STYLE: Update NAMIC website links to https versions

BRAINSia · Apr 6, 2022 · 1fecd29 · 1fecd29
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diff --git a/Applications/SlicerApp/Testing/Python/sceneImport2428.py b/Applications/SlicerApp/Testing/Python/sceneImport2428.py
@@ -26,7 +26,7 @@ def __init__(self, parent):
     """
     parent.acknowledgementText = """
     This file was originally developed by Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1.
-    This is a module to support testing of <a>http://www.na-mic.org/Bug/view.php?id=2428</a>
+    This is a module to support testing of <a>https://www.na-mic.org/Bug/view.php?id=2428</a>
 """ # replace with organization, grant and thanks.
 
 #

diff --git a/Base/Logic/Resources/ColorFiles/SPL-BrainAtlas-2009-ColorFile.txt b/Base/Logic/Resources/ColorFiles/SPL-BrainAtlas-2009-ColorFile.txt
@@ -4,7 +4,7 @@
 #Filename: CCA_Atlases_MRI_Brain_Atlas_2010_ColorFile.txt
 #Title: CCA:Atlases:MRI Brain Atlas 2010:ColorFile
 #PageName: CCA:Atlases:MRI_Brain_Atlas_2010:ColorFile
-#Source: http://www.na-mic.org/Wiki/index.php/CCA:Atlases:MRI_Brain_Atlas_2010:ColorFile
+#Source: https://www.na-mic.org/Wiki/index.php/CCA:Atlases:MRI_Brain_Atlas_2010:ColorFile
 #
 #Begin table data:
 0 background 0 0 0 255

diff --git a/Base/Python/slicer/ScriptedLoadableModule.py b/Base/Python/slicer/ScriptedLoadableModule.py
@@ -29,7 +29,7 @@ def __init__(self, parent):
 
     parent.acknowledgementText = """
 This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a>https://www.slicer.org</a> for details.
-This work is partially supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See <a href=https://www.slicer.org>http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy</a>).
+This work is partially supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See <a href=https://www.slicer.org>https://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy</a>).
 """
 
     # Set module icon from Resources/Icons/<ModuleName>.png

diff --git a/CMake/SlicerLinkerAsNeededFlagCheck.cmake b/CMake/SlicerLinkerAsNeededFlagCheck.cmake
@@ -52,6 +52,6 @@ else()
     message(STATUS "Checking if --no-as-needed linker flag is required - failed.")
     message(WARNING "Could not compile test code."
       "Linker could fail trying to resolve symbols for underlinked libraries."
-      "See issue 2321 (http://na-mic.org/Mantis/view.php?id=2321) for more details.")
+      "See issue 2321 (https://na-mic.org/Mantis/view.php?id=2321) for more details.")
   endif()
 endif()
diff --git a/CMake/SlicerMacroBuildApplication.cmake b/CMake/SlicerMacroBuildApplication.cmake
@@ -475,7 +475,7 @@ macro(slicerMacroBuildApplication)
 
   if(WIN32)
     if(Slicer_USE_PYTHONQT)
-      # HACK - See http://www.na-mic.org/Bug/view.php?id=1180
+      # HACK - See https://www.na-mic.org/Bug/view.php?id=1180
       get_filename_component(_python_library_name_we ${PYTHON_LIBRARY} NAME_WE)
       add_custom_command(
         TARGET ${slicerapp_target}

diff --git a/CMake/SlicerMacroBuildLoadableModule.cmake b/CMake/SlicerMacroBuildLoadableModule.cmake
@@ -327,7 +327,7 @@ macro(slicerMacroBuildQtModule)
     ${ARGN}
     )
 
-  # See http://www.na-mic.org/Bug/view.php?id=3332
+  # See https://www.na-mic.org/Bug/view.php?id=3332
   #message(AUTHOR_WARNING
   #  "Macro 'slicerMacroBuildQtModule' is deprecated: Use 'slicerMacroBuildLoadableModule' instead."
   #  )

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -161,7 +161,7 @@ email.
 
