added uni_tests

Former-commit-id: 532d3960

code/tests/input/extract_grayscale_image.py

-# 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/image_conversion.cfg

-% ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
-OUTPUT_FILE = ctscan_test
-LOG_DIR = ../../tests/result/logs
-MESH_FILE = ../../tests/result/ctscan_test.su2
-
-% ---- Solver specifications ----
-CFL_NUMBER = 0.5
-TIME_FINAL = 0.5
-PROBLEM = LINESOURCE
-
-% ---- Boundary Conditions ----
-BC_NEUMANN = ( void )
-QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED
-QUAD_ORDER = 10

code/tests/input/linesource.py

-import pygmsh as pg
-import numpy as np
-import itertools
-import os
-
-def add_block(x0,y0,length,char_length,geom):
-    coords = np.array([
-        [x0, y0, 0.0],
-        [x0+length, y0, 0.0],
-        [x0+length, y0+length, 0.0],
-        [x0, y0+length, 0.0]
-    ])
-    return geom.add_polygon(coords, char_length)
-
-char_length = 0.2
-geom = pg.opencascade.Geometry()
-domain = add_block(-0.6, -0.6, 1.2, char_length, geom)
-geom.add_raw_code('psource = newp;\nPoint(psource) = {0.0, 0.0, 0.0, '+str(char_length)+'};\nPoint{psource} In Surface{'+domain.id+'};')
-geom.add_physical(domain.lines, label="void")
-
-mesh_code = geom.get_code()
-with open("linesource.geo","w") as mesh_file:
-    mesh_file.write(mesh_code)
-os.system('gmsh linesource.geo -2 -format su2 -save_all')
-os.system('rm linesource.geo')

code/tests/input/phantom.csv

-0.000000000000000000e+00,0.000000000000000000e+00,1.725490196078431349e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01
-0.000000000000000000e+00,5.490196078431372473e-02,2.039215686274509776e-01,2.039215686274509776e-01,5.333333333333333259e-01,9.098039215686274384e-01,9.137254901960784048e-01,9.098039215686274384e-01,5.333333333333333259e-01,2.039215686274509776e-01
-0.000000000000000000e+00,1.333333333333333315e-01,2.039215686274509776e-01,2.039215686274509776e-01,3.215686274509804154e-01,5.098039215686274161e-01,5.098039215686274161e-01,5.098039215686274161e-01,3.215686274509804154e-01,2.078431372549019718e-01
-1.568627450980392135e-02,2.000000000000000111e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.196078431372548989e-01,2.588235294117647300e-01,2.941176470588235392e-01
-9.411764705882352811e-02,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.313725490196078538e-01,2.784313725490196179e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01
-1.725490196078431349e-01,2.039215686274509776e-01,2.039215686274509776e-01,2.352941176470588203e-01,2.823529411764705843e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01
-2.039215686274509776e-01,2.235294117647058931e-01,2.823529411764705843e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01
-2.666666666666666630e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01
-3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01
-3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01,3.019607843137254721e-01

code/tests/input/trainNN.csv.REMOVED.git-id

-7b59dd696325f2893d35bbbbcf6e1a2fd371dec5
\ No newline at end of file

code/tests/input/unit.py

-import pygmsh as pg
-import numpy as np
-import itertools
-import os
-
-def add_block(x0,y0,length,char_length,geom):
-    coords = np.array([
-        [x0, y0, 0.0],
-        [x0+length, y0, 0.0],
-        [x0+length, y0+length, 0.0],
-        [x0, y0+length, 0.0]
-    ])
-    return geom.add_polygon(coords, char_length)
-
-char_length = 0.5
-geom = pg.opencascade.Geometry()
-domain = add_block(0.0, 0.0, 1.0, char_length, geom)
-geom.add_physical(domain.lines, label="void")
-
-mesh_code = geom.get_code()
-with open("unit.geo","w") as mesh_file:
-    mesh_file.write(mesh_code)
-os.system('gmsh unit.geo -2 -format su2 -save_all')
-os.system('rm unit.geo')

