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‎src/Core/Algorithms/BrainStimulator/Tests/GenerateROIStatisticsAlgorithmTests.cc‎

Lines changed: 47 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@
2525
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
2626
DEALINGS IN THE SOFTWARE.
2727
*/
28-
28+
2929
#include <gtest/gtest.h>
3030
#include <Core/Math/MiscMath.h>
3131
#include <Core/Datatypes/Legacy/Field/VField.h>
@@ -49,46 +49,46 @@ namespace
4949
{
5050
FieldHandle CreateGetMeshSolution()
5151
{
52-
return loadFieldFromFile(TestResources::rootDir() / "generateroistatistics/mesh_sol.fld");
52+
return loadFieldFromFile(TestResources::rootDir() / "Fields/generateroistatistics/mesh_sol.fld");
5353
}
54-
54+
5555
FieldHandle CreateCoordinatesCubesShiftedBy10()
5656
{
57-
return loadFieldFromFile(TestResources::rootDir() / "generateroistatistics/coordinates_cubes_shifted_by_10.fld");
57+
return loadFieldFromFile(TestResources::rootDir() / "Fields/generateroistatistics/coordinates_cubes_shifted_by_10.fld");
5858
}
59-
59+
6060
FieldHandle CreateCoordinatesCubes()
6161
{
62-
return loadFieldFromFile(TestResources::rootDir() / "generateroistatistics/coordinates_cubes.fld");
63-
}
64-
62+
return loadFieldFromFile(TestResources::rootDir() / "Fields/generateroistatistics/coordinates_cubes.fld");
63+
}
64+
6565
FieldHandle CreateAtlas()
6666
{
67-
return loadFieldFromFile(TestResources::rootDir() / "generateroistatistics/atlas.fld");
68-
}
69-
70-
DenseMatrixHandle expected_result_no_roi_spec()
67+
return loadFieldFromFile(TestResources::rootDir() / "Fields/generateroistatistics/atlas.fld");
68+
}
69+
70+
DenseMatrixHandle expected_result_no_roi_spec()
7171
{
7272
DenseMatrixHandle expected_result(boost::make_shared<DenseMatrix>(8, 5));
7373

