Removed a bunch of TODOs and FIXMEs.

core/glsl/tools/raycasting.frag

@@ -65,16 +65,16 @@ float rayBoxIntersection(in vec3 rayOrigin, in vec3 rayDirection, in vec3 boxLlf
     return min(min(tMin.x, min(tMin.y, tMin.z))   ,    min(tMax.x, min(tMax.y, tMax.z)));
 }
 
-// compute the near and far intersections of the cube (stored in the x and y components) using the slab method
-// no intersection means vec.x > vec.y (really tNear > tFar)
-vec2 intersectAABB(vec3 rayOrigin, vec3 rayDirection, in vec3 boxLlf, in vec3 boxUrb) {
-    vec3 tMin = (boxLlf - rayOrigin) / rayDirection;
-    vec3 tMax = (boxUrb - rayOrigin) / rayDirection;
-    vec3 t1 = min(tMin, tMax);
-    vec3 t2 = max(tMin, tMax);
-    float tNear = max(max(t1.x, t1.y), t1.z);
-    float tFar = min(min(t2.x, t2.y), t2.z);
-    return vec2(tNear, tFar);
+// compute the near and far intersections of the cube (stored in the x and y components) using the slab method
+// no intersection means vec.x > vec.y (really tNear > tFar)
+vec2 intersectAABB(vec3 rayOrigin, vec3 rayDirection, in vec3 boxLlf, in vec3 boxUrb) {
+    vec3 tMin = (boxLlf - rayOrigin) / rayDirection;
+    vec3 tMax = (boxUrb - rayOrigin) / rayDirection;
+    vec3 t1 = min(tMin, tMax);
+    vec3 t2 = max(tMin, tMax);
+    float tNear = max(max(t1.x, t1.y), t1.z);
+    float tFar = min(min(t2.x, t2.y), t2.z);
+    return vec2(tNear, tFar);
 };
 
 /**

core/pipeline/abstractprocessor.cpp

@@ -57,7 +57,8 @@ namespace campvis {
 
 
     void AbstractProcessor::lockProcessor() {
-        while (_locked.compare_and_swap(true, false) == true) // TODO: busy waiting us fu**ing ugly...
+        // hopefully, it does not take too long.
+        while (_locked.compare_and_swap(true, false) == true)
             std::this_thread::yield();
         _locked = true;
         lockAllProperties();

core/tools/stringutils.h

@@ -62,7 +62,7 @@ namespace campvis {
          *
          * \param   str     Input string to parse.
          *
-         * \note    TODO: The detection algorithm is a little simplified and will not yield correct results
+         * \note    The detection algorithm is a little simplified and may not yield correct results
          *          in every case.
          **/
         static std::vector<std::string> parseFloats(const std::string& str);

ext/cgt/cgt.h

@@ -49,7 +49,6 @@
 
 //Interaction
 //#include "glcanvas.h"
-// FIXME: include glcanvas and guiapplication, include glut/qt/sdl-canvas/application/libs depending on macros
 #include "cgt/mouse.h"
 #include "cgt/camera.h"
 #include "cgt/navigation/navigation.h"

ext/cgt/filesystem.cpp

@@ -53,9 +53,6 @@
 
 using std::string;
 
-//TODO: should really switch to exceptions instead of just logging with LERROR. joerg
-// see http://en.wikipedia.org/wiki/Aliasing_%28computing%29#Conflicts_with_optimization
-
 // anonymous namespace
 namespace {
 

ext/cgt/glcanvas.cpp

@@ -48,7 +48,6 @@ GLCanvas::GLCanvas(const std::string& title,
       stereoViewing_(false),
       fullscreen_(false),
       autoFlush_(true),
-      initialized_(false),
       painter_(0) ,
       eventHandler_(new EventHandler())
 {}
@@ -78,8 +77,7 @@ void GLCanvas::paint() {
 }
 
 void GLCanvas::init() {
-    if (!initialized_)
-        initialized_ = true;
+    // nothing here, may be implemented in sub classes.
 }
 
 void GLCanvas::setPainter(Painter* p, bool initP) {

ext/cgt/glcanvas.h

@@ -179,9 +179,6 @@ public:
     /// Getter
     bool isDoubleBuffered() const { return doubleBuffered_; }
 
-    /// Getter
-    bool isInitialized() const { return initialized_; }
-
     /// Acqures this canvas as current context
     virtual void acquireAsCurrentContext() = 0;
     /// Releases this canvas as current context
@@ -204,7 +201,6 @@ protected:
     bool    stereoViewing_;
     bool    fullscreen_;
     bool    autoFlush_; ///< whether to call glFlush or swap automatically
-    bool    initialized_; // FIXME: does this make sense?
 
