Merge branch 'mergebranch_sprint1' of https://git.scc.kit.edu/rtsn/rtsn into sprint1

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/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/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/image_conversion.cfg → code/tests/input/unit_tests/common/image_conversion.cfg

 % ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
+OUTPUT_DIR = ../../../result
 OUTPUT_FILE = ctscan_test
-LOG_DIR = ../../tests/result/logs
-MESH_FILE = ../../tests/result/ctscan_test.su2
+LOG_DIR = ../../../result/logs
+MESH_FILE = ../../../result/ctscan_test.su2
 
 % ---- Solver specifications ----
 CFL_NUMBER = 0.5

code/tests/input/unit_config.cfg → code/tests/input/unit_tests/common/unit_config.cfg

@@ -18,7 +18,7 @@ OUTPUT_FILE = rtsn_test_unit_config
 % Log directory
 LOG_DIR = ../result/logs
 % Mesh File
-MESH_FILE = unit.su2
+MESH_FILE = ../../mesh_files/unit.su2
 %
 % ---- Solver specifications ----
 %

code/tests/input/unit_mesh.cfg → code/tests/input/unit_tests/common/unit_mesh.cfg

@@ -10,10 +10,10 @@
 % Only specify options that are important for this unit test!
 %
 % ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
+OUTPUT_DIR = ../../../result
 OUTPUT_FILE = rtsn_test_unit_mesh
-LOG_DIR = ../../tests/result/logs
-MESH_FILE = unit_mesh.su2
+LOG_DIR = ../../../result/logs
+MESH_FILE = ../../mesh_files/unit_mesh.su2
 %
 % ---- Boundary Conditions ----
 BC_DIRICHLET = ( void )

code/tests/input/unit_kernel.cfg → code/tests/input/unit_tests/kernels/unit_kernel.cfg

@@ -11,9 +11,9 @@
 %
 % ---- File specifications ----
 %
-OUTPUT_DIR = ../../tests/result
+OUTPUT_DIR = ../../../result
 OUTPUT_FILE = rtsn_test_unit_kernel
-LOG_DIR = ../../tests/result/logs
+LOG_DIR = ../../../result/logs
 %
 % ---- Quadrature Settings ----
 QUAD_TYPE = LEBEDEV

code/tests/input/unit_optimizerNewton.cfg → code/tests/input/unit_tests/optimizers/unit_optimizerNewton.cfg

@@ -10,9 +10,9 @@
 % Only specify options that are important for this unit test!
 %
 % ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
+OUTPUT_DIR = ../../../result
 OUTPUT_FILE = rtsn_test_unit_optimizerNewton
-LOG_DIR = ../../tests/result/logs
+LOG_DIR = ../../../result/logs
 %
 % ---- Solver specifications ----
 %

code/tests/input/unit_quadrature.cfg → code/tests/input/unit_tests/quadratures/unit_quadrature.cfg

@@ -10,9 +10,9 @@
 % Only specify options that are important for this unit test!
 %
 % ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
+OUTPUT_DIR = ../../../result
 OUTPUT_FILE = rtsn_test_unit_harmonics
-LOG_DIR = ../../tests/result/logs
+LOG_DIR = ../../../result/logs
 
 % ---- Boundary Conditions ----
 % This is just a dummy value!

code/tests/input/unit_harmonics.cfg → code/tests/input/unit_tests/solvers/unit_harmonics.cfg

@@ -9,9 +9,9 @@
 % Use this config file ONLY for test_harmonics.cpp!
 %
 % ---- File specifications ----
-OUTPUT_DIR = ../../tests/result
+OUTPUT_DIR = ../../../result
 OUTPUT_FILE = rtsn_test_unit_harmonics
-LOG_DIR = ../../tests/result/logs
+LOG_DIR = ../../../result/logs
 
 % ---- Boundary Conditions ----
 QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED

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;