stackoverflow_challenges.ipynb

Kernel: Python 3

StackOverflow Problems

Real-world problems to test your skills on!

%matplotlib inline

import matplotlib.pyplot as plt
import numpy as np
from skimage import (filters, io, color, exposure, feature,
                     segmentation, morphology, img_as_float)

Parameters of a pill

(Based on StackOverflow http://stackoverflow.com/questions/28281742/fitting-a-circle-to-a-binary-image)

Consider a pill from the [NLM Pill Image Recognition Pilot](http://pir.nlm.nih.gov/pilot/instructions.html) (``../images/round_pill.jpg``). Fit a circle to the pill outline and compute its area.

Hints:

1. Equalize (exposure.equalize_*)

2. Detect edges (filter.canny or feature.canny--depending on your version)

3. Fit the CircleModel using measure.ransac.

Alternative: morphological snakes

NOTE: this is expensive to compute, so may take a while to execute

# Initial level set
pill = color.rgb2gray(image)
pill = restoration.denoise_nl_means(pill, multichannel=False)

level_set = segmentation.circle_level_set(pill.shape, radius=200)
ls = segmentation.morphological_chan_vese(pill, 80, init_level_set=level_set, smoothing=3)

fig, ax = plt.subplots(1, 1, figsize=(8, 8))

ax.imshow(pill, cmap="gray")
ax.set_axis_off()
ax.contour(ls, [0.5], colors='r');

Counting coins

Based on StackOverflow http://stackoverflow.com/questions/28242274/count-number-of-objects-using-watershed-algorithm-scikit-image

Consider the coins image from the scikit-image example dataset, shown below. Write a function to count the number of coins.

The procedure outlined here is a bit simpler than in the notebook lecture (and works just fine!)

Hint:

1. Equalize

2. Threshold (filters.threshold_otsu)

3. Remove objects touching boundary (segmentation.clear_border)

4. Apply morphological closing (morphology.closing)

5. Remove small objects (measure.regionprops)

6. Visualize (potentially using color.label2rgb)

from skimage import data
fig, ax = plt.subplots()
ax.imshow(data.coins(), cmap='gray');

Snakes

Based on https://stackoverflow.com/q/8686926/214686

Consider the zig-zaggy snakes on the left (../images/snakes.png).
Write some code to find the begin- and end-points of each.

Hints:

1. Threshold the image to turn it into "black and white"

2. Not all lines are a single pixel thick. Use skeletonization to thin them out (morphology.skeletonize)

3. Locate all snake endpoints (I used a combination of scipy.signal.convolve2d [find all points with only one neighbor], and np.logical_and [which of those points lie on the snake?] to do that, but there are many other ways).

M&Ms

How many blue M&Ms are there in this image (../images/mm.jpg)?

Steps:

1. Denoise the image (using, e.g., restoration.denoise_nl_means)

2. Calculate how far each pixel is away from pure blue

3. Segment this distance map to give a "pill mask"

4. Fill in any holes in that mask, using scipy.ndimage.binary_fill_holes

5. Use watershed segmentation to split apart any M&Ms that were joined, as described in http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_watershed.html

Alternative approach:

• http://scikit-image.org/docs/dev/user_guide/tutorial_segmentation.html

Viscous fingers

Based on StackOverflow: http://stackoverflow.com/questions/23121416/long-boundary-detection-in-a-noisy-image

Consider the fluid experiment on the right (../images/fingers.png). Determine any kind of meaningful boundary in this noisy image.

Hints:

1. Convert to grayscale

2. Try edge detection (feature.canny)

3. If edge detection fails, denoising is needed (try restoration.denoise_tv_bregman)

4. Try edge detection (feature.canny)