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import tiffIO as tIO
import mouseVis as mv
import matplotlib.pyplot as plt
import numpy as np
import cv2

%matplotlib notebook

data = tIO.unzipChannels(tIO.loadTiff('SEP-GluA1-KI_tp1.tif'))
data2 = tIO.unzipChannels(tIO.loadTiff('SEP-GluA1-KI_tp2.tif'))
data3 = tIO.unzipChannels(tIO.loadTiff('SEP-GluA1-KI_tp3.tif'))


    

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mv.generateMultiVoxHist([data[0], data2[0], data3[0]], 'Intensity of Voxels on Chan 0 at Times 0, .25, and 24 Hours', bins=50, normed=True, xTitle='Pixel Integer Intensity', yTitle='Ratio of Image Space')
plt.show()


    

In [8]:

    

mv.generateMultiVoxHist([data[1], data2[1], data3[1]], 'Intensity of Voxels on Chan 1 at Times 0, .25, and 24 Hours', bins=50, normed=True, xTitle='Pixel Integer Intensity', yTitle='Ratio of Image Space')
plt.show()


    

In [14]:

    

testImg = data[0][0]
threshedImage = data[0][0].copy(0)
for rowInd in xrange(testImg.shape[0]):
    for colInd in xrange(testImg.shape[1]):
        if testImg[rowInd][colInd] < 21000:
            threshedImage[rowInd][colInd] = 0
            
#For some reason, this is coming up as 
#colored and not black and white through matplotlib

plt.figure()
plt.imshow(testImg)
plt.figure()
plt.imshow(threshedImage)
plt.show()


    

    




/usr/local/lib/python2.7/dist-packages/ipykernel/__main__.py:2: DeprecationWarning: Non-string object detected for the array ordering. Please pass in 'C', 'F', 'A', or 'K' instead
  from ipykernel import kernelapp as app






    















    












    















    

In [3]:

    

plt.figure()
mv.generateMultiVoxHist([data[0][0], data2[0][0], data3[0][0]], 'Intensity for Image 0 on Chan 0', 3, 50, normed=True, xTitle='Pixel Integer Intensity', yTitle='Percent of Image Area')
plt.show()


    

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