Merge branch 'master' of https://github.com/GeertLitjens/ASAP

CMakeLists.txt

@@ -4,6 +4,10 @@ PROJECT(DIAGPathology)
 SET(CMAKE_MODULE_PATH ${DIAGPathology_SOURCE_DIR}/cmakemodules)
 SET_PROPERTY(GLOBAL PROPERTY USE_FOLDERS ON)
 
+IF(NOT WIN32)
+SET(CMAKE_INSTALL_RPATH "\$ORIGIN/../lib:$ORIGIN/")
+ENDIF(NOT WIN32)
+
 # Use boost for cross-platform use of threading, file system and date_time handling
 FIND_PACKAGE(Boost REQUIRED COMPONENTS date_time filesystem program_options regex system thread)
 SET(Boost_DEFINITIONS "-DBOOST_ALL_DYN_LINK")

annotation/AnnotationToMask.cpp

@@ -88,7 +88,7 @@ void AnnotationToMask::convert(const std::shared_ptr<AnnotationList>& annotation
                   if (nameOrder.empty()) {
                     buffer[y * 512 + x] = in_poly * label > buffer[y * 512 + x] ? in_poly * label : buffer[y * 512 + x];
                   }
-                  else {
+                  else if (in_poly) {
                     buffer[y * 512 + x] = in_poly * label;
                   }
                 }

imgproc/generic/ColorDeconvolutionFilter.h

@@ -124,6 +124,12 @@ class ColorDeconvolutionFilter :  public ImageFilter<inType, double> {
     cosy[2] = cosy[2] / leng;
     cosz[2] = cosz[2] / leng;
 
+		for (int i=0; i<3; i++){
+			if (cosx[i] == 0.0) cosx[i] = 0.001;
+			if (cosy[i] == 0.0) cosy[i] = 0.001;
+			if (cosz[i] == 0.0) cosz[i] = 0.001;
+		}
+
     /* matrix inversion */
     double A = cosy[1] - cosx[1] * cosy[0] / cosx[0];
     double V = cosz[1] - cosx[1] * cosz[0] / cosx[0];

imgproc/generic/FilterBase.cpp

@@ -1,7 +1,8 @@
+#include <memory>
 #include "FilterBase.h"
 #include "core/ProgressMonitor.h"
 
-FilterBase::FilterBase() : _monitor(NULL), _cancel(false), _running(false) {
+FilterBase::FilterBase() : _cancel(false), _running(false) {
 
 }
 
@@ -41,22 +42,18 @@ void FilterBase::finish() {
 }
 
 
-const ProgressMonitor* const FilterBase::progressMonitor() const {
+std::weak_ptr<ProgressMonitor> FilterBase::progressMonitor() const {
   return _monitor;
 }
 
-void FilterBase::setProgressMonitor(ProgressMonitor* monitor) {
-  _monitorMutex.lock();
+void FilterBase::setProgressMonitor(std::shared_ptr<ProgressMonitor> monitor) {
   _monitor = monitor;
-  _monitorMutex.unlock();
 }
 
 void FilterBase::updateProgress(float progress) {
-  _monitorMutex.lock();
-  if (_monitor) {
-    _monitor->setProgress(progress);
+  if (std::shared_ptr<ProgressMonitor> shared_monitor = _monitor.lock()) {
+    shared_monitor->setProgress(progress);
   }
-  _monitorMutex.unlock();
 }
 
 void FilterBase::cancel() {

imgproc/generic/FilterBase.h

@@ -4,14 +4,14 @@
 #include "config/pathology_config.h"
 #include <mutex>
 #include <string>
+#include <memory>
 
 class ProgressMonitor;
 
 class EXPORT_BASICFILTERS FilterBase {
 
-  std::mutex _monitorMutex;
   std::mutex _cancelMutex;
-  ProgressMonitor* _monitor;
+  std::weak_ptr<ProgressMonitor> _monitor;
   bool _cancel;
   bool _running;
 
@@ -24,8 +24,8 @@ class EXPORT_BASICFILTERS FilterBase {
 
   virtual std::string name() const;
 
