[merged commit]clean ups, fixes for g++ errors and warnings, and edits for...

[merged commit]clean ups, fixes for g++ errors and warnings, and edits for cppcheck errors (except for the 480+ in the external library AlgLib)

application/gui/properties/colorpropertywidget.cpp

@@ -42,11 +42,9 @@ namespace campvis {
     }
 
     ColorPropertyWidget::~ColorPropertyWidget() {
-        ColorProperty* property = static_cast<ColorProperty*>(_property);
     }
 
     void ColorPropertyWidget::updateWidgetFromProperty() {
-        ColorProperty* prop = static_cast<ColorProperty*>(_property);
         _colorPicker->blockSignals(true);
         const tgt::vec4 val = static_cast<ColorProperty*>(_property)->getValue();
         _colorPicker->setColor(QtColorTools::toQColor(tgt::vec4(val.x *255, val.y*255, val.z*255, val.w*255)));
@@ -57,7 +55,7 @@ namespace campvis {
         ++_ignorePropertyUpdates;
         ColorProperty* prop = static_cast<ColorProperty*>(_property);
         tgt::vec4 val = QtColorTools::toTgtColor(_colorPicker->color());
-        prop->setValue(tgt::vec4(val.x/val.w, val.y/val.w, val.z/val.w, val.w/val.w));
+        prop->setValue(tgt::vec4(val.x/val.w, val.y/val.w, val.z/val.w, 1));
         --_ignorePropertyUpdates;
     }
 

core/properties/colorproperty.h

@@ -35,8 +35,6 @@ namespace campvis {
 
     typedef _ColorProperty<tgt::vec4> ColorProperty;
 
-
-
     template<typename T>
     _ColorProperty<T>::_ColorProperty(
         const std::string& name,
@@ -44,7 +42,7 @@ namespace campvis {
         const T& value,
         const T& minValue,
         const T& maxValue,
-        const T& stepValue = T(0.01f)) 
+        const T& stepValue) 
         : Vec4Property(name, title, value, minValue, maxValue, stepValue)
     {
 

core/properties/metaproperty.cpp

@@ -36,6 +36,12 @@ namespace campvis {
     MetaProperty::~MetaProperty() {
     }
 
+    void MetaProperty::deinit() {
+        for (size_t i = 0; i < _properties.size(); ++i) {
+            removeProperty(*_properties[i]);
+        }
+    }
+
     void MetaProperty::onPropertyChanged(const AbstractProperty* prop) {
         s_changed.emitSignal(this);
     }

core/properties/metaproperty.h

@@ -53,6 +53,8 @@ namespace campvis {
          **/
         virtual ~MetaProperty();
 
+        /// \see AbstractProperty::deinit
+        virtual void deinit();
 
         /// \see HasPropertyCollection::onPropertyChanged
         virtual void onPropertyChanged(const AbstractProperty* prop);

core/properties/optionproperty.h

@@ -258,7 +258,7 @@ namespace campvis {
 
     template<typename T>
     void campvis::GenericOptionProperty<T>::selectByIndex(int index) {
-        tgtAssert(index >= 0 && index < _options.size(), "Index out of bounds.");
+        tgtAssert(index >= 0 && index < static_cast<int>(_options.size()), "Index out of bounds.");
         setValue(index);
     }
 
@@ -282,17 +282,17 @@ namespace campvis {
 
     template<typename T>
     size_t campvis::GenericOptionProperty<T>::removeCurrent() {
-        int index = getValue();
+        size_t index = getValue();
         if (index == 0) return 0;
         if (index <= this->_options.size()-1)
             this->_options.erase(this->_options.begin() + index);
-        selectByIndex((index <= static_cast<int>(this->_options.size()) - 1) ? index : static_cast<int>(this->_options.size()) - 1);
-        return (index <= static_cast<int>(this->_options.size()) - 1) ? index : (static_cast<int>(this->_options.size()) - 1);
+        selectByIndex((index <= this->_options.size() - 1) ? static_cast<int>(index) : static_cast<int>(this->_options.size() - 1));
+        return (index <= this->_options.size() - 1) ? index : this->_options.size() - 1;
     }
 
