diff --git a/Applications/SlicerApp/Testing/Python/AtlasTests.py b/Applications/SlicerApp/Testing/Python/AtlasTests.py index 8ec99fa64ce..f19e0a4765d 100644 --- a/Applications/SlicerApp/Testing/Python/AtlasTests.py +++ b/Applications/SlicerApp/Testing/Python/AtlasTests.py @@ -26,9 +26,9 @@ def __init__(self, parent): For more information: - Abdominal Atlas: http://www.slicer.org/publications/item/view/1918 - Brain Atlas: http://www.slicer.org/publications/item/view/2037 - Knee Atlas: http://www.slicer.org/publications/item/view/1953 + Abdominal Atlas: https://www.slicer.org/publications/item/view/1918 + Brain Atlas: https://www.slicer.org/publications/item/view/2037 + Knee Atlas: https://www.slicer.org/publications/item/view/1953 """ parent.acknowledgementText = """ diff --git a/Applications/SlicerApp/Testing/Python/CMakeLists.txt b/Applications/SlicerApp/Testing/Python/CMakeLists.txt index e84606ae307..7232ac05f7f 100644 --- a/Applications/SlicerApp/Testing/Python/CMakeLists.txt +++ b/Applications/SlicerApp/Testing/Python/CMakeLists.txt @@ -390,7 +390,7 @@ add_test( # # SelfTests -# see http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule +# see https://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/SelfTestModule # if(Slicer_USE_QtTesting AND Slicer_USE_PYTHONQT) diff --git a/Applications/SlicerApp/Testing/Python/WebEngine.py b/Applications/SlicerApp/Testing/Python/WebEngine.py index cb165e769d2..33a0326aeae 100644 --- a/Applications/SlicerApp/Testing/Python/WebEngine.py +++ b/Applications/SlicerApp/Testing/Python/WebEngine.py @@ -63,7 +63,7 @@ def setup(self): "label": "Crowds Cure Cancer", "url": "http://cancer.crowds-cure.org" }, { - "label": "Slicer Home Page", "url": "http://slicer.org" + "label": "Slicer Home Page", "url": "https://slicer.org" }, { "label": "MorphoSource", "url": "https://www.morphosource.org" diff --git a/Base/Logic/Resources/ColorFiles/DarkBrightChartColors.txt b/Base/Logic/Resources/ColorFiles/DarkBrightChartColors.txt index b6b85e148c6..9367323d66a 100644 --- a/Base/Logic/Resources/ColorFiles/DarkBrightChartColors.txt +++ b/Base/Logic/Resources/ColorFiles/DarkBrightChartColors.txt @@ -4,7 +4,7 @@ #Filename: Slicer4_2012_DarkBrightChartColors.txt #Title: Slicer4:2012 DarkBrightChartColors #PageName: Slicer4:2012_DarkBrightChartColors -#Source: http://www.slicer.org/slicerWiki/index.php/Slicer4:2012_DarkBrightChartColors +#Source: https://www.slicer.org/slicerWiki/index.php/Slicer4:2012_DarkBrightChartColors # #Begin table data: 0 Series_1 236 44 51 255 diff --git a/Base/Logic/Resources/ColorFiles/GenericAnatomyColors.txt b/Base/Logic/Resources/ColorFiles/GenericAnatomyColors.txt index 0a6c4ca1ae7..0a9fd869e6a 100644 --- a/Base/Logic/Resources/ColorFiles/GenericAnatomyColors.txt +++ b/Base/Logic/Resources/ColorFiles/GenericAnatomyColors.txt @@ -4,7 +4,7 @@ #Filename: Slicer3_2010_GenericAnatomyColors.txt #Title: Slicer3:2010 GenericAnatomyColors #PageName: Slicer3:2010_GenericAnatomyColors -#Source: http://www.slicer.org/slicerWiki/index.php/Slicer3:2010_GenericAnatomyColors#Lookup_table +#Source: https://www.slicer.org/slicerWiki/index.php/Slicer3:2010_GenericAnatomyColors#Lookup_table # #Begin table data: 0 background 0 0 0 0 diff --git a/Base/Logic/Resources/ColorFiles/LightPaleChartColors.txt b/Base/Logic/Resources/ColorFiles/LightPaleChartColors.txt index e212db8eec2..dc7e4e19588 100644 --- a/Base/Logic/Resources/ColorFiles/LightPaleChartColors.txt +++ b/Base/Logic/Resources/ColorFiles/LightPaleChartColors.txt @@ -4,7 +4,7 @@ #Filename: Slicer4_2012_LightPaleChartColors.txt #Title: Slicer4:2012 LightPaleChartColors #PageName: Slicer4:2012_LightPaleChartColors -#Source: http://www.slicer.org/slicerWiki/index.php/Slicer4:2012_LightPaleChartColors +#Source: https://www.slicer.org/slicerWiki/index.php/Slicer4:2012_LightPaleChartColors # #Begin table data: 0 Series_1 241 175 174 255 diff --git a/Base/Logic/Resources/ColorFiles/MediumChartColors.txt b/Base/Logic/Resources/ColorFiles/MediumChartColors.txt index c4e8855a4bc..026546fd6d0 100644 --- a/Base/Logic/Resources/ColorFiles/MediumChartColors.txt +++ b/Base/Logic/Resources/ColorFiles/MediumChartColors.txt @@ -4,7 +4,7 @@ #Filename: Slicer4_2012_MediumChartColors.txt #Title: Slicer4:2012 MediumChartColors #PageName: Slicer4:2012_MediumChartColors -#Source: http://www.slicer.org/slicerWiki/index.php/Slicer4:2012_MediumChartColors +#Source: https://www.slicer.org/slicerWiki/index.php/Slicer4:2012_MediumChartColors # #Begin table data: 0 Series_1 239 89 98 255 diff --git a/Base/Logic/Resources/ColorFiles/Slicer3_2010_Brain_Labels.txt b/Base/Logic/Resources/ColorFiles/Slicer3_2010_Brain_Labels.txt index 16ec1c7fd04..f39d3276522 100644 --- a/Base/Logic/Resources/ColorFiles/Slicer3_2010_Brain_Labels.txt +++ b/Base/Logic/Resources/ColorFiles/Slicer3_2010_Brain_Labels.txt @@ -4,7 +4,7 @@ #Filename: Slicer3_2010_Brain_Labels.txt #Title: Slicer3:2010 Brain Labels #PageName: Slicer3:2010_Brain_Labels -#Source: http://www.slicer.org/slicerWiki/index.php/Slicer3:2010_Brain_Labels +#Source: https://www.slicer.org/slicerWiki/index.php/Slicer3:2010_Brain_Labels # #Begin table data: 0 Background 0 0 0 0 diff --git a/Base/Logic/Resources/ColorFiles/Slicer3_2010_Label_Colors.txt b/Base/Logic/Resources/ColorFiles/Slicer3_2010_Label_Colors.txt index 65da4cfb94a..b4182b76993 100644 --- a/Base/Logic/Resources/ColorFiles/Slicer3_2010_Label_Colors.txt +++ b/Base/Logic/Resources/ColorFiles/Slicer3_2010_Label_Colors.txt @@ -4,7 +4,7 @@ #Filename: Slicer3_2010_Label_Colors.txt #Title: Slicer3:2010 Label Colors #PageName: Slicer3:2010_Label_Colors -#Source: http://www.slicer.org/slicerWiki/index.php/Slicer3:2010_Label_Colors +#Source: https://www.slicer.org/slicerWiki/index.php/Slicer3:2010_Label_Colors # #Begin table data: 0 Background 0 0 0 0 diff --git a/Base/Python/slicer/ScriptedLoadableModule.py b/Base/Python/slicer/ScriptedLoadableModule.py index c8cd838fda7..80ed573f5f9 100644 --- a/Base/Python/slicer/ScriptedLoadableModule.py +++ b/Base/Python/slicer/ScriptedLoadableModule.py @@ -28,8 +28,8 @@ def __init__(self, parent): """ parent.acknowledgementText = """ -This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. -This work is partially supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy). +This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See https://www.slicer.org for details. +This work is partially supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy). """ # Set module icon from Resources/Icons/.png diff --git a/Base/QTApp/qSlicerAboutDialog.cxx b/Base/QTApp/qSlicerAboutDialog.cxx index 6915754624f..06b38af003f 100644 --- a/Base/QTApp/qSlicerAboutDialog.cxx +++ b/Base/QTApp/qSlicerAboutDialog.cxx @@ -55,7 +55,7 @@ qSlicerAboutDialog::qSlicerAboutDialog(QWidget* parentWidget) + " / " + slicer->repositoryRevision()); d->CreditsTextBrowser->append(""); d->CreditsTextBrowser->append(""); - d->CreditsTextBrowser->insertHtml("Download a newer version
"); + d->CreditsTextBrowser->insertHtml("Download a newer version
"); d->CreditsTextBrowser->append(""); } else diff --git a/Base/QTCore/Testing/Cxx/qSlicerUtilsTest1.cxx b/Base/QTCore/Testing/Cxx/qSlicerUtilsTest1.cxx index a488d9ae54c..ce47ed8a14c 100644 --- a/Base/QTCore/Testing/Cxx/qSlicerUtilsTest1.cxx +++ b/Base/QTCore/Testing/Cxx/qSlicerUtilsTest1.cxx @@ -763,30 +763,30 @@ int isLoadableModuleTest() { //! [replaceWikiUrlVersion example1] CHECK_QSTRING( - qSlicerUtils::replaceWikiUrlVersion("http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter", "4.4"), - "http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.4/Extensions/SlicerToKiwiExporter"); + qSlicerUtils::replaceWikiUrlVersion("https://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter", "4.4"), + "https://wiki.slicer.org/slicerWiki/index.php/Documentation/4.4/Extensions/SlicerToKiwiExporter"); //! [replaceWikiUrlVersion example1] //! [replaceWikiUrlVersion example2] CHECK_QSTRING( - qSlicerUtils::replaceWikiUrlVersion("http://wiki.slicer.org/slicerWiki/index.php/Documentation/Foo/Extensions/SlicerToKiwiExporter", "Bar"), - "http://wiki.slicer.org/slicerWiki/index.php/Documentation/Bar/Extensions/SlicerToKiwiExporter"); + qSlicerUtils::replaceWikiUrlVersion("https://wiki.slicer.org/slicerWiki/index.php/Documentation/Foo/Extensions/SlicerToKiwiExporter", "Bar"), + "https://wiki.slicer.org/slicerWiki/index.php/Documentation/Bar/Extensions/SlicerToKiwiExporter"); //! [replaceWikiUrlVersion example2] //! [replaceWikiUrlVersion