Introducing IvusTcSliceExtractor processor using Predicate Histogram Widget...

Introducing IvusTcSliceExtractor processor using Predicate Histogram Widget for classification setup.
So far just a draft - it is working but the results are not really beautiful.

modules/advancedusvis/advancedusvis.cmake

@@ -11,7 +11,7 @@ IF(${ModuleEnabled})
 
 	# Header files (including GLSL files so that they'll appear in VS projects)
 	FILE(GLOB ThisModHeaders RELATIVE ${ModulesDir}
-		modules/advancedusvis/datastructures/*.frag
+		modules/advancedusvis/datastructures/*.h
 		modules/advancedusvis/glsl/*.frag
 		modules/advancedusvis/glsl/*.vert
 		modules/advancedusvis/pipelines/*.h

modules/advancedusvis/datastructures/pointpredicatehistogram.cpp

@@ -60,10 +60,11 @@ namespace campvis {
         s_headerChanged.emitSignal();
     }
 
-    void PointPredicateHistogram::resetPredicates() {
+    void PointPredicateHistogram::resetPredicates(bool resetColors) {
         float imp = 1.f / _predicates.size();
         for (size_t i = 0; i < _predicates.size(); ++i) {
             _predicates[i]->p_importance.setValue(imp);
+            if (resetColors)
                 _predicates[i]->p_color.setValue(tgt::vec2(0.f));
         }
 
@@ -81,7 +82,7 @@ namespace campvis {
         }
 
         toReturn +=
-            "vec4 performPredicateBasedShading(in float intensity, in float gradientMagnitude, in float gradientAngle, float viewAngle, in float snr, in float vesselness, in float confidence, in uint label) {\n"
+            "vec4 performPredicateBasedShading(" + _predicateFunctionArgumentString + ") {\n"
             "    float impCount = 0.0;\n"
             "    float hueCount = 0.0;\n"
             "    vec4 impSum = vec4(0.0, 0.0, 0.0, 1.0);\n";
@@ -113,7 +114,7 @@ namespace campvis {
             "}\n\n";
 
         toReturn +=
-            "uint computePredicateBitfield(in float intensity, in float gradientMagnitude, in float gradientAngle, float viewAngle, in float snr, in float vesselness, in float confidence, in uint label) {\n"
+            "uint computePredicateBitfield(" + _predicateFunctionArgumentString + ") {\n"
             "    uint toReturn = 0U;\n";
 
         for (size_t i = 0; i < _predicates.size(); ++i) {
@@ -155,4 +156,8 @@ namespace campvis {
             _predicates[i]->unlockAllProperties();
     }
 
+    void PointPredicateHistogram::setPredicateFunctionArgumentString(const std::string& pfas) {
+        _predicateFunctionArgumentString = pfas;
+    }
+
 }
\ No newline at end of file

modules/advancedusvis/datastructures/pointpredicatehistogram.h

@@ -70,7 +70,7 @@ namespace campvis {
         /**
          * Resets the predicate histogram to default setting.
          */
-        void resetPredicates();
+        void resetPredicates(bool resetColors = true);
 
         /**
          * Returns the vector of predicates.
@@ -90,6 +90,12 @@ namespace campvis {
          */
         void setupRenderShader(tgt::Shader* shader) const;
 
+        /**
+         * Sets the GLSL predicate function argument string.
+         * \param   pfas    the GLSL predicate function argument string (without parentheses)
+         */
+        void setPredicateFunctionArgumentString(const std::string& pfas);
+
 
         /// Signal emitted when this predicate histogram's configuration (importance, color, ...) has changed
         sigslot::signal0 s_configurationChanged;
@@ -104,6 +110,8 @@ namespace campvis {
 
         /// vector of all voxel predicates
         std::vector<AbstractPointPredicate*> _predicates;
+        /// The GLSL predicate function argument string (without parentheses).
+        std::string _predicateFunctionArgumentString;
 
         static const std::string loggerCat_;
 

modules/advancedusvis/processors/pointpredicateevaluator.cpp

@@ -70,6 +70,7 @@ namespace campvis {
     }
 
     void PointPredicateEvaluator::init() {
+        p_histogram.getPredicateHistogram()->setPredicateFunctionArgumentString("in float intensity, in float gradientMagnitude, in float gradientAngle, float viewAngle, in float snr, in float vesselness, in float confidence, in uint label");
         VisualizationProcessor::init();
 
