diff --git a/Applications/SlicerApp/Testing/Python/AtlasTests.py b/Applications/SlicerApp/Testing/Python/AtlasTests.py index a7e59cbf1c7..a57a52dbf8d 100644 --- a/Applications/SlicerApp/Testing/Python/AtlasTests.py +++ b/Applications/SlicerApp/Testing/Python/AtlasTests.py @@ -12,7 +12,7 @@ class AtlasTests(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -42,7 +42,7 @@ def __init__(self, parent): class AtlasTestsWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -102,7 +102,7 @@ class AtlasTestsLogic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def hasImageData(self, volumeNode): @@ -123,7 +123,7 @@ class AtlasTestsTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/BRAINSFitRigidRegistrationCrashIssue4139.py b/Applications/SlicerApp/Testing/Python/BRAINSFitRigidRegistrationCrashIssue4139.py index 7dd62626232..a670d89e9d0 100644 --- a/Applications/SlicerApp/Testing/Python/BRAINSFitRigidRegistrationCrashIssue4139.py +++ b/Applications/SlicerApp/Testing/Python/BRAINSFitRigidRegistrationCrashIssue4139.py @@ -10,7 +10,7 @@ class BRAINSFitRigidRegistrationCrashIssue4139(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -37,7 +37,7 @@ def __init__(self, parent): class BRAINSFitRigidRegistrationCrashIssue4139Widget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -55,7 +55,7 @@ class BRAINSFitRigidRegistrationCrashIssue4139Logic(ScriptedLoadableModuleLogic) this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def hasImageData(self, volumeNode): @@ -76,7 +76,7 @@ class BRAINSFitRigidRegistrationCrashIssue4139Test(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/RSNA2012ProstateDemo.py b/Applications/SlicerApp/Testing/Python/RSNA2012ProstateDemo.py index c0c00d4b6cc..fffab47712c 100644 --- a/Applications/SlicerApp/Testing/Python/RSNA2012ProstateDemo.py +++ b/Applications/SlicerApp/Testing/Python/RSNA2012ProstateDemo.py @@ -9,7 +9,7 @@ class RSNA2012ProstateDemo(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -32,7 +32,7 @@ def __init__(self, parent): class RSNA2012ProstateDemoWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -50,7 +50,7 @@ class RSNA2012ProstateDemoTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/RSNAQuantTutorial.py b/Applications/SlicerApp/Testing/Python/RSNAQuantTutorial.py index c62a8eaf040..07aeb346505 100644 --- a/Applications/SlicerApp/Testing/Python/RSNAQuantTutorial.py +++ b/Applications/SlicerApp/Testing/Python/RSNAQuantTutorial.py @@ -12,7 +12,7 @@ class RSNAQuantTutorial(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -35,7 +35,7 @@ def __init__(self, parent): class RSNAQuantTutorialWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -131,7 +131,7 @@ class RSNAQuantTutorialTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/RSNAVisTutorial.py b/Applications/SlicerApp/Testing/Python/RSNAVisTutorial.py index 702af320008..714b986555d 100644 --- a/Applications/SlicerApp/Testing/Python/RSNAVisTutorial.py +++ b/Applications/SlicerApp/Testing/Python/RSNAVisTutorial.py @@ -13,7 +13,7 @@ class RSNAVisTutorial(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -36,7 +36,7 @@ def __init__(self, parent): class RSNAVisTutorialWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -145,7 +145,7 @@ class RSNAVisTutorialLogic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ pass @@ -154,7 +154,7 @@ class RSNAVisTutorialTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/SliceLinkLogic.py b/Applications/SlicerApp/Testing/Python/SliceLinkLogic.py index 43ee6da4ef3..f689c0621cc 100644 --- a/Applications/SlicerApp/Testing/Python/SliceLinkLogic.py +++ b/Applications/SlicerApp/Testing/Python/SliceLinkLogic.py @@ -12,7 +12,7 @@ class SliceLinkLogic(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -35,7 +35,7 @@ def __init__(self, parent): class SliceLinkLogicWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -77,7 +77,7 @@ class SliceLinkLogicLogic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def hasImageData(self, volumeNode): @@ -98,7 +98,7 @@ class SliceLinkLogicTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/Slicer4Minute.py b/Applications/SlicerApp/Testing/Python/Slicer4Minute.py index df642db1ccc..6660ec3a1f9 100644 --- a/Applications/SlicerApp/Testing/Python/Slicer4Minute.py +++ b/Applications/SlicerApp/Testing/Python/Slicer4Minute.py @@ -12,7 +12,7 @@ class Slicer4Minute(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -35,7 +35,7 @@ def __init__(self, parent): class Slicer4MinuteWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -77,7 +77,7 @@ class Slicer4MinuteLogic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def hasImageData(self, volumeNode): @@ -98,7 +98,7 @@ class Slicer4MinuteTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/SlicerBoundsTest.py b/Applications/SlicerApp/Testing/Python/SlicerBoundsTest.py index ce02708d4e7..44d49933953 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerBoundsTest.py +++ b/Applications/SlicerApp/Testing/Python/SlicerBoundsTest.py @@ -9,7 +9,7 @@ # class SlicerBoundsTest(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): diff --git a/Applications/SlicerApp/Testing/Python/SlicerCreateRulerCrashIssue4199.py b/Applications/SlicerApp/Testing/Python/SlicerCreateRulerCrashIssue4199.py index e5eb1e77020..da794982842 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerCreateRulerCrashIssue4199.py +++ b/Applications/SlicerApp/Testing/Python/SlicerCreateRulerCrashIssue4199.py @@ -10,7 +10,7 @@ class SlicerCreateRulerCrashIssue4199(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -37,7 +37,7 @@ def __init__(self, parent): class SlicerCreateRulerCrashIssue4199Widget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -55,7 +55,7 @@ class SlicerCreateRulerCrashIssue4199Logic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def hasImageData(self, volumeNode): @@ -76,7 +76,7 @@ class SlicerCreateRulerCrashIssue4199Test(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreLoopTest.py