"""Annotate the segmented tissue."""

import skimage.draw

from jicbioimage.core.transform import transformation
from jicbioimage.illustrate import AnnotatedImage
from jicbioimage.core.util.color import pretty_color

from util import argparse_get_image
from segment import segment
from transform import rotate


def annotate_segmentation(image, segmentation):
    """Return annotated segmentation."""
    annotation = AnnotatedImage.from_grayscale(image)
    for i in segmentation.identifiers:
        region = segmentation.region_by_identifier(i)
        color = pretty_color()
        annotation.mask_region(region.border.dilate(), color)

    props = skimage.measure.regionprops(segmentation)

    for p in props:

        try:
            minr, minc, maxr, maxc = p.bbox
            cval = int(p.centroid[1])
            line = skimage.draw.line(minr, cval, maxr, cval)
            annotation.mask_region(line, (0, 255, 0))
        except IndexError:
            # Don't draw line if it falls outside of the image.
            pass

    return annotation


@transformation
def annotate(image):
    """Return annotated image."""
    segmentation, angle = segment(image)

    image = rotate(image, angle)
    return annotate_segmentation(image, segmentation)


def main():
    image = argparse_get_image()
    a = annotate(image)
    with open("annotated.png", "wb") as fh:
        fh.write(a.png())


if __name__ == "__main__":
    main()

452e921791a650441791389355f7712c504b35af
<mask token>


@transformation
def annotate(image):
    """Return annotated image."""
    segmentation, angle = segment(image)
    image = rotate(image, angle)
    return annotate_segmentation(image, segmentation)


<mask token>

<mask token>


def annotate_segmentation(image, segmentation):
    """Return annotated segmentation."""
    annotation = AnnotatedImage.from_grayscale(image)
    for i in segmentation.identifiers:
        region = segmentation.region_by_identifier(i)
        color = pretty_color()
        annotation.mask_region(region.border.dilate(), color)
    props = skimage.measure.regionprops(segmentation)
    for p in props:
        try:
            minr, minc, maxr, maxc = p.bbox
            cval = int(p.centroid[1])
            line = skimage.draw.line(minr, cval, maxr, cval)
            annotation.mask_region(line, (0, 255, 0))
        except IndexError:
            pass
    return annotation


@transformation
def annotate(image):
    """Return annotated image."""
    segmentation, angle = segment(image)
    image = rotate(image, angle)
    return annotate_segmentation(image, segmentation)


def main():
    image = argparse_get_image()
    a = annotate(image)
    with open('annotated.png', 'wb') as fh:
        fh.write(a.png())


<mask token>

<mask token>


def annotate_segmentation(image, segmentation):
    """Return annotated segmentation."""
    annotation = AnnotatedImage.from_grayscale(image)
    for i in segmentation.identifiers:
        region = segmentation.region_by_identifier(i)
        color = pretty_color()
        annotation.mask_region(region.border.dilate(), color)
    props = skimage.measure.regionprops(segmentation)
    for p in props:
        try:
            minr, minc, maxr, maxc = p.bbox
            cval = int(p.centroid[1])
            line = skimage.draw.line(minr, cval, maxr, cval)
            annotation.mask_region(line, (0, 255, 0))
        except IndexError:
            pass
    return annotation


@transformation
def annotate(image):
    """Return annotated image."""
    segmentation, angle = segment(image)
    image = rotate(image, angle)
    return annotate_segmentation(image, segmentation)


def main():
    image = argparse_get_image()
    a = annotate(image)
    with open('annotated.png', 'wb') as fh:
        fh.write(a.png())


if __name__ == '__main__':
    main()

<mask token>
import skimage.draw
from jicbioimage.core.transform import transformation
from jicbioimage.illustrate import AnnotatedImage
from jicbioimage.core.util.color import pretty_color
from util import argparse_get_image
from segment import segment
from transform import rotate


def annotate_segmentation(image, segmentation):
    """Return annotated segmentation."""
    annotation = AnnotatedImage.from_grayscale(image)
    for i in segmentation.identifiers:
        region = segmentation.region_by_identifier(i)
        color = pretty_color()
        annotation.mask_region(region.border.dilate(), color)
    props = skimage.measure.regionprops(segmentation)
    for p in props:
        try:
            minr, minc, maxr, maxc = p.bbox
            cval = int(p.centroid[1])
            line = skimage.draw.line(minr, cval, maxr, cval)
            annotation.mask_region(line, (0, 255, 0))
        except IndexError:
            pass
    return annotation


@transformation
def annotate(image):
    """Return annotated image."""
    segmentation, angle = segment(image)
    image = rotate(image, angle)
    return annotate_segmentation(image, segmentation)


def main():
    image = argparse_get_image()
    a = annotate(image)
    with open('annotated.png', 'wb') as fh:
        fh.write(a.png())


if __name__ == '__main__':
    main()

"""Annotate the segmented tissue."""

import skimage.draw

from jicbioimage.core.transform import transformation
from jicbioimage.illustrate import AnnotatedImage
from jicbioimage.core.util.color import pretty_color

from util import argparse_get_image
from segment import segment
from transform import rotate


def annotate_segmentation(image, segmentation):
    """Return annotated segmentation."""
    annotation = AnnotatedImage.from_grayscale(image)
    for i in segmentation.identifiers:
        region = segmentation.region_by_identifier(i)
        color = pretty_color()
        annotation.mask_region(region.border.dilate(), color)

    props = skimage.measure.regionprops(segmentation)

    for p in props:

        try:
            minr, minc, maxr, maxc = p.bbox
            cval = int(p.centroid[1])
            line = skimage.draw.line(minr, cval, maxr, cval)
            annotation.mask_region(line, (0, 255, 0))
        except IndexError:
            # Don't draw line if it falls outside of the image.
            pass

    return annotation


@transformation
def annotate(image):
    """Return annotated image."""
    segmentation, angle = segment(image)

    image = rotate(image, angle)
    return annotate_segmentation(image, segmentation)


def main():
    image = argparse_get_image()
    a = annotate(image)
    with open("annotated.png", "wb") as fh:
        fh.write(a.png())


if __name__ == "__main__":
    main()
