.. _Measurements_page:

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Measurements as performed in python

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Amount of Tissue

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.. code-block:: python

    def QuantCore(self, image, filename, save=False):

        image = gaussian(rgb2gray(image), sigma=2)

        thresh = threshold_triangle(image[image > 0])

        binary = np.logical_and(image < thresh, image > 0)

        wholeCore = np.sum(binary)

        if save:

            self.info.emit("Saving - " + filename + '_core.tiff')

            imagesave = Image.fromarray(binary)

            imagesave.save(self.inputpath+os.sep+filename + '_core.tiff')

        return wholeCore

Amount of Signal

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.. code-block:: python

    def QuantStain(self, image, filename, save=False):

        img_hsv = rgb2hsv(image)

        img_hue = img_hsv[:, :, 0]

        image_sat = img_hsv[:, :, 1]

        hue = np.logical_and(img_hue > 0.02, img_hue < 0.10)  # BROWN PIXELS BETWEEN 0.02 and 0.10

        if self.threshold:

            stain = np.logical_and(hue, image_sat > self.threshold)  # USER DEFINED MINIMUM SATURATION THRESHOLD

        else:

            print("Defult threshold")

            stain = np.logical_and(hue, image_sat > 0.79)  #  DEFAULT SATURATION THRESHOLD APPLIED IF NO USER INPUT

        self.current_image = stain[::10, ::10].astype(float)  # SHOW A LOW RESOLUTION MASK AS A FIGURE

        self.figures.emit()

        if save:

            self.info.emit("Saving - " + filename+'_stain.tiff')  # SAVE A FIGURE IF REQUIRED

            imagesave = Image.fromarray(stain)

            imagesave.save(self.inputpath+os.sep+filename+'_stain.tiff')

        stint = np.copy(image)

        stint = exposure.rescale_intensity(stint, out_range=(0, 255))

        stint[stain == 0] = 0  # array with only the stained pixels

        stint = color.rgb2gray(stint) # convert to greyscale

        stint = np.ravel(stint) # flatten image array

        stint = stint[stint != 0] # remove all zeros

        stint_mean = stint.mean()

        stint_std = stint.std()

        stained = np.sum(stain)

        return stained, stint_mean, stint_std