b/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreLoopTest.py index 5231cd3a580..8a96b182283 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreLoopTest.py +++ b/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreLoopTest.py @@ -10,7 +10,7 @@ class SlicerMRBMultipleSaveRestoreLoopTest(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -35,7 +35,7 @@ def __init__(self, parent): class SlicerMRBMultipleSaveRestoreLoopTestWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -46,7 +46,7 @@ class SlicerMRBMultipleSaveRestoreLoop(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, methodName='runTest', numberOfIterations=5, uniqueDirectory=True, strict=False): diff --git a/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreTest.py b/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreTest.py index 202a9857020..f74e9211213 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreTest.py +++ b/Applications/SlicerApp/Testing/Python/SlicerMRBMultipleSaveRestoreTest.py @@ -10,7 +10,7 @@ class SlicerMRBMultipleSaveRestoreTest(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -35,7 +35,7 @@ def __init__(self, parent): class SlicerMRBMultipleSaveRestoreTestWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -46,7 +46,7 @@ class SlicerMRBMultipleSaveRestore(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, methodName='runTest', uniqueDirectory=True, strict=False): diff --git a/Applications/SlicerApp/Testing/Python/SlicerMRBSaveRestoreCheckPathsTest.py b/Applications/SlicerApp/Testing/Python/SlicerMRBSaveRestoreCheckPathsTest.py index 0ccc0eedf93..7cfb172fbf3 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerMRBSaveRestoreCheckPathsTest.py +++ b/Applications/SlicerApp/Testing/Python/SlicerMRBSaveRestoreCheckPathsTest.py @@ -11,7 +11,7 @@ # class SlicerMRBSaveRestoreCheckPathsTest(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -34,7 +34,7 @@ class SlicerMRBSaveRestoreCheckPaths(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, uniqueDirectory=True, strict=False): diff --git a/Applications/SlicerApp/Testing/Python/SlicerOrientationSelectorTest.py b/Applications/SlicerApp/Testing/Python/SlicerOrientationSelectorTest.py index f2683f60dc8..f5d587c8fb4 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerOrientationSelectorTest.py +++ b/Applications/SlicerApp/Testing/Python/SlicerOrientationSelectorTest.py @@ -10,7 +10,7 @@ class SlicerOrientationSelectorTest(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -35,7 +35,7 @@ def __init__(self, parent): class SlicerOrientationSelectorTestWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -53,7 +53,7 @@ class SlicerOrientationSelectorTestLogic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def hasImageData(self, volumeNode): @@ -74,7 +74,7 @@ class SlicerOrientationSelectorTestTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/SlicerRestoreSceneViewCrashIssue3445.py b/Applications/SlicerApp/Testing/Python/SlicerRestoreSceneViewCrashIssue3445.py index 17bef10c711..954330ee829 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerRestoreSceneViewCrashIssue3445.py +++ b/Applications/SlicerApp/Testing/Python/SlicerRestoreSceneViewCrashIssue3445.py @@ -9,7 +9,7 @@ class SlicerRestoreSceneViewCrashIssue3445(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -35,7 +35,7 @@ def __init__(self, parent): class SlicerRestoreSceneViewCrashIssue3445Widget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -53,7 +53,7 @@ class SlicerRestoreSceneViewCrashIssue3445Logic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ pass @@ -62,7 +62,7 @@ class SlicerRestoreSceneViewCrashIssue3445Test(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/SlicerTransformInteractionTest1.py b/Applications/SlicerApp/Testing/Python/SlicerTransformInteractionTest1.py index 0c0b12f141e..5d2de1b35c7 100644 --- a/Applications/SlicerApp/Testing/Python/SlicerTransformInteractionTest1.py +++ b/Applications/SlicerApp/Testing/Python/SlicerTransformInteractionTest1.py @@ -15,7 +15,7 @@ class SlicerTransformInteractionTest1(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): diff --git a/Applications/SlicerApp/Testing/Python/ViewControllersSliceInterpolationBug1926.py b/Applications/SlicerApp/Testing/Python/ViewControllersSliceInterpolationBug1926.py index 05579b36ca0..cbb29fd9adf 100644 --- a/Applications/SlicerApp/Testing/Python/ViewControllersSliceInterpolationBug1926.py +++ b/Applications/SlicerApp/Testing/Python/ViewControllersSliceInterpolationBug1926.py @@ -11,7 +11,7 @@ class ViewControllersSliceInterpolationBug1926(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -34,7 +34,7 @@ def __init__(self, parent): class ViewControllersSliceInterpolationBug1926Widget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -69,7 +69,7 @@ class ViewControllersSliceInterpolationBug1926Test(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/WebEngine.py b/Applications/SlicerApp/Testing/Python/WebEngine.py index ff11ca19c95..4a246650ae4 100644 --- a/Applications/SlicerApp/Testing/Python/WebEngine.py +++ b/Applications/SlicerApp/Testing/Python/WebEngine.py @@ -11,7 +11,7 @@ class WebEngine(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -34,7 +34,7 @@ def __init__(self, parent): class WebEngineWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -110,7 +110,7 @@ class WebEngineTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/Testing/Python/sceneImport2428.py b/Applications/SlicerApp/Testing/Python/sceneImport2428.py index f0979d0eb73..b36bf28e1b6 100644 --- a/Applications/SlicerApp/Testing/Python/sceneImport2428.py +++ b/Applications/SlicerApp/Testing/Python/sceneImport2428.py @@ -12,7 +12,7 @@ class sceneImport2428(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -36,7 +36,7 @@ def __init__(self, parent): class sceneImport2428Widget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -71,7 +71,7 @@ class sceneImport2428Test(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Applications/SlicerApp/qSlicerAppMainWindow.cxx