.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/02_structural_modeling/02_model_1_gempy.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_02_structural_modeling_02_model_1_gempy.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_02_structural_modeling_02_model_1_gempy.py:


Construct Model 1 with Helper Functions
---------------------------------------

This example demonstrates how to construct a 3D geological model of the Model 1 deposit using GemPy. 
It leverages custom APIs to streamline the modeling process.

.. GENERATED FROM PYTHON SOURCE LINES 8-19

.. code-block:: Python


    import time
    import os
    import xarray as xr
    from dotenv import dotenv_values
    import gempy as gp
    import gempy_viewer as gpv

    from vector_geology.model_1_builder import initialize_geo_model
    from vector_geology.omf_to_gempy import process_file








.. GENERATED FROM PYTHON SOURCE LINES 20-21

Start the timer to measure execution time

.. GENERATED FROM PYTHON SOURCE LINES 21-23

.. code-block:: Python

    start_time = time.time()








.. GENERATED FROM PYTHON SOURCE LINES 24-26

Load environment variables and path configurations
This step is crucial for setting up the directory paths for the model data.

.. GENERATED FROM PYTHON SOURCE LINES 26-29

.. code-block:: Python

    config = dotenv_values()
    path = config.get("PATH_TO_MODEL_1_Subsurface")








.. GENERATED FROM PYTHON SOURCE LINES 30-32

Initialize lists to store data
Here we prepare the containers for the structural elements and the global extent.

.. GENERATED FROM PYTHON SOURCE LINES 32-36

.. code-block:: Python

    structural_elements = []
    global_extent = None
    color_gen = gp.data.ColorsGenerator()








.. GENERATED FROM PYTHON SOURCE LINES 37-39

Process each .nc file in the specified directory
This loop reads the necessary data from each .nc file for modeling.

.. GENERATED FROM PYTHON SOURCE LINES 39-45

.. code-block:: Python

    for filename in os.listdir(path):
        base, ext = os.path.splitext(filename)
        if ext == '.nc':
            structural_element, global_extent = process_file(os.path.join(path, filename), global_extent, color_gen)
            structural_elements.append(structural_element)








.. GENERATED FROM PYTHON SOURCE LINES 46-48

Initialize the GemPy model
We use the data processed above to initialize the geological model with GemPy.

.. GENERATED FROM PYTHON SOURCE LINES 48-55

.. code-block:: Python

    geo_model = initialize_geo_model(
        structural_elements=structural_elements,
        extent=global_extent,
        topography=(xr.open_dataset(os.path.join(path, "Topography.nc"))),
        load_nuggets=True
    )





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/leguark/gempy/gempy/core/data/structural_frame.py:188: UserWarning: The basement color was already used in the structural elements.Changing the basement color to #015482.
      warnings.warn(f"The basement color was already used in the structural elements."
    Active grids: GridTypes.NONE|TOPOGRAPHY|DENSE




.. GENERATED FROM PYTHON SOURCE LINES 56-58

Display the initialized model
It's helpful to print the model to verify its initialization.

