Merge branch 'master' into master

scripts/linux-makeself

@@ -119,8 +119,7 @@ install_captk () {
   fi
 
   echo "Done."
-  echo "To run CaPTk, locate to where CaPTk is installed and enter the command \"./CaPTk/${ver}/captk\" in your console."
-
+  echo "To run CaPTk, change to the directory where CaPTk is installed and enter the command \"./CaPTk/${ver}/captk\" in your console."
 }
 
 # Print license with a reader

src/applications/individualApps/confetti_source/pyGUI/ConfettiCore.py

@@ -4,30 +4,54 @@
 import ctypes
 from  ctypes import CFUNCTYPE, c_int,c_char,c_char_p
 import numpy
+# Update 7/2/2020: Modified ConfettiCore.py to accommodate nuitka packaging. 
 class ConfettiApi():
     def __init__(self):
         try:
-          self.libraryName =self.getCoreModulePath()
-          self.CoreModule = ctypes.cdll.LoadLibrary(self.libraryName)
-          self.listner= None
-          self.txtCallback_ref = None
-        except:
+            self.libraryName = os.path.normpath(self.getCoreModulePath())
+            self.CoreModule = ctypes.cdll.LoadLibrary(self.libraryName)
+            print "Successfully loaded the ConfettiCore binary."
+            self.listner= None
+            self.txtCallback_ref = None
+        except Exception as e:
             self.CoreModule= None
-            print("Failed to load ConfettiCore binary")
+            print("Failed to load ConfettiCore binary. Exception: ")
+            print(e)
     def getCoreModulePath(self):
         if os.name is 'nt':
             libraryName = "ConfettiCore.dll"
         else:
             libraryName = "libConfettiCore.so"
-        if getattr(sys, 'frozen', False):
+        if (getattr(sys, 'frozen', False)):
             application_path = os.path.dirname(sys.executable)
         elif __file__:
-            application_path = os.path.dirname(__file__)
-        baseDir=os.path.join(application_path, '..' )
+            print "Using __file__"
+            if os.name is 'nt':
+                application_path = self.attemptWindowsLongPathFix(os.path.dirname(__file__))
+            else:
+                application_path = os.path.dirname(__file__)
+        baseDir=os.path.join(application_path, '..' ) # use to search directory above dist
+		# match if dll found in either this or one-higher directory
+        for root, dirs, files in os.walk(application_path):
+            for file in files:
+                if libraryName in file:
+                    return (os.path.join(root, file))
         for root, dirs, files in os.walk(baseDir):
             for file in files:
                 if libraryName in file:
-                     return (os.path.join(root, file))
+                    return (os.path.join(root, file))
+
+    def attemptWindowsLongPathFix(self, in_path):
+        # Do not call this on non-Windows platforms.
+        try:
+            path = unicode(in_path)
+        except Exception as e:
+            print(e) 
+        GetLongPathName = ctypes.windll.kernel32.GetLongPathNameW
+        buffer = ctypes.create_unicode_buffer(GetLongPathName(path, 0, 0))
+        GetLongPathName(path, buffer, len(buffer))
+        print buffer.value
+        return buffer.value
 
     def registerCppCallback(self):
         if self.CoreModule is None:

src/view/gui/Slicer.cpp

@@ -199,9 +199,64 @@ void Slicer::SetInitPosition()
 
