Skip to content

GitLab

Commit a9af7d2c authored by Christian Schulte zu Berge's avatar Christian Schulte zu Berge
Browse files

introduce NCC to SimilarityMeasure (somewhat dirty hack)

parent b1e6c5ec
Hide whitespace changes
Inline Side-by-side
Showing with 187 additions and 33 deletions
modules/registration/glsl/similaritymeasurencc.frag 0 → 100644
View file @ a9af7d2c
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// If not explicitly stated otherwise: Copyright (C) 2012, all rights reserved,
// Christian Schulte zu Berge <christian.szb@in.tum.de>
// Chair for Computer Aided Medical Procedures
// Technische Universitt Mnchen
// Boltzmannstr. 3, 85748 Garching b. Mnchen, Germany
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
// The licensing of this softare is not yet resolved. Until then, redistribution in source or
// binary forms outside the CAMP chair is not permitted, unless explicitly stated in legal form.
// However, the names of the original authors and the above copyright notice must retain in its
// original state in any case.
//
// Legal disclaimer provided by the BSD license:
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
// AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
//
// ================================================================================================
in vec3 ex_TexCoord;
out vec4 out_Sums;
out vec4 out_Squares;
//out float out_Value;
#include "tools/texture3d.frag"
uniform sampler3D _referenceTexture;
uniform TextureParameters3D _referenceTextureParams;
uniform sampler3D _movingTexture;
uniform TextureParameters3D _movingTextureParams;
uniform mat4 _registrationInverse;
uniform bool _applyMask = false;
uniform vec2 _xClampRange = vec2(0.0, 1.0);
uniform vec2 _yClampRange = vec2(0.0, 1.0);
uniform vec2 _zClampRange = vec2(0.0, 1.0);
void main() {
float sPixels = 0.0;
float sFixed = 0.0;
float sMoving = 0.0;
float ssFixed = 0.0;
float ssMoving = 0.0;
float spMovingFixed = 0.0;
if (ex_TexCoord.x >= _xClampRange.x && ex_TexCoord.x <= _xClampRange.y && ex_TexCoord.y >= _yClampRange.x && ex_TexCoord.y <= _yClampRange.y) {
float zStart = min(_referenceTextureParams._sizeRCP.z / 2.0, _zClampRange.x);
float zEnd = min(1.0, _zClampRange.y);
for (float z = zStart; z < zEnd; z += _referenceTextureParams._sizeRCP.z) {
// fetch value from reference volume
vec3 referenceLookupTexCoord = vec3(ex_TexCoord.xy, z);
float referenceValue = texture(_referenceTexture, referenceLookupTexCoord).a;
// apply mask if requested
if (!_applyMask || referenceValue > 0.0) {
// compute moving lookup texture coordinates
vec4 movingLookupTexCoord = _registrationInverse * vec4(referenceLookupTexCoord, 1.0);
//movingLookupTexCoord.xyz /= movingLookupTexCoord.z;
// fetch value from moving volume
float movingValue = 0.0;
if (all(greaterThanEqual(movingLookupTexCoord.xyz, vec3(0.0))) && all(lessThanEqual(movingLookupTexCoord.xyz, vec3(1.0)))) {
movingValue = texture(_movingTexture, movingLookupTexCoord.xyz).a;
}
// compute difference metrics
sPixels += 1.0;
sFixed += referenceValue;
sMoving += movingValue;
ssFixed += referenceValue * referenceValue;
ssMoving += movingValue * movingValue;
spMovingFixed += movingValue * referenceValue;
}
}
}
out_Sums = vec4(sPixels, sFixed, sMoving, 1.0);
out_Squares = vec4(ssFixed, ssMoving, spMovingFixed, 1.0);
}
modules/registration/glsl/similaritymeasure.frag → modules/registration/glsl/similaritymeasuresadssd.frag