     Painter* painter_;  ///< the painter that will be used for rendering
 

ext/cgt/manager.h

@@ -195,10 +195,9 @@ void ResourceManager<T>::dispose(T* ptr) {
 template <class T>
 void ResourceManager<T>::addPath(std::string path) {
     tbb::spin_mutex::scoped_lock lock(this->mutex_);
-
     pathList_.push_front(path);
+
     // remove duplicates
-    //TODO: better use std::set<> here
     pathList_.sort();
     pathList_.unique();
 }

ext/cgt/matrix.h

@@ -35,7 +35,7 @@
 #include "cgt/assert.h"
 
 /*
-    FIXME build a SSE-optimized mat4
+    TODO: build a SSE-optimized mat4
 */
 
 /*

ext/cgt/navigation/navigation.cpp

@@ -57,9 +57,7 @@ void Navigation::rotateView(float angle, const vec3& axis) {
 
 // Rotate the Camera about horizontal and vertical angles given by the user
 void Navigation::rotateViewHV(float anglehorz, float anglevert) {
-
-// FIXME: rotateViewHorz(anglehorz);rotateViewVert(anglevert) would be much more generic ... but maybe more expensive ...
-
+    // rotateViewHorz(anglehorz);rotateViewVert(anglevert) would be much more generic ... but maybe more expensive ...
     // for now, we use quaternion rotation... we'll have to benchmark this
     quat horz = quat::createQuat(anglehorz, getCamera()->getUpVector());
     quat vert = quat::createQuat(anglevert, getCamera()->getStrafe());
@@ -79,8 +77,6 @@ void Navigation::rotateViewHV(float anglehorz, float anglevert) {
     updateClippingPlanes();
 }
 
-// FIXME: the following few functions should be inline
-
 void Navigation::rotateView(float angle, float x, float y, float z) {
     rotateView(angle, vec3(x, y, z));
 }

ext/cgt/navigation/trackball.h

@@ -325,7 +325,7 @@ class CGT_API Trackball : public Navigation {
         KeyEvent::KeyCode keyRotateUp_              ; ///< at which key code rotate up
         KeyEvent::KeyCode keyRotateDown_            ; ///< at which key code rotate down
         int keyRotateMod_                           ; ///< at which modifiers to rotate by keys
-        bool keyRotatePressed_                      ; // FIXME: cannot remember. not in use anyway...
+        bool keyRotatePressed_                      ;
         MouseEvent::MouseButtons mouseMoveButton_   ;
         int mouseMoveMod_                           ;
         float keyMoveAcuteness_                     ;
@@ -334,7 +334,7 @@ class CGT_API Trackball : public Navigation {
         KeyEvent::KeyCode keyMoveUp_                ;
         KeyEvent::KeyCode keyMoveDown_              ;
         int keyMoveMod_                             ;
-        bool keyMovePressed_                        ; // FIXME: cannot remember, not in use
+        bool keyMovePressed_                        ;
         MouseEvent::MouseButtons mouseZoomButton_   ;
         vec2 mouseZoomInDirection_                  ;
         int mouseZoomMod_                           ;
@@ -346,7 +346,7 @@ class CGT_API Trackball : public Navigation {
         KeyEvent::KeyCode keyZoomIn_                ;
         KeyEvent::KeyCode keyZoomOut_               ;
         int keyZoomMod_                             ;
-        bool keyZoomPressed_                        ; // FIXME: cannot remember, not in use
+        bool keyZoomPressed_                        ;
         MouseEvent::MouseButtons mouseRollButton_   ;
         float mouseRollAcuteness_                   ;
         int mouseRollMod_                           ;
@@ -358,7 +358,7 @@ class CGT_API Trackball : public Navigation {
         KeyEvent::KeyCode keyRollLeft_              ;
         KeyEvent::KeyCode keyRollRight_             ;
         int keyRollMod_                             ;
-        bool keyRollPressed_                        ; // FIXME: cannot remember, not in use
+        bool keyRollPressed_                        ;
 