-  const ProgressMonitor* const progressMonitor() const;
-  void setProgressMonitor(ProgressMonitor* monitor);
+  std::weak_ptr<ProgressMonitor> progressMonitor() const;
+  void setProgressMonitor(std::shared_ptr<ProgressMonitor> monitor);
   void updateProgress(float progress);
 
   void cancel();

io/multiresolutionimageinterface/MultiResolutionImage.h

@@ -46,7 +46,7 @@ public :
   //! Obtains data as a patch, which is a basic image class containing all relevant information for further processing,
   //! like data and colortype
   template <typename T> 
-  Patch<T>* getPatch(const long long& startX, const long long& startY, const unsigned long long& width, 
+  Patch<T> getPatch(const long long& startX, const long long& startY, const unsigned long long& width,
     const unsigned long long& height, const unsigned int& level) 
   {
     std::vector<unsigned long long> dims(3,0);
@@ -60,8 +60,8 @@ public :
     for (unsigned int i = 0; i < _spacing.size(); ++i) {
       patchSpacing[i] = _spacing[i] * levelDownsample;
     }
-    Patch<T>* patch = new Patch<T>(dims, this->getColorType(), data, true);
-    patch->setSpacing(patchSpacing);
+    Patch<T> patch = Patch<T>(dims, this->getColorType(), data, true);
+    patch.setSpacing(patchSpacing);
     return patch;
   }
 

io/multiresolutionimageinterface/multiresolutionimageinterface.i

@@ -45,6 +45,7 @@
 %include "std_map.i"
 %include "std_shared_ptr.i"
 
+%shared_ptr(ImageSource)
 %shared_ptr(MultiResolutionImage)
 %shared_ptr(OpenSlideImage)
 %shared_ptr(VSIImage)
@@ -63,8 +64,8 @@ namespace std {
   %template(vector_uint) vector<unsigned int>;
   %template(vector_float) vector<float>;
   %template(vector_double) vector<double>;
-  %template(vector_annotation) vector<Annotation*>;
-  %template(vector_annotation_group) vector<AnnotationGroup*>;
+  %template(vector_annotation) vector<shared_ptr<Annotation> >;
+  %template(vector_annotation_group) vector<shared_ptr<AnnotationGroup> >;
   %template(vector_unsigned_long_long) vector<unsigned long long>;
   %template(vector_long_long) vector<long long>;
   %template(vector_string) vector<string>;

workstation/CMakeLists.txt

@@ -53,15 +53,15 @@ IF(BUILD_USING_QT4)
     resources/icons.qrc
   )
   qt4_add_resources(RESOURCE_ADDED ${RESOURCE})
-  ADD_EXECUTABLE(ASAP ${SOURCE} ${HEADERS} ${PATHOLOHWORKSTATION_MOC})
+  ADD_EXECUTABLE(ASAP WIN32 ${SOURCE} ${HEADERS} ${PATHOLOHWORKSTATION_MOC})
   TARGET_LINK_LIBRARIES(ASAP ${QT_LIBRARIES})
 ELSE()
   find_package(Qt5 COMPONENTS Core Widgets Gui OpenGL)
   set(RESOURCE
     resources/ASAP_resources.qrc
   )
   qt5_add_resources(RESOURCE_ADDED ${RESOURCE})      
-  ADD_EXECUTABLE(ASAP ${SOURCE} ${HEADERS} ${RESOURCE_ADDED})
+  ADD_EXECUTABLE(ASAP WIN32 ${SOURCE} ${HEADERS} ${RESOURCE_ADDED})
   QT5_USE_MODULES(ASAP Core Widgets OpenGL UiTools)
 ENDIF()
 

workstation/MiniMap.cpp

@@ -8,7 +8,7 @@
 
 const char* const MiniMap::coverageColors[] = { "red", "green", "yellow", "black", "purple", "orange" };
 
-MiniMap::MiniMap(QPixmap* overview, QWidget *parent) 
+MiniMap::MiniMap(const QPixmap& overview, QWidget *parent) 
   : QWidget(parent),
     _overview(overview),
     _fieldOfView(QRectF()),
@@ -21,14 +21,8 @@ MiniMap::MiniMap(QPixmap* overview, QWidget *parent)
   policy.setHorizontalPolicy(QSizePolicy::Fixed);
   policy.setVerticalPolicy(QSizePolicy::Fixed);
   setSizePolicy(policy);
-  if (_overview) {
-    _aspectRatio = static_cast<float>(_overview->width()) / _overview->height();
-  }
-}
-
-MiniMap::~MiniMap() {
-  if (_overview) {
-    delete _overview;
+  if (!overview.isNull()) {
+    _aspectRatio = static_cast<float>(_overview.width()) / _overview.height();
   }
 }
 