View file @ a9af7d2c
......@@ -47,6 +47,7 @@ uniform vec2 _yClampRange = vec2(0.0, 1.0);
uniform vec2 _zClampRange = vec2(0.0, 1.0);
void main() {
float sum = 0.0;
float sad = 0.0;
float ssd = 0.0;
......@@ -72,6 +73,7 @@ void main() {
}
// compute difference metrics
sum += 1.0;
float difference = referenceValue - movingValue;
sad += abs(difference);
ssd += difference * difference;
......@@ -79,5 +81,5 @@ void main() {
}
}
out_Color = vec4(ssd, sad, 0.0, 1.0);
out_Color = vec4(sum, sad, ssd, 1.0);
}
modules/registration/processors/similaritymeasure.cpp
View file @ a9af7d2c
......@@ -51,9 +51,11 @@ namespace campvis {
GenericOption<nlopt::algorithm>("neldermead", "Nelder-Mead Simplex", nlopt::LN_NELDERMEAD)
};
static const GenericOption<std::string> metrics[2] = {
static const GenericOption<std::string> metrics[4] = {
GenericOption<std::string>("SUM", "Sum"),
GenericOption<std::string>("SAD", "SAD"),
GenericOption<std::string>("SSD", "SSD")
GenericOption<std::string>("SSD", "SSD"),
GenericOption<std::string>("NCC", "NCC")
};
const std::string SimilarityMeasure::loggerCat_ = "CAMPVis.modules.vis.SimilarityMeasure";
......@@ -69,14 +71,16 @@ namespace campvis {
, p_translation("Translation", "Moving Image Translation", tgt::vec3(0.f), tgt::vec3(-100.f), tgt::vec3(100.f), tgt::vec3(1.f), tgt::vec3(5.f))
, p_rotation("Rotation", "Moving Image Rotation", tgt::vec3(0.f), tgt::vec3(-tgt::PIf), tgt::vec3(tgt::PIf), tgt::vec3(.01f), tgt::vec3(7.f))
, p_viewportSize("ViewportSize", "Viewport Size", tgt::ivec2(1), tgt::ivec2(1), tgt::ivec2(1000), tgt::ivec2(1), AbstractProcessor::VALID)
, p_metric("Metric", "Similarity Metric", metrics, 2)
, p_metric("Metric", "Similarity Metric", metrics, 4)
, p_computeSimilarity("ComputeSimilarity", "Compute Similarity")
, p_optimizer("Optimizer", "Optimizer", optimizers, 3)
, p_performOptimization("PerformOptimization", "Perform Optimization", AbstractProcessor::INVALID_RESULT | PERFORM_OPTIMIZATION)
, p_differenceImageId("DifferenceImageId", "Difference Image", "difference", DataNameProperty::WRITE, AbstractProcessor::VALID)
, p_computeDifferenceImage("ComputeDifferenceImage", "Compute Difference Image", AbstractProcessor::INVALID_RESULT | COMPUTE_DIFFERENCE_IMAGE)
, p_forceStop("Force Stop", "Force Stop", AbstractProcessor::VALID)
, _costFunctionShader(0)
, _sadssdCostFunctionShader(0)
, _nccCostFunctionShader(0)
, _differenceShader(0)
, _glr(0)
, _opt(0)
{
......@@ -111,9 +115,13 @@ namespace campvis {
void SimilarityMeasure::init() {
VisualizationProcessor::init();
_costFunctionShader = ShdrMgr.loadSeparate("core/glsl/passthrough.vert", "modules/registration/glsl/similaritymeasure.frag", "", false);
_costFunctionShader->setAttributeLocation(0, "in_Position");
_costFunctionShader->setAttributeLocation(1, "in_TexCoord");
_sadssdCostFunctionShader = ShdrMgr.loadSeparate("core/glsl/passthrough.vert", "modules/registration/glsl/similaritymeasuresadssd.frag", "", false);
_sadssdCostFunctionShader->setAttributeLocation(0, "in_Position");
_sadssdCostFunctionShader->setAttributeLocation(1, "in_TexCoord");
_nccCostFunctionShader = ShdrMgr.loadSeparate("core/glsl/passthrough.vert", "modules/registration/glsl/similaritymeasurencc.frag", "", false);
_nccCostFunctionShader->setAttributeLocation(0, "in_Position");
_nccCostFunctionShader->setAttributeLocation(1, "in_TexCoord");
