def mask_on_image(mask, image):
from skimage.color import label2rgb
from skimage.color import color_dict, colorlabel
from skimage.segmentation import mark_boundaries
default_colors = [
"red",
"blue",
"yellow",
"magenta",
"green",
"indigo",
"darkorange",
"cyan",
"pink",
"yellowgreen",
]
mask = mask.squeeze().astype(int)
image = hi.image_as_uint8(image) / 255.0
labels = [l for l in np.unique(mask) if l < len(color_dict)]
colors = default_colors + list(color_dict.keys())[len(default_colors) :]
colors = np.array(colors)[labels]
image_label_overlay = label2rgb(
mask, image=f2l(image).squeeze().clip(0, 1), colors=colors, bg_label=0, bg_color=None, kind="overlay"
)
return mark_boundaries(image_label_overlay, mask)
def mask_on_image(mask, image):
from skimage.color import label2rgb
from skimage.color import color_dict, colorlabel
from skimage.segmentation import mark_boundaries
default_colors = ['red', 'blue', 'yellow', 'magenta', 'green',
'indigo', 'darkorange', 'cyan', 'pink', 'yellowgreen']
mask = mask.squeeze().astype(int)
image = hi.image_as_uint8(image) / 255.
labels = [l for l in np.unique(mask) if l < len(color_dict)]
colors = (default_colors + list(color_dict.keys())[len(default_colors):])
colors = np.array(colors)[labels]
image_label_overlay = label2rgb(mask, image=f2l(image).squeeze().clip(0,1),
colors=colors, bg_label=0, bg_color=None, kind='overlay')
return mark_boundaries(image_label_overlay, mask)
import imghdr
from collections import namedtuple
import numpy as np
from skimage import io
from skimage import img_as_ubyte
from skimage.transform import resize
from skimage.color import color_dict
import six
# Convert colors from `skimage.color` to uint8 and allow access through
# dict or a named tuple.
color_dict = dict((name, tuple(int(255 * c + 0.5) for c in rgb))
for name, rgb in six.iteritems(color_dict))
colors = namedtuple('colors', color_dict.keys())(**color_dict)
def open(path):
"""Return Picture object from the given image path."""
return Picture(path=os.path.abspath(path))
def _verify_picture_index(index):
"""Raise error if picture index is not a 2D index/slice."""
if not (isinstance(index, tuple) and len(index) == 2):
raise IndexError("Expected 2D index but got {!r}".format(index))
if all(isinstance(i, int) for i in index):
return index
import os
import imghdr
from collections import namedtuple
import numpy as np
from skimage import io
from skimage import img_as_ubyte
from skimage.transform import resize
from skimage.color import color_dict
from skimage._shared import six
# Convert colors from `skimage.color` to uint8 and allow access through
# dict or a named tuple.
color_dict = dict((name, tuple(int(255 * c + 0.5) for c in rgb)) for name, rgb in six.iteritems(color_dict))
colors = namedtuple("colors", color_dict.keys())(**color_dict)
def open(path):
"""Return Picture object from the given image path."""
return Picture(path=os.path.abspath(path))
def _verify_picture_index(index):
"""Raise error if picture index is not a 2D index/slice."""
if not (isinstance(index, tuple) and len(index) == 2):
raise IndexError("Expected 2D index but got {!r}".format(index))
if all(isinstance(i, int) for i in index):
return index