 
 *The initial version of these guidelines was established during the [winter
- project week 2017](http://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week/UpdatingCommunityForums).*
+ project week 2017](https://www.na-mic.org/Wiki/index.php/2017_Winter_Project_Week/UpdatingCommunityForums).*
 
 #### Benevolent dictators for life
 

diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
@@ -2,7 +2,7 @@
 For more information, please see:
   https://www.slicer.org
 and
-  http://wiki.na-mic.org/Wiki/index.php/Slicer3
+  https://wiki.na-mic.org/Wiki/index.php/Slicer3
 
 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/Docs/cli_module_parameters_to_md.xsl b/Docs/cli_module_parameters_to_md.xsl
@@ -7,7 +7,7 @@
     <xsl:text>&#10;</xsl:text>
   </xsl:template>
 
-  <!-- See http://na-mic.org/Mantis/view.php?id=2536 -->
+  <!-- See https://na-mic.org/Mantis/view.php?id=2536 -->
   <xsl:template match="name">
     <xsl:text> (*</xsl:text>
     <xsl:value-of select="."/>

diff --git a/Docs/developer_guide/extensions.md b/Docs/developer_guide/extensions.md
@@ -537,7 +537,7 @@ The issue is that the your extension has a "non standard" layout and the wizard
 
 Similar issue has been discussed and reported for the "SPHARM-PDM" or UKF extension.
 
-First half of the solution would be to move the metadata from Common.cmake to CMakeLists.txt as it is done in [here](http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=spharm-pdm&revision=228). Then, you could make sure there is a project() statement by following what is suggested [here](http://www.na-mic.org/Bug/view.php?id=3737#c12081).
+First half of the solution would be to move the metadata from Common.cmake to CMakeLists.txt as it is done in [here](http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=spharm-pdm&revision=228). Then, you could make sure there is a project() statement by following what is suggested [here](https://www.na-mic.org/Bug/view.php?id=3737#c12081).
 
 If you prefer not to re-organize your extension, you could still contribute extension description file by creating it manually.
 

diff --git a/Docs/user_guide/modules/colors.md b/Docs/user_guide/modules/colors.md
@@ -192,7 +192,7 @@ See examples and other developer information in [Developer guide](../../develope
 
 ## Acknowledgements
 
-This work is part of the [National Alliance for Medical Image Computing](http://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
+This work is part of the [National Alliance for Medical Image Computing](https://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
 
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_namic.png)
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_spl.png)

diff --git a/Docs/user_guide/modules/data.md b/Docs/user_guide/modules/data.md
@@ -111,7 +111,7 @@ List of all nodes in the scene. Supports Edit properties, Rename, Delete.
 
 ## Tutorials
 
-- 2016: [This tutorial](http://www.na-mic.org/Wiki/index.php/Winter2016TutorialContest) demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset.
+- 2016: [This tutorial](https://www.na-mic.org/Wiki/index.php/Winter2016TutorialContest) demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset.
 - 2015: Tutorial about [loading and viewing data](https://www.slicer.org/wiki/Documentation/4.5/Training).
 
 ## Information for developers

diff --git a/Docs/user_guide/modules/dicom.md b/Docs/user_guide/modules/dicom.md
@@ -262,7 +262,7 @@ Authors:
 
 ## Acknowledgements
 
-This work is part of the [National Alliance for Medical Image Computing](http://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149, and by Quantitative Image Informatics for Cancer Research (QIICR) (U24 CA180918).
+This work is part of the [National Alliance for Medical Image Computing](https://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149, and by Quantitative Image Informatics for Cancer Research (QIICR) (U24 CA180918).
 
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_isomics.png)
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_namic.png)

diff --git a/Docs/user_guide/modules/dwiconvert.md b/Docs/user_guide/modules/dwiconvert.md
@@ -19,5 +19,5 @@
 
 ## Information for Developers
 
-- [DICOM for DWI and DTI](http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI)
+- [DICOM for DWI and DTI](https://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI)
 - [Source code on github](https://github.com/BRAINSia/BRAINSTools)
diff --git 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 https://www.slicer.org for details. Module implemented by Steve Pieper.
+This work is supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See https://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/markups.md b/Docs/user_guide/modules/markups.md
@@ -181,7 +181,7 @@ Authors:
 
 ## Acknowledgements
 
-This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [NA-MIC website](http://www.na-mic.org/).
+This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [NA-MIC website](https://www.na-mic.org/).
 
