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%matplotlib inline
import os
import numpy as np
from matplotlib import pyplot as plt
import mpld3
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import neuralyzer
from neuralyzer.im import smff
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plt.rcParams['image.cmap'] = 'gray'
plt.rcParams['image.interpolation'] = 'none'
plt.rcParams['figure.figsize'] = (8,8)
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#datafile = '/Users/michael/coding/RIKEN/data/140316/data5/data2/Image_0001_0001_channel0_13000_14000.tif'
#datafile = '/home/michael/datac/140316/data5/data2/Image_0001_0001_channel0.tif'
datafile = '/home/michael/datac/140316/data5/data2/Image_0001_0001_channel1_testdata.tif'
data = neuralyzer.get_data(datafile)
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print data.dtype
print data.shape
print data[0].shape
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mean = data.mean(axis=0)
# creating a white stripe of 20 pixels width along the first axis!!
mean[:,:20] = mean.max()
plt.imshow(mean)
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datashape = data.shape
data = data.reshape((data.shape[0], data.shape[1]*data.shape[2])).T
data.shape
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# image at timepoint 0
plt.imshow(data[:,0].reshape((256, 256)))
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