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Commit 19db932e authored by Steffen Schotthöfer's avatar Steffen Schotthöfer
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added validation_tests

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code/tests/input/checkerboard_reference.vtk deleted 100644 → 0
View file @ 2f29bd3e
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code/tests/input/extract_grayscale_image.py 0 → 100644
View file @ 19db932e
# importing PIL
from PIL import Image
import pydicom
import numpy as np
from pydicom.pixel_data_handlers.util import apply_modality_lut
from copy import deepcopy
def main():
image_name = "mini_phantom.png"
ending = image_name.split('.')[-1];
if(ending == 'dcm'): #dicom ct image
dataset = pydicom.dcmread(image_name)
hu = apply_modality_lut(dataset.pixel_array, dataset)
density = (dataset.RescaleIntercept + dataset.RescaleSlope*hu)/1000 +1
(spacingX, spacingY) = dataset.PixelSpacing
(sizeX,sizeY) = density.shape
dimensions = (spacingX*sizeX, spacingY*sizeY)
return density, dimensions
else: # jpg or png
img = Image.open(image_name).convert('L') #image data
I = np.asarray(img) # image as greyscale
I = I/255; # rescale values to [0,1]
J = deepcopy(np.flipud(I))
np.savetxt("foo.csv", J, delimiter=",")
dimensions = (1,1) # [cm]
return J , dimensions
if __name__ == '__main__':
main()
code/tests/input/validation_tests/MN_solver/checkerboard_MN.cfg 0 → 100644
View file @ 19db932e
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Checkerboard Benchmarking File MN %
% Author <Steffen Schotthöfer> %
% Date 10.11.2020 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% ---- File specifications ----
%
OUTPUT_DIR = ../../../result
OUTPUT_FILE = rtsn_test_checkerboard_MN
LOG_DIR = ../../../result/logs
MESH_FILE = ../meshes/checkerboard.su2
%
% ---- Problem specifications ----
%
PROBLEM = CHECKERBOARD
%
% ---- Solver specifications ----
%
CFL_NUMBER = 0.5
TIME_FINAL = 3.2
SOLVER = MN_SOLVER
MAX_MOMENT_SOLVER = 2
ENTROPY_FUNCTIONAL = MAXWELL_BOLTZMANN
ENTROPY_OPTIMIZER = NEWTON
%
% ----- Newton Solver Specifications ----
%
NEWTON_FAST_MODE = NO
NEWTON_ITER = 1000
NEWTON_EPSILON = 0.01
NEWTON_STEP_SIZE = 0.7
NEWTON_LINE_SEARCH_ITER = 1000
%
% ---- Boundary Conditions ----
%
BC_DIRICHLET = ( void )
%
% ---- Quadrature ----
%
QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED
QUAD_ORDER = 8
%
% ----- Output ----
%
VOLUME_OUTPUT = (MINIMAL)
code/tests/input/validation_tests/MN_solver/linesource_MN_MB.cfg 0 → 100644
View file @ 19db932e
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Linesource Benchmarking File MN %
% Author <Steffen Schotthöfer> %
% Date 01.07.2020 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% ---- File specifications ----
%
OUTPUT_DIR = ../../../result
OUTPUT_FILE = rtsn_test_linesource_MN_MB
LOG_DIR = ../../../result/logs
MESH_FILE = ../meshes/linesource.su2
%
% ---- Problem specifications ----
%
PROBLEM = LINESOURCE
SCATTER_COEFF = 1
%
% ---- Solver specifications ----
%
CFL_NUMBER = 0.7
TIME_FINAL = 0.2
SOLVER = MN_SOLVER
