void FillYSliceWith(mitk::pa::Volume::Pointer fluenceVolume, double ySlice, double value)
{
for (unsigned int x = 0; x < fluenceVolume->GetXDim(); ++x)
for (unsigned int z = 0; z < fluenceVolume->GetZDim(); ++z)
{
fluenceVolume->SetData(value, x, ySlice, z);
}
}
void AssertYSliceValue(mitk::pa::Volume::Pointer fluenceVolume, double ySlice, double value)
{
for (unsigned int x = 0; x < fluenceVolume->GetXDim(); ++x)
for (unsigned int z = 0; z < fluenceVolume->GetZDim(); ++z)
{
std::string msg = "Expected: " + std::to_string(value) + " actual: " + std::to_string(fluenceVolume->GetData(x, ySlice, z));
CPPUNIT_ASSERT_MESSAGE(msg, std::abs(fluenceVolume->GetData(x, ySlice, z) - value) < mitk::eps);
}
}
void setUp()
{
m_VolumeProperties = createTestVolumeParameters();
m_TestInSilicoVolume = mitk::pa::InSilicoTissueVolume::New(m_VolumeProperties);
m_Test3DVolume = createTest3DVolume(5);
itk::FileTools::CreateDirectory(TEST_FOLDER_PATH);
itk::FileTools::CreateDirectory(TEST_QUALIFIED_FOLDER_PATH);
itk::FileTools::CreateDirectory(TEST_FOLDER_PATH + FOLDER_FOLDER + FOLDER_FOLDER);
itk::FileTools::CreateDirectory(FCM_PATH);
CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(TEST_FOLDER_PATH));
CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(TEST_QUALIFIED_FOLDER_PATH));
CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(TEST_FOLDER_PATH + FOLDER_FOLDER + FOLDER_FOLDER));
CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(FCM_PATH));
mitk::IOUtil::Save(m_TestInSilicoVolume->ConvertToMitkImage(),
TEST_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + TEST_FILE_ENDING);
mitk::IOUtil::Save(m_Test3DVolume->AsMitkImage(),
TEST_FOLDER_PATH + TEST_3D_Volume_PATH + TEST_FILE_ENDING);
auto yo0 = createTest3DVolume(1)->AsMitkImage();
auto yo1 = createTest3DVolume(2)->AsMitkImage();
yo0->GetPropertyList()->SetStringProperty("y-offset", "0");
yo1->GetPropertyList()->SetStringProperty("y-offset", "1");
mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("y-offset"));
mitk::IOUtil::Save(yo0, TEST_QUALIFIED_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + "_yo0" + TEST_FILE_ENDING);
mitk::IOUtil::Save(yo1, TEST_QUALIFIED_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + "_yo1" + TEST_FILE_ENDING);
}
void testNoiseGenerator()
{
int size = 1000 * 100 * 100;
auto* volume = new double[size];
for (int i = 0; i < size; i++)
{
volume[i] = 1;
}
m_Volume = mitk::pa::Volume::New(volume, 1000, 100, 100, 1);
mitk::pa::NoiseGenerator::ApplyNoiseModel(m_Volume, 0.75, 0.1);
int negativecounter = 0;
for (int i = 0; i < size; i++)
{
if (m_Volume->GetData()[i] <= 0)
{
negativecounter++;
}
}
CPPUNIT_ASSERT_EQUAL_MESSAGE("More than one negative: " +
std::to_string(negativecounter) + " (" +
std::to_string((((double)negativecounter) / size) * 100) + "%)", negativecounter, 0);
}
/**
* @brief Fast 3D Gaussian convolution IIR approximation
* @param paVolume
* @param sigma
* @author Pascal Getreuer <*****@*****.**>
*
* Copyright (c) 2011, Pascal Getreuer
* All rights reserved.
*
* This program is free software: you can redistribute it and/or modify it
* under the terms of the simplified BSD license.
*
* You should have received a copy of these licenses along with this program.
* If not, see <http://www.opensource.org/licenses/bsd-license.html>.
*/
void mitk::pa::VolumeManipulator::GaussianBlur3D(mitk::pa::Volume::Pointer paVolume, double sigma)
{
double* volume = paVolume->GetData();
long width = paVolume->GetYDim();
long height = paVolume->GetXDim();
long depth = paVolume->GetZDim();
const long plane = width*height;
const long numel = plane*depth;
double lambda, dnu;
double nu, boundaryscale, postscale;
double *ptr;
long i, x, y, z;
int step;
if (sigma <= 0)
return;
lambda = (sigma*sigma) / (8.0);
dnu = (1.0 + 2.0*lambda - sqrt(1.0 + 4.0*lambda)) / (2.0*lambda);
nu = dnu;
boundaryscale = 1.0 / (1.0 - dnu);
postscale = pow(dnu / lambda, 12);
/* Filter horizontally along each row */
for (z = 0; z < depth; z++)
{
for (y = 0; y < height; y++)
{
for (step = 0; step < 4; step++)
{
ptr = volume + width*(y + height*z);
ptr[0] *= boundaryscale;
/* Filter rightwards */
for (x = 1; x < width; x++)
{
ptr[x] += nu*ptr[x - 1];
}
ptr[x = width - 1] *= boundaryscale;
/* Filter leftwards */
for (; x > 0; x--)
{
ptr[x - 1] += nu*ptr[x];
}
}
}
}
/* Filter vertically along each column */
for (z = 0; z < depth; z++)
{
for (x = 0; x < width; x++)
{
for (step = 0; step < 4; step++)
{
ptr = volume + x + plane*z;
ptr[0] *= boundaryscale;
/* Filter downwards */
for (i = width; i < plane; i += width)
{
ptr[i] += nu*ptr[i - width];
}
ptr[i = plane - width] *= boundaryscale;
/* Filter upwards */
for (; i > 0; i -= width)
{
ptr[i - width] += nu*ptr[i];
}
}
}
}
/* Filter along z-dimension */
for (y = 0; y < height; y++)
{
for (x = 0; x < width; x++)
{
for (step = 0; step < 4; step++)
{
ptr = volume + x + width*y;
ptr[0] *= boundaryscale;
for (i = plane; i < numel; i += plane)
{
ptr[i] += nu*ptr[i - plane];
}
ptr[i = numel - plane] *= boundaryscale;
for (; i > 0; i -= plane)
{
ptr[i - plane] += nu*ptr[i];
}
}
}
}
for (i = 0; i < numel; i++)
{
volume[i] *= postscale;
}
}
void assertEqual(mitk::pa::Volume::Pointer first, mitk::pa::Volume::Pointer second)
{
CPPUNIT_ASSERT(first->GetXDim() == second->GetXDim());
CPPUNIT_ASSERT(first->GetYDim() == second->GetYDim());
CPPUNIT_ASSERT(first->GetZDim() == second->GetZDim());
for (unsigned int x = 0; x < first->GetXDim(); ++x)
for (unsigned int y = 0; y < first->GetYDim(); ++y)
for (unsigned int z = 0; z < first->GetZDim(); ++z)
{
std::string message = "Expected " + std::to_string(first->GetData(x, y, z)) + " but was " + std::to_string(second->GetData(x, y, z));
CPPUNIT_ASSERT_MESSAGE(message, abs(first->GetData(x, y, z) - second->GetData(x, y, z)) < 1e-6);
}
}