b/Applications/SlicerApp/qSlicerAppMainWindow.cxx index 99c4b657038..857acce42fc 100644 --- a/Applications/SlicerApp/qSlicerAppMainWindow.cxx +++ b/Applications/SlicerApp/qSlicerAppMainWindow.cxx @@ -290,7 +290,7 @@ void qSlicerAppMainWindow::on_HelpSearchFeatureRequestsAction_triggered() //--------------------------------------------------------------------------- void qSlicerAppMainWindow::on_HelpViewLicenseAction_triggered() { - QDesktopServices::openUrl(QUrl("https://github.com/Slicer/Slicer/blob/master/License.txt")); + QDesktopServices::openUrl(QUrl("https://github.com/Slicer/Slicer/blob/main/License.txt")); } //--------------------------------------------------------------------------- diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index f47cc0491c6..49440891e48 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -21,7 +21,7 @@ If you are new to Slicer development and you don't have push access to the Slice repository, here are the steps: 1. [Fork and clone](https://docs.github.com/get-started/quickstart/fork-a-repo) the repository. -2. Run the developer setup script [`Utilities/SetupForDevelopment.sh`](https://github.com/Slicer/Slicer/blob/master/Utilities/SetupForDevelopment.sh). +2. Run the developer setup script [`Utilities/SetupForDevelopment.sh`](https://github.com/Slicer/Slicer/blob/main/Utilities/SetupForDevelopment.sh). 3. Create a branch. 4. [Push](https://docs.github.com/get-started/using-git/pushing-commits-to-a-remote-repository) the branch to your GitHub fork. 5. Create a [Pull Request](https://github.com/Slicer/Slicer/pulls). diff --git a/Docs/developer_guide/build_instructions/macos.md b/Docs/developer_guide/build_instructions/macos.md index 6341df6a2d9..2d7e40c6fda 100644 --- a/Docs/developer_guide/build_instructions/macos.md +++ b/Docs/developer_guide/build_instructions/macos.md @@ -10,7 +10,7 @@ The prerequisites listed below are required to be able to configure/build/packag xcode-select --install ``` -- A CMake version that meets at least the minimum required CMake version [here](https://github.com/Slicer/Slicer/blob/master/CMakeLists.txt#L1) +- A CMake version that meets at least the minimum required CMake version [here](https://github.com/Slicer/Slicer/blob/main/CMakeLists.txt#L1) - Qt 5: **tested and recommended**. - For building Slicer: download and execute [qt-unified-mac-x64-online.dmg](https://download.qt.io/official_releases/online_installers/qt-unified-mac-x64-online.dmg), install Qt 5.15.2, make sure to select `qtscript` and `qtwebengine` components. - For packaging and redistributing Slicer: build Qt using [qt-easy-build](https://github.com/jcfr/qt-easy-build#readme) diff --git a/Docs/developer_guide/build_instructions/overview.md b/Docs/developer_guide/build_instructions/overview.md index 7e43e4eb98e..16ca4f2467b 100644 --- a/Docs/developer_guide/build_instructions/overview.md +++ b/Docs/developer_guide/build_instructions/overview.md @@ -35,4 +35,4 @@ Customized editions of Slicer can be generated without changing Slicer source co - `Slicer_EXTENSION_SOURCE_DIRS`: Defines additional extensions that will be included in the application package as built-in modules. Full paths of extension source directories has to be specified, separated by semicolons. - `Slicer_BUILD_WIN32_CONSOLE_LAUNCHER`: Show/hide console (terminal window) on Windows. -Moreoptions are listed in CMake files, such as in [SlicerApplicationOptions.cmake](https://github.com/Slicer/Slicer/blob/master/CMake/SlicerApplicationOptions.cmake) and further customization is achievable by using [SlicerCustomAppTemplate](https://github.com/KitwareMedical/SlicerCustomAppTemplate) project maintained by Kitware. +Moreoptions are listed in CMake files, such as in [SlicerApplicationOptions.cmake](https://github.com/Slicer/Slicer/blob/main/CMake/SlicerApplicationOptions.cmake) and further customization is achievable by using [SlicerCustomAppTemplate](https://github.com/KitwareMedical/SlicerCustomAppTemplate) project maintained by Kitware. diff --git a/Docs/developer_guide/extensions.md b/Docs/developer_guide/extensions.md index a38bd3b81a4..baba02cfa13 100644 --- a/Docs/developer_guide/extensions.md +++ b/Docs/developer_guide/extensions.md @@ -308,7 +308,7 @@ Extension developers have to make sure that the extension description in each br The extensions build system allows to drive the build, test, packaging and upload of Slicer extensions. -Using the [extensions build system source code](https://github.com/Slicer/Slicer/tree/master/Extensions/CMake), it is possible to build extensions using either manual build or dashboard-driven automatic build. The extension description files must be simply placed in a folder, the same way as they are in the Extensions Index repository. +Using the [extensions build system source code](https://github.com/Slicer/Slicer/tree/main/Extensions/CMake), it is possible to build extensions using either manual build or dashboard-driven automatic build. The extension description files must be simply placed in a folder, the same way as they are in the Extensions Index repository. ### Build list of extensions manually @@ -424,7 +424,7 @@ make Continuous and nightly extension dashboards are setup on the Slicer factory machine maintained by [Kitware](https://www.kitware.com). Developers can set up similar infrastructure privately for their custom applications. -By customizing the [extension template dashboard script](https://github.com/Slicer/Slicer/blob/master/Extensions/CMake/SlicerExtensionsDashboardScript.TEMPLATE.cmake), it is possible to easily setup dashboard client submitting to [CDash](https://slicer.cdash.org/index.php?project=SlicerPreview). See example dashboard scripts that are used on official Slicer build machines [here](https://github.com/Slicer/DashboardScripts). Note that these scripts are more complex than the template to allow code reuse between different configurations, but they are tested regularly and so guaranteed