fatVolumeEstimationTest.py

import nrrd

fakeData = np.zeros((320, 260, 215), dtype=np.uint8)
fakeData[100:200, 200:300, 50:64] = 255

nrrd.write('test1.nrrd', fakeData)

# This should be L5 which for Subject0001_Final has a L5 at 50 and L4 is at 64, so that means 50-63 should be L5. (64 means where to stop in numpy array)
# Since this is a cube, trapezoidal integration should just yield the same values in between because nothing changes
# So, square area for each slice should be area = (200 - 100) * (300 - 200) * 1.40625^2 = 19775.390625mm^2
# volume = area * (64 - 50) * 3 (interpolation) = 830566.40625 mm^3
# So, you should have 39 slices of areas (trapArea variable) equal to 19775 for each one. Add those up and get the volume part.




fakeData = np.zeros((320, 260, 215), dtype=np.uint8)
fakeData[100:200, 200:300, 104:115:2] = 255

nrrd.write('test2.nrrd', fakeData)

# Same as example above but for L1 now and we only have the cube every OTHER slice. So 104, 106, 108, 110, 112, 114
# This will change the interpolation and test what you have there
# So there is a constant value at each slice that is a square, but the value is different. So here is what it looks like before
# interpolation. Assume that you scale the 255 to 1 again, which I think you do.
# 104 105 106 107 108 109 110 111 112 113 114
# 1   0   1   0   1   0   1   0   1   0   1

# Already, so interpolating by 3 means adding two space in between first.
# 104        105         106         107         108         109         110         111         112         113         114
#  1 2/3 1/3  0 1/3 2/3   1 2/3 1/3   0 1/3 2/3   1 2/3 1/3   0 1/3 2/3   1 2/3 1/3   0 1/3 2/3   1 2/3 1/3   0 1/3 2/3   1 2/3 1/3
# Linear interpolation from 1 -> 0 with two values means it just goes 1, 2/3, 1/3, 0. Make sense?

# Area for full on (1): (200 - 100) * (300 - 200) * 1 = 10000mm^2
# Area for 2/3: (200 - 100) * (300 - 200) * 2/3 = 6666.666mm^2
# Area for 1/3: (200 - 100) * (300 - 200) * 1/3 = 3333.333mm^2
# Number of slices that we have for this: 11 2/3's, 11 1/3's and 6 1s: volume = 170000mm^3


# Manually edited to add the space directions... not worth the trouble of coding for two tests