Merge branch 'dev' of github.com:freesurfer/freesurfer into dev

Author: brf2

CMakeLists.txt

@@ -253,6 +253,7 @@ if(BUILD_GUIS)
 
   # -------- qt --------
 
+if(NOT Qt6_DIR)
   if(NOT Qt5_DIR)
      if(HOST_OS MATCHES "CentOS7" OR HOST_OS MATCHES "CentOS8" OR HOST_OS MATCHES "CentOS8stream")
         set(Qt5_DIR ${FS_PACKAGES_DIR}/qt/5.12.11_LTS_cos7/lib/cmake/Qt5 CACHE PATH "Qt5 install directory")
@@ -263,9 +264,15 @@ if(BUILD_GUIS)
         set(Qt5_DIR ${FS_PACKAGES_DIR}/qt/5.12.11_LTS_cos7/lib/cmake/Qt5 CACHE PATH "Qt5 install directory")
      endif()
   endif()
+endif()
 
   find_package(QT)
-  message(STATUS "For HOST_OS=${HOST_OS} Qt5_DIR=${Qt5_DIR}")
+
+  if(Qt6_DIR)
+     message(STATUS "For HOST_OS=${HOST_OS} Qt6_DIR=${Qt6_DIR}")
+  elseif(Qt5_DIR)
+     message(STATUS "For HOST_OS=${HOST_OS} Qt5_DIR=${Qt5_DIR}")
+  endif()
 
 endif()
 
@@ -548,6 +555,7 @@ add_subdirectories(
   mris_left_right_register
   mris_make_surfaces
   mris_register
+  mris_skeletonize
   mris_smooth
   mris_sphere
   mris_surface_stats
@@ -558,6 +566,7 @@ add_subdirectories(
   mrisp_paint
   python
   samseg
+  samsegmesh2surf
   talairach_afd
   scripts
   tkregister2
@@ -834,3 +843,5 @@ if(BUILD_DNG)
   add_subdirectory(dngtester)
 endif()
 
+# add wrapper for slicedelay
+install_pyscript(./scripts/slicedelay)

cmake/FindQT.cmake

@@ -1,12 +1,14 @@
 # Qt Find Module
 
-if(NOT Qt5_DIR)
-  # default search path
-  if(EXISTS ${FS_PACKAGES_DIR}/qt/5.11/lib/cmake/Qt5)
-    set(Qt5_DIR ${FS_PACKAGES_DIR}/qt/5.11/lib/cmake/Qt5)
-  elseif(EXISTS ${FS_PACKAGES_DIR}/qt/5.6/lib/cmake/Qt5)
-    set(Qt5_DIR ${FS_PACKAGES_DIR}/qt/5.6/lib/cmake/Qt5)
-  endif()
+if(NOT Qt6_DIR)
+   if(NOT Qt5_DIR)
+     # default search path
+     if(EXISTS ${FS_PACKAGES_DIR}/qt/5.11/lib/cmake/Qt5)
+       set(Qt5_DIR ${FS_PACKAGES_DIR}/qt/5.11/lib/cmake/Qt5)
+     elseif(EXISTS ${FS_PACKAGES_DIR}/qt/5.6/lib/cmake/Qt5)
+       set(Qt5_DIR ${FS_PACKAGES_DIR}/qt/5.6/lib/cmake/Qt5)
+     endif()
+   endif()
 endif()
 
 # find Qt components
@@ -15,11 +17,30 @@ if(NOT APPLE)
   set(_qt_components ${_qt_components} X11Extras)
 endif()
 
-find_package(Qt5 COMPONENTS ${_qt_components})
+if(Qt6_DIR)
+   find_package(Qt6 COMPONENTS ${_qt_components})
+elseif(Qt5_DIR)
+   find_package(Qt5 COMPONENTS ${_qt_components})
+endif()
 