 void Slicer::SetCurrentPosition(double x, double y, double z)
 {
-	mCursor[0] = x;
-	mCursor[1] = y;
-	mCursor[2] = z;
+    double X = (x - this->GetInput()->GetOrigin()[0]) / this->GetInput()->GetSpacing()[0];
+    double Y = (y - this->GetInput()->GetOrigin()[1]) / this->GetInput()->GetSpacing()[1];
+    double Z = (z - this->GetInput()->GetOrigin()[2]) / this->GetInput()->GetSpacing()[2];
+
+    // round up pixel values
+    X = ROUND(X);
+    Y = ROUND(Y);
+    Z = ROUND(Z);
+
+    // Force pixel pos within bounds of image if not already
+#if VTK_MAJOR_VERSION <= 5
+    int minX = this->GetInput()->GetWholeExtent()[0];
+    int maxX = this->GetInput()->GetWholeExtent()[1];
+    int minY = this->GetInput()->GetWholeExtent()[2];
+    int maxY = this->GetInput()->GetWholeExtent()[3];
+    int minZ = this->GetInput()->GetWholeExtent()[4];
+    int maxZ = this->GetInput()->GetWholeExtent()[5];
+#else
+    int minX = this->GetInput()->GetExtent()[0];
+    int maxX = this->GetInput()->GetExtent()[1];
+    int minY = this->GetInput()->GetExtent()[2];
+    int maxY = this->GetInput()->GetExtent()[3];
+    int minZ = this->GetInput()->GetExtent()[4];
+    int maxZ = this->GetInput()->GetExtent()[5];
+#endif
+    if (X < minX)
+    {
+        X = minX;
+    }
+    else if (X > maxX)
+    {
+        X = maxX;
+    }
+    if (Y < minY)
+    {
+        Y = minY;
+    }
+    else if (Y > maxY)
+    {
+        Y = maxY;
+    }
+    if (Z < minZ)
+    {
+        Z = minZ;
+    }
+    else if (Z > maxZ)
+    {
+        Z = maxZ;
+    }
+    // Re-update world pos to match new pixel pos
+    x = X * this->GetInput()->GetSpacing()[0] + this->GetInput()->GetOrigin()[0];
+    y = Y * this->GetInput()->GetSpacing()[1] + this->GetInput()->GetOrigin()[1];
+    z = Z * this->GetInput()->GetSpacing()[2] + this->GetInput()->GetOrigin()[2];
+
+    // Set cursor to match new world pos
+    mCursor[0] = x;
+    mCursor[1] = y;
+    mCursor[2] = z;
 }
 
 void Slicer::SetInteractorStyle(vtkInteractorStyle * style)

src/view/gui/SlicerManager.cpp

@@ -601,21 +601,11 @@ void SlicerManager::UpdateInfoOnCursorPosition(int slicer)
   z = Z * mSlicers[slicer]->GetInput()->GetSpacing()[2] + mSlicers[slicer]->GetInput()->GetOrigin()[2];
   //
   double value = -VTK_DOUBLE_MAX;
-#if VTK_MAJOR_VERSION <= 5
-  if (X >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] && X <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
-    Y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] && Y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
-    Z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] && Z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5])
-#else
-  if (X >= mSlicers[slicer]->GetInput()->GetExtent()[0] && X <= mSlicers[slicer]->GetInput()->GetExtent()[1] &&
-    Y >= mSlicers[slicer]->GetInput()->GetExtent()[2] && Y <= mSlicers[slicer]->GetInput()->GetExtent()[3] &&
-    Z >= mSlicers[slicer]->GetInput()->GetExtent()[4] && Z <= mSlicers[slicer]->GetInput()->GetExtent()[5])
-#endif
-  {
-    //	mSlicers[slicer]->GetInput()
-    value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);
 
-    emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(), x, y, z, X, Y, Z, value);
-  }
+  value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);
+  // Update position to specified or bounded coords
+  emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(), x, y, z, X, Y, Z, value);
+
 }
 
 void SlicerManager::Activated()

src/view/gui/fHelpTutorial.cpp

@@ -87,7 +87,7 @@ fHelpTutorial::fHelpTutorial()
 
   if (!cbica::fileExists(m_helpFileFullPath))
   {
-    cbica::Logging(loggerFile, "Unable to start help page, file '" + m_helpFileFullPath + "' not found");
+    cbica::Logging(loggerFile, "Unable to start about page, file '" + m_helpFileFullPath + "' not found");
   }
   else
   {

src/view/gui/fMainWindow.cpp

@@ -344,7 +344,7 @@ fMainWindow::fMainWindow()
   {
     nonNativeAppPaths_wrap.erase(0, 1);
   }
-  nonNativeAppPaths_wrap = nonNativeAppPaths_wrap + " itksnap";
+  nonNativeAppPaths_wrap = nonNativeAppPaths_wrap + " itksnap" + " confetti";
   m_pyGUIApps = cbica::stringSplit(nonNativeAppPaths_wrap, " ");
   nonNativeAppPaths_wrap = std::string(CAPTK_APP_LIST_PY_CLI);
   if (nonNativeAppPaths_wrap[0] == ' ')
@@ -356,10 +356,6 @@ fMainWindow::fMainWindow()
   size_t allAppCounter = 0;
   for (size_t i = 0; i < m_pyGUIApps.size(); i++)
   {
-    if (m_pyGUIApps[i] == "confetti")
-    {
-      m_pyGUIApps[i] = "ConfettiGUI";
-    }
     if ((m_pyGUIApps[i] == "librabatch") || (m_pyGUIApps[i] == "librasingle"))
     {
       m_pyGUIApps[i] = "libra";
@@ -582,10 +578,13 @@ fMainWindow::fMainWindow()
   connect(supportMenu, SIGNAL(triggered(QAction*)), this, SLOT(help_Download(QAction*)));
 
   connect(actionModelLibrary, SIGNAL(triggered()), this, SLOT(OpenModelLibrary()));
+
+  mHelpDlg = new fHelpDialog();
+  mHelpTutorial = new fHelpTutorial();
 
   connect(help_systeminformation, SIGNAL(triggered()), this, SLOT(OnSystemInformationMenuClicked()));
 