.. GENERATED FROM PYTHON SOURCE LINES 58-60

.. code-block:: Python

    print(geo_model)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    {'_interpolation_options': InterpolationOptions(kernel_options={'range': 5, 'c_o': 10, 'uni_degree': 1, 'i_res': 4, 'gi_res': 2, 'number_dimensions': 3, 'kernel_function': <AvailableKernelFunctions.cubic: KernelFunction(base_function=<function cubic_function at 0x7fea8a6cd480>, derivative_div_r=<function cubic_function_p_div_r at 0x7fea8a6cd510>, second_derivative=<function cubic_function_a at 0x7fea8a6cd5a0>, consume_sq_distance=False)>, 'kernel_solver': <Solvers.DEFAULT: 1>, 'compute_condition_number': False, 'optimizing_condition_number': False, 'condition_number': None}, evaluation_options={'_number_octree_levels': 5, '_number_octree_levels_surface': 4, 'curvature_threshold': -1, 'error_threshold': 1.5, 'min_octree_level': 2, 'mesh_extraction': True, 'mesh_extraction_masking_options': <MeshExtractionMaskingOptions.INTERSECT: 3>, 'mesh_extraction_fancy': True, 'evaluation_chunk_size': 5000000, 'compute_scalar_gradient': False, 'verbose': False}, temp_interpolation_values=<gempy_engine.core.data.options.temp_interpolation_values.TempInterpolationValues object at 0x7fea2d6872e0>, debug=True, cache_mode=CacheMode.IN_MEMORY_CACHE, cache_model_name=, block_solutions_type=BlockSolutionType.OCTREE, sigmoid_slope=50000, debug_water_tight=False),
     'grid': Grid(_octree_grid=None,
                  _dense_grid=RegularGrid(resolution=array([20, 10, 20]),
                                          extent=array([ 5.59902830e+05,  5.64955682e+05,  6.44278260e+05,  6.50608735e+05,
           -1.75340000e+03,  1.60326604e+02]),
                                          values=array([[ 5.60029151e+05,  6.44594784e+05, -1.70555683e+03],
           [ 5.60029151e+05,  6.44594784e+05, -1.60987050e+03],
           [ 5.60029151e+05,  6.44594784e+05, -1.51418417e+03],
           ...,
           [ 5.64829361e+05,  6.50292212e+05, -7.88892213e+01],
           [ 5.64829361e+05,  6.50292212e+05,  1.67971089e+01],
           [ 5.64829361e+05,  6.50292212e+05,  1.12483439e+02]]),
                                          mask_topo=array([], shape=(0, 3), dtype=bool),
                                          _transform=None),
                  _custom_grid=None,
                  _topography=<gempy.core.data.grid_modules.topography.Topography object at 0x7fea789b5600>,
                  _sections=None,
                  _centered_grid=None,
                  values=array([[ 5.60029151e+05,  6.44594784e+05, -1.70555683e+03],
           [ 5.60029151e+05,  6.44594784e+05, -1.60987050e+03],
           [ 5.60029151e+05,  6.44594784e+05, -1.51418417e+03],
           ...,
           [ 5.64955682e+05,  6.49201963e+05,  1.06993262e+02],
           [ 5.64955682e+05,  6.49905349e+05,  8.89864414e+01],
           [ 5.64955682e+05,  6.50608735e+05,  7.05702308e+01]]),
                  length=array([], dtype=float64),
                  _transform=None,
                  _octree_levels=-1),
     'input_transform': {'_cached_pivot': None,
     '_is_default_transform': False,
     'position': array([-562422.65655014, -647329.31794742,     823.58712106]),
     'rotation': array([0., 0., 0.]),
     'scale': array([8.55363115e-05, 8.55363115e-05, 8.55363115e-05])},
     'meta': GeoModelMeta(name='Tutorial_ch1_1_Basics',
                          creation_date=None,
                          last_modification_date=None,
                          owner=None),
     'structural_frame': StructuralFrame(
            structural_groups=[
    StructuralGroup(
            name=Blue,
            structural_relation=StackRelationType.ERODE,
            elements=[
    Element(
            name=HBL,
            color=#ffbe00,
            is_active=True
    ),
    Element(
            name=KKR,
            color=#A46283,
            is_active=True
    )
    ]
    ),
    StructuralGroup(
            name=Red,
            structural_relation=StackRelationType.ERODE,
            elements=[
    Element(
            name=ABL,
            color=#1D3943,
            is_active=True
    ),
    Element(
            name=LGR,
            color=#6394A4,
            is_active=True
    ),
    Element(
            name=WAL,
            color=#72A473,
            is_active=True
    )
    ]
    )
    ],
            fault_relations=
    [[False, False],
     [False, False]],
    }




.. GENERATED FROM PYTHON SOURCE LINES 61-63

Modify the interpolation options
This step configures the model's interpolation settings for better accuracy.

.. GENERATED FROM PYTHON SOURCE LINES 63-69

.. code-block:: Python

    interpolation_options = geo_model.interpolation_options
    interpolation_options.mesh_extraction = True
    interpolation_options.kernel_options.range = 0.7
    interpolation_options.kernel_options.c_o = 3
    interpolation_options.kernel_options.compute_condition_number = True








.. GENERATED FROM PYTHON SOURCE LINES 70-72

Modify surface points
Adjustments to the surface points can influence the resulting geological features.

.. GENERATED FROM PYTHON SOURCE LINES 72-78

.. code-block:: Python

    gp.modify_surface_points(
        geo_model,
        slice=0,
        X=geo_model.surface_points_copy.data[0][0] + 130,
    )