 # cmake doesn't easily provide us with a cross-platform path to
 # root qt install directory, so we'll use the hidden QtCore prefix
-set(Qt5_INSTALL_DIR ${_qt5Core_install_prefix})
+if(Qt6_DIR)
+   set(Qt6_INSTALL_DIR ${_qt6Core_install_prefix})
+   if(APPLE)
+     # find_package function fails to set _qt_components with Qt6 (but not Qt5), so set Qt6 paths based upon Qt6_DIR.
+     # The bug for Qt6 being unable to find modules was supposed to have been fixed in 6.4, but still did not work for me.
+     # So the cmake command line needs to set both Qt6_DIR and Qt6GuiTools_DIR. A relative path for Qt6_INSTALL_DIR does work.
+     set(Qt6_INSTALL_DIR ${Qt6_DIR}/../../..)
+     # set(Qt6GuiTools_DIR ${Qt6_DIR}GuiTools)
+     set(MAC_QT_INSTALL_DIR ${Qt6_INSTALL_DIR})
+   endif()
+elseif(Qt5_DIR)
+   set(Qt5_INSTALL_DIR ${_qt5Core_install_prefix})
+   if(APPLE)
+     set(MAC_QT_INSTALL_DIR ${Qt5_INSTALL_DIR})
+   endif()
+endif()
 
 # install the shared libraries to the freesurfer lib directory
 if(Qt5_FOUND AND NOT APPLE)

cmake/functions.cmake

@@ -120,7 +120,8 @@ function(mac_deploy_qt)
   # run the qt deployment script
   install(CODE "
     message(STATUS \"Deploying ${APP_BUNDLE}\")
-    execute_process(COMMAND bash -c \"${CMAKE_SOURCE_DIR}/qt/mac_deploy ${Qt5_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/${APP_BUNDLE}\" RESULT_VARIABLE retcode)
+    message(STATUS \"${CMAKE_SOURCE_DIR}/qt/mac_deploy ${MAC_QT_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/${APP_BUNDLE}\")
+    execute_process(COMMAND bash -c \"${CMAKE_SOURCE_DIR}/qt/mac_deploy ${MAC_QT_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/${APP_BUNDLE}\" RESULT_VARIABLE retcode)
     if(NOT \${retcode} STREQUAL 0)
       message(FATAL_ERROR \"Could not deploy ${APP_TARGET}\")
     endif()"

diffusion_tool/CMakeLists.txt

@@ -1,14 +1,20 @@
 project(diffusion_tool)
 
-if(BUILD_GUIS AND Qt5_FOUND)
+if(BUILD_GUIS)
 
 	include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 
 	set(CMAKE_AUTOUIC ON)
 	set(CMAKE_AUTOMOC ON)
 
 	add_executable(diffusion_tool main.cpp configurationfileform.cpp)
-	target_link_libraries(diffusion_tool Qt5::Core Qt5::Widgets)
+
+  	if(Qt6_DIR)
+    		target_link_libraries(diffusion_tool Qt6::Core Qt6::Widgets)
+  	elseif(Qt5_DIR)
+    		target_link_libraries(diffusion_tool Qt5::Core Qt5::Widgets)
+  	endif()
+
 
 endif()
 

diffusion_tool/configurationfileform.cpp

@@ -3,7 +3,7 @@
 #include <QTextStream>
 #include <QFileDialog>
 #include <QMessageBox>
-#include <QRegExp>
+#include <QRegularExpression>
 
 #include "configurationfileform.h"
 
@@ -895,8 +895,9 @@ void ConfigurationFileForm::matcher(QDir directory, QString pattern, QVector<QSt
     QFileInfoList directory_contents = directory.entryInfoList(QDir::Files | QDir::Dirs | QDir::NoDotAndDotDot);
     // QTextStream(stdout) << "about to peep " << directory.absolutePath() << " and its length is " << directory_contents.length() << endl;
     QDir* temp = NULL;
-    QRegExp rx(pattern);
-    rx.setPatternSyntax(QRegExp::Wildcard);
+    QString wc_exp = QRegularExpression::wildcardToRegularExpression(pattern);
+    QRegularExpression rx(QRegularExpression::anchoredPattern(wc_exp),
+                          QRegularExpression::CaseInsensitiveOption);
     QString subject_name;
     int temp_index;
 
@@ -914,7 +915,7 @@ void ConfigurationFileForm::matcher(QDir directory, QString pattern, QVector<QSt
         else
         {
             // QTextStream(stdout) << "about to peep the contents of " << directory_contents[i].absoluteFilePath() << endl;
-            if (rx.exactMatch(directory_contents[i].absoluteFilePath()))
+            if (rx.match(directory_contents[i].absoluteFilePath()).hasMatch())
             {
                 vector.append(directory_contents[i].absoluteFilePath());
 

dissection_photo/CMakeLists.txt

@@ -1,12 +1,17 @@
 project(dissection_photo)
 
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
-if(BUILD_GUIS AND Qt5_FOUND)
+if(BUILD_GUIS)
 
   set(CMAKE_AUTOUIC ON)
   set(CMAKE_AUTOMOC ON)
   set(CMAKE_AUTORCC ON)
-  set(QT_LIBRARIES Qt5::Core Qt5::Widgets)
+
+  if(Qt6_DIR)
+    set(QT_LIBRARIES Qt6::Core Qt6::Widgets)
+  elseif(Qt5_DIR)
+    set(QT_LIBRARIES Qt5::Core Qt5::Widgets)
+  endif()
 
   add_compile_options(-Wno-deprecated -Wno-reorder -Wno-uninitialized -Wno-unused-variable -Wno-sign-compare
                       -Wno-overloaded-virtual -Wno-inconsistent-missing-override -Wno-deprecated-declarations)

dissection_photo/WidgetImageView.cpp

@@ -4,6 +4,7 @@
 #include <QDebug>
 #include "math.h"
 #include "exif.h"
+#include <QFile>
 
 WidgetImageView::WidgetImageView(QWidget *parent)
   : QWidget(parent), m_dScale(1.0), m_ptOffset(QPoint(0,0)), m_bPanning(false), m_bZooming(false), m_bDrawing(false),

dissection_photo/connected_components/CMakeLists.txt

@@ -1,6 +1,6 @@
 project(connected_components)
 
-if(BUILD_GUIS AND Qt5_FOUND)
+if(BUILD_GUIS)
 
   include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 

dissection_photo/connected_components/MainWindow.cpp

@@ -8,9 +8,9 @@
 #include <QFileInfo>
 #include <QMessageBox>
 #include <QSettings>
-#include <QDesktopWidget>
 #include "CommonDef.h"
 #include <QTemporaryDir>
+#include <QScreen>
 
 #define WND_TITLE "Connected Components"
 
@@ -49,15 +49,15 @@ MainWindow::MainWindow(QWidget *parent)
   setWindowTitle(WND_TITLE);
   QSettings s;
   QRect rc = s.value("MainWindow/Geometry").toRect();
-  if (rc.isValid() && QApplication::desktop()->screenGeometry(this).contains(rc))
+  if (rc.isValid() && QGuiApplication::primaryScreen()->geometry().contains(rc))
     setGeometry(rc);
 
   m_proc = new QProcess(this);
   connect(m_proc, SIGNAL(started()), SLOT(OnProcessStarted()));
   connect(m_proc, SIGNAL(readyReadStandardOutput()), SLOT(OnProcessOutputMessage()));
   connect(m_proc, SIGNAL(readyReadStandardError()), SLOT(OnProcessErrorMessage()));
   connect(m_proc, SIGNAL(finished(int, QProcess::ExitStatus)), SLOT(OnProcessFinished()));
-  connect(m_proc, SIGNAL(error(QProcess::ProcessError)), SLOT(OnProcessError(QProcess::ProcessError)));
+  connect(m_proc, SIGNAL(errorOccurred(QProcess::ProcessError)), SLOT(OnProcessError(QProcess::ProcessError)));
 }
 
 MainWindow::~MainWindow()
@@ -184,8 +184,8 @@ void MainWindow::LoadImage(int n)
   if (!rects.isEmpty())
   {
     QList<QPoint> pts;
-    foreach (RECT_REGION r, rects)
-      pts << r.first << r.second;
+    for (int i = 0; i < rects.size(); i++)
+      pts << rects[i].first << rects[i].second;
     m_maskProcessor.LoadSelections(pts);
     ui->widgetImageView->SetOverlay(m_maskProcessor.GetMaskImage(m_listStockColors));
     ui->pushButtonNext->setEnabled(true);

dissection_photo/fiducials_calibration/CMakeLists.txt

@@ -1,6 +1,6 @@
 project(fiducials_calibration)
 