@@ -59,7 +53,7 @@ void MiniMap::onCoverageUpdated() {
 void MiniMap::mousePressEvent(QMouseEvent *event) {
   float posX = event->pos().x();
   float posY = event->pos().y();
-  QPointF pos((_overview->width() * posX) / width() + 1, (_overview->height() * posY) / height() + 1);
+  QPointF pos((_overview.width() * posX) / width() + 1, (_overview.height() * posY) / height() + 1);
   emit positionClicked(pos);
 }
 
@@ -69,8 +63,8 @@ void MiniMap::mouseMoveEvent(QMouseEvent *event) {
 
 void MiniMap::paintEvent(QPaintEvent *event) {
   QPainter painter(this);
-  if (_overview) {
-    painter.drawPixmap(1, 1, width(), height(), *_overview);
+  if (!_overview.isNull()) {
+    painter.drawPixmap(1, 1, width(), height(), _overview);
     painter.setPen(QPen(Qt::white, 2));
     painter.drawRect(1, 1, width() - 2, height() - 2);
     painter.setPen(QPen(Qt::black, 1));
@@ -86,7 +80,7 @@ void MiniMap::paintEvent(QPaintEvent *event) {
       for (std::vector<QPainterPath>::const_iterator it = pths.begin(); it != pths.end(); ++it) {
         if (!it->isEmpty()) {
           QTransform trans;
-          trans = trans.scale(width() / static_cast<float>(_overview->width()), height() / static_cast<float>(_overview->height()));
+          trans = trans.scale(width() / static_cast<float>(_overview.width()), height() / static_cast<float>(_overview.height()));
           QPainterPath qpf2 = trans.map(*it);
           unsigned int colorIndex = (it - pths.begin()) % 6;
           painter.setPen(QPen(QColor(coverageColors[colorIndex])));
@@ -100,10 +94,10 @@ void MiniMap::paintEvent(QPaintEvent *event) {
       QPen blue = QPen(QColor("blue"));
       blue.setWidth(3);
       painter.setPen(blue);
-      float rectX = width() * (_fieldOfView.left() / _overview->width()) + 1;
-      float rectY = height() * (_fieldOfView.top() / _overview->height()) + 1;
-      float rectW = width() * (_fieldOfView.width() / _overview->width()) - 2;
-      float rectH = height() * (_fieldOfView.height() / _overview->height()) - 2;
+      float rectX = width() * (_fieldOfView.left() / _overview.width()) + 1;
+      float rectY = height() * (_fieldOfView.top() / _overview.height()) + 1;
+      float rectW = width() * (_fieldOfView.width() / _overview.width()) - 2;
+      float rectH = height() * (_fieldOfView.height() / _overview.height()) - 2;
       if (rectW > 3 && rectH > 3) {
         painter.drawRect(rectX, rectY, rectW, rectH);
       }
@@ -118,8 +112,8 @@ void MiniMap::paintEvent(QPaintEvent *event) {
 QSize MiniMap::sizeHint() const {
   QSize size(0, 0);
   unsigned int baseSize = 250;
-  if (_overview) {    
-    if (_overview->width() > _overview->height()) {
+  if (!_overview.isNull()) {    
+    if (_overview.width() > _overview.height()) {
       size = QSize(baseSize, baseSize / _aspectRatio);
     }
     else {

workstation/MiniMap.h

@@ -2,6 +2,7 @@
 #define MINIMAP_H
 
 #include <QWidget>
+#include <QPointer>
 
 class QPixmap;
 class TileManager;
@@ -10,8 +11,7 @@ class MiniMap : public QWidget {
   Q_OBJECT
 
 public:
-  MiniMap(QPixmap* overview, QWidget *parent = 0);
-  ~MiniMap();
+  MiniMap(const QPixmap& overview, QWidget *parent);
 
   QSize sizeHint() const;
   int heightForWidth(int w) const;
@@ -28,9 +28,9 @@ public slots:
   void paintEvent(QPaintEvent *event);
 
 private:
-  QPixmap* _overview;
+  QPixmap _overview;
   QRectF _fieldOfView;
-  TileManager* _manager;
+  QPointer<TileManager> _manager;
   float _aspectRatio; //Width / height
   static const char* const coverageColors[];
   bool _drawCoverageMap;