addisonElliott · March 1, 2018 03:35
diff --git a/fatVolumeEstimationTest.py b/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
	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