         _shader = ShdrMgr.loadWithCustomGlslVersion("core/glsl/passthrough.vert", "", "modules/advancedusvis/glsl/pointpredicateevaluator.frag", generateHeader(), "400");

modules/advancedusvis/processors/pointpredicateraycaster.cpp

@@ -62,8 +62,10 @@ namespace campvis {
     }
 
     void PointPredicateRaycaster::init() {
-        p_predicateHistogram.s_headerChanged.connect(this, &PointPredicateRaycaster::onHistogramHeaderChanged);
+        p_predicateHistogram.getPredicateHistogram()->setPredicateFunctionArgumentString("in float intensity, in float gradientMagnitude, in float gradientAngle, float viewAngle, in float snr, in float vesselness, in float confidence, in uint label");
+
         RaycastingProcessor::init();
+        p_predicateHistogram.s_headerChanged.connect(this, &PointPredicateRaycaster::onHistogramHeaderChanged);
     }
 
     void PointPredicateRaycaster::deinit() {

modules/ivus_tc/glsl/ivustcsliceextractor.frag

+// ================================================================================================
+// 
+// This file is part of the CAMPVis Software Framework.
+// 
+// If not explicitly stated otherwise: Copyright (C) 2012-2014, all rights reserved,
+//      Christian Schulte zu Berge <christian.szb@in.tum.de>
+//      Chair for Computer Aided Medical Procedures
+//      Technische Universitaet Muenchen
+//      Boltzmannstr. 3, 85748 Garching b. Muenchen, Germany
+// 
+// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
+// 
+// Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file 
+// except in compliance with the License. You may obtain a copy of the License at
+// 
+// http://www.apache.org/licenses/LICENSE-2.0
+// 
+// Unless required by applicable law or agreed to in writing, software distributed under the 
+// License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, 
+// either express or implied. See the License for the specific language governing permissions 
+// and limitations under the License.
+// 
+// ================================================================================================
+
+in vec3 ex_TexCoord;
+in vec4 ex_Color;
+out vec4 out_Color;
+
+#include "tools/colorspace.frag"
+#include "tools/texture3d.frag"
+#include "tools/transferfunction.frag"
+
+uniform sampler3D _ivus;
+uniform TextureParameters3D _ivusParams;
+uniform sampler3D _cm;
+uniform TextureParameters3D _cmParams;
+uniform sampler3D _tc;
+uniform TextureParameters3D _tcParams;
+uniform sampler3D _plaque;
+uniform TextureParameters3D _plaqueParams;
+
+uniform mat4 _texCoordsMatrix;
+
+uniform bool _useTexturing = true;
+uniform bool _useSolidColor = true;
+uniform vec4 _color = vec4(1.0, 1.0, 1.0, 1.0);
+
+void main() {
+    if (_useTexturing) {
+        vec3 texel = (_texCoordsMatrix * vec4(ex_TexCoord, 1.0)).xyz;
+
+        float ivus = texture(_ivus, texel).r;
+        float cm = texture(_cm, texel).r;
+        vec4 tc = texture(_tc, texel);
+        float plaque = texture(_plaque, texel).r;
+
+        vec4 pr = performPredicateBasedShading(ivus, cm, tc, plaque);
+
+        vec3 hsl = rgb2hsv(vec3(ivus));
+        hsl.xy += pr.xy;
+        hsl.x = mod(hsl.x, 1.0);
+        out_Color = vec4(hsv2rgb(hsl), 1.0);
+    }
+    else if (_useSolidColor) {
+        out_Color = _color;
+    }
+    else {
+        out_Color = ex_Color;
+    }
+}

modules/ivus_tc/pipelines/ivustcdemo.cpp

@@ -31,6 +31,8 @@
 #include "core/classification/geometry1dtransferfunction.h"
 #include "core/classification/tfgeometry1d.h"
 
+#include "modules/ivus_tc/processors/ivustcsliceextractor.h"
+
 namespace campvis {
 
     IvusTcDemo::IvusTcDemo(DataContainer* dc)
@@ -39,7 +41,7 @@ namespace campvis {
         , p_readImagesButton("ReadImagesButton", "Read Images")
         , _lsp()
         , _imageReader(&_canvasSize)
-        , _ve(&_canvasSize)
+        , _ve(&_canvasSize, new IvusTcSliceExtractor(nullptr))
     {
         // Use AbstractPipeline overload to avoid automatic evaluation of _imageReader processor
 //        AbstractPipeline::addProcessor(&_imageReader);
@@ -61,21 +63,55 @@ namespace campvis {
         _imageReader.init();
         p_readImagesButton.s_clicked.connect(this, &IvusTcDemo::readAndProcessImages);
 