74-
(*expected_result)(0, 0) = 0.5398800608953688; (*expected_result)(1, 0) = 0.7546866819823609; (*expected_result)(2, 0) = 0.3784870349158202; (*expected_result)(3, 0) = 0.5215146855270543; (*expected_result)(4, 0) = 0.6204598403245096; (*expected_result)(5, 0) = 0.4103867315361441; (*expected_result)(6, 0) = 0.6164145705872455; (*expected_result)(7, 0) = 0.3773992798882833;
75-
(*expected_result)(0, 1) = 0.2023192248404992; (*expected_result)(1, 1) = std::numeric_limits<double>::quiet_NaN(); (*expected_result)(2, 1) = 0.270036948169627; (*expected_result)(3, 1) = 0.2819928747450936; (*expected_result)(4, 1) = 0.2464919130115238; (*expected_result)(5, 1) = 0.348358459345021; (*expected_result)(6, 1) = 0.3382031144990396; (*expected_result)(7, 1) = 0.1699586184078796;
76-
(*expected_result)(0, 2) = 0.1868726045543786; (*expected_result)(1, 2) = 0.7546866819823609; (*expected_result)(2, 2) = 0.1189976815583766; (*expected_result)(3, 2) = 0.223811939491137; (*expected_result)(4, 2) = 0.2550951154592691; (*expected_result)(5, 2) = 0.1386244428286791; (*expected_result)(6, 2) = 0.2435249687249893; (*expected_result)(7, 2) = 0.1965952504312082;
77-
(*expected_result)(0, 3) = 0.7951999011370632; (*expected_result)(1, 3) = 0.7546866819823609; (*expected_result)(2, 3) = 0.6797026768536748; (*expected_result)(3, 3) = 0.9597439585160811; (*expected_result)(4, 3) = 0.8909032525357985; (*expected_result)(5, 3) = 0.9592914252054443; (*expected_result)(6, 3) = 0.9292636231872278; (*expected_result)(7, 3) = 0.6160446761466392;
74+
(*expected_result)(0, 0) = 0.5398800608953688; (*expected_result)(1, 0) = 0.7546866819823609; (*expected_result)(2, 0) = 0.3784870349158202; (*expected_result)(3, 0) = 0.5215146855270543; (*expected_result)(4, 0) = 0.6204598403245096; (*expected_result)(5, 0) = 0.4103867315361441; (*expected_result)(6, 0) = 0.6164145705872455; (*expected_result)(7, 0) = 0.3773992798882833;
75+
(*expected_result)(0, 1) = 0.2023192248404992; (*expected_result)(1, 1) = std::numeric_limits<double>::quiet_NaN(); (*expected_result)(2, 1) = 0.270036948169627; (*expected_result)(3, 1) = 0.2819928747450936; (*expected_result)(4, 1) = 0.2464919130115238; (*expected_result)(5, 1) = 0.348358459345021; (*expected_result)(6, 1) = 0.3382031144990396; (*expected_result)(7, 1) = 0.1699586184078796;
76+
(*expected_result)(0, 2) = 0.1868726045543786; (*expected_result)(1, 2) = 0.7546866819823609; (*expected_result)(2, 2) = 0.1189976815583766; (*expected_result)(3, 2) = 0.223811939491137; (*expected_result)(4, 2) = 0.2550951154592691; (*expected_result)(5, 2) = 0.1386244428286791; (*expected_result)(6, 2) = 0.2435249687249893; (*expected_result)(7, 2) = 0.1965952504312082;
77+
(*expected_result)(0, 3) = 0.7951999011370632; (*expected_result)(1, 3) = 0.7546866819823609; (*expected_result)(2, 3) = 0.6797026768536748; (*expected_result)(3, 3) = 0.9597439585160811; (*expected_result)(4, 3) = 0.8909032525357985; (*expected_result)(5, 3) = 0.9592914252054443; (*expected_result)(6, 3) = 0.9292636231872278; (*expected_result)(7, 3) = 0.6160446761466392;
7878
(*expected_result)(0, 4) = 9; (*expected_result)(1, 4) = 1; (*expected_result)(2, 4) = 5; (*expected_result)(3, 4) = 5; (*expected_result)(4, 4) = 5; (*expected_result)(5, 4) = 5; (*expected_result)(6, 4) = 5; (*expected_result)(7, 4) = 5; (*expected_result)(8, 4) = 5;
79-
79+
8080
return expected_result;
8181
}
82-
83-
DenseMatrixHandle expected_result_roi_spec()
82+
83+
DenseMatrixHandle expected_result_roi_spec()
8484
{
8585
DenseMatrixHandle expected_result(boost::make_shared<DenseMatrix>(1, 5));
8686
(*expected_result)(0, 0) = 0.5046221600763444;
8787
(*expected_result)(0, 1) = 0.2271478773489659;
8888
(*expected_result)(0, 2) = 0.1626117351946306;
8989
(*expected_result)(0, 3) = 0.7951999011370632;
9090
(*expected_result)(0, 4) = 14;
91-
91+
9292
return expected_result;
9393
}
9494
}
@@ -97,22 +97,22 @@ TEST(GenerateROIStatisticsAlgorithm, ValidInput_TestAllROI)
9797
{
9898
GenerateROIStatisticsAlgorithm algo;
9999
FieldHandle atlas = CreateAtlas();
100-
FieldHandle createcoordcubes = CreateCoordinatesCubes();
101-
FieldHandle createmeshsolution = CreateGetMeshSolution();
100+
FieldHandle createcoordcubes = CreateCoordinatesCubes();
101+
FieldHandle createmeshsolution = CreateGetMeshSolution();
102102
const std::string& atlasMeshLabelsStr = std::string("Region1;Region2;Region3;Region4;Region5;Region6;Region7;Region8");
103103
DenseMatrixHandle specROI(new DenseMatrix(5, 1));
104104
(*specROI)(0, 0) = 0;
105105
(*specROI)(1, 0) = 0;
106106
(*specROI)(2, 0) = 0;
107-
(*specROI)(3, 0) = 0;
108-
(*specROI)(4, 0) = 0;
107+
(*specROI)(3, 0) = 0;
108+
(*specROI)(4, 0) = 0;
109109
auto output = algo.run(createmeshsolution,atlas,createcoordcubes,atlasMeshLabelsStr, specROI);
110110
DenseMatrixHandle outputMatrix = output.get<0>();
111-
111+
112112
DenseMatrixHandle expected_result = expected_result_no_roi_spec();
113113
EXPECT_EQ(outputMatrix->rows(),expected_result->rows());
114-
EXPECT_EQ(outputMatrix->cols(),expected_result->cols());
115-
114+
EXPECT_EQ(outputMatrix->cols(),expected_result->cols());
115+
116116
for (int i = 0; i < outputMatrix->rows(); i++)
117117
for (int j = 0; j < outputMatrix->cols(); j++)
118118
if (i==1 && j==1)
@@ -121,62 +121,62 @@ TEST(GenerateROIStatisticsAlgorithm, ValidInput_TestAllROI)
121121
{
122122
FAIL() << "ERROR: Test on NaN failed!" << std::endl;
123123
}
124-
}
124+
}
125125
else
126126
{
127127
EXPECT_NEAR((*outputMatrix)(i, j), (*expected_result)(i,j), 1e-10);
128128
}
129-
129+
130130
}
131131