_differenceShader = ShdrMgr.loadSeparate("core/glsl/passthrough.vert", "modules/registration/glsl/differenceimage.frag", "", false);
_differenceShader->setAttributeLocation(0, "in_Position");
......@@ -124,7 +132,9 @@ namespace campvis {
void SimilarityMeasure::deinit() {
VisualizationProcessor::deinit();
ShdrMgr.dispose(_costFunctionShader);
ShdrMgr.dispose(_sadssdCostFunctionShader);
ShdrMgr.dispose(_nccCostFunctionShader);
ShdrMgr.dispose(_differenceShader);
delete _glr;
_glr = 0;
......@@ -179,7 +189,12 @@ namespace campvis {
MyFuncData_t mfd = { this, referenceImage, movingImage, 0 };
_opt = new nlopt::opt(p_optimizer.getOptionValue(), 6);
_opt->set_min_objective(&SimilarityMeasure::optimizerFunc, &mfd);
if (p_metric.getOptionValue() == "NCC") {
_opt->set_max_objective(&SimilarityMeasure::optimizerFunc, &mfd);
}
else {
_opt->set_min_objective(&SimilarityMeasure::optimizerFunc, &mfd);
}
_opt->set_xtol_rel(1e-4);
std::vector<double> x(6);
......@@ -232,27 +247,37 @@ namespace campvis {
tgt::TextureUnit referenceUnit, movingUnit;
referenceUnit.activate();
// create temporary texture for result
tgt::Texture* similarityTex = new tgt::Texture(0, tgt::ivec3(p_viewportSize.getValue(), 1), GL_RGBA, GL_RGBA32F, GL_FLOAT, tgt::Texture::NEAREST);
// create temporary texture(s) for result
tgt::Shader* leShader = _sadssdCostFunctionShader;
tgt::Texture* similarityTex = 0;
tgt::Texture* similarityTex2 = 0;
similarityTex = new tgt::Texture(0, tgt::ivec3(p_viewportSize.getValue(), 1), GL_RGBA, GL_RGBA32F, GL_FLOAT, tgt::Texture::NEAREST);
similarityTex->uploadTexture();
similarityTex->setWrapping(tgt::Texture::CLAMP);
if (p_metric.getOptionValue() == "NCC") {
similarityTex2 = new tgt::Texture(0, tgt::ivec3(p_viewportSize.getValue(), 1), GL_RGBA, GL_RGBA32F, GL_FLOAT, tgt::Texture::NEAREST);
similarityTex2->uploadTexture();
similarityTex2->setWrapping(tgt::Texture::CLAMP);
leShader = _nccCostFunctionShader;
}
// activate FBO and attach texture
_fbo->activate();
const tgt::ivec2& windowSize = p_viewportSize.getValue();
glViewport(0, 0, static_cast<GLsizei>(windowSize.x), static_cast<GLsizei>(windowSize.y));
_fbo->attachTexture(similarityTex);
//_fbo->attachTexture(&similarityTex);
if (p_metric.getOptionValue() == "NCC")
_fbo->attachTexture(similarityTex2, GL_COLOR_ATTACHMENT1);
LGL_ERROR;
// bind input images
_costFunctionShader->activate();
_costFunctionShader->setUniform("_applyMask", p_applyMask.getValue());
_costFunctionShader->setUniform("_xClampRange", tgt::vec2(p_clipX.getValue()) / static_cast<float>(size.x));
_costFunctionShader->setUniform("_yClampRange", tgt::vec2(p_clipY.getValue()) / static_cast<float>(size.y));
_costFunctionShader->setUniform("_zClampRange", tgt::vec2(p_clipZ.getValue()) / static_cast<float>(size.z));
referenceImage->bind(_costFunctionShader, referenceUnit, "_referenceTexture", "_referenceTextureParams");
movingImage->bind(_costFunctionShader, movingUnit, "_movingTexture", "_movingTextureParams");
leShader->activate();
leShader->setUniform("_applyMask", p_applyMask.getValue());
leShader->setUniform("_xClampRange", tgt::vec2(p_clipX.getValue()) / static_cast<float>(size.x));
leShader->setUniform("_yClampRange", tgt::vec2(p_clipY.getValue()) / static_cast<float>(size.y));
leShader->setUniform("_zClampRange", tgt::vec2(p_clipZ.getValue()) / static_cast<float>(size.z));
referenceImage->bind(leShader, referenceUnit, "_referenceTexture", "_referenceTextureParams");
