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test_slice_width.py
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import unittest
import pathlib
import numpy as np
import pydicom
# import hazenlib.slice_width as hazen_slice_width
from tests import TEST_DATA_DIR, TEST_REPORT_DIR
from hazenlib.tasks.slice_width import SliceWidth
from hazenlib.utils import get_dicom_files, Rod
import os
class TestSliceWidth(unittest.TestCase):
SLICE_WIDTH_DATA = pathlib.Path(TEST_DATA_DIR / "slicewidth")
"""
Notes
-----
The rod indices are ordered as:
789
456
123
"""
matlab_rods = [
Rod(71.2857, 191.5000),
Rod(130.5000, 190.5000),
Rod(190.6000, 189.4000),
Rod(69.5000, 131.5000),
Rod(128.7778, 130.5000),
Rod(189.1111, 129.2778),
Rod(69.0000, 71.5000),
Rod(128.1176, 70.4118),
Rod(188.5000, 69.2222),
]
rods = [
Rod(70.26906602941604, 190.52291430040833),
Rod(129.38344648450575, 189.5252799358382),
Rod(189.6494724536544, 188.32774808447635),
Rod(68.53084886954112, 130.56732921648214),
Rod(127.86240947286896, 129.4605302262616),
Rod(188.01124565987345, 128.2832650316875),
Rod(67.97926729691507, 70.61103769200058),
Rod(127.2060664869085, 69.42672715143607),
Rod(187.49797283835656, 68.2890101413575),
]
DISTANCES = ([119.333, 119.632, 119.522], [120.022, 120.112, 120.196])
DIST_CORR_COEFF = {"top": 0.9965, "bottom": 0.9957}
ROD_DIST = (0.13, 0.07)
TOP_CENTRE = 102
BOTTOM_CENTRE = 162
MATLAB_PROFILE = [
693,
694.75,
688.6,
685.05,
682.2,
677.65,
677.35,
675.5,
668,
665.9,
663.05,
662.05,
662.1,
657.75,
653.65,
654.75,
650.1,
648.65,
646.1,
645.9,
643.1,
639.4,
641.35,
639.1,
635.95,
633.75,
633.9,
630.7,
627.25,
628.2,
628.05,
623.4,
624.35,
622.4,
621.15,
622.45,
615,
615.8,
611.15,
605.2,
602.15,
595.75,
582.75,
573.5,
561.25,
550.4,
538.25,
524.9,
511.65,
499.9,
489.7,
487.3,
477,
476.1,
469.55,
466.9,
467.7,
466,
465.05,
468,
464.7,
467.9,
464.65,
468.85,
467.55,
468,
469.05,
473.25,
479.6,
483.8,
492.3,
500,
512.5,
523,
535.95,
548.3,
561.8,
571.95,
585.35,
593.5,
601.55,
605.45,
609.3,
612.75,
617.1,
618.8,
620.35,
623.15,
621.7,
623.35,
625.25,
628.4,
628.8,
631.55,
632.55,
633.4,
634.35,
638.1,
639.35,
640.3,
641.75,
646.7,
648.1,
647.2,
648.95,
650.2,
653.95,
659.55,
660.8,
661.95,
663,
665.6,
666.15,
670.75,
672.6,
674.15,
675.9,
677.5,
682.45,
684.3,
]
BLINE_TOP = 0.0215
BLINE_BOT = 0.0239
TRAP_FIT_COEFF_TOP = [47, 55, 153, 178]
TRAP_FIT_COEFF_BOT = [47, 55, 164, 167]
MATLAB_TRAP_FIT_COEFF = [50, 54, 153, 170, -111.7920]
MATLAB_BLINE_FIT_COEFF = [0.0216, -2.9658, 602.2568]
MATLAB_TRAP_FIT_COEFF_BOT = [55.0000, 60.0000, 155.0000, 152.0000, -136.6194]
MATLAB_BLINE_FIT_COEFF_BOT = [0.0239, -2.9389, 694.9520]
SW_MATLAB = 5.48
def setUp(self):
# self.file = str(self.SLICE_WIDTH_DATA / 'SLICEWIDTH' / 'ANNUALQA.MR.HEAD_GENERAL.tra.slice_width.IMA')
# self.dcm = pydicom.read_file(self.file)
self.slice_width = SliceWidth(