     template<typename T>
     size_t campvis::GenericOptionProperty<T>::updateCurrent(GenericOption<T> copy) {
-        std::vector< GenericOption<T> >::iterator* it = this->_options[getValue()];
+        GenericOption<T>* it = &this->_options[getValue()];
         it->_id = copy._id;
         it->_title = copy._title;
         it->_value = copy._value;

modules/devil/processors/devilimagereader.cpp

@@ -160,80 +160,24 @@ namespace campvis {
                 delete tex;
                 data.addData(p_targetImageID.getValue(), id);
             }
-            else if (p_importType.getOptionValue() == "localIntensity33") {
-                glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
-                tex->downloadTexture();
-                size_t numElements = tgt::hmul(tex->getDimensions());
-                tgt::ivec3 temp = tex->getDimensions();
-                temp.z = 100;
-                ImageData* id = new ImageData(3, temp, 3);
-
-                /*if (tex->getDataType() == GL_UNSIGNED_BYTE && tex->getNumChannels() == 3) {
-                    tgt::Vector3<uint8_t>* data = reinterpret_cast<tgt::Vector3<uint8_t>*>(tex->getPixelData());
-                    tgt::Vector3<uint8_t>* data3d = new tgt::Vector3<uint8_t>[numElements];
-                    for (size_t i = 0; i < numElements; ++i) {
-                        data3d[i].x = data[i].x;
-                        data3d[i].y = data[i].y;
-                        data3d[i].z = data[i].z;
-                    }
-                    GenericImageRepresentationLocal<uint8_t, 3>::create(id, data3d);
-                }*/
-                if (tex->getDataType() == GL_UNSIGNED_BYTE && tex->getNumChannels() == 3) {
-                    tgt::Vector3<uint8_t>* data = reinterpret_cast<tgt::Vector3<uint8_t>*>(tex->getPixelData());
-                    tgt::Vector3<uint8_t>* data3d = new tgt::Vector3<uint8_t>[temp.y * temp.x*temp.z];
-                    //for(int i =0; i < temp.z; i++)
-                    //    data3d[i] = new tgt::Vector3<uint8_t>[temp.y * temp.x];
-                    for (size_t i = 0; i < numElements; ++i) {
-                        for(int k = 0; k < temp.z; k++){
-                        data3d[k*numElements + i].x = data[i].x;
-                        data3d[k*numElements + i].y = data[i].y;
-                        data3d[k*numElements + i].z = data[i].z;}
-                    }
-                    GenericImageRepresentationLocal<uint8_t, 3>::create(id, data3d);
-                }
-
-                delete tex;
-                data.addData(p_targetImageID.getValue(), id);
-            }
             else if (p_importType.getOptionValue() == "localIntensity3") {
                 glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
                 tex->downloadTexture();
                 size_t numElements = tgt::hmul(tex->getDimensions());
                 tgt::ivec3 temp = tex->getDimensions();
-                //temp.z = 1;
                 int zee = 0;
 
-                /*if (tex->getDataType() == GL_UNSIGNED_BYTE && tex->getNumChannels() == 3) {
-                    tgt::Vector3<uint8_t>* data = reinterpret_cast<tgt::Vector3<uint8_t>*>(tex->getPixelData());
-                    tgt::Vector3<uint8_t>* data3d = new tgt::Vector3<uint8_t>[numElements];
-                    for (size_t i = 0; i < numElements; ++i) {
-                        data3d[i].x = data[i].x;
-                        data3d[i].y = data[i].y;
-                        data3d[i].z = data[i].z;
-                    }
-                    GenericImageRepresentationLocal<uint8_t, 3>::create(id, data3d);
-                }*/
-
-                //tgt::Vector3<uint8_t>* data3d;
-                std::vector<tgt::Vector3<uint8_t> > vdata;// = new std::vector<tgt::Vector3<uint8_t> >();
+                std::vector<tgt::Vector3<uint8_t> > vdata;
                 while (nullptr != tex) {
                     if (tex->getDataType() == GL_UNSIGNED_BYTE && tex->getNumChannels() == 3) {
                         tgt::Vector3<uint8_t>* data = reinterpret_cast<tgt::Vector3<uint8_t>*>(tex->getPixelData());
-                        //data3d = new tgt::Vector3<uint8_t>[temp.y * temp.x*temp.z];
                         for (size_t i = 0; i < numElements*1; ++i) {
                             for(int k = 0; k < temp.z; k++){
-                                //data3d[k*numElements + i].x = data[i].x;
-                                //data3d[k*numElements + i].y = data[i].y;
-                                //data3d[k*numElements + i].z = data[i].z;
                                 vdata.push_back(data[i % numElements]);
                             }
                         }
-                        //std::vector<tgt::Vector3<uint8_t> > x(data, data+numElements);
-                        //vdata->push_back(x);
                         zee+=1;
-                        //GenericImageRepresentationLocal<uint8_t, 3>::create(id, data3d);
                     }
-
                     delete tex;
 
