Commit 19db932e authored by Steffen Schotthöfer's avatar Steffen Schotthöfer
Browse files

added validation_tests

parent 2f29bd3e
This diff is collapsed.
# 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()
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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)
# vtk DataFile Version 4.2
vtk output
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 61 double
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-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
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
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5
5
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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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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)
# 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
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
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