MAX_MOMENT_SOLVER = 2
ENTROPY_FUNCTIONAL = MAXWELL_BOLTZMANN
ENTROPY_OPTIMIZER = NEWTON
%
% ----- Newton Solver Specifications ----
%
NEWTON_FAST_MODE = NO
NEWTON_ITER = 1000
NEWTON_EPSILON = 0.01
NEWTON_STEP_SIZE = 0.7
NEWTON_LINE_SEARCH_ITER = 1000
%
% ---- Boundary Conditions ----
%
BC_DIRICHLET = ( void )
%
% ---- Quadrature ----
%
QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED
QUAD_ORDER = 8
%
% ----- Output ----
%
VOLUME_OUTPUT = (MINIMAL)
code/tests/input/validation_tests/MN_solver/linesource_MN_MB_reference.vtk 0 → 100644
View file @ 19db932e
# vtk DataFile Version 4.2
vtk output
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 61 double
-0.6 -0.6 0 0.6 -0.6 0 0.6 0.6 0
-0.6 0.6 0 0 0 0 -0.4 -0.6 0
-0.2 -0.6 0 6.6613381478e-16 -0.6 0 0.2 -0.6 0
0.4 -0.6 0 0.6 -0.4 0 0.6 -0.2 0
0.6 6.6613381478e-16 0 0.6 0.2 0 0.6 0.4 0
0.4 0.6 0 0.2 0.6 0 -6.6613381478e-16 0.6 0
-0.2 0.6 0 -0.4 0.6 0 -0.6 0.4 0
-0.6 0.2 0 -0.6 -6.6613381478e-16 0 -0.6 -0.2 0
-0.6 -0.4 0 -0.088332399106 0.43353121176 0 -0.43353121176 -0.088332399106 0
0.40841747107 -0.28277700638 0 0.098365396477 -0.42773865803 0 0.42773865803 0.098365396477 0
-0.29915252614 -0.43064559099 0 0.28277700638 0.40841747107 0 -0.43064559099 0.29915252614 0
-0.10013118828 -0.42759398766 0 -0.20781352442 -0.27458104075 0 -0.0060623725765 -0.26932681281 0
0.19654300579 -0.27981612736 0 -0.42855941329 0.10180335451 0 -0.27474194502 0.20809221879 0
-0.27627251382 0.017148940826 0 0.42968185474 -0.087368937613 0 0.25358983849 9.3513224001e-16 0
0.27719329831 0.19755340122 0 0.089041103842 0.43064728037 0 -9.3611199873e-16 0.25358983849 0
0.44021646687 0.29298768454 0 0.2928192853 -0.44065360504 0 -0.4176849844 -0.28566219856 0
-0.28567861737 0.4177134226 0 0.1 -0.12679491924 0 0.12679491924 0.1 0
-0.10384694829 0.12210748587 0 -0.12288196948 -0.10311927111 0 0.45358983849 -0.45358983849 0
-0.45358983849 -0.45358983849 0 0.45358983849 0.45358983849 0 -0.45358983849 0.45358983849 0
0.1476383677 0.28308824116 0 0.28288662677 -0.14773537411 0 -0.28834516088 -0.13980201577 0
-0.13980201577 0.28834516088 0
CELLS 96 384
3 38 48 32
3 34 47 30
3 42 45 31
3 36 46 27
3 44 51 50
3 38 60 48
3 34 59 47
3 39 52 51
3 27 58 36
3 31 57 42
3 50 51 4
3 41 50 49
3 51 52 4
3 49 52 35
3 6 33 30
3 33 35 34
3 8 28 7
3 11 40 27
3 13 29 12
3 18 25 17
3 23 26 22
3 37 38 32
3 16 43 31
3 21 37 32
3 33 34 30
3 37 39 38
3 11 27 10
3 6 30 5
3 7 33 6
3 16 31 15
3 21 32 20
3 25 44 43
3 26 39 37
3 28 33 7
3 25 43 17
3 26 37 22
3 28 35 33
3 29 41 40
3 12 40 11
3 29 40 12
3 17 43 16
3 22 37 21
3 28 36 35
3 29 42 41
3 49 50 4
3 4 52 49
3 14 45 13
3 9 46 8
3 19 48 18
3 24 47 23
3 28 46 36
3 29 45 42
3 13 45 29
3 23 47 26
3 8 46 28
3 18 48 25
3 5 54 0
3 10 53 1
3 15 55 2
3 20 56 3
3 0 54 24
3 1 53 9
3 2 55 14
3 3 56 19
3 40 58 27
3 43 57 31
3 35 52 34
3 39 51 38
3 48 60 25
3 47 59 26
3 50 57 44
3 49 58 41
3 36 49 35
3 42 50 41
3 14 55 45
3 9 53 46
3 19 56 48
3 24 54 47
3 30 54 5
3 27 53 10
3 31 55 15
3 32 56 20
3 25 60 44
3 26 59 39
3 41 58 40
3 44 57 43
3 46 53 27
3 47 54 30
3 45 55 31