132-
TEST(GenerateROIStatisticsAlgorithm, ValidInput_TestSpecROI)
132+
TEST(GenerateROIStatisticsAlgorithm, ValidInput_TestSpecROI)
133133
{
134134
GenerateROIStatisticsAlgorithm algo;
135135
FieldHandle atlas = CreateAtlas();
136-
FieldHandle createcoordcubes = CreateCoordinatesCubes();
137-
FieldHandle createmeshsolution = CreateGetMeshSolution();
136+
FieldHandle createcoordcubes = CreateCoordinatesCubes();
137+
FieldHandle createmeshsolution = CreateGetMeshSolution();
138138
const std::string& atlasMeshLabelsStr = std::string("Region1;Region2;Region3;Region4;Region5;Region6;Region7;Region8");
139139
DenseMatrixHandle specROI(new DenseMatrix(5, 1));
140140
(*specROI)(0, 0) = 0.5;
141141
(*specROI)(1, 0) = 0.5;
142142
(*specROI)(2, 0) = 0.5;
143-
(*specROI)(3, 0) = 0;
144-
(*specROI)(4, 0) = 1;
143+
(*specROI)(3, 0) = 0;
144+
(*specROI)(4, 0) = 1;
145145
auto output = algo.run(createmeshsolution,atlas,createcoordcubes,atlasMeshLabelsStr, specROI);
146146
DenseMatrixHandle outputMatrix = output.get<0>();
147-
147+
148148
DenseMatrixHandle expected_result = expected_result_roi_spec();
149149
EXPECT_EQ(outputMatrix->rows(),expected_result->rows());
150-
EXPECT_EQ(outputMatrix->cols(),expected_result->cols());
151-
150+
EXPECT_EQ(outputMatrix->cols(),expected_result->cols());
151+
152152
for (int i = 0; i < outputMatrix->rows(); i++)
153153
for (int j = 0; j < outputMatrix->cols(); j++)
154154
EXPECT_NEAR((*outputMatrix)(i, j), (*expected_result)(i,j), 1e-10);
155-
155+
156156
}
157157

