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Commit a9af7d2c authored by Christian Schulte zu Berge's avatar Christian Schulte zu Berge
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introduce NCC to SimilarityMeasure (somewhat dirty hack)

parent b1e6c5ec
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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;
......
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