Hi Jean-Patrick,

Y is the known corresponding digit identity. The function to "jitter" the digit images around a bit just takes digits.target as Y and concatenates it with itself five times, so the expanded dataset has known identities to compare against.

Regards,
Josh

On Wednesday, February 25, 2015 at 7:09:39 AM UTC-6, Jean-Patrick Pommier wrote:

Regarding the rbm classifier in the following example. At first sight I don't understand what is Y array (X array seems to be the set of images).

Jean-Patrick

Le mardi 24 février 2015 17:21:10 UTC+1, Jean-Patrick Pommier a écrit :

Dear All,

I am trying to make pairs of images from the following set of images (chromosomes sorted by size after rotation). The idea is to make a feature vector for unsupervised classification (kmeans with 19 clusters)

From each chromosome an integral image was calculated:

plt.figure(figsize = (15,15))
gs1 = gridspec.GridSpec(6,8)
gs1.update(wspace=0.0, hspace=0.0) # set the spacing between axes.
for i in range(38):
# i = i + 1 # grid spec indexes from 0
ax1 = plt.subplot(gs1[i])
plt.axis('off')
ax1.set_xticklabels([])
ax1.set_yticklabels([])
ax1.set_aspect('equal')
image = sk.transform.integral_image(reallysorted[i][:,:,2])
imshow(image , interpolation='nearest')

Then each integral image was flatten and combined with the others:

Features =[]

for i in range(38):
Feat = np.ndarray.flatten(sk.transform.integral_image(reallysorted[i][:,:,2]))
Features.append(Feat)
X = np.asarray(Features)
print X.shape

The X array contains 38 lines and 9718 features, which is not good. However, I trried to submit these raw features to kmeans classification with sklearn using a direct example :

from sklearn.neighbors import NearestNeighbors
nbrs = NearestNeighbors(n_neighbors=19, algorithm='ball_tree').fit(X)
distances, indices = nbrs.kneighbors(X)
connection = nbrs.kneighbors_graph(X).toarray()
Ploting the connection graph shows that a chromosomes is similar to more than one ...
• Do you think that integral images can be used to discriminate the chromosomes pairs?
• If so, how to reduce the number of features to 10~20? (to get a better discrimination)