example3] CHECK_QSTRING( - qSlicerUtils::replaceWikiUrlVersion("http://wiki.slicer.org/slicerWiki/index.php/Documentation/Foo/Extensions/SlicerToKiwiExporter/Foo", "Bar"), - "http://wiki.slicer.org/slicerWiki/index.php/Documentation/Bar/Extensions/SlicerToKiwiExporter/Foo"); + qSlicerUtils::replaceWikiUrlVersion("https://wiki.slicer.org/slicerWiki/index.php/Documentation/Foo/Extensions/SlicerToKiwiExporter/Foo", "Bar"), + "https://wiki.slicer.org/slicerWiki/index.php/Documentation/Bar/Extensions/SlicerToKiwiExporter/Foo"); //! [replaceWikiUrlVersion example3] //! [replaceWikiUrlVersion example4] QString input = "Read documentation at " - "http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.4/Extensions/SlicerToKiwiExporter." + "https://wiki.slicer.org/slicerWiki/index.php/Documentation/4.4/Extensions/SlicerToKiwiExporter." "You will learn how to ..."; QString expectedOutput = "Read documentation at " - "http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter." + "https://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter." "You will learn how to ..."; CHECK_QSTRING(qSlicerUtils::replaceWikiUrlVersion(input, "Nightly"), expectedOutput); //! [replaceWikiUrlVersion example4] diff --git a/Base/QTCore/qSlicerAbstractCoreModule.h b/Base/QTCore/qSlicerAbstractCoreModule.h index f3a576a14ac..e6718bced1f 100644 --- a/Base/QTCore/qSlicerAbstractCoreModule.h +++ b/Base/QTCore/qSlicerAbstractCoreModule.h @@ -204,7 +204,7 @@ class Q_SLICER_BASE_QTCORE_EXPORT qSlicerAbstractCoreModule : public QObject virtual void printAdditionalInfo(); /// Convenience method to return slicer wiki URL - QString slicerWikiUrl()const{ return "http://www.slicer.org/slicerWiki/index.php"; } + QString slicerWikiUrl()const{ return "https://www.slicer.org/slicerWiki/index.php"; } /// Convenience method that returns a string that can be inserted into the application help text that contains /// link to the module's documentation in current Slicer version's documentation on ReadTheDocs. diff --git a/Base/QTGUI/qSlicerApplication.cxx b/Base/QTGUI/qSlicerApplication.cxx index 01b5a1d1a1b..4d6d21010c8 100644 --- a/Base/QTGUI/qSlicerApplication.cxx +++ b/Base/QTGUI/qSlicerApplication.cxx @@ -142,8 +142,8 @@ class qSlicerApplicationPrivate : public qSlicerCoreApplicationPrivate QPointer LayoutManager; ctkToolTipTrapper* ToolTipTrapper; - // If MainWindow exists and the dialog is displayed then the MainWindow - // must be set as parent to ensure correct Z order; + // If MainWindow exists and the dialog is displayed then the MainWindow + // must be set as parent to ensure correct Z order; // but that also transfers the ownership of the object, therefore we use QPointer // to keep track if the object is deleted already by the MainWindow. QPointer SettingsDialog; @@ -182,7 +182,7 @@ qSlicerApplicationPrivate::qSlicerApplicationPrivate( qSlicerApplicationPrivate::~qSlicerApplicationPrivate() { // Delete settings dialog. deleteLater would cause memory leaks on exit. - // Settings dialog is displayed then MainWindow becomes its parent and + // Settings dialog is displayed then MainWindow becomes its parent and // thus MainWindow is responsible for deleting it. // Set the parent to 'nullptr' removes this responsibility. if (this->SettingsDialog) @@ -448,7 +448,7 @@ bool qSlicerApplication::notify(QObject *receiver, QEvent *event) errorMessage += tr("Adding more RAM may fix this issue.\n\n"); } errorMessage += tr("If you have a repeatable sequence of steps that causes this message, "); - errorMessage += tr("please report the issue following instructions available at http://slicer.org\n\n\n"); + errorMessage += tr("please report the issue following instructions available at https://slicer.org\n\n\n"); errorMessage += tr("The message detail is:\n\n"); errorMessage += tr("Exception thrown in event: ") + exception.what(); qCritical() << errorMessage; @@ -467,7 +467,7 @@ bool qSlicerApplication::notify(QObject *receiver, QEvent *event) errorMessage = tr("%1 has caught an application error, ").arg(this->applicationName()); errorMessage += tr("please save your work and restart.\n\n"); errorMessage += tr("If you have a repeatable sequence of steps that causes this message, "); - errorMessage += tr("please report the issue following instructions available at http://slicer.org\n\n\n"); + errorMessage += tr("please report the issue following instructions available at https://slicer.org\n\n\n"); errorMessage += tr("The message detail is:\n\n"); errorMessage += tr("Exception thrown in event: ") + exception.what(); qCritical() << errorMessage; diff --git a/CMake/SlicerCTestUploadURL.cmake b/CMake/SlicerCTestUploadURL.cmake index ff2cb129049..0f705fab660 100644 --- a/CMake/SlicerCTestUploadURL.cmake +++ b/CMake/SlicerCTestUploadURL.cmake @@ -41,7 +41,7 @@ # Supported hash algorithms depends on the version of CMake. # See https://cmake.org/cmake/help/latest/command/string.html#supported-hash-algorithms # -# FILEPATH +# FILEPATH # File for computing the cryptographic hash and substituting ``%(hash)`` in # specified URL template. # diff --git a/CMake/pre-commit b/CMake/pre-commit index 9e20832ae56..cedda1b1c65 100644 --- a/CMake/pre-commit +++ b/CMake/pre-commit @@ -5,6 +5,6 @@ Paste the following commands into a shell: ./Utilities/SetupForDevelopment.sh See -http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/DevelopmentWithGit +https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/DevelopmentWithGit for more information.' exit 1 diff --git a/CMakeLists.txt b/CMakeLists.txt index 6fe54474919..85b0895886e 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -62,7 +62,7 @@ set(Slicer_CMAKE_DIR ${Slicer_SOURCE_DIR}/CMake) set(Slicer_EXTENSIONS_CMAKE_DIR ${Slicer_SOURCE_DIR}/Extensions/CMake) #----------------------------------------------------------------------------- -# http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/DevelopmentWithGit +# https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/DevelopmentWithGit #----------------------------------------------------------------------------- include(SlicerCheckSourceTree) diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt index 01122fafe44..0d1c0bb8cf1 100644 --- a/COPYRIGHT.txt +++ b/COPYRIGHT.txt @@ -1,6 +1,6 @@ For more information, please see: - http://www.slicer.org + https://www.slicer.org and http://wiki.na-mic.org/Wiki/index.php/Slicer3 diff --git a/Docs/developer_guide/api.md b/Docs/developer_guide/api.md index 08d5851caa4..ae00e8b38ce 100644 --- a/Docs/developer_guide/api.md +++ b/Docs/developer_guide/api.md @@ -7,7 +7,7 @@ Check out these [developer tutorials](https://www.slicer.org/wiki/Documentation/ ## C++ Majority of Slicer core modules and all basic infrastructure are implemented in C++. -Documentation of these classes are available at: http://apidocs.slicer.org/master +Documentation of these classes are available at: https://apidocs.slicer.org/master ## Python @@ -30,11 +30,11 @@ vtkITK ### Doxygen-style documentation Slicer core infrastructure is mostly implemented in C++ and it is made available in Python in the `slicer` namespace. -Documentation of these classes is available at: http://apidocs.slicer.org/master/ +Documentation of these classes is available at: https://apidocs.slicer.org/master/ C++ classes are made available in Python using two mechanisms: PythonQt and VTK Python wrapper. They have a few slight differences: -- Qt classes (class name starts with `q` or `Q`): for example, [qSlicerMarkupsPlaceWidget](http://apidocs.slicer.org/master/classqSlicerMarkupsPlaceWidget.html). These classes are all derived from QObject and follow [Qt](https://www.qt.io/) conventions. They support properties, signals, and slots. -- VTK classes (class name starts with `vtk`): for example, [vtkMRMLModelDisplayNode](http://apidocs.slicer.org/master/classvtkMRMLModelDisplayNode.html). These classes are all derived from vtkObject and follow [VTK](https://vtk.org/) conventions. +- Qt classes (class name starts with `q` or `Q`): for example, [qSlicerMarkupsPlaceWidget](https://apidocs.slicer.org/master/classqSlicerMarkupsPlaceWidget.html). These classes are all derived from QObject and follow [Qt](https://www.qt.io/) conventions. They support properties, signals, and slots. +- VTK classes (class name starts with `vtk`): for example, [vtkMRMLModelDisplayNode](https://apidocs.slicer.org/master/classvtkMRMLModelDisplayNode.html). These classes are all derived from vtkObject and follow [VTK](https://vtk.org/) conventions. This documentation is generated using the Doxygen tool, which uses C++ syntax. The following rules can help in interpreting this documentation for Python: diff --git a/Docs/developer_guide/extensions.md b/Docs/developer_guide/extensions.md index a2692d2c7e1..c165e669eca 100644 --- a/Docs/developer_guide/extensions.md +++ b/Docs/developer_guide/extensions.md @@ -169,7 +169,7 @@ Extension documentation examples: - [SegmentMesher](https://github.com/lassoan/SlicerSegmentMesher) - [SequenceRegistration](https://github.com/moselhy/SlicerSequenceRegistration) - [AI-assisted annotation client](https://github.com/NVIDIA/ai-assisted-annotation-client/tree/master/slicer-plugin) -- [SlicerDMRI](http://dmri.slicer.org/) - large extension documented using Github pages +- [SlicerDMRI](https://dmri.slicer.org/) - large extension documented using Github pages Thumbnails to YouTube videos can be generated by downloading the image from [here](https://img.youtube.com/vi/your-youtube-video-id/0.jpg) and adding a playback button using [this free service](http://addplaybuttontoimage.way4info.net/) (the second red arrow is recommended). @@ -564,7 +564,7 @@ if(NOT Slicer_SOURCE_DIR) set(EXTENSION_CONTRIBUTORS "Jean-Christophe Fillion-Robin (Kitware)") set(EXTENSION_DESCRIPTION "This is an example of extension bundling N module(s)") set(EXTENSION_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/EmptyExtensionTemplate/EmptyExtensionTemplate.png?revision=21746&view=co") - set(EXTENSION_SCREENSHOTURLS "http://www.slicer.org/w/img_auth.php/4/42/Slicer-r19441-EmptyExtensionTemplate-screenshot.png") + set(EXTENSION_SCREENSHOTURLS "https://www.slicer.org/w/img_auth.php/4/42/Slicer-r19441-EmptyExtensionTemplate-screenshot.png") endif() if(NOT Slicer_SOURCE_DIR) @@ -592,7 +592,7 @@ set(EXTENSION_HOMEPAGE "https://www.slicer.org/wiki/Documentation/Nightly/Extens set(EXTENSION_CONTRIBUTORS "Jean-Christophe Fillion-Robin (Kitware)") set(EXTENSION_DESCRIPTION "This is an example of empty extension") set(EXTENSION_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/EmptyExtensionTemplate/EmptyExtensionTemplate.png?revision=21746&view=co") -set(EXTENSION_SCREENSHOTURLS "http://www.slicer.org/w/img_auth.php/4/42/Slicer-r19441-EmptyExtensionTemplate-screenshot.png") +set(EXTENSION_SCREENSHOTURLS "https://www.slicer.org/w/img_auth.php/4/42/Slicer-r19441-EmptyExtensionTemplate-screenshot.png") find_package(Slicer REQUIRED) include(${Slicer_USE_FILE}) diff --git a/Docs/developer_guide/modules/colors.md b/Docs/developer_guide/modules/colors.md index cf7f618d7dc..ea603fb54d1 100644 --- a/Docs/developer_guide/modules/colors.md +++ b/Docs/developer_guide/modules/colors.md @@ -2,7 +2,7 @@ ## Color table file format (.txt, .ctbl) -The color file format can store a [color node](http://apidocs.slicer.org/master/classvtkMRMLColorNode.html) in a plain text file with the `.txt` or `.ctbl` extension. It is a text file with values separated by space, with a custom header to specify lookup table type. Header lines are prefixed with `#`. +The color file format can store a [color node](https://apidocs.slicer.org/master/classvtkMRMLColorNode.html) in a plain text file with the `.txt` or `.ctbl` extension. It is a text file with values separated by space, with a custom header to specify lookup table type. Header lines are prefixed with `#`. ### Discrete scale color lookup table diff --git a/Docs/developer_guide/modules/transforms.md b/Docs/developer_guide/modules/transforms.md index ebe3ace12c7..265aead47e8 100644 --- a/Docs/developer_guide/modules/transforms.md +++ b/Docs/developer_guide/modules/transforms.md @@ -1,11 +1,11 @@ # Transforms ## Related MRML nodes -- [vtkMRMLTransformableNode](http://slicer.org/doc/html/classvtkMRMLTransformableNode.html): any node that can be transformed -- [vtkMRMLTransformNode](http://slicer.org/doc/html/classvtkMRMLTransformNode.html): it can store any linear or deformable transform or composite of multiple transforms - - [vtkMRMLLinearTransformNode](http://slicer.org/doc/html/classvtkMRMLLinearTransformNode.html): Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed. A vtkMRMLLinearTransformNode may contain non-linear components after a non-linear transform is hardened on it. Therefore, to check linearity of a transform the vtkMRMLTransformNode::IsLinear() and vtkMRMLTransformNode::IsTransformToWorldLinear() and vtkMRMLTransformNode::IsTransformToNodeLinear() methods must be used instead of using vtkMRMLLinearTransformNode::SafeDownCast(transform)!=NULL. - - [vtkMRMLBSplineTransformNode](http://slicer.org/doc/html/classvtkMRMLBSplineTransformNode.html): Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed. - - [vtkMRMLGridTransformNode](http://slicer.org/doc/html/classvtkMRMLGridTransformNode.html): Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed. +- [vtkMRMLTransformableNode](https://slicer.org/doc/html/classvtkMRMLTransformableNode.html): any node that can be transformed +- [vtkMRMLTransformNode](https://slicer.org/doc/html/classvtkMRMLTransformNode.html): it can store any linear or deformable transform or composite of multiple transforms + - [vtkMRMLLinearTransformNode](https://slicer.org/doc/html/classvtkMRMLLinearTransformNode.html): Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed. A vtkMRMLLinearTransformNode may contain non-linear components after a non-linear transform is hardened on it. Therefore, to check linearity of a transform the vtkMRMLTransformNode::IsLinear() and vtkMRMLTransformNode::IsTransformToWorldLinear() and vtkMRMLTransformNode::IsTransformToNodeLinear() methods must be used instead of using vtkMRMLLinearTransformNode::SafeDownCast(transform)!=NULL. + - [vtkMRMLBSplineTransformNode](https://slicer.org/doc/html/classvtkMRMLBSplineTransformNode.html): Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed. + - [vtkMRMLGridTransformNode](https://slicer.org/doc/html/classvtkMRMLGridTransformNode.html): Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed. ## Transform files @@ -19,7 +19,7 @@ ## Events -When a transform node is observed by a transformable node, [vtkMRMLTransformableNode::TransformModifiedEvent](http://slicer.org/doc/html/classvtkMRMLTransformableNode.html#ace1c30fc9df552543f00d51a20c038a6a4993bf6e23a6dfc138cb2efc1b9ce43b) is fired on the transformable node at observation time. Anytime a transform is modified, vtkCommand::ModifiedEvent is fired on the transform node and [vtkMRMLTransformableNode::TransformModifiedEvent](http://slicer.org/doc/html/classvtkMRMLTransformableNode.html#ace1c30fc9df552543f00d51a20c038a6a4993bf6e23a6dfc138cb2efc1b9ce43b) is fired on the transformable node. +When a transform node is observed by a transformable node, [vtkMRMLTransformableNode::TransformModifiedEvent](https://slicer.org/doc/html/classvtkMRMLTransformableNode.html#ace1c30fc9df552543f00d51a20c038a6a4993bf6e23a6dfc138cb2efc1b9ce43b) is fired on the transformable node at observation time. Anytime a transform is modified, vtkCommand::ModifiedEvent is fired on the transform node and [vtkMRMLTransformableNode::TransformModifiedEvent](https://slicer.org/doc/html/classvtkMRMLTransformableNode.html#ace1c30fc9df552543f00d51a20c038a6a4993bf6e23a6dfc138cb2efc1b9ce43b) is fired on the transformable node. ## Examples diff --git a/Docs/developer_guide/modules/volumerendering.md b/Docs/developer_guide/modules/volumerendering.md index e36813bb653..35a46d10cc9 100644 --- a/Docs/developer_guide/modules/volumerendering.md +++ b/Docs/developer_guide/modules/volumerendering.md @@ -1,13 +1,13 @@ # Volume rendering ## Key classes -- [vtkMRMLVolumeRenderingDisplayNode](http://apidocs.slicer.org/master/classvtkMRMLVolumeRenderingDisplayNode.html) controls the volume rendering properties. Each volume rendering technique has its own subclass. -- [vtkSlicerVolumeRenderingLogic](http://apidocs.slicer.org/master/classvtkSlicerVolumeRenderingLogic.html) contains utility functions -- [vtkMRMLScalarVolumeNode](http://apidocs.slicer.org/master/classvtkMRMLScalarVolumeNode.html) contains the volume itself -- [vtkMRMLVolumePropertyNode](http://apidocs.slicer.org/master/classvtkMRMLVolumePropertyNode.html) points to the transfer functions -- [vtkMRMLMarkupsROINode](http://apidocs.slicer.org/master/classvtkMRMLMarkupsROINode.html) controls the clipping planes -- [vtkMRMLAnnotationROINode](http://apidocs.slicer.org/master/classvtkMRMLAnnotationROINode.html) controls the clipping planes (legacy, use vtkMRMLMarkupsROINode instead) -- [vtkMRMLVolumeRenderingDisplayableManager](http://apidocs.slicer.org/master/classvtkMRMLVolumeRenderingDisplayableManager.html) responsible for adding VTK actors to the renderers +- [vtkMRMLVolumeRenderingDisplayNode](https://apidocs.slicer.org/master/classvtkMRMLVolumeRenderingDisplayNode.html) controls the volume rendering properties. Each volume rendering technique has its own subclass. +- [vtkSlicerVolumeRenderingLogic](https://apidocs.slicer.org/master/classvtkSlicerVolumeRenderingLogic.html) contains utility functions +- [vtkMRMLScalarVolumeNode](https://apidocs.slicer.org/master/classvtkMRMLScalarVolumeNode.html) contains