input.py

# Copyright CNRS/Inria/UNS
# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
#
# eric.debreuve@cnrs.fr
#
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# "http://www.cecill.info".
#
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from brick.general.type import array_t
import numpy as np_
import math as mt_
import sys as sy_
from PIL import Image
from PIL.ExifTags import TAGS
import re

size_voxel_in_micron = None


def ImageVerification(image: array_t, channel: str) -> array_t:
    #
    # The image must not be constant
    if image.max() == image.min():
        raise ValueError('The input image should not be constant.')

    # Verification of the dimension of the image and its coherence with the parameters (channel)
    elif image.ndim == 3:
        print('The image has only one color channel.')
        if channel is not None:
            raise ValueError('The image has only 3 dimensions. However, a value for the "channel" parameter is '
                             'specified. Give the channel the value None')

    elif image.ndim == 4:
        if channel == 'R' or channel == 'G' or channel == 'B':
            # not changed into if --channel in 'RGB'-- because if channel='RG' => True.
            print('The image has multiple color channels. The channel', channel,
                  'is specified in the parameters.')
            image = image[:, :, :, 'RGB'.find(channel)]

            # The obtained image must not be constant
            if image.max() == image.min():
                raise ValueError('The input image should not be constant.')

            return image

        else:
            raise ValueError('The image has multiple color channels. Error in the value of the parameter channel.')

    elif image.ndim != 4 and image.ndim != 3:
        raise ValueError(f'The image dimensions are not correct: {image.ndim}, instead of 3 or 4.')


def NormalizedImage(image: array_t) -> array_t:
    #
    print(
        "This normalization does not bring anything; BUT IT CHANGES THE NB OF EXT DETECTED BY FRANGI - left as is for "
        "now to avoid the need for changing prms "
    )
    nonextreme_values = image[np_.logical_and(image > 0.0, image < image.max())]

    if nonextreme_values.size > 0:
        nonextreme_avg = nonextreme_values.mean()
        result = image.astype(np_.float32) / nonextreme_avg
    else:
        result = image.astype(np_.float32)

    return result


def IntensityNormalizedImage(image: array_t) -> array_t:
    '''
    Relative normalization of the image between 0 and 1.
    No division per 0 since the image should not be constant (ImageVerification function).
    '''
    #
    print('Relative Intensity Normalization between 0 and 1. Need to reevaluate the parameters !!! IS NOT SUPPORTED '
          'BY THE FRANGI ALGO')

    value_max = image.max()
    value_min = image.min()

    result = (image.astype(np_.float32) - value_min) / float(value_max - value_min)

    return result

    # print(
    #     "This normalization does not bring anything; left as is for now to avoid the need for changing prms"
    # )
    # nonextreme_values = image[np_.logical_and(image > 0.0, image < image.max())]
    #
    # if nonextreme_values.size > 0:
    #     nonextreme_avg = nonextreme_values.mean()
    #     result = image.astype(np_.float32) / nonextreme_avg
    # else:
    #     result = image.astype(np_.float32)
    #
    # return result


def FindVoxelDimensionInMicron(data_path: str) -> array_t:
    #
    if size_voxel_in_micron is not None:
        return np_.array(size_voxel_in_micron)

    else:
        print('/!\ The size of a voxel is not specified in the parameters.')

        try:
            with Image.open(data_path) as img:  # Find the voxels dimensions in micron in the metadata.
                meta_dict = {TAGS.get(key, 'missing'): img.tag[key] for key in
                             img.tag}  # Use the exif tags into the image metadata

            # Decode the tags text
            metadata = meta_dict['missing'].decode('utf8')  # Decode the tags text
            metadata = metadata.replace('\x00', '')

            voxel_size = []  # Initialize the list of voxel size in str
            for axe in 'XYZ':
                pattern = 'Voxel' + axe + '.+\= (\d.+E.\d.)'  # Regular expression
                voxel_size.append(re.findall(pattern, metadata)[0])

            voxel_size = np_.array(list(map(float, voxel_size)))
            voxel_size_micron = 1.0e6 * voxel_size  # Conversion meters in micron
            print('VOXEL DIM: [X Y Z] =', voxel_size_micron, 'micron.')
            return voxel_size_micron

        except:
            print('/!\ Unable to find the voxel dimensions in micron in the metadata. Please specify it in the parameters.')


def ToPixel(micron: float, voxel_size_micron: array_t, dimension: tuple = (0,)) -> int:
    '''
    Dimension correspond to the axis (X,Y,Z) = (0,1,2). Can be used for distance, area and volumes.
    '''
    # Conversion of pixels into micron.
    return round(micron/(mt_.prod(voxel_size_micron[axis] for axis in dimension)))


def ToMicron(pixel: int, voxel_size_micron: array_t, dimension: tuple = (0,)) -> float:
    '''
    Dimension correspond to the axis (X,Y,Z) = (0,1,2). Can be used for distance, area and volumes.
    '''
    # May not be used. if not used, delete.
    # Conversion of micron into pixels.
    return float(pixel * (mt_.prod(voxel_size_micron[axis] for axis in dimension)))


def DijkstraCosts(image: array_t, som_map: array_t, ext_map: array_t) -> array_t:
    #
    # TODO: Ideally, the extension part should be dilated
    # but in ext-ext connections, there must not be dilation around the current or the other exts
    # (current ext plays the role of a soma in soma-ext step)
    #
    dijkstra_costs = 1.0 / (image + 1.0)
    dijkstra_costs[np_.logical_or(som_map > 0, ext_map > 0)] = np_.inf

    return dijkstra_costs