input_data=[
os.path.join(
self.SLICE_WIDTH_DATA,
"SLICEWIDTH",
"ANNUALQA.MR.HEAD_GENERAL.tra.slice_width.IMA",
)
],
report_dir=pathlib.PurePath.joinpath(TEST_REPORT_DIR),
)
def test_get_rods(self):
arr = self.slice_width.single_dcm.pixel_array
rods, _ = self.slice_width.get_rods(arr)
# print("rods")
# print(rods)
for n in range(len(rods)):
np.testing.assert_almost_equal(self.rods[n].centroid, rods[n].centroid, 3)
def test_get_rod_distances(self):
# From MATLAB Rods
distances = self.slice_width.get_rod_distances(self.matlab_rods)
np.testing.assert_almost_equal(distances, self.DISTANCES, 3)
def test_get_rod_distortion_correction_coefficients(self):
distances = self.slice_width.get_rod_distances(self.matlab_rods)
# print("rod distortion correction coefficient")
# print(hazen_slice_width.get_rod_distortion_correction_coefficients(distances[0], self.dcm.PixelSpacing[0]))
dist_corr_coeff = self.slice_width.get_rod_distortion_correction_coefficients(
distances[0]
)
np.testing.assert_almost_equal(
dist_corr_coeff["top"], self.DIST_CORR_COEFF["top"], 3
)
np.testing.assert_almost_equal(
dist_corr_coeff["bottom"], self.DIST_CORR_COEFF["bottom"], 3
)
def test_rod_distortions(self):
horz_dist, vert_dist = self.slice_width.get_rod_distances(self.matlab_rods)
(
horizontal_distortion,
vertical_distortion,
) = self.slice_width.get_rod_distortions(horz_dist, vert_dist)
# print("rod distortion")
# print(horizontal_distortion, vertical_distortion)
assert (
round(horizontal_distortion, 2),
round(vertical_distortion, 2),
) == self.ROD_DIST
def test_get_ramp_profiles(self):
ramp_profiles = self.slice_width.get_ramp_profiles(
self.slice_width.single_dcm.pixel_array, self.matlab_rods
)
bottom_profiles = ramp_profiles["bottom"]
mean_bottom_profile = np.mean(bottom_profiles, axis=0).tolist()
# print("bottom centre ramp profile")
# print(ramp_profiles["bottom-centre"])
# print("top centre ramp profile")
# print(ramp_profiles["top-centre"])
# print("mean bottom profile")
# print(mean_bottom_profile)
assert ramp_profiles["bottom-centre"] == self.BOTTOM_CENTRE
assert ramp_profiles["top-centre"] == self.TOP_CENTRE
assert mean_bottom_profile == self.MATLAB_PROFILE
def test_baseline_correction(self):
# matlab top 0.0215 -2.9668 602.4568
# matlab bottom [0.0239, -2.9349, 694.9520]
ramps = self.slice_width.get_ramp_profiles(
self.slice_width.single_dcm.pixel_array, self.matlab_rods
)
top_mean_ramp = np.mean(ramps["top"], axis=0)
top_coefficients = list(
self.slice_width.baseline_correction(top_mean_ramp, sample_spacing=0.25)[
"f"
]
)
# print("top bline corr coeff")
# print(round(top_coefficients[0], 4))
assert round(top_coefficients[0], 4) == self.BLINE_TOP
bottom_mean_ramp = np.mean(ramps["bottom"], axis=0)