                     if (this->p_importSimilar.getValue() == true) {
@@ -246,20 +190,13 @@ namespace campvis {
                     else {
                         break;
                     }
-                    //break;
-                } //while
+                }
 
                 temp.z = zee;
                 ImageData* id = new ImageData(3, temp, 3);
 
-                //uint8_t* data3d = new uint8_t[temp.x * temp.y * temp.z+100];
-                //for (size_t i = 0; i < temp.x*temp.y*temp.z; ++i) {
-                //    data3d[i] = vdata->at(i).x;
-                //}
-                //GenericImageRepresentationLocal<uint8_t, 1>::create(id, data3d);
-
                 tgt::Vector3<uint8_t>* data3d = new tgt::Vector3<uint8_t>[temp.x * temp.y * temp.z];
-                memcpy_s(data3d, temp.x*temp.y*temp.z *3, &vdata.front(), temp.x*temp.y*temp.z*3);
+                memcpy(data3d, &vdata.front(), temp.x*temp.y*temp.z *3);
                 GenericImageRepresentationLocal<uint8_t, 3>::create(id, data3d);
 
                 id->setMappingInformation(ImageMappingInformation(id->getSize(), id->getMappingInformation().getOffset(), id->getMappingInformation().getVoxelSize() * tgt::vec3(1, 1, 1) ));

modules/io/processors/genericimagereader.cpp

@@ -56,6 +56,10 @@ namespace campvis {
     }
     
     GenericImageReader::~GenericImageReader() {
+        for(std::map<AbstractImageReader*, MetaProperty*>::iterator it = this->_readers.begin(); it != this->_readers.end(); ++it) {
+            delete it->second;
+            delete it->first;
+        }
     }
 
     void GenericImageReader::init() {
@@ -64,8 +68,14 @@ namespace campvis {
 
     void GenericImageReader::deinit() {
         for(std::map<AbstractImageReader*, MetaProperty*>::iterator it = this->_readers.begin(); it != this->_readers.end(); ++it) {
-            if (nullptr != it->first) delete it->first;
-            if (nullptr != it->second) delete it->second;
+            // deinit MetaProperty first!
+            if (nullptr != it->second) {
+                it->second->deinit();
+            }
+            // then we can delete the reader!
+            if (nullptr != it->first) {
+                dynamic_cast<AbstractProcessor*>(it->first)->deinit();
+            }
         }
     }
 

modules/microscopysegmentation/ext/alglib/CMakeLists.txt

@@ -12,12 +12,12 @@
 project(alglib CXX C)
 cmake_minimum_required(VERSION 2.6.2)
 
-# Where Google Test's .h files can be found.
+# Where .h files can be found.
 include_directories(
   ${alglib_SOURCE_DIR}
   ${alglib_SOURCE_DIR})
 
-# Where Google Test's libraries can be found.
+# Where libraries can be found.
 link_directories(${gtest_BINARY_DIR})
 
 LIST(APPEND AlglibHeaders
@@ -54,13 +54,9 @@ LIST(APPEND AlglibSources
 
 
 ########################################################################
-#
-# Defines the alglib & gtest_main libraries.  User tests should link
-# with one of them.
 