-  connect(&mHelpTutorial, SIGNAL(skipTutorialOnNextRun(bool)), this, SLOT(skipTutorial(bool)));
+  connect(mHelpTutorial, SIGNAL(skipTutorialOnNextRun(bool)), this, SLOT(skipTutorial(bool)));
 
   for (size_t i = 0; i < vectorOfGBMApps.size(); i++)
   {
@@ -944,7 +943,7 @@ fMainWindow::fMainWindow()
   statusBar()->addPermanentWidget(m_progressBar);
   m_progressBar->setValue(0);
 
-  mHelpDlg = new fHelpDialog();
+
 
   recurrencePanel.SetCurrentLoggerPath(m_tempFolderLocation);
   msubtypePanel.SetCurrentLoggerPath(m_tempFolderLocation);
@@ -1014,6 +1013,9 @@ fMainWindow::~fMainWindow()
     file.close();
   }
 
+  if (mHelpTutorial)
+    delete mHelpTutorial;
+
   if (mHelpDlg)
     delete mHelpDlg;
 
@@ -1133,7 +1135,7 @@ std::string fMainWindow::ConversionFrom2Dto3D(const std::string &fileName)
 void fMainWindow::about()
 {
 //#if CAPTK_PACKAGE_PROJECT
-  mHelpTutorial.show();
+  mHelpTutorial->show();
 //#endif
 }
 
@@ -2290,6 +2292,7 @@ void fMainWindow::CloseImage(QTableWidgetItem* item)
 
 void fMainWindow::MousePositionChanged(int visibility, double x, double y, double z, double X, double Y, double Z, double value)
 {
+
   infoPanel->setCurrentInfo(visibility, x, y, z, X, Y, Z, value);
   tumorPanel->HighlightCurrentSelctedPoints(x, y, z, X, Y, Z, value);
 }
@@ -2725,9 +2728,10 @@ void fMainWindow::MoveSlicerCursor(double x, double y, double z, int mode)
     mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0)->SetCurrentPosition(x, y, z);
     //
     mSlicerManagers[mCurrentPickedImageIndex]->Picked();
+    mSlicerManagers[mCurrentPickedImageIndex]->UpdateInfoOnCursorPosition(0);
     mSlicerManagers[mCurrentPickedImageIndex]->UpdateViews(0);
     mSlicerManagers[mCurrentPickedImageIndex]->UpdateLinked(0);
-    mSlicerManagers[mCurrentPickedImageIndex]->UpdateInfoOnCursorPosition(0);
+
   }
   else if (mode == 1)
   {
@@ -2739,9 +2743,9 @@ void fMainWindow::MoveSlicerCursor(double x, double y, double z, int mode)
     mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0)->SetCurrentPosition(x, y, z);
     //
     mSlicerManagers[mCurrentPickedImageIndex]->Picked();
+    mSlicerManagers[mCurrentPickedImageIndex]->UpdateInfoOnCursorPosition(0);
     mSlicerManagers[mCurrentPickedImageIndex]->UpdateViews(0);
     mSlicerManagers[mCurrentPickedImageIndex]->UpdateLinked(0);
-    mSlicerManagers[mCurrentPickedImageIndex]->UpdateInfoOnCursorPosition(0);
   }
   propogateSlicerPosition();
 }
@@ -6124,8 +6128,8 @@ void fMainWindow::ApplicationLIBRASingle()
 
 void fMainWindow::ApplicationConfetti()
 {
-  std::string scriptToCall = m_allNonNativeApps["ConfettiGUI"];
-
+  std::string scriptToCall = m_allNonNativeApps["confetti"];
+   
   if (startExternalProcess(scriptToCall.c_str(), QStringList()) != 0)
   {
     ShowErrorMessage("Confetti failed to execute. Please check installation requirements and retry.", this);

src/view/gui/fMainWindow.h

@@ -1563,7 +1563,7 @@ public slots:
   Fetalbrain mfetalbrain;
 
   fHelpDialog* mHelpDlg;
-  fHelpTutorial mHelpTutorial;
+  fHelpTutorial* mHelpTutorial;
 
   std::string t1cePath;
   std::string m_imagetype_string;