to work. +By customizing the [extension template dashboard script](https://github.com/Slicer/Slicer/blob/main/Extensions/CMake/SlicerExtensionsDashboardScript.TEMPLATE.cmake), it is possible to easily setup dashboard client submitting to [CDash](https://slicer.cdash.org/index.php?project=SlicerPreview). See example dashboard scripts that are used on official Slicer build machines [here](https://github.com/Slicer/DashboardScripts). Note that these scripts are more complex than the template to allow code reuse between different configurations, but they are tested regularly and so guaranteed to work. ## Frequently asked questions @@ -440,7 +440,7 @@ We suggest to use the `Slicer` prefix in the extension name, too, when the exten ### Where can I find the extension templates? -The module and extension templates are available in the Slicer source tree: +The module and extension templates are available in the Slicer source tree: Using the [Extension Wizard module](https://www.slicer.org/wiki/Documentation/Nightly/Developers/ExtensionWizard), developers can easily create a new extension without having to copy, rename and update manually every files. @@ -515,8 +515,8 @@ To help fixing-up the libraries, executables and plugins so that they reference This module is used in two situations: -- Fixup of Slicer application itself. See [SlicerCPack.cmake#L36-68](https://github.com/Slicer/Slicer/blob/master/CMake/SlicerCPack.cmake#L36-68) and [SlicerCPackBundleFixup.cmake.in](https://github.com/Slicer/Slicer/blob/master/CMake/SlicerCPackBundleFixup.cmake.in). -- Fixup of an extension package. See [SlicerExtensionCPack.cmake#L126-143](https://github.com/Slicer/Slicer/blob/master/CMake/SlicerExtensionCPack.cmake#L126-143) and [SlicerExtensionCPackBundleFixup.cmake.in](https://github.com/Slicer/Slicer/blob/master/CMake/SlicerExtensionCPackBundleFixup.cmake.in). +- Fixup of Slicer application itself. See [SlicerCPack.cmake#L36-68](https://github.com/Slicer/Slicer/blob/main/CMake/SlicerCPack.cmake#L36-68) and [SlicerCPackBundleFixup.cmake.in](https://github.com/Slicer/Slicer/blob/main/CMake/SlicerCPackBundleFixup.cmake.in). +- Fixup of an extension package. See [SlicerExtensionCPack.cmake#L126-143](https://github.com/Slicer/Slicer/blob/main/CMake/SlicerExtensionCPack.cmake#L126-143) and [SlicerExtensionCPackBundleFixup.cmake.in](https://github.com/Slicer/Slicer/blob/main/CMake/SlicerExtensionCPackBundleFixup.cmake.in). ### How to check if an extension is built by Slicer Extensions build system? @@ -639,7 +639,7 @@ To build Slicer with SSL support, you need to build (or download) Qt with SSL su ### How to package third party libraries? -Extensions integrating third party libraries should follow the [SuperBuild extension template](https://github.com/Slicer/Slicer/tree/master/Utilities/Templates/Extensions/SuperBuild). +Extensions integrating third party libraries should follow the [SuperBuild extension template](https://github.com/Slicer/Slicer/tree/main/Utilities/Templates/Extensions/SuperBuild). Each third party libraries will be configured and built using a dedicated `External_MyLib.cmake` file, the install location of binaries and libraries should be set to `Slicer_INSTALL_BIN_DIR` and `Slicer_INSTALL_LIB_DIR`. diff --git a/Docs/developer_guide/modules/markups.md b/Docs/developer_guide/modules/markups.md index 944350a8984..087499fc5fa 100644 --- a/Docs/developer_guide/modules/markups.md +++ b/Docs/developer_guide/modules/markups.md @@ -2,7 +2,7 @@ ## Markups json file format (.mrk.json) -All markups node types (point list, line, angle, curve, etc.) can be saved to and loaded from json files. Detailed specification of all elements of the file is available in the [JSON schema](https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Markups/Resources/Schema). +All markups node types (point list, line, angle, curve, etc.) can be saved to and loaded from json files. Detailed specification of all elements of the file is available in the [JSON schema](https://github.com/Slicer/Slicer/blob/main/Modules/Loadable/Markups/Resources/Schema). A simple example that specifies a markups point list with 3 points that can be saved to a `myexample.mrk.json` file and loaded into Slicer: diff --git a/Docs/developer_guide/modules/transforms.md b/Docs/developer_guide/modules/transforms.md index 265aead47e8..b453186c921 100644 --- a/Docs/developer_guide/modules/transforms.md +++ b/Docs/developer_guide/modules/transforms.md @@ -11,7 +11,7 @@ - Slicer stores transforms in VTK classes in memory, but uses ITK transform IO classes to read/write transforms to files. ITK's convention is to use LPS coordinate system as opposed to RAS coordinate system in Slicer (see Coordinate systems page for details). Conversion between VTK and ITK transform classes are implemented in vtkITKTransformConverter. - ITK stores the transform in resampling (a.k.a., image processing) convention, i.e., that transforms points from fixed to moving coordinate system. This transform is usable as is for resampling a moving image in the coordinate system of a fixed image. For transforming points and surface models to the fixed coordinate system, one needs the transform in the modeling (a.k.a. computer graphics) convention, i.e., transform from moving to fixed coordinate system (which is the inverse of the "image processing" convention). -- Transform nodes in Slicer can store transforms in both modeling (when "to parent" transform is set) and resampling way (when "from parent" transform is set). When writing transform to ITK files, linear transforms are inverted as needed and written as an AffineTransform. Non-linear transforms cannot be inverted without losing information (in general), therefore if a non-linear transform is defined in resampling convention in Slicer then it is written to ITK file using special "Inverse" transform types (e.g., InverseDisplacementFieldTransform instead of DisplacementFieldTransform). Definition of the inverse