158-
TEST(GenerateROIStatisticsAlgorithm, ValidInput_TestCoordinateSpace)
158+
TEST(GenerateROIStatisticsAlgorithm, ValidInput_TestCoordinateSpace)
159159
{
160160
GenerateROIStatisticsAlgorithm algo;
161-
FieldHandle atlas = CreateAtlas();
161+
FieldHandle atlas = CreateAtlas();
162162
FieldHandle createcoordcubesshiftby10 = CreateCoordinatesCubesShiftedBy10();
163-
FieldHandle createmeshsolution = CreateGetMeshSolution();
163+
FieldHandle createmeshsolution = CreateGetMeshSolution();
164164
const std::string& atlasMeshLabelsStr = std::string("Region1;Region2;Region3;Region4;Region5;Region6;Region7;Region8");
165165
DenseMatrixHandle specROI(new DenseMatrix(5, 1));
166166
(*specROI)(0, 0) = 10.5;
167167
(*specROI)(1, 0) = 10.5;
168168
(*specROI)(2, 0) = 10.5;
169-
(*specROI)(3, 0) = 0;
170-
(*specROI)(4, 0) = 1.0;
169+
(*specROI)(3, 0) = 0;
170+
(*specROI)(4, 0) = 1.0;
171171
auto output = algo.run(createmeshsolution,atlas,createcoordcubesshiftby10,atlasMeshLabelsStr, specROI);
172172
DenseMatrixHandle outputMatrix = output.get<0>();
173-
173+
174174
DenseMatrixHandle expected_result = expected_result_roi_spec();
175175
EXPECT_EQ(outputMatrix->rows(),expected_result->rows());
176-
EXPECT_EQ(outputMatrix->cols(),expected_result->cols());
177-
176+
EXPECT_EQ(outputMatrix->cols(),expected_result->cols());
177+
178178
for (int i = 0; i < outputMatrix->rows(); i++)
179179
for (int j = 0; j < outputMatrix->cols(); j++)
180180
EXPECT_NEAR((*outputMatrix)(i, j), (*expected_result)(i,j), 1e-10);
181-
181+
182182
}

‎src/Core/Algorithms/BrainStimulator/Tests/SetConductivitiesToTetMeshAlgorithmTests.cc‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@
2525
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
2626
DEALINGS IN THE SOFTWARE.
2727
*/
28-
28+
2929
#include <gtest/gtest.h>
3030

3131
#include <Core/Datatypes/Legacy/Field/VField.h>
@@ -47,39 +47,39 @@ namespace
4747
{
4848
FieldHandle CreateTetMeshVectorOnElem()
4949
{
50-
return loadFieldFromFile(TestResources::rootDir() / "_etfielddata/tet_mesh/data_defined_on_elem/vector/tet_vector_on_elem.fld");
50+
return loadFieldFromFile(TestResources::rootDir() / "Fields/tet_mesh/data_defined_on_elem/vector/tet_vector_on_elem.fld");
5151
}
5252
FieldHandle CreateTetMeshScalarSevenElem()
5353
{
54-
return loadFieldFromFile(TestResources::rootDir() / "_etfielddata/tet_mesh_7elem.fld");
54+
return loadFieldFromFile(TestResources::rootDir() / "Fields/tet_mesh/tet_mesh_7elem.fld");
5555
}
5656
FieldHandle CreateTetMeshScalarOnElem()
5757
{
58-
return loadFieldFromFile(TestResources::rootDir() / "_etfielddata/tet_mesh/data_defined_on_elem/scalar/tet_scalar_on_elem.fld");
58+
return loadFieldFromFile(TestResources::rootDir() / "Fields/tet_mesh/data_defined_on_elem/scalar/tet_scalar_on_elem.fld");
5959
}
6060
FieldHandle CreateTetMeshScalarOnNode()
6161
{
62-
return loadFieldFromFile(TestResources::rootDir() / "_etfielddata/tet_mesh/data_defined_on_node/scalar/tet_scalar_on_node.fld");
62+
return loadFieldFromFile(TestResources::rootDir() / "Fields/tet_mesh/data_defined_on_node/scalar/tet_scalar_on_node.fld");
6363
}
6464
}
6565