         bool tracking_; ///< Are we tracking mouse move events? Only when we received a
                         ///< mousePressEvent before.

ext/cgt/qt/qtcanvas.cpp

@@ -84,10 +84,6 @@ QtCanvas::QtCanvas(QWidget* parent, bool shared, Qt::WFlags f, char* /*name*/)
 
 QtCanvas::~QtCanvas() {}
 
-void QtCanvas::init() {
-    GLCanvas::init();
-}
-
 void QtCanvas::initializeGL() {
 }
 
@@ -273,7 +269,7 @@ KeyEvent::KeyCode QtCanvas::getKey(int key) {
         case Qt::Key_Down     : return cgt::KeyEvent::K_DOWN;
         case Qt::Key_PageUp   : return cgt::KeyEvent::K_PAGEUP;
         case Qt::Key_PageDown     : return cgt::KeyEvent::K_PAGEDOWN;
-        case Qt::Key_Shift    : return cgt::KeyEvent::K_LSHIFT;  //TODO: qt only knows one shift, control, meta and alt
+        case Qt::Key_Shift    : return cgt::KeyEvent::K_LSHIFT;  // Qt only knows one shift, control, meta and alt
         case Qt::Key_Control : return cgt::KeyEvent::K_LCTRL;//...
         case Qt::Key_Meta : return cgt::KeyEvent::K_RMETA;//...
         case Qt::Key_Alt  : return cgt::KeyEvent::K_LALT;//...

ext/cgt/qt/qtcanvas.h

@@ -70,9 +70,6 @@ public:
     virtual ~QtCanvas();
 
 
-    /// initialize canvas
-    virtual void init();
-
     /**
      * Called by the Qt framework once at the beginning, before rendering starts.
      * This function calls the corresponding GLCanvas method \a initialize.

ext/cgt/shadermanager.cpp

@@ -951,14 +951,7 @@ bool Shader::setUniform(const string& name, Vector2f* vectors, GLsizei count) {
     GLint l = getUniformLocation(name);
     if (l == -1)
         return false;
-    //TODO: use the adress directly, without copying, same below. joerg
-    GLfloat* values = new GLfloat[2*count];
-    for (int i=0; i < count; i++){
-        values[2*i] = vectors[i].x;
-        values[2*i+1] = vectors[i].y;
-    }
-    glUniform2fv(l, count, values);
-    delete[] values;
+    glUniform2fv(l, count, vectors[0].elem);
     return true;
 }
 
@@ -974,14 +967,7 @@ bool Shader::setUniform(const string& name, Vector3f* vectors, GLsizei count) {
     GLint l = getUniformLocation(name);
     if (l == -1)
         return false;
-    GLfloat* values = new GLfloat[3*count];
-    for (int i=0; i < count; i++) {
-        values[3*i] = vectors[i].x;
-        values[3*i+1] = vectors[i].y;
-        values[3*i+2] = vectors[i].z;
-    }
-    glUniform3fv(l, count, values);
-    delete[] values;
+    glUniform3fv(l, count, vectors[0].elem);
     return true;
 }
 
@@ -997,15 +983,7 @@ bool Shader::setUniform(const string& name, Vector4f* vectors, GLsizei count) {
     GLint l = getUniformLocation(name);
     if (l == -1)
         return false;
-    GLfloat* values = new GLfloat[4*count];
-    for (int i=0; i < count; i++) {
-        values[4*i] = vectors[i].x;
-        values[4*i+1] = vectors[i].y;
-        values[4*i+2] = vectors[i].z;
-        values[4*i+3] = vectors[i].a;
-    }
-    glUniform4fv(l, count, values);
-    delete[] values;
+    glUniform4fv(l, count, vectors[0].elem);
     return true;
 }
 