the volume itself +- [vtkMRMLVolumePropertyNode](https://apidocs.slicer.org/master/classvtkMRMLVolumePropertyNode.html) points to the transfer functions +- [vtkMRMLMarkupsROINode](https://apidocs.slicer.org/master/classvtkMRMLMarkupsROINode.html) controls the clipping planes +- [vtkMRMLAnnotationROINode](https://apidocs.slicer.org/master/classvtkMRMLAnnotationROINode.html) controls the clipping planes (legacy, use vtkMRMLMarkupsROINode instead) +- [vtkMRMLVolumeRenderingDisplayableManager](https://apidocs.slicer.org/master/classvtkMRMLVolumeRenderingDisplayableManager.html) responsible for adding VTK actors to the renderers ## Format of Volume Property (.vp) file diff --git a/Docs/developer_guide/mrml_overview.md b/Docs/developer_guide/mrml_overview.md index 9a82a48c5f7..c94ca0ae052 100644 --- a/Docs/developer_guide/mrml_overview.md +++ b/Docs/developer_guide/mrml_overview.md @@ -19,19 +19,19 @@ Medical Reality Modeling Language (MRML) is a data model developed to represent ### Basic MRML node types - **Data nodes** store basic properties of a data set. Since the same data set can be displayed in different ways (even within the same application, you may want to show the same data set differently in each view), display properties are not stored in the data node. Similarly, the same data set can be stored in various file formats, therefore file storage properties are not stored in a data node. Data nodes are typically thin wrappers over VTK objects, such as vtkPolyData, vtkImageData, vtkTable. Most important Slicer core data nodes are the following: - - **Volume** ([vtkMRMLVolume](http://apidocs.slicer.org/master/classvtkMRMLVolumeNode.html) and its subclasses): stores a 3D image. Each voxel of a volume may be a scalar (to store images with continuous grayscale values, such as a CT image), label (to store discrete labels, such as a segmentation result), vector (for storing displacement fields or RGB color images), or tensor (MRI diffusion images). 2D image volumes are represented as single-slice 3D volumes. 4D volumes are stored in sequence nodes (vtkMRMLSequenceNode). - - **Model** ([vtkMRMLModelNode](http://apidocs.slicer.org/master/classvtkMRMLModelNode.html)): stores a surface mesh (polygonal elements, points, lines, etc.) or volumetric mesh (tetrahedral, wedge elements, unstructured grid, etc.) - - **Segmentation** ([vtkMRMLSegmentationNode](http://apidocs.slicer.org/master/classvtkMRMLSegmentationNode.html)): complex data node that can store image segmentation (also known as contouring, labeling). It can store multiple representations internally, for example it can store both binary labelmap image and closed surface mesh. - - **Markups** ([vtkMRMLMarkupsNode](http://apidocs.slicer.org/master/classvtkMRMLMarkupsNode.html) and subclasses): store simple geometrical objects, such as point lists (formerly called "fiducial lists"), lines, angles, curves, planes for annotation and measurements. Annotations module is the old generation of markups functionality and is being phased out. - - **Transform** ([vtkMRMLTransformNode](http://apidocs.slicer.org/master/classvtkMRMLTransformNode.html)): stores geometrical transformation that can be applied to any [transformable nodes](http://apidocs.slicer.org/master/classvtkMRMLTransformableNode.html). A transformation can contain any number of linear or non-linear (warping) transforms chained together. In general, it is recommended to use vtkMRMLTransformNode. Child types (vtkMRMLLinearTransformNode, vtkMRMLBSplineTransformNode, vtkMRMLGridTransformNode) are kept for backward compatibility and to allow filtering for specific transformation types in user interface widgets. - - **Text** ([vtkMRMLTextNode](http://apidocs.slicer.org/master/classvtkMRMLTextNode.html)): stores text data, such as configuration files, descriptive text, etc. - - **Table** ([vtkMRMLTableNode](http://apidocs.slicer.org/master/classvtkMRMLTableNode.html)): stores tabular data (multiple scalar or vector arrays), used mainly for showing quantitative results in tables and plots -- **Display nodes** ([vtkMRMLDisplayNode](http://apidocs.slicer.org/master/classvtkMRMLDisplayNode.html) and its subclasses) specify properties how to display data nodes. For example, a model node's color is stored in a display node associated with a model node. + - **Volume** ([vtkMRMLVolume](https://apidocs.slicer.org/master/classvtkMRMLVolumeNode.html) and its subclasses): stores a 3D image. Each voxel of a volume may be a scalar (to store images with continuous grayscale values, such as a CT image), label (to store discrete labels, such as a segmentation result), vector (for storing displacement fields or RGB color images), or tensor (MRI diffusion images). 2D image volumes are represented as single-slice 3D volumes. 4D volumes are stored in sequence nodes (vtkMRMLSequenceNode). + - **Model** ([vtkMRMLModelNode](https://apidocs.slicer.org/master/classvtkMRMLModelNode.html)): stores a surface mesh (polygonal elements, points, lines, etc.) or volumetric mesh (tetrahedral, wedge elements, unstructured grid, etc.) + - **Segmentation** ([vtkMRMLSegmentationNode](https://apidocs.slicer.org/master/classvtkMRMLSegmentationNode.html)): complex data node that can store image segmentation (also known as contouring, labeling). It can store multiple representations internally, for example it can store both binary labelmap image and closed surface mesh. + - **Markups** ([vtkMRMLMarkupsNode](https://apidocs.slicer.org/master/classvtkMRMLMarkupsNode.html) and subclasses): store simple geometrical objects, such as point lists (formerly called "fiducial lists"), lines, angles, curves, planes for annotation and measurements. Annotations module is the old generation of markups functionality and is being phased out. + - **Transform** ([vtkMRMLTransformNode](https://apidocs.slicer.org/master/classvtkMRMLTransformNode.html)): stores geometrical transformation that can be applied to any [transformable nodes](https://apidocs.slicer.org/master/classvtkMRMLTransformableNode.html). A transformation can contain any number of linear or non-linear (warping) transforms chained together. In general, it is recommended to use vtkMRMLTransformNode. Child types (vtkMRMLLinearTransformNode, vtkMRMLBSplineTransformNode, vtkMRMLGridTransformNode) are kept for backward compatibility and to allow filtering for specific transformation types in user interface widgets. + - **Text** ([vtkMRMLTextNode](https://apidocs.slicer.org/master/classvtkMRMLTextNode.html)): stores text data, such as configuration files, descriptive text, etc. + - **Table** ([vtkMRMLTableNode](https://apidocs.slicer.org/master/classvtkMRMLTableNode.html)): stores tabular data (multiple scalar or vector arrays), used mainly for showing quantitative results in tables and plots +- **Display nodes** ([vtkMRMLDisplayNode](https://apidocs.slicer.org/master/classvtkMRMLDisplayNode.html) and its subclasses) specify properties how to display data nodes. For example, a model node's color is stored in a display node associated with a model node. - Multiple display nodes may be added for a single data, each specifying different display properties and view nodes. Built-in Slicer modules typically only show and allow editing of the *first* display node associated with a data node. - If a display node specifies a list of view nodes then the associated data node is only displayed in those views. - Display nodes may refer to *color nodes* to specify a list of colors or color look-up-tables. - When a data node is created then default display node can be added by calling its `CreateDefaultDisplayNodes()` method. In some cases, Slicer detects if the display and storage node is missing and tries to create a default nodes, but the developers should not rely on this error-recovery mechanism. -- **Storage nodes** ([vtkMRMLStorageNode](http://apidocs.slicer.org/master/classvtkMRMLStorageNode.html) and its subclasses) specify how to store a data node in file. It can store one or more file name, compression options, coordinate system information, etc. +- **Storage nodes** ([vtkMRMLStorageNode](https://apidocs.slicer.org/master/classvtkMRMLStorageNode.html) and its subclasses) specify how to store a data node in file. It can store one or more file name, compression options, coordinate system information, etc. - Default storage node may be created for a data node by calling its `CreateDefaultStorageNode()` method. - **View nodes** ([vtkMRMLAbstractViewNode](https://apidocs.slicer.org/v4.8/classvtkMRMLAbstractViewNode.html) and subclasses) specify view layout and appearance of views, such as background color. Additional