data=md, + ) + # is thickness calc alpha the label? + assert ( + thickness_calculator.thickness_calculator_label == 'InterpolatedStructure' + ), 'InterpolatedStructure: thickness calculator name not set correctly' -@pytest.fixture -def samples(project): - return project.structure_samples + # is the result a pandas dataframe? + assert isinstance( + result, pandas.DataFrame + ), 'InterpolatedStructure result not a pandas DataFrame' + # Check if there is mean, std, and median in results + required_columns = ['ThicknessMean', 'ThicknessMedian', 'ThicknessStdDev'] + for column in required_columns: + assert column in result.columns, f'{column} not in InterpolatedStructure result' -@pytest.fixture -def map_data(project): - return project.map_data + # check if all units are in the results + assert 'name' in result.columns, 'unit_name not in InterpolatedStructure result' + assert all( + name in result['name'].values for name in st_units['name'].values + ), 'units missing from in InterpolatedStructure result' + # are bottom and top units being assigned -1 + for column, description in [ + ('ThicknessMean', 'mean'), + ('ThicknessMedian', 'median'), + ('ThicknessStdDev', 'std dev'), + ]: + check_thickness_values(result, column, description) -def test_compute( - interpolated_structure_thickness, - units, - stratigraphic_order, - basal_contacts, - samples, - map_data, - project, -): - result = interpolated_structure_thickness.compute( - units, stratigraphic_order, basal_contacts, samples, map_data - ) - assert ( - interpolated_structure_thickness.thickness_calculator_label == "InterpolatedStructure" - ), 'Thickness_calc interpolated structure not being set properly' - assert isinstance( - result, pd.DataFrame - ), 'InterpolatedStructure calculator is not returning a DataFrame' - assert ( - 'ThicknessMedian' in result.columns - ), 'Thickness not being calculated in InterpolatedStructure calculator' - assert ( - 'ThicknessMean' in result.columns - ), 'Thickness not being calculated in InterpolatedStructure calculator' - - assert result['ThicknessMedian'].dtypes is float or int, 'ThicknessMedian column is not float' - assert ( - 'ThicknessStdDev' in result.columns - ), 'Thickness std not being calculated in InterpolatedStructure calculator' - assert np.issubdtype( - result['ThicknessStdDev'].dtypes, np.floating - ), 'ThicknessStdDev column is not float' + # are the dtypes numpy.float? + for column in required_columns: + assert ( + result[column].dtype == numpy.float64 + ), f'InterpolatedStructure: result column {column} not numpy.float64' - # check for nas in thickness - assert result['ThicknessMedian'].isna().sum() == 0, 'ThicknessMedian column has NaNs' + # check for nans in the results + for column in required_columns: + assert ( + not result[column].isnull().values.any() + ), f'InterpolatedStructure: result column {column} has NaN values' diff --git a/tests/thickness/StructurePoint/test_ThicknessStructuralPoint.py b/tests/thickness/StructurePoint/test_ThicknessStructuralPoint.py new file mode 100644 index 00000000..a71ebb7b --- /dev/null +++ b/tests/thickness/StructurePoint/test_ThicknessStructuralPoint.py @@ -0,0 +1,1718 @@ +import pandas +import geopandas +import numpy + +from map2loop.mapdata import MapData +from map2loop.thickness_calculator import StructuralPoint +from map2loop._datasets.geodata_files.load_map2loop_data import load_hamersley_geology +from map2loop.m2l_enums import Datatype + +#################################################################### +### Define the test data for ThicknessCalculator StructuralPoint ### +#################################################################### + +# Sample stratigraphic units data +st_units = pandas.DataFrame( + { + 'Unnamed: 0': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], + 'layerId': [7, 0, 10, 8, 1, 5, 9, 4, 3, 2, 6], + 'name': [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + ], + 'minAge': [0.0] * 11, + 'maxAge': [100000.0] * 11, + 'group': [None] * 11, + 