movingImage->bind(leShader, movingUnit, "_movingTexture", "_movingTextureParams");
tgt::mat4 registrationMatrix = tgt::mat4::createTranslation(translation) * euleranglesToMat4(rotation);
tgt::mat4 registrationInverse;
......@@ -265,9 +290,18 @@ namespace campvis {
// render quad to compute similarity measure by shader
_costFunctionShader->setUniform("_registrationInverse", registrationInverse);
QuadRdr.renderQuad();
_costFunctionShader->deactivate();
leShader->setUniform("_registrationInverse", registrationInverse);
if (p_metric.getOptionValue() == "NCC") {
static const GLenum buffers[] = { GL_COLOR_ATTACHMENT0, GL_COLOR_ATTACHMENT1};
glDrawBuffers(2, buffers);
QuadRdr.renderQuad();
glDrawBuffers(1, buffers);
}
else {
QuadRdr.renderQuad();
}
leShader->deactivate();
// detach texture and reduce it
//data.addData("All glory to the HYPNOTOAD!", new RenderData(_fbo));
......@@ -275,19 +309,44 @@ namespace campvis {
_fbo->deactivate();
// reduce the juice
std::vector<float> similarities = _glr->reduce(similarityTex);
float toReturn = 0.f;
if (p_metric.getOptionValue() == "NCC") {
std::vector<float> similarities = _glr->reduce(similarityTex);
std::vector<float> similarities2 = _glr->reduce(similarityTex2);
if (similarities.size() >= 3 && similarities2.size() >= 3) {
float countRCP = 1.f / similarities[0];
float meanFixed = similarities[1] * countRCP;
float meanMoving = similarities[2] * countRCP;
float varFixed = (similarities2[1] - (similarities[2] * similarities[2]) * countRCP) * countRCP;
float _varMoving = (similarities2[0] - (similarities[1] * similarities[1]) * countRCP) * countRCP;
float correlation = 0.0f;
if (varFixed > 0.0f && _varMoving > 0.0f)
{
correlation = (similarities2[2] - (similarities[1] * similarities[2]) * countRCP) * countRCP;
toReturn = correlation / sqrt(varFixed * _varMoving);
}
}
delete similarityTex;
}
else {
std::vector<float> similarities = _glr->reduce(similarityTex);
if (p_metric.getOptionValue() == "SUM")
toReturn = similarities[0];
else if (p_metric.getOptionValue() == "SAD")
toReturn = similarities[1];
else if (p_metric.getOptionValue() == "SSD")
toReturn = similarities[2];
}
delete similarityTex;
delete similarityTex2;
tgt::TextureUnit::setZeroUnit();
LGL_ERROR;
if (similarities.empty())
return 0.f;
if (p_metric.getOptionValue() == "SAD")
return similarities[0];
if (p_metric.getOptionValue() == "SSD")
return similarities[1];
return toReturn;
}
double SimilarityMeasure::optimizerFunc(const std::vector<double>& x, std::vector<double>& grad, void* my_func_data) {
......@@ -301,7 +360,7 @@ namespace campvis {
float similarity = mfd->_object->computeSimilarity(mfd->_reference, mfd->_moving, translation, rotation);
GLGC.deleteGarbage();
std::cout << translation << rotation << " : " << similarity << "\n";
LDEBUG(translation << rotation << " : " << similarity);
return similarity;
}
......
modules/registration/processors/similaritymeasure.h
View file @ a9af7d2c
......@@ -141,7 +141,8 @@ namespace campvis {
IVec2Property p_viewportSize;
tgt::Shader* _costFunctionShader; ///< Shader for slice rendering
tgt::Shader* _sadssdCostFunctionShader; ///< Shader for computing SAD/SSD
tgt::Shader* _nccCostFunctionShader; ///< Shader for computing NCC
tgt::Shader* _differenceShader; ///< Shader for computing the difference image
GlReduction* _glr;
nlopt::opt* _opt;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment