Merge pull request #1201 from AlexanderGetka-cbica/confetti-change-mi…

…sc-fixes

Confetti change misc fixes

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;