3 48 56 32
3 42 57 50
3 36 58 49
3 44 60 51
3 39 59 52
3 52 59 34
3 51 60 38
CELL_TYPES 96
5
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5
CELL_DATA 96
FIELD FieldData 1
radiation%20flux%20density 1 96 double
0.023075686389 0.023075686389 0.023075686389 0.023075686389 3.2567884905 0.023075686389 0.023075686389 2.9000325329 0.023075686389
0.023075686389 4.0517913501 3.1542357631 3.9630162161 2.7957825828 0.023075686389 0.023075686389 5.0580418059e-101 0.023075686389
5.0580418059e-101 1.6357402065e-101 1.6357402065e-101 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389 1.0925488099e-124
1.67533772e-128 4.807237643e-101 1.0925488099e-124 1.67533772e-128 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389
0.023075686389 0.023075686389 5.1070999977e-101 0.023075686389 3.5741746143e-101 3.353049222e-101 0.023075686389 0.023075686389 3.9616384051
3.9219732906 2.8869513693e-129 2.6164279107e-129 5.1807883453e-126 5.2355333002e-126 0.023075686389 0.023075686389 0.023075686389 0.023075686389
0.023075686389 0.023075686389 1.609494535e-180 1.609494535e-180 1.609494535e-180 1.609494535e-180 1.609494535e-180 1.609494535e-180 1.609494535e-180
1.609494535e-180 0.023075686389 0.023075686389 0.76456256015 0.79934508806 0.023075686389 0.023075686389 1.48065084 1.2673622482
0.65568641859 0.81185421685 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389
0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389 0.023075686389
0.023075686389 0.023075686389 1.2625328905 0.94584263198 0.023075686389 0.023075686389
POINT_DATA 61
FIELD FieldData 1
radiation%20flux%20density 1 61 double
1.609494535e-180 1.609494535e-180 1.609494535e-180 1.609494535e-180 3.9746048155 0.007691895463 0.007691895463 0.007691895463 0.007691895463
0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463
0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.007691895463 0.019229738658 0.019229738658
0.019779159762 0.019229738658 0.019229738658 0.019229738658 0.019779159762 0.019229738658 0.019229738658 0.14665683202 0.71420977012
0.12851080842 0.019229738658 0.15245392 0.78574121868 0.019229738658 0.88377988122 0.1545387748 0.019229738658 1.0115332134
0.019229738658 0.019229738658 0.019779159762 0.019779159762 2.2542506278 2.391433536 2.3223688935 2.1877550716 0.013845411833
0.013845411833 0.013845411833 0.013845411833 0.31459071711 0.27193299875 0.20762907551 0.27096712721
code/tests/input/validation_tests/MN_solver/linesource_MN_Quad.cfg 0 → 100644
View file @ 19db932e
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Linesource Benchmarking File MN %
% Author <Steffen Schotthöfer> %
% Date 01.07.2020 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% ---- File specifications ----
%
OUTPUT_DIR = ../../../result
OUTPUT_FILE = rtsn_test_linesource_MN_Quad
LOG_DIR = ../../../result/logs
MESH_FILE = ../meshes/linesource.su2
%
% ---- Problem specifications ----
%
PROBLEM = LINESOURCE
SCATTER_COEFF = 1
%
% ---- Solver specifications ----
%
CFL_NUMBER = 0.7
TIME_FINAL = 0.2
SOLVER = MN_SOLVER
MAX_MOMENT_SOLVER = 2
ENTROPY_FUNCTIONAL = QUADRATIC