+        _ve.p_inputVolume.setValue("image.ivus");
         _ve.p_outputImage.setValue("combine");
         _renderTargetID.setValue("combine");
         
-        _imageReader.p_inputDirectory.setValue("D:/Medical Data/IVUS/H52 LAD1/IVUS");
         _imageReader.p_fileExtension.setValue("bmp");
-        _imageReader.p_outputImage.setValue("reader.output");
-        _imageReader.p_outputImage.addSharedProperty(&_ve.p_inputVolume);
 
+        // initialize predicates with default config
+        PointPredicateHistogramProperty* php = dynamic_cast<PointPredicateHistogramProperty*>(_ve.getNestedProperty("SliceExtractorProperties::PredicateHistogram"));
+        if (php != nullptr) {
+            PointPredicateHistogram* histogram = php->getPredicateHistogram();
+
+            AbstractPointPredicate* vpToAdd = 0;
+//             vpToAdd = new RangePointPredicate("ivus", "IvusIntensity", "IVUS Intensity Range");
+//             static_cast<RangePointPredicate*>(vpToAdd)->p_range.setValue(tgt::vec2(0.f, 1.f));
+//             histogram->addPredicate(vpToAdd);
+
+            vpToAdd = new RangePointPredicate("cm", "ConfidenceMap", "Confidence");
+            static_cast<RangePointPredicate*>(vpToAdd)->p_range.setValue(tgt::vec2(0.25f, 1.f));
+            histogram->addPredicate(vpToAdd);
+
+            vpToAdd = new RangePointPredicate("tc.r", "Calcified", "Calcified Tissue");
+            static_cast<RangePointPredicate*>(vpToAdd)->p_range.setValue(tgt::vec2(0.15f, 1.f));
+            vpToAdd->p_color.setValue(tgt::vec2(0.f, 1.f));
+            histogram->addPredicate(vpToAdd);
+
+            vpToAdd = new RangePointPredicate("tc.g", "Fibrotic", "Fibrotic Tissue");
+            static_cast<RangePointPredicate*>(vpToAdd)->p_range.setValue(tgt::vec2(0.15f, 1.f));
+            vpToAdd->p_color.setValue(tgt::vec2(0.2f, 1.f));
+            histogram->addPredicate(vpToAdd);
+
+            vpToAdd = new RangePointPredicate("tc.b", "Lipidic", "Lipidic Tissue");
+            static_cast<RangePointPredicate*>(vpToAdd)->p_range.setValue(tgt::vec2(0.15f, 1.f));
+            vpToAdd->p_color.setValue(tgt::vec2(0.4f, 1.f));
+            histogram->addPredicate(vpToAdd);
+
+            vpToAdd = new RangePointPredicate("tc.a", "Necrotic", "Necrotic Tissue");
+            static_cast<RangePointPredicate*>(vpToAdd)->p_range.setValue(tgt::vec2(0.15f, 1.f));
+            vpToAdd->p_color.setValue(tgt::vec2(0.6f, 1.f));
+            histogram->addPredicate(vpToAdd);
+
+            vpToAdd = new RangePointPredicate("plaque", "Plaque", "Plaque Mask");
+            static_cast<RangePointPredicate*>(vpToAdd)->p_range.setValue(tgt::vec2(0.5f, 1.f));
+            vpToAdd->p_color.setValue(tgt::vec2(0.8f, 1.f));
+            histogram->addPredicate(vpToAdd);
+
+            histogram->resetPredicates(false);
+            addProperty(*php);
+        }
 
-        Geometry1DTransferFunction* dvrTF = new Geometry1DTransferFunction(128, tgt::vec2(0.f, .05f));
-        dvrTF->addGeometry(TFGeometry1D::createQuad(tgt::vec2(.12f, .15f), tgt::col4(85, 0, 0, 128), tgt::col4(255, 0, 0, 128)));
-        dvrTF->addGeometry(TFGeometry1D::createQuad(tgt::vec2(.19f, .28f), tgt::col4(89, 89, 89, 155), tgt::col4(89, 89, 89, 155)));
-        dvrTF->addGeometry(TFGeometry1D::createQuad(tgt::vec2(.41f, .51f), tgt::col4(170, 170, 128, 64), tgt::col4(192, 192, 128, 64)));
-        static_cast<TransferFunctionProperty*>(_ve.getNestedProperty("VolumeRendererProperties::RaycasterProps::TransferFunction"))->replaceTF(dvrTF);
-        static_cast<FloatProperty*>(_ve.getNestedProperty("VolumeRendererProperties::RaycasterProps::SamplingRate"))->setValue(4.f);
     }
 