@@ -1021,13 +999,7 @@ bool Shader::setUniform(const string& name, ivec2* vectors, GLsizei count) {
     GLint l = getUniformLocation(name);
     if (l == -1)
         return false;
-    GLint* values = new GLint[2*count];
-    for (int i=0; i < count; i++) {
-        values[2*i] = vectors[i].x;
-        values[2*i+1] = vectors[i].y;
-    }
-    glUniform2iv(l, count, values);
-    delete[] values;
+    glUniform2iv(l, count, vectors[0].elem);
     return true;
 }
 
@@ -1043,14 +1015,7 @@ bool Shader::setUniform(const string& name, ivec3* vectors, GLsizei count) {
     GLint l = getUniformLocation(name);
     if (l == -1)
         return false;
-    GLint* values = new GLint[3*count];
-    for (int i=0; i < count; i++) {
-        values[3*i] = vectors[i].x;
-        values[3*i+1] = vectors[i].y;
-        values[3*i+2] = vectors[i].z;
-    }
-    glUniform3iv(l, count, values);
-    delete[] values;
+    glUniform3iv(l, count, vectors[0].elem);
     return true;
 }
 
@@ -1066,15 +1031,7 @@ bool Shader::setUniform(const string& name, ivec4* vectors, GLsizei count) {
     GLint l = getUniformLocation(name);
     if (l == -1)
         return false;
-    GLint* values = new GLint[4*count];
-    for (int i=0; i < count; i++) {
-        values[4*i] = vectors[i].x;
-        values[4*i+1] = vectors[i].y;
-        values[4*i+2] = vectors[i].z;
-        values[4*i+3] = vectors[i].a;
-    }
-    glUniform4iv(l, count, values);
-    delete[] values;
+    glUniform4iv(l, count, vectors[0].elem);
     return true;
 }
 

modules/devil/processors/devilimagereader.cpp

@@ -246,7 +246,6 @@ namespace campvis {
             rd->addColorTexture(id);
 
             // create fake depth image
-            // TODO: think of a better solution to this...
             ImageData* idDepth = new ImageData(dimensionality, imageSize, 1);
             float* ptr = new float[cgt::hmul(imageSize)];
             memset(ptr, 0, cgt::hmul(imageSize) * sizeof(float));

modules/io/processors/niftiimagereader.cpp

@@ -719,7 +719,6 @@ namespace campvis {
 
         // Nifti transformations give us the center of the first voxel, we translate to correct:
         // pToW = pToW * cgt::mat4::createTranslation(-spacing * 0.5f);
-        // TODO: implement arbitrary transformations into ImageMappingInformation
 
         cgt::svec3 imageSize(dimensions);
         if (numVolumes <= 1) {

modules/preprocessing/processors/imagefilter.cpp

@@ -34,9 +34,8 @@
 
 namespace campvis {
 
-    static const GenericOption<std::string> filterModes[2] = {
-        GenericOption<std::string>("median", "Median"),
-        GenericOption<std::string>("gauss", "Gauss"),
+    static const GenericOption<std::string> filterModes[1] = {
+        GenericOption<std::string>("median", "Median")
     };
 
     const std::string ImageFilter::loggerCat_ = "CAMPVis.modules.classification.ImageFilter";
@@ -45,7 +44,7 @@ namespace campvis {
         : AbstractProcessor()
         , p_sourceImageID("InputVolume", "Input Volume ID", "volume", DataNameProperty::READ)
         , p_targetImageID("OutputGradients", "Output Gradient Volume ID", "gradients", DataNameProperty::WRITE)
-        , p_filterMode("FilterMode", "Filter Mode", filterModes, 2)
+        , p_filterMode("FilterMode", "Filter Mode", filterModes, 1)
         , p_kernelSize("KernelSize", "Kernel Size", 3, 3, 15)
         , p_sigma("Sigma", "Sigma", 1.f, .1f, 10.f, 0.1f)
     {
@@ -72,11 +71,6 @@ namespace campvis {
                     tbb::blocked_range<size_t>(0, input->getNumElements()), 
                     ImageFilterMedian(input, output, p_kernelSize.getValue()));
             }
-            else if (p_filterMode.getOptionValue() == "gauss") {
-                tbb::parallel_for(
-                    tbb::blocked_range<size_t>(0, input->getNumElements()), 
-                    ImageFilterGauss(input, output, p_kernelSize.getValue(), p_sigma.getValue()));
-            }
 