'supergroup': [None] * 11, + 'ThicknessMean_ThicknessCalculatorAlpha': [0.0] * 11, + 'ThicknessMedian_ThicknessCalculatorAlpha': [0.0] * 11, + 'ThicknessStdDev_ThicknessCalculatorAlpha': [0.0] * 11, + 'stratigraphic_Order': list(range(11)), + 'colour': [ + '#5d7e60', + '#387866', + '#628304', + '#a2f290', + '#0c2562', + '#5fb3c5', + '#f48b70', + '#1932e2', + '#106e8a', + '#d0d47c', + '#e7f2f3', + ], + } +) + +st_column = [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + 'Fortescue_Group', +] + +# 3. map_data.basal_contacts +basal_c = [ + {'ID': 0, 'basal_unit': 'Turee_Creek_Group', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Boolgeeda_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Brockman_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Weeli_Wolli_Formation', 'type': 'BASAL'}, + {'ID': 4, 'basal_unit': 'Jeerinah_Formation', 'type': 'BASAL'}, + {'ID': 5, 'basal_unit': 'Bunjinah_Formation', 'type': 'BASAL'}, + {'ID': 6, 'basal_unit': 'Marra_Mamba_Iron_Formation', 'type': 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'0', + '1', + '1', + '1', + '0', + '0', + '1', + '1', + '1', + '1', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', + '4', + '5', + '5', + '5', + '5', + '5', + '5', + '0', + '1', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', + '4', + '5', + '5', + '5', + '5', + '5', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', +] + +s_c = pandas.DataFrame({'X': X, 'Y': Y, 'Z': Z, 'featureId': featureid}) + + +############################ +### TEST StructuralPoint ### +############################ + +geology = load_hamersley_geology() +geology.rename(columns={'unitname': 'UNITNAME', 'code': 'CODE'}, inplace=True) + + +def check_thickness_values(result, column, description): + for order, position in [ + (max(st_units['stratigraphic_Order']), 'bottom'), + (min(st_units['stratigraphic_Order']), 'top'), + ]: + assert ( + result[result['stratigraphic_Order'] == order][column].values == -1 + ), f"StructuralPoint: {position} unit not assigned as -1 ({description})" + + +def test_calculate_thickness_structural_point(): + # Run the calculation + thickness_calculator = StructuralPoint() + + md = MapData() + md.sampled_contacts = s_c + md.sampled_contacts = s_c + md.raw_data[Datatype.GEOLOGY] = geology + md.load_map_data(Datatype.GEOLOGY) + md.check_map(Datatype.GEOLOGY) + md.parse_geology_map() + + result = thickness_calculator.compute( + units=st_units, + stratigraphic_order=st_column, + basal_contacts=bc_gdf, + structure_data=structures, + map_data=md, + ) + + # is thickness calc alpha the label? + assert ( + thickness_calculator.thickness_calculator_label == 'StructuralPoint' + ), 'StructuralPoint: thickness calculator name not set correctly' + + # is the result a pandas dataframe? + assert isinstance(result, pandas.DataFrame), 'StructuralPoint result not a pandas DataFrame' + + # Check if there is mean, std, and median in results + required_columns = ['ThicknessMean', 'ThicknessMedian', 'ThicknessStdDev'] + for column in required_columns: + assert column in result.columns, f'{column} not in StructuralPoint result' + + # check if all units are in the results + assert 'name' in result.columns, 'unit_name not in StructuralPoint result' + assert all( + name in result['name'].values for name in st_units['name'].values + ), 'units missing from in StructuralPoint result' + + # are bottom and top units being assigned -1 + for column, description in [ + ('ThicknessMean', 'mean'), + ('ThicknessMedian', 'median'), + ('ThicknessStdDev', 'std dev'), + ]: + check_thickness_values(result, column, description) + + # are the dtypes numpy.float? + for column in required_columns: + assert ( + result[column].dtype == numpy.float64 + ), f'StructuralPoint: result column {column} not numpy.float64' + + # check for nans in the results + for column in required_columns: + assert ( + not result[column].isnull().values.any() + ), f'StructuralPoint: result column {column} has NaN values' diff --git a/tests/thickness/StructurePoint/test_thickness_StructuralPoint_local_source.py b/tests/thickness/StructurePoint/test_thickness_StructuralPoint_local_source.py deleted file mode 100644 index 9407af65..00000000 --- a/tests/thickness/StructurePoint/test_thickness_StructuralPoint_local_source.py +++ /dev/null @@ -1,261 +0,0 @@ -# This test runs on a portion of the dataset in https://github.com/Loop3D/m2l3_examples/tree/main/Laurent2016_V2_variable_thicknesses (only for lithologies E, F, and G) -# structures are confined to litho_F, and the test confirms if the StructuralPoint thickness is calculated, for all lithologies, if the thickness is correct for F (~90 m), and top/bottom units are assigned -1 -# this creates a temp folder in Appdata to store the data to run the proj, checks the thickness, and then deletes the temp folder -# this was done to avoid overflow of file creation in the tests folder - -# this tests the thickness calculator Structural Point from local source - -from map2loop.thickness_calculator import StructuralPoint -from osgeo import gdal, osr -import os -import shapely -import geopandas -import tempfile -import pathlib -from map2loop.sampler import SamplerSpacing, SamplerDecimator -from map2loop.project import Project -from map2loop.m2l_enums import Datatype -import map2loop - - -def create_raster(output_path, bbox, epsg, pixel_size, value=100): - minx, miny, maxx, maxy = bbox - cols = int((maxx - minx) / pixel_size) - rows = int((maxy - miny) / pixel_size) - driver = gdal.GetDriverByName('GTiff') - out_raster = driver.Create(output_path, cols, rows, 1, gdal.GDT_Byte) - out_raster.SetGeoTransform([minx, pixel_size, 0, maxy, 0, -pixel_size]) - srs = osr.SpatialReference() - srs.ImportFromEPSG(epsg) - out_raster.SetProjection(srs.ExportToWkt()) - out_band = out_raster.GetRasterBand(1) - out_band.Fill(value) - out_band.FlushCache() - out_raster = None - - -# build geology file - -geology = [ - { - 'UNITNAME': 'Litho_E', - 'geometry': 'POLYGON ((9795.91836734694 9931.26849738919, 9860.73785898637 9795.91836734694, 9935.33621028978 9591.836734693878, 9950.618354641661 9387.755102040817, 10000 9210.342095822705, 10000 8757.661313426739, 9957.613263811385 8571.428571428572, 9795.91836734694 8453.228230379065, 9591.836734693878 8459.27180076132, 9387.755102040817 8424.58063242387, 9183.673469387755 8396.186050103635, 8979.591836734695 8375.328219666773, 8775.510204081633 8142.6900746871015, 8533.835897640307 7959.183673469388, 8367.34693877551 7832.006337691327, 8271.702357700893 7755.102040816327, 8163.265306122449 7660.1472192881065, 8074.276982521525 7551.0204081632655, 7959.183673469388 7424.887053820552, 7876.85861392897 7346.938775510204, 7755.102040816327 7225.488935198103, 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8331.792968313717 987.0163842928032, 8460.484987971584 920.4515465387335, 8713.43137143705 845.0113970841217, 8855.43635864573 782.8842151803237, 8975.253066603054 671.9428189235414, 9010.754313405225 565.4390785170299, 9046.255560207395 410.1211237575353, 9068.443839458752 281.4291040996677, 9050.693216057667 179.36301954342798, 9006.316657554953 90.60990253800173, 8972.337944103203 0, 8858.95553900271 0, 8979.591836734695 180.16181430038142, 8979.591836734695 360.74278305987923)), ((9935.33621028978 9591.836734693878, 9860.73785898637 9795.91836734694, 9795.91836734694 9931.26849738919, 9765.614100864956 10000, 9959.7366093588 10000, 10000 9899.990932923472, 10000 9210.342095822705, 9950.618354641661 9387.755102040817, 9935.33621028978 9591.836734693878)))', - 'GROUP': 'A', - 'ID': 1, - }, - { - 'UNITNAME': 'Litho_G', - 'geometry': 'MULTIPOLYGON (((9591.836734693878 7392.409188406808, 9387.755102040817 7366.494159309232, 9183.673469387755 7310.6236360511, 8979.591836734695 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9736.033069844148 1224.4897959183675, 10000 887.0183205117985, 10000 0, 8972.337944103203 0, 9006.316657554953 90.60990253800173, 9050.693216057667 179.36301954342798, 