6666
TEST(SetConductivitiesToTetMeshAlgorithmTest, TetMeshScalars)
6767
{
6868
SetConductivitiesToTetMeshAlgorithm algo;
69-
69+
7070
double conductivities[] = {9.25, 25.1988, 18.99999, 3.5, 5.1988, 5.22, 22.2013};
71-
71+
7272
algo.set(Parameters::Skin, conductivities[0]);
7373
algo.set(Parameters::SoftBone, conductivities[1]);
7474
algo.set(Parameters::HardBone, conductivities[2]);
7575
algo.set(Parameters::CSF, conductivities[3]);
7676
algo.set(Parameters::GM, conductivities[4]);
7777
algo.set(Parameters::WM, conductivities[5]);
7878
algo.set(Parameters::Electrode, conductivities[6]);
79-
79+
8080
auto input = CreateTetMeshScalarSevenElem();
8181
auto output = algo.run(input);
82-
82+
8383
VField* ivfield = input->vfield();
8484
VField* ovfield = output->vfield();
8585
int ival = 0;
@@ -96,9 +96,9 @@ TEST(SetConductivitiesToTetMeshAlgorithmTest, TetMeshScalars)
9696
TEST(SetConductivitiesToTetMeshAlgorithmTest, TetMeshScalarSevenElem)
9797
{
9898
SetConductivitiesToTetMeshAlgorithm algo;
99-
99+
100100
double conductivities[] = {9.25, 25.1988, 18.99999, 3.5, 5.1988, 5.22, 22.2013};
101-
101+
102102
algo.set(Parameters::Skin, conductivities[0]);
103103
algo.set(Parameters::SoftBone, conductivities[1]);
104104
algo.set(Parameters::HardBone, conductivities[2]);
@@ -109,7 +109,7 @@ TEST(SetConductivitiesToTetMeshAlgorithmTest, TetMeshScalarSevenElem)
109109

110110
FieldHandle input = CreateTetMeshScalarSevenElem();
111111
FieldHandle output = algo.run(CreateTetMeshScalarSevenElem());
112-
112+
113113
VField* ivfield = input->vfield();
114114
VField* ovfield = output->vfield();
115115
int ival = 0;
@@ -136,7 +136,7 @@ TEST(SetConductivitiesToTetMeshAlgorithmTest, TetMeshScalarThreeElem)
136136

137137
FieldHandle input = CreateTetMeshScalarOnElem();
138138
FieldHandle output = algo.run(CreateTetMeshScalarOnElem());
139-
139+
140140
VField* ivfield = input->vfield();
141141
VField* ovfield = output->vfield();
142142
int ival = 0;

‎src/Core/Algorithms/BrainStimulator/Tests/SimulateForwardMagneticFieldAlgorithmTests.cc‎

Lines changed: 23 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -55,77 +55,76 @@ using namespace SCIRun::Core::Algorithms::Fields;
5555
using namespace SCIRun::Core::Algorithms::BrainStimulator;
5656

5757
FieldHandle LoadFieldFirstModuleInput()
58-
{
59-
return loadFieldFromFile(TestResources::rootDir() / "simulateforwardmagneticfield/first.fld");
58+
{
59+
return loadFieldFromFile(TestResources::rootDir() / "Fields/simulateforwardmagneticfield/first.fld");
6060
}
6161

6262
FieldHandle LoadFieldSecondModuleInput()
63-
{
64-
return loadFieldFromFile(TestResources::rootDir() / "simulateforwardmagneticfield/second.fld");
63+
{
64+
return loadFieldFromFile(TestResources::rootDir() / "Fields/simulateforwardmagneticfield/second.fld");
6565
}
6666

6767
FieldHandle LoadFieldThirdModuleInput()
68-
{
69-
return loadFieldFromFile(TestResources::rootDir() / "simulateforwardmagneticfield/third.fld");
68+
{
69+
return loadFieldFromFile(TestResources::rootDir() / "Fields/simulateforwardmagneticfield/third.fld");
7070
}
7171