nodes related to view nodes include: - vtkMRMLCameraNode stores properties of camera of a 3D view. @@ -40,11 +40,11 @@ Medical Reality Modeling Language (MRML) is a data model developed to represent - vtkMRMLLayoutNode defines the current view layout: what views (slice, 3D, table, etc.) are display and where. In addition to switching between built-in view layouts, custom view layouts can be specified using an XML description. - vtkMRMLInteractionNode specifies interaction mode of viewers (view/transform, window/level, place markups), such as what happens the user clicks in a view - vtkMRMLSelectionNode stores global state information of the scene, such as active markup (that is being placed), units (length, time, etc.) used in the scene, etc -- **Plot nodes** specify how to display table node contents as plots. [Plot series node](http://apidocs.slicer.org/master/classvtkMRMLPlotSeriesNode.html) specifies a data series using one or two columns of a table node. [Plot chart node](http://apidocs.slicer.org/master/classvtkMRMLPlotChartNode.html) specifies which series to plot and how. [Plot view node](http://apidocs.slicer.org/master/classvtkMRMLPlotViewNode.html) specifies which plot chart to show in a view and how user can interact with it. -- **Subject hierarchy node** ([vtkMRMLSubjectHierarchyNode](http://apidocs.slicer.org/master/classvtkMRMLSubjectHierarchyNode.html)) allows organization of data nodes into folders. Subject hierarchy folders may be associated with display nodes, which can be used to override display properties of all children in that folder. It replaces all previous hierarchy management methods, such as model or annotation hierarchies. +- **Plot nodes** specify how to display table node contents as plots. [Plot series node](https://apidocs.slicer.org/master/classvtkMRMLPlotSeriesNode.html) specifies a data series using one or two columns of a table node. [Plot chart node](https://apidocs.slicer.org/master/classvtkMRMLPlotChartNode.html) specifies which series to plot and how. [Plot view node](https://apidocs.slicer.org/master/classvtkMRMLPlotViewNode.html) specifies which plot chart to show in a view and how user can interact with it. +- **Subject hierarchy node** ([vtkMRMLSubjectHierarchyNode](https://apidocs.slicer.org/master/classvtkMRMLSubjectHierarchyNode.html)) allows organization of data nodes into folders. Subject hierarchy folders may be associated with display nodes, which can be used to override display properties of all children in that folder. It replaces all previous hierarchy management methods, such as model or annotation hierarchies. - [**Sequence node**](https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkMRMLSequenceNode.h) stores a list of data nodes to represent time sequences or other multidimensional data sets in the scene. [Sequence browser node](https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Sequences/MRML/vtkMRMLSequenceBrowserNode.h) specifies which one of the internal data node should be copied to the scene so that it can be displayed or edited. The node that represents a node of the internal scene is called a *proxy node*. When a proxy node is modified in the scene, all changes can be saved into the internal scene. -Detailed documentation of MRML API can be found in [here](http://apidocs.slicer.org/master/classes.html). +Detailed documentation of MRML API can be found in [here](https://apidocs.slicer.org/master/classes.html). ### MRML node attributes @@ -102,7 +102,7 @@ The following methods on the MRML scene are used to manage Undo/Redo stacks: If you are adding new functionality to 3D Slicer either via extensions, or even updates to the core, most of the time the existing MRML nodes will be sufficient. Many powerful C++ and Python extensions simply use and combine existing the node types to create new functionality. Other extensions, instead of creating new MRML nodes from scratch, derive from existing nodes and add just a few methods to get the needed functionality. That said, if the existing MRML nodes don't offer enough (or almost enough) functionality to enable what needs to be done, it is possible to create custom MRML node classes with a little bit of effort. -There are a number of different MRML nodes and helper classes that can be implemented to enable new MRML data type functionality. Here is the not-so-short list. We will go over each of these in detail. +There are a number of different MRML nodes and helper classes that can be implemented to enable new MRML data type functionality. Here is the not-so-short list. We will go over each of these in detail. 1. [Data node](#the-data-node) 2. [Display node](#the-display-node) @@ -127,7 +127,7 @@ MRML nodes can be implemented in a Slicer extension. :::{note} -All links to API class and function documentation redirecting to `https://apidocs.slicer.org` correspond to documentation generated from the latest commit of the `master` branch of Slicer. This means that versions of this documentation associated with an older version of Slicer may be out of sync with the linked API. +All links to API class and function documentation redirecting to `https://apidocs.slicer.org` correspond to documentation generated from the latest commit of the `master` branch of Slicer. This means that versions of this documentation associated with an older version of Slicer may be out of sync with the linked API. ::: @@ -519,9 +519,9 @@ A layout manager ([qSlicerLayoutManager][qSlicerLayoutManager-apidoc]) shows or - Pre-defined layouts are described using XML and are registered in `vtkMRMLLayoutLogic::AddDefaultLayouts()`. - Developer may register additional layout. -[qSlicerLayoutManager-apidoc]: http://apidocs.slicer.org/master/classqSlicerLayoutManager.html -[vtkMRMLLayoutNode-apidoc]: http://apidocs.slicer.org/master/classvtkMRMLLayoutNode.html -[vtkMRMLLayoutLogic-apidoc]: http://apidocs.slicer.org/master/classvtkMRMLLayoutLogic.html +[qSlicerLayoutManager-apidoc]: https://apidocs.slicer.org/master/classqSlicerLayoutManager.html +[vtkMRMLLayoutNode-apidoc]: https://apidocs.slicer.org/master/classvtkMRMLLayoutNode.html +[vtkMRMLLayoutLogic-apidoc]: https://apidocs.slicer.org/master/classvtkMRMLLayoutLogic.html #### Registering a custom layout diff --git a/Docs/developer_guide/python_faq.md b/Docs/developer_guide/python_faq.md index 9c95c0efa84..e5f96dc1928 100644 --- a/Docs/developer_guide/python_faq.md +++ b/Docs/developer_guide/python_faq.md @@ -71,7 +71,7 @@ cliNode = slicer.cli.runSync(slicer.modules.simpleregiongrowingsegmentation, Non ### Running CLI in the background -If the CLI module is executed using `slicer.cli.run` method then the CLI module runs in a background thread, so the call to `startProcessing` will return right away and the user interface will not be blocked. The `slicer.cli.run` call returns a cliNode (an instance of [vtkMRMLCommandLineModuleNode](http://slicer.org/doc/html/classvtkMRMLCommandLineModuleNode.html)) which can be used to monitor the progress of the module. +If the CLI module is executed using `slicer.cli.run` method then the CLI module runs in a background thread, so the call to `startProcessing` will return right away and the user interface will not be blocked. The `slicer.cli.run` call returns a cliNode (an instance of [vtkMRMLCommandLineModuleNode](https://slicer.org/doc/html/classvtkMRMLCommandLineModuleNode.html)) which can be used to monitor the progress of the module. In this example we create a simple callback `onProcessingStatusUpdate` that will be called whenever the cliNode is modified. The status will tell you if the nodes is Pending, Running, or Completed. diff --git a/Docs/developer_guide/script_repository/markups.md b/Docs/developer_guide/script_repository/markups.md index 34b98923cec..a96e7b455ac 100644 --- a/Docs/developer_guide/script_repository/markups.md +++ b/Docs/developer_guide/script_repository/markups.md @@ -68,7 +68,7 @@ slicer.util.updateMarkupsControlPointsFromArray(curveNode, pointPositions) This code snippet creates a toggle button, which activates control point placement when pressed (and deactivates when released). -The [qSlicerMarkupsPlaceWidget widget](http://apidocs.slicer.org/master/classqSlicerMarkupsPlaceWidget.html) can automatically activate placement of multiple points and can show buttons for deleting points, changing colors, lock, and hide points. +The [qSlicerMarkupsPlaceWidget widget](https://apidocs.slicer.org/master/classqSlicerMarkupsPlaceWidget.html) can automatically activate placement of multiple points and can show buttons for deleting points, changing colors, lock, and hide points. ```python w=slicer.qSlicerMarkupsPlaceWidget() @@ -585,7 +585,7 @@ Markups have `Color` and `SelectedColor` properties. `SelectedColor` is used if ### Display list of control points in my module's GUI -The [qSlicerSimpleMarkupsWidget](http://apidocs.slicer.org/master/classqSlicerSimpleMarkupsWidget.html) can be integrated into module widgets to display list of markups control points and initiate placement. An example of this use is in [Gel Dosimetry module](https://www.slicer.org/wiki/Documentation/Nightly/Modules/GelDosimetry). +The [qSlicerSimpleMarkupsWidget](https://apidocs.slicer.org/master/classqSlicerSimpleMarkupsWidget.html) can be integrated into module widgets to display list of markups control points and initiate placement. An example of this use is in [Gel Dosimetry module](https://www.slicer.org/wiki/Documentation/Nightly/Modules/GelDosimetry). ### Pre-populate the scene with measurements diff --git a/Docs/developer_guide/script_repository/tractography.md b/Docs/developer_guide/script_repository/tractography.md index 98ae9062f54..bd1500a1384 100644 --- a/Docs/developer_guide/script_repository/tractography.md +++ b/Docs/developer_guide/script_repository/tractography.md @@ -4,7 +4,7 @@ :::{note} -An interactive version of this script is now included in the [SlicerDMRI extension](http://dmri.slicer.org) ([module code](https://github.com/SlicerDMRI/SlicerDMRI/tree/master/Modules/Scripted/TractographyExportPLY)). After installing SlicerDMRI, go to *Modules -> Diffusion -> Import and Export -> Export tractography to PLY (mesh)*. +An interactive version of this script is now included in the [SlicerDMRI extension](https://dmri.slicer.org) ([module code](https://github.com/SlicerDMRI/SlicerDMRI/tree/master/Modules/Scripted/TractographyExportPLY)). After installing SlicerDMRI, go to *Modules -> Diffusion -> Import and Export -> Export tractography to PLY (mesh)*. ::: diff --git a/Docs/developer_guide/script_repository/volumes.md b/Docs/developer_guide/script_repository/volumes.md index 7d423d396c2..d54a076f15a 100644 --- a/Docs/developer_guide/script_repository/volumes.md +++ b/Docs/developer_guide/script_repository/volumes.md @@ -836,7 +836,7 @@ propertyNode->SetScalarOpacity(opacities); // optionally set the gradients opacities with SetGradientOpacity ``` -Volume rendering logic has utility functions to help you create those transfer functions: [SetWindowLevelToVolumeProp](http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#ab8dbda38ad81b39b445b01e1bf8c7a86), [SetThresholdToVolumeProp](http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a1dcbe614493f3cbb9aa50c68a64764ca), [SetLabelMapToVolumeProp](http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a359314889c2b386fd4c3ffe5414522da). +Volume rendering logic has utility functions to help you create those transfer functions: [SetWindowLevelToVolumeProp](https://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#ab8dbda38ad81b39b445b01e1bf8c7a86), [SetThresholdToVolumeProp](https://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a1dcbe614493f3cbb9aa50c68a64764ca), [SetLabelMapToVolumeProp](https://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a359314889c2b386fd4c3ffe5414522da). ### Limit volume rendering to a specific region of the volume @@ -856,7 +856,7 @@ displayNode->SetCroppingEnabled(1); ### Register a new Volume Rendering mapper -You need to derive from [vtkMRMLVolumeRenderingDisplayNode](http://apidocs.slicer.org/master/classvtkMRMLVolumeRenderingDisplayNode.html) and register your class within [vtkSlicerVolumeRenderingLogic](http://apidocs.slicer.org/master/classvtkSlicerVolumeRenderingLogic.html). +You need to derive from [vtkMRMLVolumeRenderingDisplayNode](https://apidocs.slicer.org/master/classvtkMRMLVolumeRenderingDisplayNode.html) and register your class within [vtkSlicerVolumeRenderingLogic](https://apidocs.slicer.org/master/classvtkSlicerVolumeRenderingLogic.html). C++: @@ -885,7 +885,7 @@ void qSlicerMyABCVolumeRenderingModule::setup() } ``` -If you want to expose control widgets for your volume rendering method, then register your widget with [addRenderingMethodWidget()](http://apidocs.slicer.org/master/classqSlicerVolumeRenderingModuleWidget.html#acd9cdb60f1fd260f3ebf74428bb7c45b). +If you want to expose control widgets for your volume rendering method, then register your widget with [addRenderingMethodWidget()](https://apidocs.slicer.org/master/classqSlicerVolumeRenderingModuleWidget.html#acd9cdb60f1fd260f3ebf74428bb7c45b). ### Register custom volume rendering presets diff --git a/Docs/user_guide/about.md b/Docs/user_guide/about.md index c7fd3e03bbc..3f6304299ff 100644 --- a/Docs/user_guide/about.md +++ b/Docs/user_guide/about.md @@ -51,7 +51,7 @@ The discussion concluded that bundling the contribution agreement in the license ### 3D Slicer as a platform -To acknowledge 3D Slicer as a platform, please cite the [Slicer web site](http://www.slicer.org/) and the following publications when publishing work that uses or incorporates 3D Slicer: +To acknowledge 3D Slicer as a platform, please cite the [Slicer web site](https://www.slicer.org/) and the following publications when publishing work that uses or incorporates 3D Slicer: **Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [3D Slicer as an Image Computing Platform for the Quantitative Imaging Network](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466397/pdf/nihms383480.pdf). Magnetic Resonance Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.** diff --git a/Docs/user_guide/getting_started.md b/Docs/user_guide/getting_started.md index f618b98bfed..6102e640ac2 100644 --- a/Docs/user_guide/getting_started.md +++ b/Docs/user_guide/getting_started.md @@ -25,7 +25,7 @@ GPU: Graphics must support minimum OpenGL 3.2. Integrated graphics card is suffi ## Installing 3D Slicer -To download Slicer, click [here](http://download.slicer.org/). +To download Slicer, click [here](https://download.slicer.org/). ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/getting_started_download.png) @@ -209,7 +209,7 @@ Terms used in various fields of medical and biomedical image computing and clini - **MRML**: [Medical Reality Markup Language](https://en.wikipedia.org/wiki/Medical_Reality_Markup_Language): Software library for storage, visualization, and processing of information objects that may be used in medical applications. The library is designed to be reusable in various software applications, but 3D Slicer is the only major application that is known to use it. - **Model** (or model node): MRML node storing surface mesh (consists of triangle, polygon, or other 2D cells) or volumetric mesh (consists of tetrahedral, wedge, or other 3D cells) - **Module** (or Slicer module): A Slicer module is a software component consisting of a graphical user interface (that is displayed in the module panel when the module is selected), a logic (that implements algorithms that operate on MRML nodes), and may provide new MRML node types, displayable managers (that are responsible for displaying those nodes in views), input/output plugins (that are responsible for load/save MRML nodes in files), and various other plugins. Modules are typically independent and only communicate with each other via modifying MRML nodes, but sometimes a module use features provided by other modules by calling methods in its logic. -- **Node** (or MRML node): One data object in the scene. A node can represent data (such as an image or a mesh), describe how it is displayed (color, opacity, etc.), stored on disk, spatial transformations applied on them, etc. There is a C++ class hierarchy to define the common behaviors of nodes, such as the property of being storable on disk or being geometrically transformable. The structure of this class hierarchy can be inspected in the code or in the [API documentation](http://apidocs.slicer.org/master/classvtkMRMLStorableNode.html). +- **Node** (or MRML node): One data object in the scene. A node can represent data (such as an image or a mesh), describe how it is displayed (color, opacity, etc.), stored on disk, spatial transformations applied on them, etc. There is a C++ class hierarchy to define the common behaviors of nodes, such as the property of being storable on disk or being geometrically transformable. The structure of this class hierarchy can be inspected in the code or in the [API documentation](https://apidocs.slicer.org/master/classvtkMRMLStorableNode.html). - **Orientation marker**: Arrow, box, or human shaped marker to show axis directions in slice views and 3D views. - **RAS**: Right-anterior-superior anatomical coordinate system. Coordinate system used internally in Slicer. It can be converted to/from LPS coordinate system by