classes are available in [vtkITKTransformInverse](https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkITKTransformInverse.h). The inverse classes are only usable for file IO, because currently ITK does not provide a generic inverse transform computation method. Options to manage inverse transforms in applications: +- Transform nodes in Slicer can store transforms in both modeling (when "to parent" transform is set) and resampling way (when "from parent" transform is set). When writing transform to ITK files, linear transforms are inverted as needed and written as an AffineTransform. Non-linear transforms cannot be inverted without losing information (in general), therefore if a non-linear transform is defined in resampling convention in Slicer then it is written to ITK file using special "Inverse" transform types (e.g., InverseDisplacementFieldTransform instead of DisplacementFieldTransform). Definition of the inverse classes are available in [vtkITKTransformInverse](https://github.com/Slicer/Slicer/blob/main/Libs/MRML/Core/vtkITKTransformInverse.h). The inverse classes are only usable for file IO, because currently ITK does not provide a generic inverse transform computation method. Options to manage inverse transforms in applications: - Create VTK transforms from ITK transforms: VTK transforms can compute their inverse, transform can be changed dynamically, the inverse will be always updated automatically in real-time (this approach is used by Slicer) - Invert transform in ITK statically: by converting to displacement field and inverting the displacement field; whenever the forward transform changes, the complete inverse transform has to be computed again (which is typically very time consuming) - Avoid inverse non-linear transforms: make sure that non-linear transforms are only set as FromParent diff --git a/Docs/developer_guide/script_repository.md b/Docs/developer_guide/script_repository.md index 4f73a6b5f75..395e2f045f0 100644 --- a/Docs/developer_guide/script_repository.md +++ b/Docs/developer_guide/script_repository.md @@ -11,9 +11,9 @@ To run a Python code snippet automatically at each application startup, add it t :::{note} **More reference code**: -The Slicer source code has Python [scripted modules](https://github.com/Slicer/Slicer/tree/master/Modules/Scripted) and [scripted Segmentation Editor effects](https://github.com/Slicer/Slicer/tree/master/Modules/Loadable/Segmentations/EditorEffects/Python) that can be used as working examples. +The Slicer source code has Python [scripted modules](https://github.com/Slicer/Slicer/tree/main/Modules/Scripted) and [scripted Segmentation Editor effects](https://github.com/Slicer/Slicer/tree/main/Modules/Loadable/Segmentations/EditorEffects/Python) that can be used as working examples. * Most [Slicer Extensions](https://github.com/topics/3d-slicer-extension) are written in Python to address specific use cases. Looking at their source code can be informative. -* The [Slicer Discourse forum](https://discourse.slicer.org/) has many code snippets and discussions. +* The [Slicer Discourse forum](https://discourse.slicer.org/) has many code snippets and discussions. ::: diff --git a/Docs/developer_guide/script_repository/gui.md b/Docs/developer_guide/script_repository/gui.md index d4b6e5824a0..ea43292a348 100644 --- a/Docs/developer_guide/script_repository/gui.md +++ b/Docs/developer_guide/script_repository/gui.md @@ -532,7 +532,7 @@ layoutManager.layoutLogic().GetLayoutNode().AddLayoutDescription(customLayoutId, layoutManager.setLayout(customLayoutId) ``` -See description of standard layouts (that can be used as examples) here: https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx +See description of standard layouts (that can be used as examples) here: https://github.com/Slicer/Slicer/blob/main/Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx You can use this code snippet to add a button to the layout selector toolbar: diff --git a/Docs/developer_guide/script_repository/markups.md b/Docs/developer_guide/script_repository/markups.md index f46fcc2ce38..1a318b03265 100644 --- a/Docs/developer_guide/script_repository/markups.md +++ b/Docs/developer_guide/script_repository/markups.md @@ -145,7 +145,7 @@ for i in range(numControlPoints): print(i,": RAS =",ras,", world =",world) ``` -You can also look at the sample code in the [Endoscopy module](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Endoscopy/Endoscopy.py#L287) to see how python is used to access control points from a scripted module. +You can also look at the sample code in the [Endoscopy module](https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/Endoscopy/Endoscopy.py#L287) to see how python is used to access control points from a scripted module. ### Define/edit a circular region of interest in a slice viewer diff --git a/Docs/developer_guide/script_repository/subjecthierarchy.md b/Docs/developer_guide/script_repository/subjecthierarchy.md index 4a935a07085..dae3e70a69f 100644 --- a/Docs/developer_guide/script_repository/subjecthierarchy.md +++ b/Docs/developer_guide/script_repository/subjecthierarchy.md @@ -102,7 +102,7 @@ class MyListenerClass(VTKObservationMixin): ### Subject hierarchy plugin offering view context menu action -If an object that supports view context menus (e.g. markups) is right-clicked in a slice or 3D view, it can offer custom actions. Due to internal limitations these plugins must be set up differently, as explained [here](https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Annotations/SubjectHierarchyPlugins/AnnotationsSubjectHierarchyPlugin.py#L96-L107). This example makes it easier to create such a plugin. +If an object that supports view context menus (e.g. markups) is right-clicked in a slice or 3D view, it can offer custom actions. Due to internal limitations these plugins must be set up differently, as explained [here](https://github.com/Slicer/Slicer/blob/main/Modules/Loadable/Annotations/SubjectHierarchyPlugins/AnnotationsSubjectHierarchyPlugin.py#L96-L107). This