```
>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>> from scipy import ndimage
```

# 1.6.11.4. Example of solution for the image processing exercise: unmolten grains in glass¶

Open the image file MV_HFV_012.jpg and display it. Browse through the keyword arguments in the docstring of

`imshow`

to display the image with the “right” orientation (origin in the bottom left corner, and not the upper left corner as for standard arrays).>>> dat = plt.imread('data/MV_HFV_012.jpg')

Crop the image to remove the lower panel with measure information.

>>> dat = dat[:-60]

Slightly filter the image with a median filter in order to refine its histogram. Check how the histogram changes.

>>> filtdat = ndimage.median_filter(dat, size=(7,7)) >>> hi_dat = np.histogram(dat, bins=np.arange(256)) >>> hi_filtdat = np.histogram(filtdat, bins=np.arange(256))

Using the histogram of the filtered image, determine thresholds that allow to define masks for sand pixels, glass pixels and bubble pixels. Other option (homework): write a function that determines automatically the thresholds from the minima of the histogram.

>>> void = filtdat <= 50 >>> sand = np.logical_and(filtdat > 50, filtdat <= 114) >>> glass = filtdat > 114

Display an image in which the three phases are colored with three different colors.

>>> phases = void.astype(np.int) + 2*glass.astype(np.int) + 3*sand.astype(np.int)

Use mathematical morphology to clean the different phases.

>>> sand_op = ndimage.binary_opening(sand, iterations=2)

Attribute labels to all bubbles and sand grains, and remove from the sand mask grains that are smaller than 10 pixels. To do so, use

`ndimage.sum`

or`np.bincount`

to compute the grain sizes.>>> sand_labels, sand_nb = ndimage.label(sand_op) >>> sand_areas = np.array(ndimage.sum(sand_op, sand_labels, np.arange(sand_labels.max()+1))) >>> mask = sand_areas > 100 >>> remove_small_sand = mask[sand_labels.ravel()].reshape(sand_labels.shape)

Compute the mean size of bubbles.

>>> bubbles_labels, bubbles_nb = ndimage.label(void) >>> bubbles_areas = np.bincount(bubbles_labels.ravel())[1:] >>> mean_bubble_size = bubbles_areas.mean() >>> median_bubble_size = np.median(bubbles_areas) >>> mean_bubble_size, median_bubble_size (1699.875, 65.0)