inverting the direction of the first two axes. - **Reference**: Has no specific meaning, but typically refers to a secondary input (data object, coordinate frame, geometry, etc.) for an operation. diff --git a/Docs/user_guide/modules/endoscopy.md b/Docs/user_guide/modules/endoscopy.md index 0863fa200dd..931298e4285 100644 --- a/Docs/user_guide/modules/endoscopy.md +++ b/Docs/user_guide/modules/endoscopy.md @@ -30,4 +30,4 @@ Steve Pieper (Isomics), Jean-Christophe Fillion-Robin (Kitware) ## Acknowledgements -This work is supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy) NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. Module implemented by Steve Pieper. +This work is supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy) NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See https://www.slicer.org for details. Module implemented by Steve Pieper. diff --git a/Docs/user_guide/modules/volumes.md b/Docs/user_guide/modules/volumes.md index be5e45c948e..cb8ff45ae2c 100644 --- a/Docs/user_guide/modules/volumes.md +++ b/Docs/user_guide/modules/volumes.md @@ -87,7 +87,7 @@ Note: Consumer file formats, such as jpg, png, and tiff are not well suited for - Volume Information: Information about the selected volume. Some fields can be edited to correctly describe the volume, for example, when loading incompletely specified image data such as a sequence of jpeg files. Use caution however, since changing properties such as Image Spacing will impact the physical accuracy of some calculations such as Label Statistics. - Image Dimensions: The number of pixels in "IJK" space - this is the way the data is arranged in memory. The IJK indices (displayed in the DataProbe) go from 0 to dimension-1 in each direction. - Image Spacing: The physical distance between pixel centers when mapped to patient space expressed in millimeters. - - Image Origin: The location of the center of the 0,0,0 (IJK) pixel expressed with respect to patient space. Patient space is organized with respect to the subject's Right, Anterior, and Superior anatomical directions. See [coordinate systems page](http://www.slicer.org/slicerWiki/index.php/Coordinate_systems) for more information. + - Image Origin: The location of the center of the 0,0,0 (IJK) pixel expressed with respect to patient space. Patient space is organized with respect to the subject's Right, Anterior, and Superior anatomical directions. See [coordinate systems page](https://www.slicer.org/slicerWiki/index.php/Coordinate_systems) for more information. - IJK to RAS Direction Matrix: The trasnform matrix from the IJK to RAS coordinate systems - Center Volume: This button will apply a transform to the volume that shifts its center to the origin in patient space. Harden the transform on the volume to permanently change the image origin. - Scan Order: Describes the image orientation (how the IJK space is oriented with respect to patient RAS. diff --git a/Extensions/CMake/SlicerFunctionExtractExtensionDescription.cmake b/Extensions/CMake/SlicerFunctionExtractExtensionDescription.cmake index 195d1c91ce3..a51ea88d127 100644 --- a/Extensions/CMake/SlicerFunctionExtractExtensionDescription.cmake +++ b/Extensions/CMake/SlicerFunctionExtractExtensionDescription.cmake @@ -131,12 +131,12 @@ function(slicer_extract_extension_description_test) set(expected_CONTRIBUTORS "Jean-Christophe Fillion-Robin (Kitware), Pat Marion (Kitware), Steve Pieper (Isomics), Atsushi Yamada (Shiga University of Medical Science)") set(expected_DESCRIPTION "The SlicerToKiwiExporter module provides Slicer user with any easy way to export models into a KiwiViewer scene file.") set(expected_ENABLED "1") - set(expected_HOMEPAGE "http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter") - set(expected_ICONURL "http://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png") + set(expected_HOMEPAGE "https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter") + set(expected_ICONURL "https://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png") set(expected_SCM "git") set(expected_SCMREVISION "9d7341e978df954a2c875240290833d7528ef29c") set(expected_SCMURL "https://github.com/jcfr/SlicerToKiwiExporter.git") - set(expected_SCREENSHOTURLS "http://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG http://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG http://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png") + set(expected_SCREENSHOTURLS "https://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG https://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG https://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png") set(expected_STATUS "") # Extract extension description without depends diff --git a/Extensions/CMake/SlicerFunctionGenerateExtensionDescription.cmake b/Extensions/CMake/SlicerFunctionGenerateExtensionDescription.cmake index 076da3311b7..50e10cd5da9 100644 --- a/Extensions/CMake/SlicerFunctionGenerateExtensionDescription.cmake +++ b/Extensions/CMake/SlicerFunctionGenerateExtensionDescription.cmake @@ -131,10 +131,10 @@ function(slicer_generate_extension_description_test) EXTENSION_DESCRIPTION "The SlicerToKiwiExporter module provides Slicer user with any easy way to export models into a KiwiViewer scene file." EXTENSION_CATEGORY "Exporter" EXTENSION_CONTRIBUTORS "Jean-Christophe Fillion-Robin (Kitware), Pat Marion (Kitware), Steve Pieper (Isomics), Atsushi Yamada (Shiga University of Medical Science)" - EXTENSION_HOMEPAGE "http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter" - EXTENSION_ICONURL "http://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png" + EXTENSION_HOMEPAGE "https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter" + EXTENSION_ICONURL "https://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png" EXTENSION_NAME "SlicerToKiwiExporter" - EXTENSION_SCREENSHOTURLS "http://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG http://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG http://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png" + EXTENSION_SCREENSHOTURLS "https://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG https://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG https://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png" EXTENSION_STATUS "Development" EXTENSION_WC_REVISION "9d7341e978df954a2c875240290833d7528ef29c" EXTENSION_WC_ROOT "https://github.com/jcfr/SlicerToKiwiExporter.git" diff --git a/Extensions/CMake/Testing/extension_description_with_depends.s4ext b/Extensions/CMake/Testing/extension_description_with_depends.s4ext index 84ca2bec83e..df9215c5221 100644 --- a/Extensions/CMake/Testing/extension_description_with_depends.s4ext +++ b/Extensions/CMake/Testing/extension_description_with_depends.s4ext @@ -18,7 +18,7 @@ depends Foo Bar build_subdirectory inner/inner-inner-build # homepage -homepage http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter +homepage https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter # Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2) # For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware) @@ -28,7 +28,7 @@ contributors Jean-Christophe Fillion-Robin (Kitware), Pat Marion (Kitware), Stev category Exporter # url to icon (png, size 128x128 pixels) -iconurl http://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png +iconurl https://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png # Give people an idea what to expect from this code # - Is it just a test or something you stand behind? @@ -38,7 +38,7 @@ status Development description The SlicerToKiwiExporter module provides Slicer user with any easy way to export models into a KiwiViewer scene file. # Space separated list of urls -screenshoturls http://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG http://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG http://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png +screenshoturls https://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG https://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG https://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png # 0 or 1: Define if the extension should be enabled after its installation. enabled 0 diff --git a/Extensions/CMake/Testing/extension_description_without_depends.s4ext b/Extensions/CMake/Testing/extension_description_without_depends.s4ext index d78af756ca9..45a0ddf113f 100644 --- a/Extensions/CMake/Testing/extension_description_without_depends.s4ext +++ b/Extensions/CMake/Testing/extension_description_without_depends.s4ext @@ -18,7 +18,7 @@ depends NA build_subdirectory . # homepage -homepage http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter +homepage