example makes it easier to create such a plugin. This text must be saved as `ViewContextMenu.py` and placed in a folder that is added to "Additional module paths" in Application Settings / Modules section. diff --git a/Docs/developer_guide/script_repository/volumes.md b/Docs/developer_guide/script_repository/volumes.md index a94d18960d0..78b5880a5a9 100644 --- a/Docs/developer_guide/script_repository/volumes.md +++ b/Docs/developer_guide/script_repository/volumes.md @@ -656,7 +656,7 @@ slicer.util.setSliceViewerLayers(background=outputVolumeNode) More information: - See the SimpleITK documentation for SimpleITK examples: https://simpleitk.org/doxygen/latest/html/examples.html -- sitkUtils in Slicer is used for pushing and pulling images from Slicer to SimpleITK: https://github.com/Slicer/Slicer/blob/master/Base/Python/sitkUtils.py +- sitkUtils in Slicer is used for pushing and pulling images from Slicer to SimpleITK: https://github.com/Slicer/Slicer/blob/main/Base/Python/sitkUtils.py ### Get axial slice as numpy array diff --git a/Docs/user_guide/about.md b/Docs/user_guide/about.md index 2d2c0c91042..94b08fa8df0 100644 --- a/Docs/user_guide/about.md +++ b/Docs/user_guide/about.md @@ -20,7 +20,7 @@ Highlights: The 3D Slicer software is distributed under a BSD-style open source license that is broadly compatible with the Open Source Definition by [The Open Source Initiative](https://opensource.org/) and contains no restrictions on legal uses of the software. -To use Slicer, please read the [3D Slicer Software License Agreement](https://github.com/Slicer/Slicer/blob/master/License.txt) before downloading any binary releases of the Slicer. +To use Slicer, please read the [3D Slicer Software License Agreement](https://github.com/Slicer/Slicer/blob/main/License.txt) before downloading any binary releases of the Slicer. ### Historical notes about the license diff --git a/Docs/user_guide/data_loading_and_saving.md b/Docs/user_guide/data_loading_and_saving.md index 9f9fbd7a9da..39236412ff7 100644 --- a/Docs/user_guide/data_loading_and_saving.md +++ b/Docs/user_guide/data_loading_and_saving.md @@ -125,7 +125,7 @@ Surface or volumetric meshes. ### Markups -- **Markups JSON** (.mkp.json): point list, line, curve, closed curve, plane, etc. Default coordinate system: LPS. Coordinate system (LPS/RAS) can be specified in image header. JSON schema is available [here](https://github.com/Slicer/Slicer/tree/master/Modules/Loadable/Markups/Resources/Schema). +- **Markups JSON** (.mkp.json): point list, line, curve, closed curve, plane, etc. Default coordinate system: LPS. Coordinate system (LPS/RAS) can be specified in image header. JSON schema is available [here](https://github.com/Slicer/Slicer/tree/main/Modules/Loadable/Markups/Resources/Schema). - **Markups CSV** (.fcsv): legacy file format for storing point list. Default coordinate system: LPS. Coordinate system (LPS/RAS) can be specified in image header. - **Annotation CSV** (.acsv): legacy file format for storing annotation ruler, ROI. diff --git a/Docs/user_guide/get_help.md b/Docs/user_guide/get_help.md index 9c9eb6123d6..b4ff8987577 100644 --- a/Docs/user_guide/get_help.md +++ b/Docs/user_guide/get_help.md @@ -12,13 +12,13 @@ If you are not sure if Slicer behaves incorrectly or you are not using it properly then [ask about it on the Slicer Forum](https://discourse.slicer.org/c/support) (in the `Support` category). If you are _sure_ that Slicer is not working as intended then [submit a bug report in the Slicer issue tracker](https://github.com/Slicer/Slicer/issues/new?assignees=&labels=type%3Abug&template=bug_report.md). -In your question/report provide all the information that is described in the [bug reporting template](https://github.com/Slicer/Slicer/blob/master/.github/ISSUE_TEMPLATE/bug_report.md#summary). +In your question/report provide all the information that is described in the [bug reporting template](https://github.com/Slicer/Slicer/blob/main/.github/ISSUE_TEMPLATE/bug_report.md#summary). :::{tip} Don't be anonymous: real people trying hard to solve real problems are more likely to get valuable help. If you tell about yourself and your project then it may get more attention and the problem may be resolved sooner. -::: +::: ## I would like to request enhancement or new feature diff --git a/Docs/user_guide/modules/data.md b/Docs/user_guide/modules/data.md index 601fb8c1668..2bfbd311d54 100644 --- a/Docs/user_guide/modules/data.md +++ b/Docs/user_guide/modules/data.md @@ -121,7 +121,7 @@ List of all nodes in the scene. Supports Edit properties, Rename, Delete. To create a C++ plugin, implement a child class of qSlicerSubjectHierarchyAbstractPlugin, for Python plugin see below. Many examples can be found in Slicer core and in the SlicerRT extension, look for folders named SubjectHierarchyPlugins. - Writing plugins in **Python**: - Child class of AbstractScriptedSubjectHierarchyPlugin which is a Python adaptor of the C++ qSlicerSubjectHierarchyScriptedPlugin class - - Example: [Annotations](https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Annotations/SubjectHierarchyPlugins/AnnotationsSubjectHierarchyPlugin.py) role plugin, [function plugin](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/SegmentEditor/SubjectHierarchyPlugins/SegmentEditorSubjectHierarchyPlugin.py) + - Example: [Annotations](https://github.com/Slicer/Slicer/blob/main/Modules/Loadable/Annotations/SubjectHierarchyPlugins/AnnotationsSubjectHierarchyPlugin.py) role plugin, [function plugin](https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/SegmentEditor/SubjectHierarchyPlugins/SegmentEditorSubjectHierarchyPlugin.py) - **Role** plugins: add support for new data node types - Defines: ownership, icon, tooltip, edit properties, help text (in the yellow question mark popup), visibility icon, set/get display visibility, displayed node name (if different than