From b1007f019675621a372066433b2a374e62c3b1b1 Mon Sep 17 00:00:00 2001
From: Tony S Yu <tsyu80@gmail.com>
Date: Sun, 19 Aug 2012 17:46:22 -0400
Subject: [PATCH] ENH: Add regional maxima example

---
 doc/examples/plot_regional_maxima.py | 113 +++++++++++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 doc/examples/plot_regional_maxima.py

diff --git a/doc/examples/plot_regional_maxima.py b/doc/examples/plot_regional_maxima.py
new file mode 100644
index 00000000..9d4de9b1
--- /dev/null
+++ b/doc/examples/plot_regional_maxima.py
@@ -0,0 +1,113 @@
+"""
+=========================
+Filtering regional maxima
+=========================
+
+Here, we use morphological reconstruction to create a background image, which
+we can subtract from the original image to isolate bright features (regional
+maxima).
+
+First we try reconstruction by dilation starting at the edges of the image. We
+initialize a seed image to the minimum intensity of the image, and set its
+border to be the pixel values in the original image. These maximal pixels will
+get dilated in order to reconstruct the background image.
+"""
+import numpy as np
+
+from skimage import data
+from skimage import img_as_float
+from skimage.morphology import reconstruction
+from scipy.ndimage import gaussian_filter
+import matplotlib.pyplot as plt
+
+# Convert to float: Important for subtraction later which won't work with uint8
+image = img_as_float(data.coins())
+image = gaussian_filter(image, 1)
+
+seed = np.copy(image)
+seed[1:-1, 1:-1] = image.min()
+mask = image
+
+dilated = reconstruction(seed, mask, method='dilation')
+
+"""
+Subtracting the dilated image leaves an image with just the coins and a flat,
+black background, as shown below.
+"""
+
+fig, (ax1, ax2, ax3) = plt.subplots(ncols=3, figsize=(8, 2.5))
+
+ax1.imshow(image)
+ax1.set_title('original image')
+ax1.axis('off')
+
+ax2.imshow(dilated, vmin=image.min(), vmax=image.max())
+ax2.set_title('dilated')
+ax2.axis('off')
+
+ax3.imshow(image - dilated)
+ax3.set_title('image - dilated')
+ax3.axis('off')
+
+plt.tight_layout()
+
+"""
+
+.. image:: PLOT2RST.current_figure
+
+Although the features (i.e. the coins) are clearly isolated, the coins
+surrounded by a bright background in the original image are dimmer in the
+subtracted image. We can attempt to correct this using a different seed image.
+
+Instead of creating a seed image with maxima along the image border, we can use
+the features of the image itself to seed the reconstruction process. Here, the
+seed image is the original image minus a fixed value, ``h``.
+"""
+
+h = 0.4
+seed = image - h
+dilated = reconstruction(seed, mask, method='dilation')
+hdome = image - dilated
+
+"""
+To get a feel for the reconstruction process, we plot the intensity of the
+mask, seed, and dilated images along a slice of the image (indicated by red
+line).
+"""
+
+fig, (ax1, ax2, ax3) = plt.subplots(ncols=3, figsize=(8, 2.5))
+
+yslice = 197
+
+ax1.plot(mask[yslice], '0.5', label='mask')
+ax1.plot(seed[yslice], 'k', label='seed')
+ax1.plot(dilated[yslice], 'r', label='dilated')
+ax1.set_ylim(-0.2, 2)
+ax1.set_title('image slice')
+ax1.set_xticks([])
+ax1.legend()
+
+ax2.imshow(dilated, vmin=image.min(), vmax=image.max())
+ax2.axhline(yslice, color='r', alpha=0.4)
+ax2.set_title('dilated')
+ax2.axis('off')
+
+ax3.imshow(hdome)
+ax3.axhline(yslice, color='r', alpha=0.4)
+ax3.set_title('image - dilated')
+ax3.axis('off')
+
+plt.tight_layout()
+plt.show()
+
+"""
+.. image:: PLOT2RST.current_figure
+
+As you can see in the image slice, each coin is given a different baseline
+intensity in the reconstructed image; this is because we used the local
+intensity (shifted by ``h``) as a seed value. As a result, the coins in the
+subtracted image have similar pixel intensities. The final result is known as
+the h-dome of an image since this tends to isolate regional maxima of height
+``h``. This operation is particularly useful when your images are unevenly
+illuminated.
+"""