-if(BUILD_GUIS AND Qt5_FOUND)
+if(BUILD_GUIS)
 
   include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 

dissection_photo/fiducials_calibration/MainWindow.cpp

@@ -6,7 +6,7 @@
 #include <QMessageBox>
 #include <QSettings>
 #include <QDebug>
-#include <QDesktopWidget>
+#include <QScreen>
 #include <QFileDialog>
 #include "DialogWelcome.h"
 #include <QTimer>
@@ -45,15 +45,15 @@ MainWindow::MainWindow(QWidget *parent)
   QSettings s;
   QRect rc = s.value("MainWindow/Geometry").toRect();
   m_strLastDir = s.value("LastDir").toString();
-  if (rc.isValid() && QApplication::desktop()->screenGeometry(this).contains(rc))
+  if (rc.isValid() && QGuiApplication::primaryScreen()->geometry().contains(rc))
     setGeometry(rc);
 
   m_proc = new QProcess(this);
   connect(m_proc, SIGNAL(started()), SLOT(OnProcessStarted()));
   connect(m_proc, SIGNAL(readyReadStandardOutput()), SLOT(OnProcessOutputMessage()));
   connect(m_proc, SIGNAL(readyReadStandardError()), SLOT(OnProcessErrorMessage()));
   connect(m_proc, SIGNAL(finished(int, QProcess::ExitStatus)), SLOT(OnProcessFinished()));
-  connect(m_proc, SIGNAL(error(QProcess::ProcessError)), SLOT(OnProcessError(QProcess::ProcessError)));
+  connect(m_proc, SIGNAL(errorOccurred(QProcess::ProcessError)), SLOT(OnProcessError(QProcess::ProcessError)));
 }
 
 MainWindow::~MainWindow()

dissection_photo/fiducials_correction/CMakeLists.txt

@@ -1,6 +1,6 @@
 project(fiducials_correction)
 
-if(BUILD_GUIS AND Qt5_FOUND)
+if(BUILD_GUIS)
 
   include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 

dissection_photo/fiducials_correction/MainWindow.cpp

@@ -5,9 +5,9 @@
 #include <QSettings>
 #include <QFileInfo>
 #include <QMessageBox>
-#include <QDesktopWidget>
 #include <QTimer>
 #include <QFileDialog>
+#include <QScreen>
 #include <QDebug>
 
 #define WND_TITLE "Correction With Fiducials"
@@ -28,7 +28,7 @@ MainWindow::MainWindow(QWidget *parent)
 
   QSettings s;
   QRect rc = s.value("MainWindow/Geometry").toRect();
-  if (rc.isValid() && QApplication::desktop()->screenGeometry(this).contains(rc))
+  if (rc.isValid() && QGuiApplication::primaryScreen()->geometry().contains(rc))
     setGeometry(rc);
 
   m_proc = new QProcess(this);

dissection_photo/py_scripts/func_fiducials_correction.py

@@ -42,8 +42,8 @@ def fiducials_correction(args):
             size=point[2],
             angle=point[3],
             response=point[4],
-            octave=point[5],
-            class_id=point[6],
+            octave=int(point[5]),
+            class_id=int(point[6]),
         )
         kp_template.append(temp)
 

dissection_photo/retrospective_correction/CMakeLists.txt

@@ -1,6 +1,6 @@
 project(retrospective_correction)
 
-if(BUILD_GUIS AND Qt5_FOUND)
+if(BUILD_GUIS)
 
   include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 

dissection_photo/retrospective_correction/MainWindow.cpp

@@ -8,7 +8,7 @@
 #include <QFileInfo>
 #include <QMessageBox>
 #include <QSettings>
-#include <QDesktopWidget>
+#include <QScreen>
 #include "CommonDef.h"
 #include <QTemporaryDir>
 
@@ -25,7 +25,7 @@ MainWindow::MainWindow(QWidget *parent)
 
   QSettings s;
   QRect rc = s.value("MainWindow/Geometry").toRect();
-  if (rc.isValid() && QApplication::desktop()->screenGeometry(this).contains(rc))
+  if (rc.isValid() && QGuiApplication::primaryScreen()->geometry().contains(rc))
     setGeometry(rc);
 
   SetupScriptPath();