name of the node object) - Existing plugins in Slicer core: Markups, Models, SceneViews, Charts, Folder, Tables, Transforms, LabelMaps, Volumes diff --git a/Docs/user_guide/modules/dicompatcher.md b/Docs/user_guide/modules/dicompatcher.md index c6c3ce30dd0..26eb58177f5 100644 --- a/Docs/user_guide/modules/dicompatcher.md +++ b/Docs/user_guide/modules/dicompatcher.md @@ -34,7 +34,7 @@ DICOM is a large and complex standard and device manufacturers and third-party s ## Information for Developers -This is a Python scripted module. Source code is available [here](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/DICOMPatcher/DICOMPatcher.py). +This is a Python scripted module. Source code is available [here](https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/DICOMPatcher/DICOMPatcher.py). ## Contributors diff --git a/Docs/user_guide/modules/screencapture.md b/Docs/user_guide/modules/screencapture.md index dac3df94bd0..060d54c1785 100644 --- a/Docs/user_guide/modules/screencapture.md +++ b/Docs/user_guide/modules/screencapture.md @@ -119,7 +119,7 @@ On Windows, Screen Capture model can automatically download and install ffmpeg w ## Information for developers -- This is a Python scripted module. Source code is available [here](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/ScreenCapture/ScreenCapture.py). +- This is a Python scripted module. Source code is available [here](https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/ScreenCapture/ScreenCapture.py). - Examples of capturing images are available in the [Script Repository](../../developer_guide/script_repository.md#screen-capture) ## Contributors diff --git a/Docs/user_guide/modules/segmentations.md b/Docs/user_guide/modules/segmentations.md index b3af1d5cde9..a5457df5347 100644 --- a/Docs/user_guide/modules/segmentations.md +++ b/Docs/user_guide/modules/segmentations.md @@ -186,8 +186,8 @@ See Script repository's [Segmentations section](../../developer_guide/script_rep ## Information for developers -- [vtkSegmentationCore on GitHub](https://github.com/Slicer/Slicer/tree/master/Libs/vtkSegmentationCore) (within Slicer) -- [Segmentations Slicer module on GitHub](https://github.com/Slicer/Slicer/tree/master/Modules/Loadable/Segmentations) +- [vtkSegmentationCore on GitHub](https://github.com/Slicer/Slicer/tree/main/Libs/vtkSegmentationCore) (within Slicer) +- [Segmentations Slicer module on GitHub](https://github.com/Slicer/Slicer/tree/main/Modules/Loadable/Segmentations) - [Segmentations Labs page](https://www.slicer.org/wiki/Documentation/Labs/Segmentations) - [Manipulation of segmentations from Python scripts - examples in script repository](../../developer_guide/script_repository.md#segmentations) diff --git a/Docs/user_guide/modules/segmentstatistics.md b/Docs/user_guide/modules/segmentstatistics.md index 5514e25b770..d55336e374c 100644 --- a/Docs/user_guide/modules/segmentstatistics.md +++ b/Docs/user_guide/modules/segmentstatistics.md @@ -44,7 +44,7 @@ Labelmap statistics are calculated using the binary labelmap representation of t ## Information for developers See examples for calculating statistics from your own modules in the [Slicer script repository](../../developer_guide/script_repository.md#quantifying-segments). -Additional plugins for computation of other statistical measurements may be registered by subclassing [SegmentStatisticsPluginBase.py](https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/SegmentStatistics/SegmentStatisticsPlugins/SegmentStatisticsPluginBase.py), and registering the plugin with SegmentStatisticsLogic. +Additional plugins for computation of other statistical measurements may be registered by subclassing [SegmentStatisticsPluginBase.py](https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/SegmentStatistics/SegmentStatisticsPlugins/SegmentStatisticsPluginBase.py), and registering the plugin with SegmentStatisticsLogic. ## Contributors diff --git a/Docs/user_guide/modules/terminologies.md b/Docs/user_guide/modules/terminologies.md index d4e3fc8ec0f..a086737356b 100644 --- a/Docs/user_guide/modules/terminologies.md +++ b/Docs/user_guide/modules/terminologies.md @@ -40,7 +40,7 @@ Opening up the panes on the left and right, additional options become visible: - Find items: Start typing the name of the category/type/region in the search box above the column. - Load new terminology/anatomical context: click the Load button next to the context drop-down and select JSON from local storage. -- Create custom terminology/anatomical context: Start from an existing JSON file, such as the DICOM master list for [terminologies](https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Terminologies/Resources/SegmentationCategoryTypeModifier-DICOM-Master.json) or [anatomical contexts](https://github.com/Slicer/Slicer/blob/master/Modules/Loadable/Terminologies/Resources/AnatomicRegionAndModifier-DICOM-Master.json). Remove the entries you do not need. Validate the JSON file with the [validator online tool](https://qiicr.org/dcmqi/#/validators). +- Create custom terminology/anatomical context: Start from an existing JSON file, such as the DICOM master list for [terminologies](https://github.com/Slicer/Slicer/blob/main/Modules/Loadable/Terminologies/Resources/SegmentationCategoryTypeModifier-DICOM-Master.json) or [anatomical contexts](https://github.com/Slicer/Slicer/blob/main/Modules/Loadable/Terminologies/Resources/AnatomicRegionAndModifier-DICOM-Master.json). Remove the entries you do not need. Validate the JSON file with the [validator online tool](https://qiicr.org/dcmqi/#/validators). ## References diff --git a/Docs/user_guide/modules/webserver.md b/Docs/user_guide/modules/webserver.md index 9239b643c01..0ad7ef4e19d 100644 --- a/Docs/user_guide/modules/webserver.md +++ b/Docs/user_guide/modules/webserver.md @@ -14,9 +14,9 @@ There are three types of endpoints: | [Slicer](#slicer-endpoints) | Give read/write access to features in Slicer's MRML scene and GUI.