             data.addData(p_targetImageID.getValue(), id);
         }

modules/preprocessing/tools/abstractimagefilter.cpp

@@ -32,9 +32,12 @@
 namespace campvis {
 
     ImageFilterMedian::ImageFilterMedian(const ImageRepresentationLocal* input, ImageRepresentationLocal* output, size_t kernelSize)
-        : AbstractImageFilter(input, output)
+        : _input(input)
+        , _output(output)
         , _kernelSize(kernelSize)
     {
+        cgtAssert(input != 0, "Input image must not be 0.");
+        cgtAssert(output != 0, "Output image must not be 0.");
         cgtAssert(kernelSize > 0, "Kernel Size must be greater 0.");
     }
 
@@ -67,81 +70,4 @@ namespace campvis {
         }
     }
 
-
-// ================================================================================================
-    
-    ImageFilterGauss::ImageFilterGauss(const ImageRepresentationLocal* input, ImageRepresentationLocal* output, size_t kernelSize, float sigma)
-        : AbstractImageFilter(input, output)
-        , _kernelSize(kernelSize)
-        , _halfKernelSize(kernelSize / 2)
-        , _sigma(sigma)
-        , _norm(0.f)
-    {
-        cgtAssert(kernelSize > 0, "Kernel Size must be greater 0.");
-
-        // compute Gauss kernel and corresponding norm
-        // it is sufficient to compute only one half of the 1D kernel
-        _kernel.resize(_halfKernelSize + 1, 0.f);
-        for (size_t i = 0; i <= _halfKernelSize; ++i) {
-            float f = static_cast<float>(i);
-            _kernel[i] = exp(-(f * f) / (2.f * _sigma * _sigma));
-            _norm += _kernel[i];
-        }
-
-        _norm = (2.f * _norm) - _kernel[0];
-    }
-
-
-    void ImageFilterGauss::operator()(const tbb::blocked_range<size_t>& range) const {
-        size_t halfKernelDim = static_cast<size_t>(_kernelSize / 2);
-        const cgt::svec3& size = _input->getSize();
-
-        for (size_t index = range.begin(); index < range.end(); ++index) {
-            cgt::svec3 position = _input->getParent()->indexToPosition(index);
-            cgt::svec3 npos = position;
-            float sum = 0.f;
-
-            // The gauss convolution filter is separable so it is sufficient to perform
-            // three 1D convolutions - one for each axis.
-
-            size_t zmin = position.z >= halfKernelDim ? position.z - halfKernelDim : 0;
-            size_t zmax = std::min(position.z+halfKernelDim, size.z-1);
-            for (npos.z = zmin; npos.z <= zmax; npos.z++) {
-                int i = abs(static_cast<int>(position.z) - static_cast<int>(npos.z));
-                sum += _input->getElementNormalized(npos, 0) * _kernel[i];
-            }
-            sum /= _norm;
-            _output->setElementNormalized(index, 0, sum);
-            npos.z = position.z;
-            sum = 0.f;
-
-            // FIXME: barrier sync needed!
-
-            size_t ymin = position.y >= halfKernelDim ? position.y - halfKernelDim : 0;
-            size_t ymax = std::min(position.y+halfKernelDim, size.y-1);
-            for (npos.y=ymin; npos.y<=ymax; npos.y++) {
-                int i = abs(static_cast<int>(position.y) - static_cast<int>(npos.y));
-                sum += _output->getElementNormalized(npos, 0) * _kernel[i];
-            }
-            sum /= _norm;
-            _output->setElementNormalized(index, 0, sum);
-            npos.y = position.y;
-            sum = 0.f;
-
-            // FIXME: barrier sync needed!
-
-            size_t xmin = position.x >= halfKernelDim ? position.x - halfKernelDim : 0;
-            size_t xmax = std::min(position.x+halfKernelDim, size.x-1);
-            for (npos.x=xmin; npos.x<=xmax; npos.x++) {
-                int i = abs(static_cast<int>(position.x) - static_cast<int>(npos.x));
-                sum += _output->getElementNormalized(npos, 0) * _kernel[i];
-            }
-            sum /= _norm;
-            _output->setElementNormalized(index, 0, sum);
-
-        }
-    }
-
-
-
 }

