Source code for pyfibre.core.base_multi_image_analyser

from abc import abstractmethod
import os

from traits.api import ABCHasTraits, Instance, provides

from .i_multi_image import IMultiImage
from .i_multi_image_analyser import IMultiImageAnalyser


@provides(IMultiImageAnalyser)
class BaseMultiImageAnalyser(ABCHasTraits):
    """Class that provides analysis instructions for a particular
    BaseMultiImage class"""

    #: Reference to multi image under analysis
    multi_image = Instance(IMultiImage)

    database_names = []

    @abstractmethod
    def image_analysis(self, *args, **kwargs):
        """Perform analysis on data"""

    @abstractmethod
    def create_metrics(self, *args, **kwargs):
        """Create metrics from multi-image components that can be
        generated upon end of analysis"""

    @abstractmethod
    def create_figures(self, *args, **kwargs):
        """Create figures from multi-image components that can be
        generated upon end of analysis"""

    @abstractmethod
    def save_databases(self, databases):
        """Save databases that have been generated by the analysis

        Parameters
        ----------
         databases: list(pd.DataFrame)
            List of pandas dataframes generated by the analysis
        """

    @abstractmethod
    def load_databases(self):
        """Loads and returns databases that have been generated by
         the analysis

         Returns
         -------
         databases: list(pd.DataFrame)
            List of pandas dataframes generated by the analysis
         """

    @property
    def analysis_path(self):
        """Identifies folder that will be used to store analysis
        files"""
        return os.path.join(
            self.multi_image.path,
            '-'.join([self.multi_image.name, 'pyfibre', 'analysis'])
        )

    def make_directories(self):
        """Creates required directories for analysis"""
        if not os.path.exists(self.analysis_path):
            os.mkdir(self.analysis_path)