9068.443839458752 281.4291040996677, 9046.255560207395 410.1211237575353, 9010.754313405225 565.4390785170299, 8975.253066603054 671.9428189235414, 8855.43635864573 782.8842151803237, 8713.43137143705 845.0113970841217, 8460.484987971584 920.4515465387335, 8331.792968313717 987.0163842928032, 8052.220649746626 1093.5201246993138, 7870.2767598855025 1155.6473066031122, 7666.144590773023 1160.0849624533835, 7444.261798259459 1168.960274153926, 7311.13212275132 1195.5862092555535, 6978.307933980974 1275.4640145604371, 6822.989979221478 1324.2782289134211, 6641.046089360355 1435.2196251702035, 6246.09471868621 1776.9191256410927, 5744.639607605554 2273.9365808714774, 5465.067289038463 2611.198425492096, 5358.563548631952 2673.3256073958946, 5189.932626321643 2766.5163802515917, 4897.047340203738 2886.333088208916, 4684.039859390716 2983.9615169148847, 4542.034872182035 3028.338075417598, 4320.15207966847 3032.7757312678687, 4013.9538259997507 3037.2133871181404, 3845.322903689442 3028.338075417598, 3379.369039410956 3170.343062626279, 3082.0460974427792 3294.5974264338747, 2944.4787660843695 3361.162264187944, 2842.4126815281297 3560.8567774501525, 2780.285499624332 3840.429096017244, 2735.908941121619 4088.937823632436, 2846.850337378401 4315.258271996272, 2993.2929804373534 4554.891687910922, 3263.9899873039026 4830.026350627742, 3494.7480915180095 5020.8455521894075, 3734.3815074326594 5176.163506948902, 3925.2007089943236 5389.170987761928, 4129.332878106803 5593.303156874407, 4324.58973551874 5824.061261088515, 4542.034872182033 6063.6946770031645, 4777.230632246412 6223.450287612931, 4910.36030775455 6347.704651420527, 5145.556067818929 6445.333080126496, 5376.314172033036 6489.709638629209, 5673.6371140012125 6480.834326928666, 5984.273023520203 6427.582456725404, 6294.908933039194 6432.020112575675, 6805.239355820393 6449.77073597676, 7209.066038195081 6636.152281688155, 7683.89521417411 6951.225847057416, 8078.846584848256 7359.490185282376, 8398.357806067788 7714.50265330408, 8771.120897490577 7976.324348470085, 8984.1283783036 8184.894173432836, 9143.883988913365 8300.273225539891, 9383.517404828015 8331.33681649179, 9796.219398903246 8371.275719144232, 10000 8427.640566256101, 10000 7398.084317291527, 9795.91836734694 7385.734246701611, 9591.836734693878 7392.409188406808)), ((10000 10000, 10000 9899.990932923472, 9959.7366093588 10000, 10000 10000)))', - 'GROUP': 'A', - 'ID': 2, - }, -] -for row in geology: - row['geometry'] = shapely.wkt.loads(row['geometry']) - -geology = geopandas.GeoDataFrame(geology, crs='epsg:7854') - -# build structures file -structures = [ - { - 'x': 2775.287768202244933, - 'y': 4330.15, - 'strike2': 45.00, - 'dip_2': 45.70, - 'id': 147.00, - 'sf': 's0', - }, - { - 'x': 3529.794754080061011, - 'y': 3091.192011237949828, - 'strike2': 288.50, - 'dip_2': 41.70, - 'id': 204.00, - 'sf': 's0', - }, - { - 'x': 7928.315269200518742, - 'y': 7234.561058065713951, - 'strike2': 48.80, - 'dip_2': 41.10, - 'id': 229.00, - 'sf': 's0', - }, - { - 'x': 8003.966104268994968, - 'y': 7421.634268009857806, - 'strike2': 48.80, - 'dip_2': 41.10, - 'id': 235.00, - 'sf': 's0', - }, - { - 'x': 6881.165236574942355, - 'y': 1213.128646564158771, - 'strike2': 299.10, - 'dip_2': 44.70, - 'id': 252.00, - 'sf': 's0', - }, - { - 'x': 3674.015651128655009, - 'y': 5266.677487068354822, - 'strike2': 41.20, - 'dip_2': 40.10, - 'id': 347.00, - 'sf': 's0', - }, - { - 'x': 3970.895076049027921, - 'y': 2944.223069901633608, - 'strike2': 273.00, - 'dip_2': 46.00, - 'id': 408.00, - 'sf': 's0', - }, -] -for row in structures: - row['geometry'] = shapely.Point(row['x'], row['y']) - del row['x'], row['y'] - -structures = geopandas.GeoDataFrame(structures, crs='epsg:7854') - -faults = geopandas.GeoDataFrame(columns=['geometry'], crs='epsg:7854') - -f_path = tempfile.mkdtemp() - -bounding_box = {"minx": 0, "miny": 0, "maxx": 10000, "maxy": 10000, "base": 