import skimage

skimage.__version__

from matplotlib import pyplot as plt

import numpy as np

bright_raw = plt.imread('Pos60051.png')

plt.imshow(bright_raw)

bright_raw.dtype

bright_raw.shape

from skimage.filter import gaussian_filter

bright_blurred = gaussian_filter(bright_raw, sigma=30)

plt.imshow(bright_blurred)

np.max(bright_blurred)

np.max(bright_raw)

# skimage.filter.

from skimage.morphology import label

# Threshold
bright_regions = bright_blurred > 0.12

bright_regions.dtype

np.unique(bright_regions[:, :, 2])
# Only G channel contains data

label_regions = label(bright_regions[:, :, 1], neighbors=4, background=0)

label_regions.dtype

# Number of labels
np.unique(label_regions)
# or, simply,
np.max(label_regions)
# + 1

# plt.imshow(label_regions)
plt.colorbar(plt.imshow(label_regions))

from skimage import measure

intensity_regions = measure.regionprops(label_regions, ['MeanIntensity'], intensity_image=bright_raw[:, :, 1])

len(intensity_regions)

coord_regions = measure.regionprops(label_regions, ['coords'], intensity_image=bright_raw[:, :, 1])

coord_regions[0]['coords']

np.where(label_regions==0)

for i in xrange(len(intensity_regions)):
    print(intensity_regions[i]['MeanIntensity'])

from skimage.feature import match_template

np.where(label_regions==4)

region_4 = bright_raw[720:780, 780:840]

plt.imshow(region_4)

region_matching = match_template(bright_raw[:, :, 1], region_4[:, :, 1])

plt.imshow(region_matching)

plt.gray()

plt.imshow(region_matching)

plt.imshow(plt.imread('longtime_z006.png'))
plt.axis('off')