https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerToKiwiExporter # Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2) # For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware) @@ -28,7 +28,7 @@ contributors Jean-Christophe Fillion-Robin (Kitware), Pat Marion (Kitware), Stev category Exporter # url to icon (png, size 128x128 pixels) -iconurl http://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png +iconurl https://www.slicer.org/slicerWiki/images/6/64/SlicerToKiwiExporterLogo.png # Give people an idea what to expect from this code # - Is it just a test or something you stand behind? @@ -38,7 +38,7 @@ status Development description The SlicerToKiwiExporter module provides Slicer user with any easy way to export models into a KiwiViewer scene file. # Space separated list of urls -screenshoturls http://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG http://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG http://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png +screenshoturls https://www.slicer.org/slicerWiki/images/9/9e/SlicerToKiwiExporter_Kiwiviewer_8.PNG https://www.slicer.org/slicerWiki/images/a/ab/SlicerToKiwiExporter_Kiwiviewer_9.PNG https://www.slicer.org/slicerWiki/images/9/9a/SlicerToKiwiExporter_SaveDialog_Select-file-format_1.png # 0 or 1: Define if the extension should be enabled after its installation. enabled 1 diff --git a/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py b/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py index 88062d09f3e..ea7de2a680d 100644 --- a/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py +++ b/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py @@ -19,7 +19,7 @@ def __init__(self, parent): self.parent.hidden = True self.parent.helpText = "This hidden module registers the segment editor effect" self.parent.helpText += self.getDefaultModuleDocumentationLink() - self.parent.acknowledgementText = "Supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details." + self.parent.acknowledgementText = "Supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See https://www.slicer.org for details." slicer.app.connect("startupCompleted()", self.registerEditorEffect) def registerEditorEffect(self): diff --git a/Libs/MRML/Widgets/qMRMLNodeComboBox.cxx b/Libs/MRML/Widgets/qMRMLNodeComboBox.cxx index 375f89dff24..45220cc48ca 100644 --- a/Libs/MRML/Widgets/qMRMLNodeComboBox.cxx +++ b/Libs/MRML/Widgets/qMRMLNodeComboBox.cxx @@ -506,7 +506,7 @@ void qMRMLNodeComboBox::addAttribute(const QString& nodeType, if (nodeType=="vtkMRMLScalarVolumeNode" && attributeName=="LabelMap") { qWarning("vtkMRMLScalarVolumeNode does not have a LabelMap attribute anymore. Update your code according to " - "http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/Segmentations#Module_update_instructions"); + "https://www.slicer.org/slicerWiki/index.php/Documentation/Labs/Segmentations#Module_update_instructions"); return; } diff --git a/License.txt b/License.txt index 14285be7ea0..8216cf628de 100644 --- a/License.txt +++ b/License.txt @@ -1,7 +1,7 @@ For more information, please see: - http://www.slicer.org + https://www.slicer.org The 3D Slicer license below is a BSD style license, with extensions to cover contributions and other issues specific to 3D Slicer. diff --git a/Modules/Loadable/SlicerWelcome/qSlicerWelcomeModule.cxx b/Modules/Loadable/SlicerWelcome/qSlicerWelcomeModule.cxx index afeb2adcb94..c100c9fa4f9 100644 --- a/Modules/Loadable/SlicerWelcome/qSlicerWelcomeModule.cxx +++ b/Modules/Loadable/SlicerWelcome/qSlicerWelcomeModule.cxx @@ -61,7 +61,7 @@ QString qSlicerWelcomeModule::helpText()const QString qSlicerWelcomeModule::acknowledgementText()const { return "This work was supported by NA-MIC, NAC, BIRN, NCIGT, CTSC and the Slicer Community. " - "See http://www.slicer.org for details. We would also like to express our sincere " + "See https://www.slicer.org for details. We would also like to express our sincere " "thanks to members of the Slicer User Community who have helped us to design the contents " "of this Welcome Module, and whose feedback continues to improve functionality, usability " "and Slicer user experience\n."; diff --git a/Modules/Scripted/DMRIInstall/DMRIInstall.py b/Modules/Scripted/DMRIInstall/DMRIInstall.py index a2fcc5c39c6..e7f11abe83b 100644 --- a/Modules/Scripted/DMRIInstall/DMRIInstall.py +++ b/Modules/Scripted/DMRIInstall/DMRIInstall.py @@ -30,7 +30,7 @@ class DMRIInstall(ScriptedLoadableModule): For more information, please visit:

-    http://dmri.slicer.org +    https://dmri.slicer.org

Questions are welcome on the Slicer forum: diff --git a/Modules/Scripted/SegmentStatistics/SegmentStatistics.py b/Modules/Scripted/SegmentStatistics/SegmentStatistics.py index 4039203ceb0..076d42d8b8e 100644 --- a/Modules/Scripted/SegmentStatistics/SegmentStatistics.py +++ b/Modules/Scripted/SegmentStatistics/SegmentStatistics.py @@ -34,7 +34,7 @@ def __init__(self, parent): """ self.parent.helpText += parent.defaultDocumentationLink self.parent.acknowledgementText = """ -Supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. +Supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See https://www.slicer.org for details. """ def setup(self): diff --git a/README.txt b/README.txt index 403dbb6319f..781387ffc35 100644 --- a/README.txt +++ b/README.txt @@ -14,6 +14,6 @@ For Slicer community announcements and support, visit: For documentation, tutorials, and more information, please see: - http://www.slicer.org + https://www.slicer.org See License.txt for information on using and contributing. diff --git a/Utilities/Scripts/SlicerWizard/ExtensionWizard.py b/Utilities/Scripts/SlicerWizard/ExtensionWizard.py index 8892069f3bc..77a0eb61f48 100644 --- a/Utilities/Scripts/SlicerWizard/ExtensionWizard.py +++ b/Utilities/Scripts/SlicerWizard/ExtensionWizard.py @@ -675,7 +675,7 @@ def _execute(self, args): Option '%s' is not available. Consider re-building Slicer with SSL support or downloading - Slicer from http://download.slicer.org + Slicer from https://download.slicer.org """ % option)) # Add built-in templates diff --git a/Utilities/Scripts/SlicerWizard/doc/conf.py b/Utilities/Scripts/SlicerWizard/doc/conf.py index c401b68c831..92f01715470 100644 --- a/Utilities/Scripts/SlicerWizard/doc/conf.py +++ b/Utilities/Scripts/SlicerWizard/doc/conf.py @@ -29,7 +29,7 @@ #=============================================================================== class WikidocRole: - wiki_root = 'http://wiki.slicer.org/slicerWiki/index.php' + wiki_root = 'https://wiki.slicer.org/slicerWiki/index.php' #----------------------------------------------------------------------------- def __call__(self, role, rawtext, text, lineno, inliner, diff --git a/Utilities/Scripts/genqrc.py b/Utilities/Scripts/genqrc.py index eff6833563c..9b39aed740d 100755 --- a/Utilities/Scripts/genqrc.py +++ b/Utilities/Scripts/genqrc.py @@ -71,7 +71,7 @@ def main(argv): " This file was automatically generated by %s %r" % (os.path.basename(__file__), args.resource_directories), " See %s/%s for more information." % - ("http://www.slicer.org/slicerWiki/index.php", + ("https://www.slicer.org/slicerWiki/index.php", "Documentation/Nightly/Developers/Build_system/Qt_resource_files"), "-->", "", diff --git a/Utilities/SetupForDevelopment.sh b/Utilities/SetupForDevelopment.sh index ac4215a50eb..70728f83993 100755 --- a/Utilities/SetupForDevelopment.sh +++ b/Utilities/SetupForDevelopment.sh @@ -2,7 +2,7 @@ # Run this script to set up development with git. # For more information, see: -# http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DevelopmentWithGit +# https://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DevelopmentWithGit # printErrorAndExit() { diff --git a/Utilities/Templates/Modules/ScriptedSegmentEditorEffect/SegmentEditorTemplateKey.py b/Utilities/Templates/Modules/ScriptedSegmentEditorEffect/SegmentEditorTemplateKey.py index 882d1bad150..10360cb74d0 100644 --- a/Utilities/Templates/Modules/ScriptedSegmentEditorEffect/SegmentEditorTemplateKey.py +++ b/Utilities/Templates/Modules/ScriptedSegmentEditorEffect/SegmentEditorTemplateKey.py @@ -20,7 +20,7 @@ def __init__(self, parent): self.parent.hidden = True self.parent.helpText = "This hidden module registers the segment editor effect" self.parent.helpText += self.getDefaultModuleDocumentationLink() - self.parent.acknowledgementText = "Supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details." + self.parent.acknowledgementText = "Supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See https://www.slicer.org for details." slicer.app.connect("startupCompleted()", self.registerEditorEffect) def registerEditorEffect(self):