code/tests/input/unit_config.cfg

-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%													%
-%	Unit: Configuration File reader 				%
-%	Author: Steffen Schotthöfer						%
-% 	Date: 13.08.2020								%
-%													%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Use this config file ONLY for test_config.cpp!
-% Only specify options that are important for this unit test!
-%
-% ---- File specifications ----
-% 
-% Output directory
-OUTPUT_DIR = ../result
-% Output file
-OUTPUT_FILE = rtsn_test_unit_config
-% Log directory
-LOG_DIR = ../result/logs
-% Mesh File
-MESH_FILE = unit.su2
-%
-% ---- Solver specifications ----
-%
-% CFL number
-CFL_NUMBER = 0.4
-% Final time for simulation
-TIME_FINAL = 0.3
-%
-% ---- Problem Specifications ----
-%
-% Preselected Problem for Physics Settings
-PROBLEM = LINESOURCE
-%
-% Scattering Kernel
-KERNEL = ISOTROPIC
-%
-%% Quadrature Specifications
-% Quadrature Type
-QUAD_TYPE = MONTE_CARLO
-% Quadrature Order
-QUAD_ORDER = 5000 
-%
-%
-% ---- Boundary Conditions ----
-%
-% Example: BC_DIRICLET = (dummyMarker1, dummyMarker2)
-% Dirichlet Boundary
-BC_DIRICHLET = ( DirichletTestMarker1, DirichletTestMarker2 )
-%
-% Neumann Boundary
-BC_NEUMANN =  (NeumannTestMarker1, NeumannTestMarker2)
-%

code/tests/input/unit_harmonics.cfg

-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%													%
-%	Unit: Spherical Harmonics		 				%
-%	Author: Steffen Schotthöfer						%
-% 	Date: 08.06.2020								%
-%													%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Use this config file ONLY for test_harmonics.cpp!
-%
-% ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
-OUTPUT_FILE = rtsn_test_unit_harmonics
-LOG_DIR = ../../tests/result/logs
-
-% ---- Boundary Conditions ----
-QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED
-QUAD_ORDER = 12
-%
-% Use this option, since default solver is SN. (Solver is not used in this unit test)
-SN_ALL_GAUSS_PTS = YES

code/tests/input/unit_kernel.cfg

-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%													%
-%	Unit: Kernel		 							%
-%	Author: Steffen Schotthöfer						%
-% 	Date: 13.08.2020								%
-%													%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Use this config file ONLY for test_kernel.cpp!
-% Only specify options that are important for this unit test!
-%
-% ---- File specifications ----
-%
-OUTPUT_DIR = ../../tests/result
-OUTPUT_FILE = rtsn_test_unit_kernel
-LOG_DIR = ../../tests/result/logs
-%
-% ---- Quadrature Settings ----
-QUAD_TYPE = LEBEDEV
-QUAD_ORDER = 5
-

code/tests/input/unit_mesh.cfg

-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%													%
-%	Unit: Mesh										%
-%	Author: Steffen Schotthöfer						%
-% 	Date: 13.08.2020								%
-%													%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Use this config file ONLY for test_mesh.cpp!
-% Only specify options that are important for this unit test!
-%
-% ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
-OUTPUT_FILE = rtsn_test_unit_mesh
-LOG_DIR = ../../tests/result/logs
-MESH_FILE = unit_mesh.su2
-%
-% ---- Boundary Conditions ----
-BC_DIRICHLET = ( void )
-

code/tests/input/unit_mesh.su2

-NDIME= 2
-NELEM= 14
-5 1 9 4 0
-5 5 9 1 1
-5 3 11 6 2
-5 7 11 3 3
-5 2 10 5 4
-5 6 10 2 5
-5 4 8 0 6
-5 0 8 7 7
-5 9 11 8 8
-5 8 11 7 9
-5 4 9 8 10
-5 10 11 9 11
-5 6 11 10 12
-5 5 10 9 13
-NPOIN= 12
-0 0 0
-1 0 1
-1 1 2
-0 1 3
-0.5 0 4
-1 0.5 5
-0.5 1 6
-0 0.5 7
-0.25 0.25 8
-0.625 0.3750000000000001 9
-0.71875 0.7187500000000001 10
-0.345703125 0.654296875 11
-NMARK= 1
-MARKER_TAG= void
-MARKER_ELEMS= 8
-3 0 4 
-3 4 1 
-3 1 5 
-3 5 2 
-3 2 6 
-3 6 3 
-3 3 7 
-3 7 0 