     void IvusTcDemo::deinit() {

modules/ivus_tc/processors/ivustcsliceextractor.cpp

+// ================================================================================================
+// 
+// This file is part of the CAMPVis Software Framework.
+// 
+// If not explicitly stated otherwise: Copyright (C) 2012-2014, all rights reserved,
+//      Christian Schulte zu Berge <christian.szb@in.tum.de>
+//      Chair for Computer Aided Medical Procedures
+//      Technische Universitaet Muenchen
+//      Boltzmannstr. 3, 85748 Garching b. Muenchen, Germany
+// 
+// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
+// 
+// Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file 
+// except in compliance with the License. You may obtain a copy of the License at
+// 
+// http://www.apache.org/licenses/LICENSE-2.0
+// 
+// Unless required by applicable law or agreed to in writing, software distributed under the 
+// License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, 
+// either express or implied. See the License for the specific language governing permissions 
+// and limitations under the License.
+// 
+// ================================================================================================
+
+#include "ivustcsliceextractor.h"
+#include "tgt/logmanager.h"
+#include "tgt/shadermanager.h"
+#include "tgt/textureunit.h"
+
+#include "core/datastructures/imagedata.h"
+#include "core/datastructures/imagerepresentationgl.h"
+#include "core/datastructures/renderdata.h"
+#include "core/classification/simpletransferfunction.h"
+
+#include "core/tools/quadrenderer.h"
+
+namespace campvis {
+    const std::string IvusTcSliceExtractor::loggerCat_ = "CAMPVis.modules.vis.IvusTcSliceExtractor";
+
+    IvusTcSliceExtractor::IvusTcSliceExtractor(IVec2Property* viewportSizeProp)
+        : SliceRenderProcessor(viewportSizeProp, "modules/ivus_tc/glsl/ivustcsliceextractor.frag", "400")
+        , p_cmImage("CmImage", "Confidence Map Image", "image.cm", DataNameProperty::READ)
+        , p_tcImage("TcImage", "Tissue Classification Image", "image.tc", DataNameProperty::READ)
+        , p_plaqueImage("PlaqueImage", "Plaque Mask Image", "image.plaque", DataNameProperty::READ)
+        , p_predicateHistogram("PredicateHistogram", "predicate Histogram")
+    {
+        addProperty(p_cmImage);
+        addProperty(p_tcImage);
+        addProperty(p_plaqueImage);
+        addProperty(p_predicateHistogram);
+
+        invalidate(AbstractProcessor::INVALID_SHADER);
+
+        p_predicateHistogram.getPredicateHistogram()->setPredicateFunctionArgumentString("in float ivus, in float cm, in vec4 tc, in float plaque");
+    }
+
+    IvusTcSliceExtractor::~IvusTcSliceExtractor() {
+
+    }
+
+    void IvusTcSliceExtractor::renderImageImpl(DataContainer& dataContainer, const ImageRepresentationGL::ScopedRepresentation& img) {
+        ImageRepresentationGL::ScopedRepresentation cm(dataContainer, p_cmImage.getValue());
+        ImageRepresentationGL::ScopedRepresentation tc(dataContainer, p_tcImage.getValue());
+        ImageRepresentationGL::ScopedRepresentation plaque(dataContainer, p_plaqueImage.getValue());
+
+        if (cm && tc && plaque) {
+            // prepare OpenGL
+            _shader->activate();
+            tgt::TextureUnit ivusUnit, cmUnit, tcUnit, plaqueUnit;
+            img->bind(_shader, ivusUnit, "_ivus", "_ivusParams");
+            cm->bind(_shader, cmUnit, "_cm", "_cmParams");
+            tc->bind(_shader, tcUnit, "_tc", "_tcParams");
+            plaque->bind(_shader, plaqueUnit, "_plaque", "_plaqueParams");
+
+            {
+                tgt::Shader::IgnoreUniformLocationErrorGuard guard(_shader);
+                p_predicateHistogram.getPredicateHistogram()->setupRenderShader(_shader);
+            }
+            
+            tgt::mat4 identity = tgt::mat4::identity;
+
+            _shader->setUniform("_texCoordsMatrix", _texCoordMatrix);
+            _shader->setUniform("_modelMatrix", identity);
+            _shader->setUniform("_viewMatrix", _viewMatrix);
+            _shader->setUniform("_projectionMatrix", identity);
+            _shader->setUniform("_useTexturing", true);
+            _shader->setUniform("_useSolidColor", true);
+
+            // render slice
+            FramebufferActivationGuard fag(this);
+            createAndAttachColorTexture();
+            createAndAttachDepthTexture();
+            glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
+            QuadRdr.renderQuad();
+
+            if (p_renderCrosshair.getValue())
+                renderCrosshair(img);
+
+            renderGeometry(dataContainer, img);
+
+            _shader->deactivate();
+            tgt::TextureUnit::setZeroUnit();
+
+            dataContainer.addData(p_targetImageID.getValue(), new RenderData(_fbo));
+        }
+    }
+
+    void IvusTcSliceExtractor::onHistogramHeaderChanged() {
+        invalidate(INVALID_SHADER);
+    }
+
+    std::string IvusTcSliceExtractor::getGlslHeader() {
+        return SliceRenderProcessor::getGlslHeader() + p_predicateHistogram.getPredicateHistogram()->getGlslHeader();
+    }
+
+}