This interface also exposes the Python interpreter so that arbitrary python code may be executed in the Slicer application. | `/slicer` | [SlicerRequestHandler][SlicerRequestHandler] | | [DICOMweb](#dicom-endpoints) | Exposes the Slicer dicom database as a DICOMweb services | `/dicom` | [DICOMRequestHandler][DICOMRequestHandler] | -[StaticPagesRequestHandler]: https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/WebServer/WebServerLib/StaticPagesRequestHandler.py -[SlicerRequestHandler]: https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/WebServer/WebServerLib/SlicerRequestHandler.py -[DICOMRequestHandler]: https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/WebServer/WebServerLib/DICOMRequestHandler.py +[StaticPagesRequestHandler]: https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/WebServer/WebServerLib/StaticPagesRequestHandler.py +[SlicerRequestHandler]: https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/WebServer/WebServerLib/SlicerRequestHandler.py +[DICOMRequestHandler]: https://github.com/Slicer/Slicer/blob/main/Modules/Scripted/WebServer/WebServerLib/DICOMRequestHandler.py :::{note} The web server is integrated with the Qt event loop so it can be used together with the interactive session. diff --git a/Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate/ScriptedLoadableModuleTemplate.py b/Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate/ScriptedLoadableModuleTemplate.py index 70f8f06df5f..f1d54e20414 100644 --- a/Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate/ScriptedLoadableModuleTemplate.py +++ b/Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate/ScriptedLoadableModuleTemplate.py @@ -14,7 +14,7 @@ class ScriptedLoadableModuleTemplate(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -40,7 +40,7 @@ def __init__(self, parent): class ScriptedLoadableModuleTemplateWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -150,7 +150,7 @@ class ScriptedLoadableModuleTemplateLogic(ScriptedLoadableModuleLogic): this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def hasImageData(self, volumeNode): @@ -204,7 +204,7 @@ class ScriptedLoadableModuleTemplateTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py b/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py index be4b2ceb6c3..7e2beb7d064 100644 --- a/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py +++ b/Extensions/Testing/ScriptedSegmentEditorEffectExtensionTemplate/ScriptedSegmentEditorEffectModuleTemplate/SegmentEditorScriptedSegmentEditorEffectModuleTemplate.py @@ -7,7 +7,7 @@ class SegmentEditorScriptedSegmentEditorEffectModuleTemplate(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -34,7 +34,7 @@ class SegmentEditorScriptedSegmentEditorEffectModuleTemplateTest(ScriptedLoadabl """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Modules/Loadable/CropVolume/Testing/Python/CropVolumeSelfTest.py b/Modules/Loadable/CropVolume/Testing/Python/CropVolumeSelfTest.py index 86e140c6983..000c4a13ab5 100644 --- a/Modules/Loadable/CropVolume/Testing/Python/CropVolumeSelfTest.py +++ b/Modules/Loadable/CropVolume/Testing/Python/CropVolumeSelfTest.py @@ -26,7 +26,7 @@ def __init__(self, parent): class CropVolumeSelfTestWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): diff --git a/Modules/Loadable/Markups/Testing/Python/AddManyMarkupsFiducialTest.py b/Modules/Loadable/Markups/Testing/Python/AddManyMarkupsFiducialTest.py index 9b4241428e6..4d6ac394649 100644 --- a/Modules/Loadable/Markups/Testing/Python/AddManyMarkupsFiducialTest.py +++ b/Modules/Loadable/Markups/Testing/Python/AddManyMarkupsFiducialTest.py @@ -33,7 +33,7 @@ def __init__(self, parent): class AddManyMarkupsFiducialTestWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -216,7 +216,7 @@ class AddManyMarkupsFiducialTestTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Modules/Loadable/SceneViews/Testing/Python/AddStorableDataAfterSceneViewTest.py b/Modules/Loadable/SceneViews/Testing/Python/AddStorableDataAfterSceneViewTest.py index dddf5cb5e39..f13a3ababcd 100644 --- a/Modules/Loadable/SceneViews/Testing/Python/AddStorableDataAfterSceneViewTest.py +++ b/Modules/Loadable/SceneViews/Testing/Python/AddStorableDataAfterSceneViewTest.py @@ -13,7 +13,7 @@ class AddStorableDataAfterSceneViewTest(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): @@ -39,7 +39,7 @@ def __init__(self, parent): class AddStorableDataAfterSceneViewTestWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): @@ -95,7 +95,7 @@ def onApplyButton(self): class AddStorableDataAfterSceneViewTestLogic(ScriptedLoadableModuleLogic): """ Uses ScriptedLoadableModuleLogic base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def run(self, enableScreenshots=0): @@ -124,7 +124,7 @@ class AddStorableDataAfterSceneViewTestTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: - https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py + https://github.com/Slicer/Slicer/blob/main/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): diff --git a/Modules/Loadable/SlicerWelcome/Resources/HTML/About.html b/Modules/Loadable/SlicerWelcome/Resources/HTML/About.html index 674b87fcfbf..1721cd796d7 100644 --- a/Modules/Loadable/SlicerWelcome/Resources/HTML/About.html +++ b/Modules/Loadable/SlicerWelcome/Resources/HTML/About.html @@ -11,7 +11,7 @@

- 3D Slicer is distributed under a BSD-style license; for details about the contribution and software license agreement, please see the 3D Slicer Software License Agreement. This software has been designed for research purposes only and has not been reviewed or approved by the Food and Drug Administration, or by any other agency. + 3D Slicer is distributed under a BSD-style license; for details about the contribution and software license agreement, please see the 3D Slicer Software License Agreement. This software has been designed for research purposes only and has not been reviewed or approved by the Food and Drug Administration, or by any other agency.

diff --git a/Modules/Loadable/SlicerWelcome/Resources/HTML/OtherUsefulHints.html b/Modules/Loadable/SlicerWelcome/Resources/HTML/OtherUsefulHints.html index 02a953f1bcd..bbe94a5cc9a 100644 --- a/Modules/Loadable/SlicerWelcome/Resources/HTML/OtherUsefulHints.html +++ b/Modules/Loadable/SlicerWelcome/Resources/HTML/OtherUsefulHints.html @@ -31,7 +31,7 @@

About 3D Slicer