Source code for darsia.manager.co2analysis

"""Structure for analyzing images of multi-component multi-phase experiments.

The goal of such analysis is to identify distinct components/phases. In practice, it may
have to be tailored to the specific scenario by inheritance. For more general use, a
generalized multicomponent analysis manager should be used. This module is tailored to
CO2 experiments in water, strongly motivated by the International FluidFlower Benchmark
study.

"""

from __future__ import annotations

from abc import ABC, abstractmethod
from pathlib import Path
from typing import Union
from warnings import warn

import darsia




class CO2Analysis(ABC, darsia.ConcentrationAnalysisBase):
    """
    General setup for an image analysis of time series aiming at analyzing CO2 evolution.
    This class inherits from darsia.TracerAnalysis.
    """

    def __init__(
        self,
        baseline: Union[str, Path, list[str], list[Path]],
        config: Union[str, Path],
        update_setup: bool = False,
    ) -> None:
        """
        Constructor for two-component analysis, where the two specific components
        are identified with CO2(g) and CO2 saturated water. Pure water will be treated
        as neutral (third) phase.

        Args:
            baseline (str, Path or list of such): see darsia.AnalysisBase.
            config_source (str or Path): see darsia.AnalysisBase.
            update_setup (bool): see darsia.AnalysisBase.

        """
        # Call constructor of TracerAnalysis
        super().__init__(baseline, config, update_setup)

        # Define the specific components - use external methods to allow for further tailoring.
        # The main philosophy is to first separate water from the rest, which here will be
        # simply called CO2. In the CO2 region, additional separation will be required to
        # separate CO2(g) from CO2 saturated water.

        # Yet, only proceed if the config contains required keywords.
        if "co2" in self.config.keys():
            # Define the concentration analysis
            self.co2_analysis = self.define_co2_analysis()

            # Safety check
            if not isinstance(self.co2_analysis, darsia.ConcentrationAnalysis):
                raise ValueError("co2_analysis has wrong type.")

            # Setup standard data including the cleaning filter
            co2_cleaning_filter = self.config["co2"].get(
                "cleaning_filter", "cache/cleaning_filter_co2.npy"
            )
            self._setup_concentration_analysis(
                self.co2_analysis,
                co2_cleaning_filter,
                baseline,
                update_setup,
            )
        else:
            warn("CO2 analysis not well-defined.")

        if "co2(g)" in self.config.keys():
            # Define the concentration analysis
            self.co2_gas_analysis = self.define_co2_gas_analysis()

            # Safety check
            if not isinstance(self.co2_gas_analysis, darsia.ConcentrationAnalysis):
                raise ValueError("co2_gas_analysis has wrong type.")

            # Setup standard data including the cleaning filter
            co2_gas_cleaning_filter = self.config["co2(g)"].get(
                "cleaning_filter", "cache/cleaning_filter_co2_gas.npy"
            )
            self._setup_concentration_analysis(
                self.co2_gas_analysis,
                co2_gas_cleaning_filter,
                baseline,
                update_setup,
            )
        else:
            warn("CO2(g) analysis not well-defined.")



    @abstractmethod
    def define_co2_analysis(self) -> darsia.ConcentrationAnalysis:
        """
        Empty method which should define self.co2_analysis of type
        darsia.ConcentrationAnalysis.

        """
        pass




    @abstractmethod
    def define_co2_gas_analysis(self) -> darsia.ConcentrationAnalysis:
        """
        Empty method which should define self.co2_gas_analysis of type
        darsia.ConcentrationAnalysis.

        """
        pass




    def determine_co2(self) -> darsia.Image:
        """
        Extract CO2 from currently loaded image, based on a reference image.

        Returns:
            darsia.Image: binary image of spatial CO2 distribution.
        """
        # Make a copy of the current image
        img = self.img.copy()

        # Extract binary concentration
        co2 = self.co2_analysis(img)

        return co2




    def determine_co2_gas(self) -> darsia.Image:
        """
        Extract CO2(g) from currently loaded image, based on a reference image.

        Returns:
            darsia.Image: binary image of spatial CO2(g) distribution.
        """
        # Make a copy of the current image
        img = self.img.copy()

        # Extract binary concentration
        co2 = self.co2_gas_analysis(img)

        return co2