modules/ivus_tc/processors/ivustcsliceextractor.h

+// ================================================================================================
+// 
+// This file is part of the CAMPVis Software Framework.
+// 
+// If not explicitly stated otherwise: Copyright (C) 2012-2014, all rights reserved,
+//      Christian Schulte zu Berge <christian.szb@in.tum.de>
+//      Chair for Computer Aided Medical Procedures
+//      Technische Universitaet Muenchen
+//      Boltzmannstr. 3, 85748 Garching b. Muenchen, Germany
+// 
+// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
+// 
+// Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file 
+// except in compliance with the License. You may obtain a copy of the License at
+// 
+// http://www.apache.org/licenses/LICENSE-2.0
+// 
+// Unless required by applicable law or agreed to in writing, software distributed under the 
+// License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, 
+// either express or implied. See the License for the specific language governing permissions 
+// and limitations under the License.
+// 
+// ================================================================================================
+
+#ifndef IVUSTCSLICEEXTRACTOR_H__
+#define IVUSTCSLICEEXTRACTOR_H__
+
+#include "core/pipeline/slicerenderprocessor.h"
+
+#include "modules/advancedusvis/properties/pointpredicatehistogramproperty.h"
+
+namespace campvis {
+    /**
+     * IVUS Tissue Classification Slice Rendering with Predicate Histogram-based classification.
+     */
+    class IvusTcSliceExtractor : public SliceRenderProcessor {
+    public:
+        /**
+         * Constructs a new IvusTcSliceExtractor Processor
+         **/
+        IvusTcSliceExtractor(IVec2Property* viewportSizeProp);
+
+        /**
+         * Destructor
+         **/
+        virtual ~IvusTcSliceExtractor();
+
+        /// \see AbstractProcessor::getName()
+        virtual const std::string getName() const { return "IvusTcSliceExtractor"; };
+        /// \see AbstractProcessor::getDescription()
+        virtual const std::string getDescription() const { return "IVUS Tissue Classification Slice Rendering with Predicate Histogram-based classification."; };
+        /// \see AbstractProcessor::getAuthor()
+        virtual const std::string getAuthor() const { return "Christian Schulte zu Berge <christian.szb@in.tum.de>"; };
+        /// \see AbstractProcessor::getProcessorState()
+        virtual ProcessorState getProcessorState() const { return AbstractProcessor::EXPERIMENTAL; };
+
+        DataNameProperty p_cmImage;
+        DataNameProperty p_tcImage;
+        DataNameProperty p_plaqueImage;
+
+        PointPredicateHistogramProperty p_predicateHistogram;
+
+    protected:
+        /// \see SliceRenderProcessor::renderImageImpl
+        virtual void renderImageImpl(DataContainer& dataContainer, const ImageRepresentationGL::ScopedRepresentation& img);
+
+        virtual std::string getGlslHeader();
+
+    private:
+        void onHistogramHeaderChanged();
+
+        static const std::string loggerCat_;
+    };
+
+}
+
+#endif // IVUSTCSLICEEXTRACTOR_H__