bottom_coefficients = list(
self.slice_width.baseline_correction(bottom_mean_ramp, sample_spacing=0.25)[
"f"
]
)
# print("bottom bline corr coeff")
# print(round(bottom_coefficients[0], 4))
assert round(bottom_coefficients[0], 4) == self.BLINE_BOT
def test_trapezoid(self):
"""
Notes
-----
variables from one iteration of the original matlab script
n_ramp, n_plateau, n_left_baseline, n_right_baseline, plateau_amplitude =
55.0000 58.0000 156.0000 153.0000 -136.6194 and fwhm 113
"""
assert self.slice_width.trapezoid(55, 58, 156, 153, -136.6194)[1] == 113
def test_get_initial_trapezoid_fit_and_coefficients(self):
"""
Notes
-----
Trapezoid_Fit_Coefficients_Initial = 48.0000 56.0000 153.0000 172.0000 -116.4920
fwhm = 104
"""
sample_spacing = 0.25
slice_thickness = self.slice_width.single_dcm.SliceThickness
ramps = self.slice_width.get_ramp_profiles(
self.slice_width.single_dcm.pixel_array, self.matlab_rods
)
top_mean_ramp = np.mean(ramps["top"], axis=0)
bottom_mean_ramp = np.mean(ramps["bottom"], axis=0)
ramps_baseline_corrected = {
"top": self.slice_width.baseline_correction(top_mean_ramp, sample_spacing),
"bottom": self.slice_width.baseline_correction(
bottom_mean_ramp, sample_spacing
),
}
(
trapezoid_fit,
trapezoid_fit_coefficients,
) = self.slice_width.get_initial_trapezoid_fit_and_coefficients(
ramps_baseline_corrected["top"]["profile_corrected_interpolated"],
slice_thickness,
)
# print("trap fit coeff top initial")
# print(trapezoid_fit_coefficients[:4])
assert trapezoid_fit_coefficients[:4] == self.TRAP_FIT_COEFF_TOP
(
trapezoid_fit,
trapezoid_fit_coefficients,
) = self.slice_width.get_initial_trapezoid_fit_and_coefficients(
ramps_baseline_corrected["bottom"]["profile_corrected_interpolated"],
slice_thickness,
)
# print("trap fit coeff bottom initial")
# print(trapezoid_fit_coefficients[:4])
assert trapezoid_fit_coefficients[:4] == self.TRAP_FIT_COEFF_BOT
def test_fit_trapezoid(self):
sample_spacing = 0.25
slice_thickness = self.slice_width.single_dcm.SliceThickness
ramps = self.slice_width.get_ramp_profiles(
self.slice_width.single_dcm.pixel_array, self.matlab_rods
)
top_mean_ramp = np.mean(ramps["top"], axis=0)
bottom_mean_ramp = np.mean(ramps["bottom"], axis=0)
ramps_baseline_corrected = {
"top": self.slice_width.baseline_correction(top_mean_ramp, sample_spacing),
"bottom": self.slice_width.baseline_correction(
bottom_mean_ramp, sample_spacing
),
}
(
trapezoid_fit_coefficients,
baseline_fit_coefficients,
) = self.slice_width.fit_trapezoid(
profiles=ramps_baseline_corrected["top"], slice_thickness=slice_thickness
)
# print("top trap fit coeff")
# print(trapezoid_fit_coefficients)
# print("top bline fit coeff")
# print(baseline_fit_coefficients)
# check top profile first
matlab_trapezoid_fit_coefficients = self.MATLAB_TRAP_FIT_COEFF
matlab_baseline_fit_coefficients = self.MATLAB_BLINE_FIT_COEFF
for idx, value in enumerate(trapezoid_fit_coefficients):
assert abs(value - matlab_trapezoid_fit_coefficients[idx]) <= 5
for idx, value in enumerate(matlab_baseline_fit_coefficients):
assert abs(value - matlab_baseline_fit_coefficients[idx]) <= 5
# residual error is 3735.6
## check bottom profile now
(
trapezoid_fit_coefficients,
baseline_fit_coefficients,
) = self.slice_width.fit_trapezoid(
profiles=ramps_baseline_corrected["bottom"], slice_thickness=slice_thickness
)
# print("bottom trap fit coeff")
# print(trapezoid_fit_coefficients)
# print("bottom bline fit coeff")
# print(baseline_fit_coefficients)
matlab_trapezoid_fit_coefficients = self.MATLAB_TRAP_FIT_COEFF_BOT
matlab_baseline_fit_coefficients = self.MATLAB_BLINE_FIT_COEFF_BOT
for idx, value in enumerate(trapezoid_fit_coefficients):
assert abs(value - matlab_trapezoid_fit_coefficients[idx]) <= 5
for idx, value in enumerate(matlab_baseline_fit_coefficients):
assert abs(value - matlab_baseline_fit_coefficients[idx]) <= 5
def test_slice_width(self):
result = self.slice_width.run()
slice_width_mm = result["measurement"]["slice width mm"]
print("\ntest_slice_width.py::TestSliceWidth::test_slice_width")
print("new_release_value:", slice_width_mm)
print("fixed_value:", self.SW_MATLAB)
assert abs(slice_width_mm - self.SW_MATLAB) < 0.1
class Test512Matrix(TestSliceWidth):
SLICE_WIDTH_DATA = pathlib.Path(TEST_DATA_DIR / "slicewidth")
"""
Notes
-----
The rod indices are ordered as:
789
456
123
"""
matlab_rods = [
Rod(134.19422395407386, 376.3297092734241),
Rod(255.5191606119133, 374.7890799840584),
Rod(376.45583336255567, 373.7479398253673),
Rod(133.73482492069846, 255.9592867481753),
Rod(254.49068286441252, 254.33374023796569),
Rod(375.15134878569734, 254.0979036468634),
Rod(133.07301997760993, 136.86070859809843),
Rod(253.53888071406627, 135.75358569280274),
Rod(374.00513210724, 135.12370483098044),
]
rods = [
Rod(134.50715482125025, 376.39901305569873),
Rod(255.46730860444976, 374.7645374009015),
Rod(376.3508021809186, 373.6769436835617),
Rod(133.58289022243835, 256.06611582258665),
Rod(254.51562676421784, 254.61914241989848),
Rod(375.3779965519839, 253.83655980142507),
Rod(132.7380060479853, 137.19733440032368),
Rod(253.45972063728271, 135.83081591213042),
Rod(374.31705777525144, 135.3055747931858),
]
DISTANCES = ([242.275, 241.424, 240.938], [239.472, 239.044, 238.637])
DIST_CORR_COEFF = {"top": 1.0049, "bottom": 1.0077}
ROD_DIST = (0.28, 0.17)
TOP_CENTRE = 196
BOTTOM_CENTRE = 316
MATLAB_PROFILE = [
7970.0,
7912.7,
7884.8,
7858.8,
7812.95,
7759.8,
7717.925,
7686.575,
7658.275,
7625.375,
7578.45,
7522.275,
7472.325,
7439.35,
7408.325,
7364.875,
7327.475,
7311.0,
7299.025,
7265.475,
7213.525,
7166.7,
7122.625,
7070.875,
7022.25,
6998.95,
6990.05,
6965.325,
6923.2,
6891.6,
6880.05,
6856.425,
6809.975,
6770.95,
6759.55,
6752.15,
6721.55,
6682.175,
6658.075,
6642.175,
6611.75,
6562.325,
6512.85,
6485.575,
6479.45,
6478.3,
6467.8,
6439.45,
6396.675,
6351.825,
6320.7,
6309.525,
6310.175,
6303.0,
6267.3,
6214.1,
6173.725,
6167.0,
6176.825,
6171.4,
6152.0,
6146.4,
6147.425,
6127.85,
6090.75,
6065.175,
6055.675,
6031.15,
5991.975,
5977.125,
5996.25,
5998.8,
5951.0,
5895.325,
5883.475,
5903.65,
5899.7,
5861.825,
5843.075,
5860.825,
5872.95,
5857.625,
5835.2,
5828.275,
5816.95,
5783.475,
5752.975,
5753.025,
5766.5,
5768.75,
5773.775,
5794.775,
5802.7,
5757.25,
5684.375,
5638.1,
5624.1,
5593.575,
5519.275,
5428.525,
5351.5,
5274.45,
5169.925,
5045.75,
4932.65,
4839.15,
4757.825,
4684.975,
4621.675,
4577.3,
4547.775,
4529.55,
4515.15,
4495.7,
4479.775,
4484.425,
4501.25,
4487.35,
4437.025,
4392.075,
4386.55,
4401.175,
4401.925,
4386.75,
4388.975,
4402.075,
4395.4,
4376.25,
4384.05,
4419.075,
4443.875,
4436.9,
4423.475,
4437.25,
4467.7,
4485.775,
4490.65,
4499.55,
4522.525,
4556.525,
4594.4,
4634.55,
4662.325,
4658.45,
4645.775,
4675.325,
4746.475,
4802.05,
4809.95,
4813.95,
4874.025,
4968.925,
5048.425,
5119.975,
5236.2,
5398.2,
5542.675,
5632.375,
5706.4,
5813.375,
5943.575,
6056.1,
6135.025,
6193.7,
6246.75,
6291.075,
6325.35,
6353.55,
6371.325,
6382.85,
6403.925,
6445.9,
6493.45,
6522.275,
6531.15,
6535.175,
6541.625,
6544.275,
6557.0,
6593.725,
6651.325,
6703.0,
6725.95,
6732.325,
6745.5,
6774.625,
6811.225,
6843.275,
6863.175,
6874.65,
6893.3,
6934.7,
6985.0,
7019.45,
7049.125,
7095.475,
7143.35,
7165.65,
7169.85,
7197.3,
7255.65,
7304.35,
7319.925,
7333.55,
7385.35,
7466.05,
7530.7,
7559.15,
7579.95,
7614.85,
7657.725,
7699.05,
7747.975,
7805.1,
7855.1,
7888.925,
7913.6,
7947.425,
7996.65,
8051.65,
8105.075,
8160.575,
8215.6,
8258.975,
8284.975,
8312.85,
8364.925,
8438.1,
8501.675,
8547.175,
8597.825,
8665.9,
8731.175,
8776.475,
8814.125,
8864.925,
8922.575,
8972.85,
9023.675,
9093.4,
9167.25,
9216.7,
]
BLINE_TOP = 0.1686
BLINE_BOT = 0.2072
TRAP_FIT_COEFF_TOP = [47, 55, 398, 421]
TRAP_FIT_COEFF_BOT = [47, 55, 442, 377]
MATLAB_TRAP_FIT_COEFF = [81, 125, 331, 350, -1448.2731999293467]
MATLAB_BLINE_FIT_COEFF = [
0.16890305013478935,
-39.18378191113812,
8256.387981752052,
]
MATLAB_TRAP_FIT_COEFF_BOT = [80, 115, 382, 311, -1331.3180036312333]
MATLAB_BLINE_FIT_COEFF_BOT = [
0.20707462357475487,
-44.91849057042588,
8014.213383072912,
]
SW_MATLAB = 4.972852917690252
def setUp(self):
self.slice_width = SliceWidth(
input_data=[
os.path.join(self.SLICE_WIDTH_DATA, "512_matrix", "512_matrix")
],
report_dir=pathlib.PurePath.joinpath(TEST_REPORT_DIR),
)
# self.file = str(TEST_DATA_DIR / 'slicewidth' / 'SLICEWIDTH' / '512_matrix')
# self.dcm = pydicom.read_file(self.file)