-# Google Test libraries.  We build them using more strict warnings than what
-# are used for other targets, to ensure that alglib can be compiled by a user
-# aggressive about warnings.
+# Defines the alglib librarie.  
+
 ADD_LIBRARY(alglib STATIC 
     ${AlglibSources} ${AlglibHeaders} )
 #cxx_library(gtest_main "${cxx_strict}" src/gtest_main.cc)
@@ -70,9 +66,11 @@ ADD_LIBRARY(alglib STATIC
 if ( CMAKE_COMPILER_IS_GNUCC )
     # This is tested
     set_property( TARGET alglib APPEND_STRING PROPERTY COMPILE_FLAGS -Wall )
+	SET(CMAKE_CXX_FLAGS "-fPIC -fno-strict-aliasing")
 endif ( CMAKE_COMPILER_IS_GNUCC )
 if ( MSVC )
     # This is untested
-    set_property( TARGET alglib APPEND_STRING PROPERTY COMPILE_FLAGS /W1 )
+    set_property( TARGET alglib APPEND_STRING PROPERTY COMPILE_FLAGS "/W1 /EHsc" )
+	SET(CMAKE_CXX_FLAGS "-fno-strict-aliasing")
 endif ( MSVC )
 

modules/microscopysegmentation/ext/alglib/ap.cpp

@@ -139,9 +139,9 @@ __declspec(align(AE_LOCK_ALIGNMENT)) volatile ae_int64_t _ae_dbg_lock_yields = 0
  * you can remove them, if you want - they are not used anywhere.
  *
  */
-static char _ae_int32_t_must_be_32_bits_wide[1-2*((int)(sizeof(ae_int32_t))-4)*((int)(sizeof(ae_int32_t))-4)];
-static char _ae_int64_t_must_be_64_bits_wide[1-2*((int)(sizeof(ae_int64_t))-8)*((int)(sizeof(ae_int64_t))-8)];
-static char _ae_int_t_must_be_pointer_sized [1-2*((int)(sizeof(ae_int_t))-(int)sizeof(void*))*((int)(sizeof(ae_int_t))-(int)(sizeof(void*)))];  
+// static char _ae_int32_t_must_be_32_bits_wide[1-2*((int)(sizeof(ae_int32_t))-4)*((int)(sizeof(ae_int32_t))-4)];
+// static char _ae_int64_t_must_be_64_bits_wide[1-2*((int)(sizeof(ae_int64_t))-8)*((int)(sizeof(ae_int64_t))-8)];
+// static char _ae_int_t_must_be_pointer_sized [1-2*((int)(sizeof(ae_int_t))-(int)sizeof(void*))*((int)(sizeof(ae_int_t))-(int)(sizeof(void*)))];  
 
 /*
  * This variable is used to prevent some tricky optimizations which may degrade multithreaded performance.

modules/microscopysegmentation/ext/alglib/linalg.cpp

@@ -7071,8 +7071,8 @@ bool rmatrixschur(real_2d_array &a, const ae_int_t n, real_2d_array &s)
 /////////////////////////////////////////////////////////////////////////
 namespace alglib_impl
 {
-static ae_int_t ablas_rgemmparallelsize = 64;
-static ae_int_t ablas_cgemmparallelsize = 64;
+// static ae_int_t ablas_rgemmparallelsize = 64;
+// static ae_int_t ablas_cgemmparallelsize = 64;
 static void ablas_ablasinternalsplitlength(ae_int_t n,
      ae_int_t nb,
      ae_int_t* n1,
@@ -26936,15 +26936,15 @@ static void rcond_cmatrixestimatenorm(ae_int_t n,
 {
     ae_int_t itmax;
     ae_int_t i;
-    ae_int_t iter;
-    ae_int_t j;
-    ae_int_t jlast;
+    ae_int_t iter = 0;
+    ae_int_t j=0;
+    ae_int_t jlast = 0;
     ae_int_t jump;
-    double absxi;
-    double altsgn;
-    double estold;
+    double absxi = 0;
+    double altsgn = 0;
+    double estold = 0;
     double safmin;
-    double temp;
+    double temp = 0;
     

modules/microscopysegmentation/pipelines/microscopyimagesegmentationdemo.cpp

@@ -42,7 +42,6 @@ namespace campvis {
     {
         addProcessor(&_lsp);
 