7272
FieldHandle LoadFieldFourthModuleInput()
73-
{
74-
return loadFieldFromFile(TestResources::rootDir() / "simulateforwardmagneticfield/fourth.fld");
73+
{
74+
return loadFieldFromFile(TestResources::rootDir() / "Fields/simulateforwardmagneticfield/fourth.fld");
7575
}
7676

7777
FieldHandle LoadFieldMagneticFieldResult()
78-
{
79-
return loadFieldFromFile(TestResources::rootDir() / "simulateforwardmagneticfield/result_magnetic_field.fld");
78+
{
79+
return loadFieldFromFile(TestResources::rootDir() / "Fields/simulateforwardmagneticfield/result_magnetic_field.fld");
8080
}
8181

8282
FieldHandle LoadFieldMagneticFieldMagnitudesResult()
83-
{
84-
return loadFieldFromFile(TestResources::rootDir() / "simulateforwardmagneticfield/result_magnetic_field_magnitudes.fld");
83+
{
84+
return loadFieldFromFile(TestResources::rootDir() / "Fields/simulateforwardmagneticfield/result_magnetic_field_magnitudes.fld");
8585
}
8686

8787

8888
TEST(SimulateForwardMagneticFieldAlgoTest, TestOnLatVol)
8989
{
9090
FieldHandle first = LoadFieldFirstModuleInput();
91-
FieldHandle second = LoadFieldSecondModuleInput();
91+
FieldHandle second = LoadFieldSecondModuleInput();
9292
FieldHandle third = LoadFieldThirdModuleInput();
9393
FieldHandle fourth = LoadFieldFourthModuleInput();
9494
long nr_nodes = (long)second->vmesh()->num_nodes();
9595
DenseMatrixHandle tensor_matrix(boost::make_shared<DenseMatrix>(nr_nodes,9));
96-
96+
9797
for (long i=0;i<nr_nodes;i++)
9898
{
9999
for (int j=0;j<7;j++)
100100
{
101101
if (j==0 || j==4 || j==8)
102102
(*tensor_matrix)(i,j)=1;
103103
else
104-
(*tensor_matrix)(i,j)=0;
104+
(*tensor_matrix)(i,j)=0;
105105
}
106106
}
107-
107+
108108
SetFieldDataAlgo algo;
109109

110-
FieldHandle second_with_tensor = algo.run(second, tensor_matrix);
110+
FieldHandle second_with_tensor = algo.run(second, tensor_matrix);
111111

112112
SimulateForwardMagneticFieldAlgo algo2;
113-
113+
114114
FieldHandle MField, MFieldMagnitudes;
115115
boost::tie(MField,MFieldMagnitudes) = algo2.run(first,second_with_tensor,third,fourth);
116-
116+
117117
GetFieldDataAlgo algo3;
118-
118+
119119
DenseMatrixHandle MField_matrix = algo3.run(MField);
120120
DenseMatrixHandle MFieldMagnitudes_matrix = algo3.run(MFieldMagnitudes);
121-
121+
122122
FieldHandle MField_expected = LoadFieldMagneticFieldResult();
123123
FieldHandle MFieldMagnitudes_expected = LoadFieldMagneticFieldMagnitudesResult();
124-
124+
125125
DenseMatrixHandle MField_expected_matrix = algo3.run(MField_expected);
126126
DenseMatrixHandle MFieldMagnitudes_expected_matrix = algo3.run(MFieldMagnitudes_expected);
127-
127+
128128
EXPECT_MATRIX_EQ_TOLERANCE(*MField_matrix, *MField_expected_matrix, 1e-16);
129129
EXPECT_MATRIX_EQ_TOLERANCE(*MFieldMagnitudes_matrix, *MFieldMagnitudes_expected_matrix, 1e-16);
130130
}
131-

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