0, "top": -5000} - -create_raster( - os.path.join(f_path, "DEM.tif"), - (bounding_box['minx'], bounding_box['miny'], bounding_box['maxx'], bounding_box['maxy']), - 7854, - 1000, -) - -geology.to_file(os.path.join(f_path, "geology.shp")) -structures.to_file(os.path.join(f_path, "structures.shp")) -faults.to_file(os.path.join(f_path, "faults.shp")) - -loop_project_filename = os.path.join(f_path, "local_source.loop3d") - -config = { - "structure": { - "orientation_type": "strike", - "dipdir_column": "strike2", - "dip_column": "dip_2", - "description_column": "DESCRIPTION", - "bedding_text": "Bed", - "overturned_column": "structypei", - "overturned_text": "BEOI", - "objectid_column": "objectid", - "desciption_column": "feature", - }, - "geology": { - "unitname_column": "UNITNAME", - "alt_unitname_column": "UNITNAME", - "group_column": "GROUP", - "supergroup_column": "supersuite", - "description_column": "descriptn", - "minage_column": "min_age_ma", - "maxage_column": "max_age_ma", - "rocktype_column": "rocktype1", - "alt_rocktype_column": "rocktype2", - "sill_text": "sill", - "intrusive_text": "intrusive", - "volcanic_text": "volcanic", - "objectid_column": "ID", - "ignore_codes": ["cover"], - }, - "fault": { - "structtype_column": "feature", - "fault_text": "Fault", - "dip_null_value": "0", - "dipdir_flag": "num", - "dipdir_column": "dip_dir", - "dip_column": "dip", - "orientation_type": "dip direction", - "dipestimate_column": "dip_est", - "dipestimate_text": "gentle,moderate,steep", - "name_column": "name", - "objectid_column": "objectid", - }, - "fold": { - "structtype_column": "feature", - "fold_text": "Fold axial trace", - "description_column": "type", - "synform_text": "syncline", - "foldname_column": "NAME", - "objectid_column": "objectid", - }, -} - - -proj = Project( - geology_filename=os.path.join(f_path, "geology.shp"), - fault_filename=os.path.join(f_path, "faults.shp"), - fold_filename=os.path.join(f_path, "faults.shp"), - structure_filename=os.path.join(f_path, "structures.shp"), - dtm_filename=os.path.join(f_path, 'DEM.tif'), - clut_filename=pathlib.Path( - os.path.join(os.path.dirname(map2loop.__file__), "_datasets/clut_files/WA_clut.csv") - ), - config_dictionary=config, - clut_file_legacy=False, - working_projection="EPSG:7854", - bounding_box=bounding_box, - loop_project_filename=loop_project_filename, - overwrite_loopprojectfile=True, -) - -proj.set_thickness_calculator(StructuralPoint()) - -column = ['Litho_G', 'Litho_F', 'Litho_E'] -proj.set_sampler(Datatype.GEOLOGY, SamplerSpacing(100.0)) -proj.set_sampler(Datatype.STRUCTURE, SamplerDecimator(0)) -proj.run_all(user_defined_stratigraphic_column=column) - - -def test_thickness_structuralPoint(proj=proj): - # 1. are all lithologies in the geology returned? - assert all( - element in geology['UNITNAME'].unique().tolist() - for element in proj.stratigraphic_column.stratigraphicUnits['name'].to_list() - ), " thickness calculator not calculating for all lithologies in geology" - - # 2. is ThicknessMedian a column in the stratigraphicUnits? - assert ( - 'ThicknessMedian' in proj.stratigraphic_column.stratigraphicUnits.columns.to_list() - ), "ThicknessMedian not in resulting stratigraphicUnits" - - # 2. are bottom and top units assigned as -1? - assert ( - proj.stratigraphic_column.stratigraphicUnits[ - proj.stratigraphic_column.stratigraphicUnits['Order'] - == min(proj.stratigraphic_column.stratigraphicUnits['Order']) - ]['ThicknessMedian'].values - == -1 - ), "StructuralPoint thickness calculator: top unit not assigned as -1" - assert ( - proj.stratigraphic_column.stratigraphicUnits[ - proj.stratigraphic_column.stratigraphicUnits['Order'] - == max(proj.stratigraphic_column.stratigraphicUnits['Order']) - ]['ThicknessMedian'].values - == -1 - ), "thickness calculator StructuralPoint: bottom unit not assigned as -1" - - # 3. Is the thickness being calculated correctly? Should be ~ 89 - assert ( - round( - proj.stratigraphic_column.stratigraphicUnits[ - proj.stratigraphic_column.stratigraphicUnits['name'] == 'Litho_F' - ]['ThicknessMedian'] - ).values - == 89.0 - ), "thickness calculator StructuralPoint not calculating thickness correctly" diff --git a/tests/thickness/StructurePoint/test_thickness_StructuralPoint_server.py b/tests/thickness/StructurePoint/test_thickness_StructuralPoint_server.py deleted file mode 100644 index 84492ec5..00000000 --- a/tests/thickness/StructurePoint/test_thickness_StructuralPoint_server.py +++ /dev/null @@ -1,65 +0,0 @@ -# This test runs on a portion of the dataset in https://github.com/Loop3D/m2l3_examples/tree/main/Laurent2016_V2_variable_thicknesses (only for lithologies E, F, and G) -# structures are confined to litho_F, and the test confirms if the StructuralPoint thickness is calculated, for all lithologies, if the thickness is correct for F (~90 m), and top/bottom units are assigned -1 -# this creates a temp folder in Appdata to store the data to run the proj, checks the thickness, and then deletes the temp folder -# this was done to avoid overflow of file creation in the tests folder - -# this tests the thickness calculator Structural Point from a server - -#internal imports -from map2loop.thickness_calculator import StructuralPoint -from map2loop.project import Project -from map2loop.m2l_enums import VerboseLevel - -#external imports -import pathlib -import pytest -import requests -import map2loop - - -def test_from_aus_state(): - - bbox_3d = { - "minx": 515687.31005864, - "miny": 7493446.76593407, - "maxx": 562666.860106543, - "maxy": 7521273.57407786, - "base": -3200, - "top": 3000, - } - loop_project_filename = "wa_output.loop3d" - module_path = map2loop.__file__.replace("__init__.py", "") - - try: - proj = Project( - use_australian_state_data="WA", - working_projection="EPSG:28350", - bounding_box=bbox_3d, - config_filename=pathlib.Path(module_path) - / pathlib.Path('_datasets') - / pathlib.Path('config_files') - / pathlib.Path('WA.json'), - clut_filename=pathlib.Path(module_path) - / pathlib.Path('_datasets') - / pathlib.Path('clut_files') - / pathlib.Path('WA_clut.csv'), - # clut_file_legacy=False, - verbose_level=VerboseLevel.NONE, - loop_project_filename=loop_project_filename, - overwrite_loopprojectfile=True, - ) - except requests.exceptions.ReadTimeout: - pytest.skip("Connection to the server timed out, skipping test") - - proj.set_thickness_calculator(StructuralPoint()) - proj.run_all() - print("from the test", proj.stratigraphic_column.stratigraphicUnits.columns) - assert ( - proj.thickness_calculator.thickness_calculator_label == "StructuralPoint" - ), 'Thickness_calc structural point not being set properly' - assert ( - "ThicknessMedian" in proj.stratigraphic_column.stratigraphicUnits.columns - ), 'Thickness not being calculated in StructuralPointCalculator' - assert ( - "ThicknessStdDev" in proj.stratigraphic_column.stratigraphicUnits.columns - ), 'Thickness std not being calculated in StructuralPointCalculator' diff --git a/tests/thickness/ThicknessCalculatorAlpha/test_ThicknessCalculatorAlpha.py b/tests/thickness/ThicknessCalculatorAlpha/test_ThicknessCalculatorAlpha.py new file mode 100644 index 00000000..a169b3ce --- /dev/null +++ b/tests/thickness/ThicknessCalculatorAlpha/test_ThicknessCalculatorAlpha.py @@ -0,0 +1,1713 @@ +import pandas +import geopandas +import numpy + +from map2loop.mapdata import MapData +from map2loop.m2l_enums import Datatype +from map2loop.thickness_calculator import ThicknessCalculatorAlpha +from map2loop._datasets.geodata_files.load_map2loop_data import load_hamersley_geology + + +######################################################### +### Define the test data for ThicknessCalculatorAlpha ### +######################################################### + +# Sample stratigraphic units data +st_units = pandas.DataFrame( + { + 'Unnamed: 0': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10], + 'layerId': [7, 0, 10, 8, 1, 5, 9, 4, 3, 2, 6], + 'name': [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + ], + 'minAge': [0.0] * 11, + 'maxAge': [100000.0] * 11, + 