-        //_ve.getProperty()->addSharedProperty(_imageReader.getProperty("imgReaderViewport"));
         addProcessor(&_imageReader);
         addProcessor(&_ve);
 
@@ -58,20 +57,15 @@ namespace campvis {
         _ve.p_outputImage.setValue("mscopy");
         _renderTargetID.setValue("mscopy");
 
-        //_imageReader.setURL(CAMPVIS_SOURCE_DIR "/modules/vis/sampledata/smallHeart.mhd");
-        _imageReader.p_url.setValue(CAMPVIS_SOURCE_DIR "/../lymph/LymphP1_0086.tif");
+        _imageReader.setURL(CAMPVIS_SOURCE_DIR "/../lymph/LymphP1_0086.tif");
         MetaProperty *metaProp = dynamic_cast<MetaProperty*>(_imageReader.getProperty("DevilImageReaderMetaProp"));
         tgtAssert(nullptr != metaProp, "This should not happen.");
         BoolProperty *bp = dynamic_cast<BoolProperty*>(metaProp->getProperty("ImportSimilar"));
         tgtAssert(nullptr != bp, "This should not happen.");
         bp->setValue(true);
-        
-        _imageReader.setTargetImageId("mscopy.output");
-        _imageReader.setTargetImageIdSharedProperty(&_ve.p_inputVolume);        
-        //_imageReader.p_importType.selectById("localIntensity3");//selectByIndex(2);
-        //_imageReader.p_targetImageID.setValue("reader.output");
-        //_imageReader.p_targetImageID.addSharedProperty(&_ve.p_inputVolume);
 
+        _imageReader.setTargetImageId("mscopy.output");
+        _imageReader.setTargetImageIdSharedProperty(&_ve.p_inputVolume);
 
         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)));
@@ -84,9 +78,4 @@ namespace campvis {
     void MicroscopyImageSegmentationDemo::deinit() {
         AutoEvaluationPipeline::deinit();
     }
-
-    //void MicroscopyImageSegmentation::updateProperties(DataContainer &dc) {
-
-    //}
-
-}
\ No newline at end of file
+}

modules/microscopysegmentation/processors/microscopyimagesegmentation.cpp

@@ -95,19 +95,19 @@ namespace campvis {
         , _zSliceHandler(&_sliceExtractor.p_zSliceNumber)
         , _windowingHandler(&_sliceExtractor.p_transferFunction)
         , _trackballEH(0)
-        , _mousePressedInRaycaster(false)
         , p_paintColor("PaintColor", "Change Color", tgt::vec4(255), tgt::vec4(0.0f), tgt::vec4(255))
         , p_axisScaling("AxisScaling", "Axis Scale", tgt::vec3(1), tgt::vec3(1), tgt::vec3(25), tgt::vec3(1))
-        , p_objectList(0)
+        , p_fitToWindow("FitToWindow", "Fit to Window", true)
+        , p_scalingFactor("ScalingFactor", "Scaling Factor", 1.f, 0.f, 10.f, .1f, 2)
+        , p_offset("Offset", "Offset", tgt::ivec2(0), tgt::ivec2(0), tgt::ivec2(100))
         , p_addObject("addObjectButton", "Add Object")
         , p_deleteObject("deleteObjectButton", "Delete Current Object")
         , p_csvPath("csvPath", "File Name", "", StringProperty::SAVE_FILENAME)
         , p_saveCSV("saveCSV", "Save")
+        , p_objectList(0)
+        , _mousePressedInRaycaster(false)        
         , _objectNamePrefix("Object ")
         , _objectNameSuffix(0) 
-        , p_fitToWindow("FitToWindow", "Fit to Window", true)
-        , p_scalingFactor("ScalingFactor", "Scaling Factor", 1.f, 0.f, 10.f, .1f, 2)
-        , p_offset("Offset", "Offset", tgt::ivec2(0), tgt::ivec2(0), tgt::ivec2(100))
 
