TNO Intern

Commit c23a55e5 authored by Zanne Korevaar's avatar Zanne Korevaar
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Merge branch '13-fix-bug-lithology_properties-table' into 'main' 

Resolve "fix bug lithology_properties table"

Closes #13

See merge request !14
parents a08e080b 516acf7d

docs/manual/lithology_configuration.md

+21 −19
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@@ -14,9 +14,10 @@ except `config_file_path`. 
The input JSON file for the lithology module includes the following parameters:



| Parameter                 | Description                                                                                | Unit    | Type           | Remark                                                                                  |

|-------------------------|---------------------------------------------------------------------------------------------|------|------|---------|

|---------------------------|--------------------------------------------------------------------------------------------|---------|----------------|-----------------------------------------------------------------------------------------|

| input_dir_lithology       | Path to folder with Excel file containing lithology properties for the borehole            | —       | string         | —                                                                                       |

| out_dir_lithology         | Path to folder where lithology output is stored                                            | —       | string         | Output includes tables with bulk subsurface thermal conductivity over depth and figures |

| lithology_properties_path | Path to Excel file containing user-defined soil/rock properties                            | -       | string         | Optional; default table with properties is included in the lithology package            |

| borehole_lithology_path   | Path to Excel file with subsurface lithology data                                          | —       | string         | —                                                                                       |

| borhole_litho_sheetname   | Name of tab in Excel file with subsurface lithology data                                   | —       | string         | —                                                                                       |

| out_table                 | Name of HDF5 (.h5) file to store lithology and thermal conductivity data                   | —       | string         | —                                                                                       |
@@ -78,10 +79,11 @@ The lithology types (for `Lithology_a` and `Lithology_b`) currently supported by 


### Excel Format for Lithological Thermal Properties from Literature



The lithology module relies on an Excel file (`resources/lithology_properties/lithology_properties.xlsx`) that contains 

The lithology module relies on an Excel file (`lithology/resources/lithology_properties.xlsx`) that contains 

physical and thermal parameters for each lithology type, from Hantschel & Kauerauf (2009). This table acts as the reference 

database from which all lithology-dependent thermal-conductivity calculations draw their input values. This table

should be edited for additional lithologies and/or customization of the rock properties. 

database from which all lithology-dependent thermal-conductivity calculations draw their input values. Optionally,

the path to a similar table is user-defined in the configuration of the lithology module, with additional or edited soil

and/or rock properties. 



The Excel file includes the following columns:

src/geoloop/configuration.py

+20 −0
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@@ -19,6 +19,8 @@ class LithologyConfig(BaseModel): 
        Path to the JSON configuration file that created this object.

    out_dir_lithology : str or Path

        Directory where lithology outputs will be written.

    lithology_properties_path: str or Path

        Path to the Excel table  with lithology properties.

    borehole_lithology_path : str or Path

        Path to the Excel or CSV file containing lithology data.

    borehole_lithology_sheetname : str
@@ -48,6 +50,7 @@ class LithologyConfig(BaseModel): 
    config_file_path: str | Path

    out_dir_lithology: str | Path

    input_dir_lithology: str | Path

    lithology_properties_path: str |Path | None = None

    borehole_lithology_path: str | Path

    borehole_lithology_sheetname: str

    out_table: str
@@ -89,6 +92,23 @@ class LithologyConfig(BaseModel): 
        if not isinstance(self.out_dir_lithology, Path):

            self.out_dir_lithology = base_dir_lithology / Path(self.out_dir_lithology)



        # Lithology properties table

        # Resolve user-supplied path

        if self.lithology_properties_path is not None:

            if not isinstance(self.lithology_properties_path, Path):

                self.lithology_properties_path = Path(self.lithology_properties_path)



            if not self.lithology_properties_path.is_absolute():

                self.lithology_properties_path = (

                        base_dir_lithology / self.lithology_properties_path

                ).resolve()



            if not self.lithology_properties_path.exists():

                raise FileNotFoundError(

                    f"Lithology properties file not found: "

                    f"{self.lithology_properties_path}"

                )



        return self

src/geoloop/constants.py

+0 −5
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@@ -10,11 +10,6 @@ test_output_path = test_dir / "output" 
# Resources directory

resources_path = repo_path / "resources"



# Lithology resources directory

lithology_properties_xlsx = (

    resources_path / "lithology_properties" / "lithology_properties.xlsx"

)



# Dictionary of units for various parameters in the model.

units_dict = {

    "Q_b": "W",

src/geoloop/lithology/process_lithology.py

+15 −5
Original line number Diff line number Diff line 
import math

from pathlib import Path

from importlib.resources import files



import numpy as np

import pandas as pd

import xarray as xr



from geoloop.configuration import LithologyConfig

from geoloop.constants import lithology_properties_xlsx

from geoloop.geoloopcore.strat_interpolator import TgInterpolator
@@ -257,6 +257,7 @@ class ProcessLithologyToThermalConductivity: 


    def __init__(

        self,

        lithology_properties_df: pd.DataFrame,

        borehole_df: pd.DataFrame,

        Tg: float,

        Tgrad: float,
@@ -270,8 +271,7 @@ class ProcessLithologyToThermalConductivity: 
        out_table: str,

        read_from_table: bool,

    ) -> None:

        # Read lithology properties reference table (Excel)

        self.lithology_props_df = pd.read_excel(lithology_properties_xlsx)

        self.lithology_props_df = lithology_properties_df



        self.borehole_df = borehole_df

        self.lithology_props_dict = self.create_lithology_props_dict()
@@ -385,12 +385,22 @@ class ProcessLithologyToThermalConductivity: 
            Initialized instance.

        """



        borehole_path = config.borehole_lithology_path

        # Read borehole lithology table (Excel)

        borehole_df = pd.read_excel(

            borehole_path, sheet_name=config.borehole_lithology_sheetname

            config.borehole_lithology_path, sheet_name=config.borehole_lithology_sheetname

        )

        # Read lithology properties reference table (Excel)

        if config.lithology_properties_path is not None:

            lithology_properties_df = pd.read_excel(

                config.lithology_properties_path

            )

        else:

            lithology_properties_df = pd.read_excel(

                files("geoloop.lithology.resources").joinpath("lithology_properties.xlsx")

            )



        return cls(

            lithology_properties_df=lithology_properties_df,

            borehole_df=borehole_df,

            Tg=config.Tg,

            Tgrad=config.Tgrad,

src/geoloop/lithology/resources/__init__.py

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