Finding and resizing pixel data from segmented images using skimage

Question

import matplotlib.pyplot as plt
import matplotlib.patches as mpatches

from skimage import data
from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label, regionprops
from skimage.morphology import closing, square
from skimage.color import label2rgb


image = data.coins()[50:-50, 50:-50]

# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(3))

# remove artifacts connected to image border
cleared = clear_border(bw)

# label image regions
label_image = label(cleared)
# to make the background transparent, pass the value of `bg_label`,
# and leave `bg_color` as `None` and `kind` as `overlay`
image_label_overlay = label2rgb(label_image, image=image, bg_label=0)

fig, ax = plt.subplots(figsize=(10, 6))
ax.imshow(image_label_overlay)

for region in regionprops(label_image):
    # take regions with large enough areas
    if region.area >= 100:
        # draw rectangle around segmented coins
        minr, minc, maxr, maxc = region.bbox
        rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
                                  fill=False, edgecolor='red', linewidth=2)
        ax.add_patch(rect)

ax.set_axis_off()
plt.tight_layout()
plt.show()

Hi all,

I am trying to use this code to segment, resize and load pixel data into an array. I think I should be using region.image though I am not sure how to resize it (all seperate images to the same size) and load all the separate images into one array. I am trying to get to the same data as the data in the MNIST data.

Thanks in advance for any help.

Answer 1

you can use resize method from skimage to resize your segment

from skimage.transform import resize

# initialize segments list
segments = []
for region in regionprops(label_image):
    # take regions with large enough areas
    if region.area >= 100:
        # draw rectangle around segmented coins
        minr, minc, maxr, maxc = region.bbox
        # crop the segment
        segment = image_label_overlay[minr:maxr,minc:maxc,:]
        # resize to 28x28 (MNIST is 28x28)
        segment = resize(segment, (28, 28))
        segments.append(segment)
# convert to numpy array
segments = np.array(segments)