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">

            <table>
              <tr><td>Structural Groups:</td><td>
        <table style="border-left:1.2px solid black;>
          <tr><th colspan="2"><b>StructuralGroup:</b></th></tr>
          <tr><td>Name:</td><td>Blue</td></tr>
          <tr><td>Structural Relation:</td><td>StackRelationType.ERODE</td></tr>
          <tr><td>Elements:</td><td>
        <table width="50%" style="border-left:15px solid #ffbe00;">
          <tr><th colspan="2"><b>StructuralElement:</b></th></tr>
          <tr><td>Name:</td><td>HBL</td></tr>
        </table>
            <br>
        <table width="50%" style="border-left:15px solid #A46283;">
          <tr><th colspan="2"><b>StructuralElement:</b></th></tr>
          <tr><td>Name:</td><td>KKR</td></tr>
        </table>
            </td></tr>
        </table>
            <br>
        <table style="border-left:1.2px solid black;>
          <tr><th colspan="2"><b>StructuralGroup:</b></th></tr>
          <tr><td>Name:</td><td>Red</td></tr>
          <tr><td>Structural Relation:</td><td>StackRelationType.ERODE</td></tr>
          <tr><td>Elements:</td><td>
        <table width="50%" style="border-left:15px solid #1D3943;">
          <tr><th colspan="2"><b>StructuralElement:</b></th></tr>
          <tr><td>Name:</td><td>ABL</td></tr>
        </table>
            <br>
        <table width="50%" style="border-left:15px solid #6394A4;">
          <tr><th colspan="2"><b>StructuralElement:</b></th></tr>
          <tr><td>Name:</td><td>LGR</td></tr>
        </table>
            <br>
        <table width="50%" style="border-left:15px solid #72A473;">
          <tr><th colspan="2"><b>StructuralElement:</b></th></tr>
          <tr><td>Name:</td><td>WAL</td></tr>
        </table>
            </td></tr>
        </table>
            </td></tr>
              <tr><td>Fault Relations:</td><td><table style="border-collapse: collapse; table-layout: fixed;"><th></th><th style="transform: rotate(-35deg); height:150px; vertical-align: bottom; text-align: center;">Blue</th><th style="transform: rotate(-35deg); height:150px; vertical-align: bottom; text-align: center;">Red</th><tr><th>Blue</th><td style="background-color: #FFB6C1; width: 20px; height: 20px; border: 1px solid black;"></td><td style="background-color: #FFB6C1; width: 20px; height: 20px; border: 1px solid black;"></td></tr><tr><th>Red</th><td style="background-color: #FFB6C1; width: 20px; height: 20px; border: 1px solid black;"></td><td style="background-color: #FFB6C1; width: 20px; height: 20px; border: 1px solid black;"></td></tr></table></td></tr>
              <tr><td></td><td>
            <table>
              <tr>
                <td><div style="display: inline-block; background-color: #527682; width: 20px; height: 20px; border: 1px solid black;"></div> True</td>
                <td><div style="display: inline-block; background-color: #FFB6C1; width: 20px; height: 20px; border: 1px solid black;"></div> False</td>
              </tr>
            </table>
            </td></tr>
            </table>
        
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 79-81

Compute the model
This is where the model computation happens, utilizing the GemPy engine.

.. GENERATED FROM PYTHON SOURCE LINES 81-90

.. code-block:: Python

    before_compute_time = time.time()
    gp.compute_model(
        geo_model,
        engine_config=gp.data.GemPyEngineConfig(
            backend=gp.data.AvailableBackends.PYTORCH,
            dtype="float32"
        ),
    )





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Setting Backend To: AvailableBackends.PYTORCH
    Condition number: 146825.828125.
    Condition number: 276737.5.


.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <b>Solutions:</b> 5 Octree Levels, 5 DualContouringMeshes
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 91-93

Plot 2D model visualization
Visualizing the model in 2D helps in understanding the geological layers.

.. GENERATED FROM PYTHON SOURCE LINES 93-95

.. code-block:: Python

    gpv.plot_2d(geo_model, show_scalar=False)




.. image-sg:: /examples/02_structural_modeling/images/sphx_glr_02_model_1_gempy_001.png
   :alt: Cell Number: mid Direction: y
   :srcset: /examples/02_structural_modeling/images/sphx_glr_02_model_1_gempy_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    <gempy_viewer.modules.plot_2d.visualization_2d.Plot2D object at 0x7fea2d483790>



.. GENERATED FROM PYTHON SOURCE LINES 96-98

3D visualization with gempy_viewer
A 3D view provides a comprehensive look at the model's structure.

.. GENERATED FROM PYTHON SOURCE LINES 98-104

.. code-block:: Python

    gempy_vista = gpv.plot_3d(
        model=geo_model,
        show=True,
        kwargs_plot_structured_grid={'opacity': 0.8}
    )




.. image-sg:: /examples/02_structural_modeling/images/sphx_glr_02_model_1_gempy_002.png
   :alt: 02 model 1 gempy
   :srcset: /examples/02_structural_modeling/images/sphx_glr_02_model_1_gempy_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 105-107

Calculate and print execution times
It's useful to know how long different parts of the process take.

.. GENERATED FROM PYTHON SOURCE LINES 107-117

.. code-block:: Python

    end_time = time.time()
    prep_time = before_compute_time - start_time
    compute_time = end_time - before_compute_time
    execution_time = end_time - start_time

    print(f"Preparation time: {prep_time} seconds.")
    print(f"Computation time: {compute_time} seconds.")
    print(f"Total execution time: {execution_time} seconds.")

    # sphinx_gallery_thumbnail_number = -2  




.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Preparation time: 1.0133297443389893 seconds.
    Computation time: 4.729570627212524 seconds.
    Total execution time: 5.742900371551514 seconds.





.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 5.802 seconds)


.. _sphx_glr_download_examples_02_structural_modeling_02_model_1_gempy.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: 02_model_1_gempy.ipynb <02_model_1_gempy.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: 02_model_1_gempy.py <02_model_1_gempy.py>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_