Source code for ddd_pylib.labels_manip._labels_properties_operator

from ddd_pylib._base import MeasurementsOperator
from skimage.measure import regionprops
from tifffile import imread
import pandas as pd
import numpy as np
import xarray as xr





class LabelsPropertiesOperator(MeasurementsOperator):
    def __init__(self):
        super().__init__()
        self.secondary_image = None
        self.properties = []
        self.dataframe = None



    def getSecondaryImage(self):
        return self.secondary_image




    def setProperties(self, properties):
        self.properties = [] if properties is None else properties




    def getProperties(self):
        return self.properties




    def getDataFrame(self):
        return self.dataframe

    



    def setSecondaryImage(self, image):
        if not image is None:
            self.secondary_image = image


    def _measureLabel(self, image, secondary_image=None):
        region_props = regionprops(label_image=image.values, intensity_image=secondary_image)
        if self.properties != []:
            if "measure" in self.properties:
                measure = "volume" if "Z" in image.dims else "area"
            data = {}
            for prop in self.properties:
                if prop == "measure":
                    prop = measure
                data[prop] = []
            for key in self.properties:
                key1 = key
                if key=="measure":
                    key=measure
                    key1="area"
                for e in region_props:
                    data[key].append(getattr(e, key1, None))
            result = self._createDataFrame(data)
        else:
            result = self._createDataFrame(region_props)
        return result

    def _createDataFrame(self, array):
        self.dataframe = pd.DataFrame(data=array)
        return self.dataframe



    def getPrefix(self):
        return "DataFrameMeasure - "


    def _applyToFrame(self, frameData, t, nT):
        if self.secondary_image is None:
            image1 = frameData[0]
            return self._measureLabel(image1)
        else:
            image1, image2 = frameData
            return self._measureLabel(image1, image2)

    def _zipInputs(self):
        if self.secondary_image is None:
            return super()._zipInputs()
        else:
            imA = self.getMainImage()
            imB = self.getSecondaryImage()
            if "T" in imA.dims:
                return [
                    (imA.isel(T=t), imB.isel(T=t)) for t in range(self.getNTimePoints())
                ]
            else:
                return [(imA, imB)]