code/tests/input/unit_optimizerNewton.cfg

-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%													%
-%	Unit: Optimizer			 						%
-%	Author: Steffen Schotthöfer						%
-% 	Date: 13.08.2020								%
-%													%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Use this config file ONLY for test_optimizer.cpp!
-% Only specify options that are important for this unit test!
-%
-% ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
-OUTPUT_FILE = rtsn_test_unit_optimizerNewton
-LOG_DIR = ../../tests/result/logs
-%
-% ---- Solver specifications ----
-%
-MAX_MOMENT_SOLVER = 1
-%
-ENTROPY_OPTIMIZER = NEWTON
-ENTROPY_FUNCTIONAL = QUADRATIC
-%
-% ----- Newton Solver Specifications ----
-%
-NEWTON_FAST_MODE = NO
-NEWTON_ITER = 100
-NEWTON_EPSILON = 0.01
-NEWTON_STEP_SIZE = 0.5
-NEWTON_LINE_SEARCH_ITER = 100
-%
-% ---- Quadrature Specs ----
-%
-QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED
-QUAD_ORDER = 4
-%
-% Use this option, since default solver is SN. (Solver is not used in this unit test)
-SN_ALL_GAUSS_PTS = YES

code/tests/input/unit_quadrature.cfg

-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%													%
-%	Unit: Quadrature		 						%
-%	Author: Steffen Schotthöfer						%
-% 	Date: 13.08.2020								%
-%													%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Use this config file ONLY for test_quadrature.cpp!
-% Only specify options that are important for this unit test!
-%
-% ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
-OUTPUT_FILE = rtsn_test_unit_harmonics
-LOG_DIR = ../../tests/result/logs
-
-% ---- Boundary Conditions ----
-% This is just a dummy value!
-QUAD_TYPE = MONTE_CARLO
-% This is just a dummy value!
-QUAD_ORDER = 1
-%
-% Use this option, since default solver is SN. (Solver is not used in this unit test)
-SN_ALL_GAUSS_PTS = YES

code/tests/test_config.cpp

@@ -2,7 +2,7 @@
 #include "common/config.h"
 
 TEST_CASE( "Read in Config Template" ) {
-    std::string filename = std::string( TESTS_PATH ) + "input/unit_config.cfg";
+    std::string filename = std::string( TESTS_PATH ) + "input/unit_tests/common/unit_config.cfg";
 
     // Load Settings from File
     Config* config = new Config( filename );

code/tests/test_harmonics.cpp

@@ -30,7 +30,7 @@ double P2_2( double my ) { return sqrt( 15 / ( 16 * M_PI ) ) * ( 1 - my * my );
 
 TEST_CASE( "test the spherical harmonics basis computation", "[spherical_harmonics]" ) {
 
-    std::string filename = std::string( TESTS_PATH ) + "input/unit_harmonics.cfg";
+    std::string filename = std::string( TESTS_PATH ) + "input/unit_tests/solvers/unit_harmonics.cfg";
 
     // Load Settings from File
     Config* config = new Config( filename );
@@ -86,7 +86,7 @@ TEST_CASE( "test the spherical harmonics basis computation", "[spherical_harmoni
         Vector values( 9, 0.0 );
         Vector result( 4, 0.0 );
 
-        case_file.open( "harmonicBasis_reference.csv", std::ios::in );
+        case_file.open( "unit_test/solvers/harmonicBasis_reference.csv", std::ios::in );
 
         getline( case_file, text_line );
 

code/tests/test_image_conversion.cpp

@@ -9,11 +9,11 @@
 #include "toolboxes/textprocessingtoolbox.h"
 
 TEST_CASE( "convert image data to grayscale matrix", "[image I/O]" ) {
-    std::string config_file_name = std::string( TESTS_PATH ) + "input/image_conversion.cfg";
+    std::string config_file_name = std::string( TESTS_PATH ) + "input/unit_tests/common/image_conversion.cfg";
 
     Config* config = new Config( config_file_name );    // just to init spdlog
 
-    std::string testImage = std::string( TESTS_PATH ) + "input/mini_phantom.png";
+    std::string testImage = std::string( TESTS_PATH ) + "input/unit_tests/common/mini_phantom.png";
     std::string testMesh  = config->GetMeshFile();
 
     Matrix gsImage = createSU2MeshFromImage( testImage, testMesh );
@@ -26,7 +26,7 @@ TEST_CASE( "convert image data to grayscale matrix", "[image I/O]" ) {
         REQUIRE( blaze::max( gsImage ) <= 1.0 );           // upper bound
 
         // load reference matrix from csv file
-        std::string refMatrixFile = std::string( TESTS_PATH ) + "input/phantom.csv";
+        std::string refMatrixFile = std::string( TESTS_PATH ) + "input/unit_tests/common/phantom.csv";
         std::ifstream data( refMatrixFile );
         REQUIRE( data.is_open() );
         std::string line;