     {
         addProperty(p_inputVolume, INVALID_PROPERTIES);
@@ -254,7 +254,7 @@ namespace campvis {
                     float pos = 0;
                     vertices.clear();
                     colors.clear();
-                    for (int gg = 0; gg < selectedObject._points.size() * 5; gg++ ) {
+                    for (size_t gg = 0; gg < selectedObject._points.size() * 5; gg++ ) {
                         double x, y, z = selectedObject._points[0].z;
                         alglib::pspline2calc(p, pos, x, y);
                         pos += stepSize;
@@ -292,7 +292,7 @@ namespace campvis {
                             float pos = 0;
                             vertices.clear();
                             colors.clear();
-                            for (int gg= 0; gg < it.size() * 5; gg++ ) {
+                            for (size_t gg= 0; gg < it.size() * 5; gg++ ) {
                                 double x, y, z = it[0].z;
                                 alglib::pspline2calc(p, pos, x, y);
                                 pos += stepSize;
@@ -556,7 +556,7 @@ namespace campvis {
                     }
 
                     // lock this processor, so that the slice orientation's setting does not change
-                    AbstractProcessor::ScopedLock lock(this, false);
+                    AbstractProcessor::ScopedLock lock(this);
 
                     if (me->y() <= blockSize.y * 2 && me->x() >= leftPane.x) {
                         _sliceExtractor.p_sliceOrientation.selectByOption(SliceExtractor::XZ_PLANE);//xz
@@ -632,10 +632,10 @@ namespace campvis {
                     return;
                 }
 
-                for (int i = 0; i < selectedObject._points.size(); i++) {
+                for (size_t i = 0; i < selectedObject._points.size(); i++) {
                     unsigned long dist2 = distanceSqr(selectedObject._points[i], voxel);
                     if (dist > dist2) {
-                        insertNextVoxelAt = i;
+                        insertNextVoxelAt = static_cast<int>(i);
                         dist = dist2;
                     }
                 }
@@ -672,14 +672,14 @@ namespace campvis {
     }
 
     void MicroscopyImageSegmentation::onPaintColorChanged(const AbstractProperty *prop) {
-        ContourObject &obj = this->p_objectList->getOptionValue();
+        ContourObject &obj = this->p_objectList->getOptionReference();
         obj._color.setValue(p_paintColor.getValue());
         this->p_objectList->updateCurrent(obj);
 
         invalidate(INVALID_RESULT | SCRIBBLE_INVALID);
     }
     void MicroscopyImageSegmentation::onObjectSelectionChanged (const AbstractProperty *prop) {
-        ContourObject &obj = this->p_objectList->getOptionValue();
+        const ContourObject &obj = this->p_objectList->getOptionValue();
         this->p_paintColor.setValue(obj._color.getValue());
 
         invalidate(INVALID_RESULT | SCRIBBLE_INVALID);

modules/microscopysegmentation/processors/microscopyimagesegmentation.h

@@ -182,6 +182,12 @@ namespace campvis {
         IVec2Property p_leftPaneSize;                   ///< Used to define space for zslice
         IVec2Property p_zSize;                          ///< Actual size for zslice
 
+        MWheelToNumericPropertyEventListener _xSliceHandler;
+        MWheelToNumericPropertyEventListener _ySliceHandler;
+        MWheelToNumericPropertyEventListener _zSliceHandler;
+        TransFuncWindowingEventListener _windowingHandler;
+        TrackballNavigationEventListener* _trackballEH;
+
         ColorProperty p_paintColor;                     ///< Color picker for active object
         Vec3Property p_axisScaling;                     ///< Asis ratio. Used to change ImageMappingInformation
         tgt::vec3 _oldScaling;
@@ -195,12 +201,6 @@ namespace campvis {
         StringProperty p_csvPath;                       ///< Filepath to save CSV
         ButtonProperty p_saveCSV;                       ///< Save changes in CSV
         GenericOptionProperty<ContourObject> *p_objectList; ///< List of drawn contours
-
-        MWheelToNumericPropertyEventListener _xSliceHandler;
-        MWheelToNumericPropertyEventListener _ySliceHandler;
-        MWheelToNumericPropertyEventListener _zSliceHandler;
-        TransFuncWindowingEventListener _windowingHandler;
-        TrackballNavigationEventListener* _trackballEH;
         bool _mousePressedInRaycaster;                  ///< Flag whether mouse was pressed in raycaster
 
         static const std::string loggerCat_;