comparison overlay_images.py @ 6:2495f8b2aefd draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit c86a1b93cb7732f7331a981d13465653cc1a2790

5:002f7bad3e82

See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
"""

import argparse

import matplotlib.colors
import matplotlib.pyplot as plt
import numpy as np
import skimage.color
import skimage.io

import tifffile
from contours import ContourPaint


def read_im_gray(fn):
    img = skimage.io.imread(fn)
    nDims = len(img.shape)
    assert nDims in [2, 3], 'this tool only supports single 2D images'
    if nDims == 3 and img.shape[-1] in [3, 4]:
        img = skimage.color.rgb2gray(img)
    if len(img.shape) == 3:

    out_im[:, :, 1] = (im2 - vmin) * scal
    skimage.io.imsave(out_fn, out_im)  # output is RGB


def blending(im1_fn, im2_fn, out_fn, alpha=0.5):
    im1 = skimage.io.imread(im1_fn)
    im2 = skimage.io.imread(im2_fn)
    assert im1.shape == im2.shape, 'Two images should have the same dimension'
    out_im = (1 - alpha) * im1 + alpha * im2
    if len(im1.shape) > 3:
        tifffile.imwrite(out_fn, out_im.astype(im1.dtype), imagej=True)
    else:
        skimage.io.imsave(out_fn, out_im.astype(im1.dtype))  # format of output is the same as input


def seg_contour(im1_fn, im2_fn, out_fn, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'):
    img = skimage.io.imread(im1_fn)
    labels = skimage.io.imread(im2_fn)

    result = get_rgb8_copy(img)
    cp = ContourPaint(labels, linewidth, where='center')
    color_rgb = np.multiply(255, matplotlib.colors.to_rgb(color))

6:2495f8b2aefd

See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
"""

import argparse

import giatools.io
import matplotlib.colors
import matplotlib.pyplot as plt
import numpy as np
import skimage.color
import skimage.io

import tifffile
from contours import ContourPaint


def read_im_gray(fn):
    img = giatools.io.imread(fn)
    nDims = len(img.shape)
    assert nDims in [2, 3], 'this tool only supports single 2D images'
    if nDims == 3 and img.shape[-1] in [3, 4]:
        img = skimage.color.rgb2gray(img)
    if len(img.shape) == 3:

    out_im[:, :, 1] = (im2 - vmin) * scal
    skimage.io.imsave(out_fn, out_im)  # output is RGB


def blending(im1_fn, im2_fn, out_fn, alpha=0.5):
    im1 = giatools.io.imread(im1_fn)
    im2 = giatools.io.imread(im2_fn)
    assert im1.shape == im2.shape, 'Two images should have the same dimension'
    out_im = (1 - alpha) * im1 + alpha * im2
    if len(im1.shape) > 3:
        tifffile.imwrite(out_fn, out_im.astype(im1.dtype), imagej=True)
    else:
        skimage.io.imsave(out_fn, out_im.astype(im1.dtype))  # format of output is the same as input


def seg_contour(im1_fn, im2_fn, out_fn, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'):
    img = giatools.io.imread(im1_fn)
    labels = giatools.io.imread(im2_fn)

    result = get_rgb8_copy(img)
    cp = ContourPaint(labels, linewidth, where='center')
    color_rgb = np.multiply(255, matplotlib.colors.to_rgb(color))