modules/preprocessing/tools/abstractimagefilter.h

@@ -34,49 +34,18 @@
 namespace campvis {
     class ImageRepresentationLocal;
 
-    struct CAMPVIS_MODULES_API AbstractImageFilter {
-        AbstractImageFilter(const ImageRepresentationLocal* input, ImageRepresentationLocal* output)
-            : _input(input)
-            , _output(output)
-        {
-            cgtAssert(input != 0, "Input image must not be 0.");
-            cgtAssert(output != 0, "Output image must not be 0.");
-        }
-
-        virtual void operator() (const tbb::blocked_range<size_t>& range) const = 0;
-
-    protected:
-        const ImageRepresentationLocal* _input;
-        ImageRepresentationLocal* _output;
-    };
-
-// ================================================================================================
-
-    struct CAMPVIS_MODULES_API ImageFilterMedian : public AbstractImageFilter {
+    struct CAMPVIS_MODULES_API ImageFilterMedian {
     public:
         ImageFilterMedian(const ImageRepresentationLocal* input, ImageRepresentationLocal* output, size_t kernelSize);
 
         void operator() (const tbb::blocked_range<size_t>& range) const;
 
     protected:
+        const ImageRepresentationLocal* _input;
+        ImageRepresentationLocal* _output;
         size_t _kernelSize;
     };
 
-// ================================================================================================
-
-    struct CAMPVIS_MODULES_API ImageFilterGauss : public AbstractImageFilter {
-    public:
-        ImageFilterGauss(const ImageRepresentationLocal* input, ImageRepresentationLocal* output, size_t kernelSize, float sigma);
-
-        void operator() (const tbb::blocked_range<size_t>& range) const;
-
-    protected:
-        size_t _kernelSize;
-        size_t _halfKernelSize;
-        float _sigma;
-        std::vector<float> _kernel;
-        float _norm;
-    };
 }
 
 #endif // ABSTRACTIMAGEFILTER_H__

modules/vis/glsl/contextpreservingraycaster.frag

@@ -67,7 +67,6 @@ uniform float _maxDepth;    ///< Maximum depth of exit points
 uniform float _kappaS;      ///< k_s parameter from the paper
 uniform float _kappaT;      ///< l_t parameter from the paper
 
-// TODO: copy+paste from Voreen - eliminate or improve.
 const float SAMPLING_BASE_INTERVAL_RCP = 200.0;
 
 /**

modules/vis/glsl/drrraycaster.frag

@@ -52,7 +52,6 @@ uniform float _samplingStepSize;
 uniform float _shift;
 uniform float _scale;
 
-// TODO: copy+paste from Voreen - eliminate or improve.
 const float SAMPLING_BASE_INTERVAL_RCP = 200.0;
 
 /**

modules/vis/glsl/optimizedraycaster.frag

@@ -76,7 +76,6 @@ bool _inVoid = false;
 uniform float _shadowIntensity;
 #endif
 
-// TODO: copy+paste from Voreen - eliminate or improve.
 const float SAMPLING_BASE_INTERVAL_RCP = 200.0;
 
 ivec3 voxelToBrick(in vec3 voxel) {

modules/vis/glsl/simpleraycaster.frag

@@ -65,7 +65,6 @@ uniform float _samplingStepSize;
 uniform float _shadowIntensity;
 #endif
 
-// TODO: copy+paste from Voreen - eliminate or improve.
 const float SAMPLING_BASE_INTERVAL_RCP = 200.0;
 
 /**