input.py

# Copyright CNRS/Inria/UNS
# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
#
# eric.debreuve@cnrs.fr
#
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# modify and/ or redistribute the software under the terms of the CeCILL
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# "http://www.cecill.info".
#
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from brick.general.type import array_t
import numpy as np_
import sys as sy_
from PIL import Image
from PIL.ExifTags import TAGS


def ImageVerification(image: array_t, channel: str) -> array_t:
    if image.ndim == 3:
        print('Your image has only one color channel.')
        if channel == 'RGB':
            print('"RGB" channels are specified in the parameters. The image dimensions are not correct:', image.ndim,
                  ', instead of 4.')
            sy_.exit(0)

    elif image.ndim == 4:
        if channel == 'R' or channel == 'G' or channel == 'B':
            print('The image has multiple color channels. The channel', channel,
                  'is specified in the parameters.')
            for idx, color in enumerate('RGB'):
                if channel == color:
                    image = image[:, :, :, idx]
            return image
        elif channel == 'RGB':
            print('"RGB" channels are specified in the parameters. The program does not handle multiple channels for '
                  'now.')
            sy_.exit(0)

    elif image.ndim != 4 and image.ndim != 3:
        print('The image dimensions are not correct:', image.ndim, ', instead of 3 or 4.')
        sy_.exit(0)


# if channel != 'RGB' and image.ndim == 4:
#     print('The image has multiple color channels. The channel', channel, 'was specified in the parameters.')
#     for idx, color in enumerate('RGB'):
#         if channel == color:
#             image = image[:, :, :, idx]
# elif channel == 'RGB' and image.ndim == 3:
#     print('WARNING. The 3 RGB color channels were selected in the parameters but the image has only one channel.')


def IntensityNormalizedImage(image: array_t) -> array_t:
    #
    print(
        'Relative Intensity Normalization between 0 and 1 (Not a standardization). Need to reevaluate the parameters !!!')

    value_max = image.astype(np_.float32).max()
    value_min = image.astype(np_.float32).min()

    result = (image.astype(np_.float32) - value_min) / (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 VoxelDimensionInMicrons(data_path: str) -> array_t:
    # TODO Verify if metadata are in the same format for all the images - if not, add a raise error ?

    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 idaxe, axe in enumerate('XYZ'):
        idvox = metadata.find('dblVoxel' + axe)  # Get the index of the voxel size for the axe X, Y, Z
        idvox += 15
        while metadata[idvox] != '\n':
            voxel_size[idaxe] += metadata[idvox]
            idvox += 1
    voxel_size = np_.asarray(list(map(float, voxel_size)))
    voxel_size_microns = 1.0e6 * voxel_size
    print('Voxel dimension in the image is [X Y Z] =', voxel_size_microns, 'in microns. WARNING this method highly '
                                                                           'depends on the format of the metadata.')

    return voxel_size_microns


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