ENTROPY_OPTIMIZER = NEWTON
%
% ----- Newton Solver Specifications ----
%
NEWTON_FAST_MODE = YES
%
% ---- Boundary Conditions ----
%
BC_DIRICHLET = ( void )
%
% ---- Quadrature ----
%
QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED
QUAD_ORDER = 8
%
% ----- Output ----
%
VOLUME_OUTPUT = (MINIMAL)
code/tests/input/validation_tests/MN_solver/linesource_MN_Quad_reference.vtk 0 → 100644
View file @ 19db932e
# vtk DataFile Version 4.2
vtk output
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 61 double
-0.6 -0.6 0 0.6 -0.6 0 0.6 0.6 0
-0.6 0.6 0 0 0 0 -0.4 -0.6 0
-0.2 -0.6 0 6.6613381478e-16 -0.6 0 0.2 -0.6 0
0.4 -0.6 0 0.6 -0.4 0 0.6 -0.2 0
0.6 6.6613381478e-16 0 0.6 0.2 0 0.6 0.4 0
0.4 0.6 0 0.2 0.6 0 -6.6613381478e-16 0.6 0
-0.2 0.6 0 -0.4 0.6 0 -0.6 0.4 0
-0.6 0.2 0 -0.6 -6.6613381478e-16 0 -0.6 -0.2 0
-0.6 -0.4 0 -0.088332399106 0.43353121176 0 -0.43353121176 -0.088332399106 0
0.40841747107 -0.28277700638 0 0.098365396477 -0.42773865803 0 0.42773865803 0.098365396477 0
-0.29915252614 -0.43064559099 0 0.28277700638 0.40841747107 0 -0.43064559099 0.29915252614 0
-0.10013118828 -0.42759398766 0 -0.20781352442 -0.27458104075 0 -0.0060623725765 -0.26932681281 0
0.19654300579 -0.27981612736 0 -0.42855941329 0.10180335451 0 -0.27474194502 0.20809221879 0
-0.27627251382 0.017148940826 0 0.42968185474 -0.087368937613 0 0.25358983849 9.3513224001e-16 0
0.27719329831 0.19755340122 0 0.089041103842 0.43064728037 0 -9.3611199873e-16 0.25358983849 0
0.44021646687 0.29298768454 0 0.2928192853 -0.44065360504 0 -0.4176849844 -0.28566219856 0
-0.28567861737 0.4177134226 0 0.1 -0.12679491924 0 0.12679491924 0.1 0
-0.10384694829 0.12210748587 0 -0.12288196948 -0.10311927111 0 0.45358983849 -0.45358983849 0
-0.45358983849 -0.45358983849 0 0.45358983849 0.45358983849 0 -0.45358983849 0.45358983849 0
0.1476383677 0.28308824116 0 0.28288662677 -0.14773537411 0 -0.28834516088 -0.13980201577 0
-0.13980201577 0.28834516088 0
CELLS 96 384
3 38 48 32
3 34 47 30
3 42 45 31
3 36 46 27
3 44 51 50
3 38 60 48
3 34 59 47
3 39 52 51
3 27 58 36
3 31 57 42
3 50 51 4
3 41 50 49
3 51 52 4
3 49 52 35
3 6 33 30
3 33 35 34
3 8 28 7
3 11 40 27
3 13 29 12
3 18 25 17
3 23 26 22
3 37 38 32
3 16 43 31
3 21 37 32
3 33 34 30
3 37 39 38
3 11 27 10
3 6 30 5
3 7 33 6
3 16 31 15
3 21 32 20
3 25 44 43
3 26 39 37
3 28 33 7
3 25 43 17
3 26 37 22
3 28 35 33
3 29 41 40
3 12 40 11
3 29 40 12
3 17 43 16
3 22 37 21
3 28 36 35
3 29 42 41
3 49 50 4
3 4 52 49
3 14 45 13
3 9 46 8
3 19 48 18
3 24 47 23
3 28 46 36
3 29 45 42
3 13 45 29
3 23 47 26
3 8 46 28
3 18 48 25
3 5 54 0
3 10 53 1
3 15 55 2
3 20 56 3
3 0 54 24
3 1 53 9
3 2 55 14
3 3 56 19
3 40 58 27
3 43 57 31
3 35 52 34
3 39 51 38
3 48 60 25
3 47 59 26
3 50 57 44
3 49 58 41
3 36 49 35
3 42 50 41
3 14 55 45
3 9 53 46
3 19 56 48
3 24 54 47
3 30 54 5
3 27 53 10
3 31 55 15
3 32 56 20
3 25 60 44
3 26 59 39
3 41 58 40
3 44 57 43
3 46 53 27
3 47 54 30
3 45 55 31
3 48 56 32
3 42 57 50
3 36 58 49
3 44 60 51
3 39 59 52
3 52 59 34
3 51 60 38
CELL_TYPES 96
5
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