'group': [None] * 11, + 'supergroup': [None] * 11, + 'ThicknessMean_ThicknessCalculatorAlpha': [0.0] * 11, + 'ThicknessMedian_ThicknessCalculatorAlpha': [0.0] * 11, + 'ThicknessStdDev_ThicknessCalculatorAlpha': [0.0] * 11, + 'stratigraphic_Order': list(range(11)), + 'colour': [ + '#5d7e60', + '#387866', + '#628304', + '#a2f290', + '#0c2562', + '#5fb3c5', + '#f48b70', + '#1932e2', + '#106e8a', + '#d0d47c', + '#e7f2f3', + ], + } +) + +st_column = [ + 'Turee_Creek_Group', + 'Boolgeeda_Iron_Formation', + 'Woongarra_Rhyolite', + 'Weeli_Wolli_Formation', + 'Brockman_Iron_Formation', + 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', + 'Wittenoom_Formation', + 'Marra_Mamba_Iron_Formation', + 'Jeerinah_Formation', + 'Bunjinah_Formation', + 'Pyradie_Formation', + 'Fortescue_Group', +] + +# 3. map_data.basal_contacts +basal_c = [ + {'ID': 0, 'basal_unit': 'Turee_Creek_Group', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Boolgeeda_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Brockman_Iron_Formation', 'type': 'BASAL'}, + {'ID': 1, 'basal_unit': 'Weeli_Wolli_Formation', 'type': 'BASAL'}, + {'ID': 4, 'basal_unit': 'Jeerinah_Formation', 'type': 'BASAL'}, + {'ID': 5, 'basal_unit': 'Bunjinah_Formation', 'type': 'BASAL'}, + {'ID': 6, 'basal_unit': 'Marra_Mamba_Iron_Formation', 'type': 'BASAL'}, + {'ID': 7, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'ABNORMAL'}, + {'ID': 8, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'ABNORMAL'}, + {'ID': 9, 'basal_unit': 'Wittenoom_Formation', 'type': 'BASAL'}, + {'ID': 10, 'basal_unit': 'Mount_McRae_Shale_and_Mount_Sylvia_Formation', 'type': 'BASAL'}, + {'ID': 11, 'basal_unit': 'Woongarra_Rhyolite', 'type': 'BASAL'}, +] +bc_geoms = geopandas.GeoSeries.from_wkt( + [ + 'MULTILINESTRING ((520000.0000000000000000 7506463.0589317083358765, 520000.0000000000000000 7506464.0583261400461197, 521798.5784270099829882 7506667.5086746597662568, 524292.0583883899962530 7507105.0368000296875834, 525888.7772752699675038 7507345.5593877695500851, 526916.8410634599858895 7507564.5817003501579165, 528098.0088455299846828 7507783.0997126800939441, 529344.8316910399589688 7507958.1297348998486996, 530263.5311044099507853 7508220.6498684398829937, 531357.2706492099678144 7508395.6678343201056123, 532013.4010351699544117 7508548.6697535198181868, 532538.3520777500234544 7508548.6775182196870446, 532932.1086069300072268 7508483.1717491699382663, 533085.1519033299991861 7508308.1688938299193978, 533107.0194513100432232 7508045.6694244500249624, 533041.4099823100259528 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'2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', + '4', + '5', + '5', + '5', + '5', + '5', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '0', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '1', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '2', + '3', +] + +s_c = pandas.DataFrame({'X': X, 'Y': Y, 'Z': Z, 'featureId': featureid}) + + +##################################### +### TEST ThicknessCalculatorAlpha ### +##################################### + + +def check_thickness_values(result, column, description): + for order, position in [ + (max(st_units['stratigraphic_Order']), 'bottom'), + (min(st_units['stratigraphic_Order']), 'top'), + ]: + assert ( + result[result['stratigraphic_Order'] == order][column].values == -1 + ), f"ThicknessCalculatorAlpha: {position} unit not assigned as -1 ({description})" + + +geology = load_hamersley_geology() + + +def test_calculate_thickness_thickness_calculator_alpha(): + # Run the calculation + md = MapData() + md.sampled_contacts = s_c + md.data[Datatype.GEOLOGY] = geology + + print('GERE', md.get_map_data(Datatype.GEOLOGY)) + + thickness_calculator = ThicknessCalculatorAlpha() + result = thickness_calculator.compute( + units=st_units, + stratigraphic_order=st_column, + basal_contacts=bc_gdf, + structure_data=structures, + map_data=md, + ) + + # is thickness calc alpha the label? + assert ( + thickness_calculator.thickness_calculator_label == 'ThicknessCalculatorAlpha' + ), 'ThicknessCalcAlpha: thickness calculator name not set correctly' + + # is the result a pandas dataframe? + assert isinstance(result, pandas.DataFrame), 'ThicknessCalcAlpha result not a pandas DataFrame' + + # Check if there is mean, std, and median in results + required_columns = ['ThicknessMean', 'ThicknessMedian', 'ThicknessStdDev'] + for column in required_columns: + assert column in result.columns, f'{column} not in ThicknessCalcAlpha result' + + # check if all units are in the results + assert 'name' in result.columns, 'unit_name not in ThicknessCalcAlpha result' + assert all( + name in result['name'].values for name in st_units['name'].values + ), 'units missing from in ThicknessCalcAlpha result' + + # are bottom and top units being assigned -1 + for column, description in [ + ('ThicknessMean', 'mean'), + ('ThicknessMedian', 'median'), + ('ThicknessStdDev', 'median'), + ]: + check_thickness_values(result, column, description) + + # are the dtypes numpy.float? + for column in required_columns: + assert result[column].dtype == numpy.float64, f'{column} not numpy.float64' + + # check for nans in the results + for column in required_columns: + assert not result[column].isnull().values.any(), f'{column} has NaN values' diff --git a/tests/utils/test_rgb_and_hex_functions.py b/tests/utils/test_rgb_and_hex_functions.py index cce2059b..a4d82fd9 100644 --- a/tests/utils/test_rgb_and_hex_functions.py +++ b/tests/utils/test_rgb_and_hex_functions.py @@ -4,11 +4,14 @@ import re from map2loop.utils import generate_random_hex_colors, hex_to_rgb -#does it return the right number of colors? +# does it return the right number of colors? def test_generate_random_hex_colors_length(): n = 5 colors = generate_random_hex_colors(n) - assert len(colors) == n, f"utils function generate_random_hex_colors not returning the right number of hex codes.Expected {n} colors, got {len(colors)}" + assert ( + len(colors) == n + ), f"utils function generate_random_hex_colors not returning the right number of hex codes.Expected {n} colors, got {len(colors)}" + # are the returned hex strings the right format? def test_generate_random_hex_colors_format(): @@ -16,21 +19,29 @@ def test_generate_random_hex_colors_format(): hex_pattern = re.compile(r'^#[0-9A-Fa-f]{6}$') colors = generate_random_hex_colors(n) for color in colors: - assert hex_pattern.match(color), f"utils function generate_random_hex_colors not returning hex strings in the right format. Got {color} instead." + assert hex_pattern.match( + color + ), f"utils function generate_random_hex_colors not returning hex strings in the right format. Got {color} instead." + # is hex conversion to rgba working as expected? def test_hex_to_rgba_long_hex(): - hex_color = "#1a2b3c" # long hex versions + hex_color = "#1a2b3c" # long hex versions expected_output = (0.10196078431372549, 0.16862745098039217, 0.23529411764705882, 1.0) - assert hex_to_rgb(hex_color) == expected_output, f"utils function hex_to_rgba not doing hex to rgba conversion correctly. Expected {expected_output}, got {hex_to_rgb(hex_color)}" + assert ( + hex_to_rgb(hex_color) == expected_output + ), f"utils function hex_to_rgba not doing hex to rgba conversion correctly. Expected {expected_output}, got {hex_to_rgb(hex_color)}" def test_hex_to_rgba_short_hex(): - hex_color = "#abc" # short hex versions + hex_color = "#abc" # short hex versions expected_output = (0.6666666666666666, 0.7333333333333333, 0.8, 1.0) assert hex_to_rgb(hex_color) == expected_output + # does it handle invalid inputs correctly? def test_hex_to_rgba_invalid_hex(): with pytest.raises(ValueError): - hex_to_rgb("12FF456"), "utils function hex_to_rgba is expected to raise a ValueError when an invalid hex string is passed, but it did not." \ No newline at end of file + hex_to_rgb( + "12FF456" + ), "utils function hex_to_rgba is expected to raise a ValueError when an invalid hex string is passed, but it did not."