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_spl.png)
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_perklab.png)
diff --git a/Docs/user_guide/modules/segmenteditor.md b/Docs/user_guide/modules/segmenteditor.md
@@ -285,7 +285,7 @@ Authors:
 ## Acknowledgements
 
 This module is partly funded by an Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.
-The work is part of the [National Alliance for Medical Image Computing](http://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
+The work is part of the [National Alliance for Medical Image Computing](https://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
 
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_perklab.png)
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_isomics.png)

diff --git a/Docs/user_guide/modules/segmentstatistics.md b/Docs/user_guide/modules/segmentstatistics.md
@@ -58,7 +58,7 @@ Authors:
 ## Acknowledgements
 
 This module is partly funded by an Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.
-The work is part of the [National Alliance for Medical Image Computing](http://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
+The work is part of the [National Alliance for Medical Image Computing](https://www.na-mic.org/) (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
 
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_perklab.png)
 ![](https://github.com/Slicer/Slicer/releases/download/docs-resources/logo_isomics.png)

diff --git a/Libs/MRML/Core/vtkEventBroker.h b/Libs/MRML/Core/vtkEventBroker.h
@@ -39,7 +39,7 @@ class vtkObservation;
 /// It caches tags returned by AddObserver method so that observers can be
 /// removed properly.
 /// See also:
-/// http://wiki.na-mic.org/Wiki/index.php/Slicer3:EventBroker
+/// https://wiki.na-mic.org/Wiki/index.php/Slicer3:EventBroker
 /// http://en.wikipedia.org/wiki/Observer_pattern
 //
 /// Other interesting observer implementations:

diff --git a/Libs/MRML/Core/vtkMRMLNRRDStorageNode.cxx b/Libs/MRML/Core/vtkMRMLNRRDStorageNode.cxx
@@ -555,7 +555,7 @@ int vtkMRMLNRRDStorageNode::ParseDiffusionInformation(
     cur_grad.copy_in(tmp_grads->GetTuple3(i));
 
     // note: this is norm^2, per the NA-MIC NRRD DWI convention
-    // http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
+    // https://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format
     double cur_bval = ref_bvalue * pow(cur_grad.two_norm() / max_grad_norm, 2);
     bvalues_array->SetValue(i, cur_bval);
 

diff --git a/Modules/CLI/FiducialRegistration/Testing/CMakeLists.txt b/Modules/CLI/FiducialRegistration/Testing/CMakeLists.txt
@@ -1,4 +1,4 @@
-# See http://www.na-mic.org/Bug/view.php?id=3340
+# See https://www.na-mic.org/Bug/view.php?id=3340
 # message(WARNING "warning: Module ${MODULE_NAME} doesn't have any test !")
 
 #-----------------------------------------------------------------------------

diff --git a/Modules/CLI/ProbeVolumeWithModel/Testing/CMakeLists.txt b/Modules/CLI/ProbeVolumeWithModel/Testing/CMakeLists.txt
@@ -1,4 +1,4 @@
-# See http://www.na-mic.org/Bug/view.php?id=3334
+# See https://www.na-mic.org/Bug/view.php?id=3334
 # message(WARNING "warning: Module ${MODULE_NAME} doesn't have any test !")
 
 #-----------------------------------------------------------------------------

diff --git a/Modules/Loadable/SlicerWelcome/Resources/HTML/Acknowledgment.html b/Modules/Loadable/SlicerWelcome/Resources/HTML/Acknowledgment.html
@@ -8,7 +8,7 @@
     <center>
       <table cellpadding="5" cellspacing="0"><tr>
         <td align="center" valign="middle">
-          <a href="http://www.na-mic.org/">
+          <a href="https://www.na-mic.org/">
             <img width="80" src="qrc:Logos/NAMIC.png"/>
           </a>
         </td>
@@ -30,7 +30,7 @@
       </tr></table>
     </center>
 
-    <p align="justify">Development of 3D Slicer is supported by <a href="http://www.na-mic.org/">NA-MIC</a>, <a href="http://nac.spl.harvard.edu/">NAC</a>, <a href="http://www.ncigt.org/">NCIGT</a>, <a href="http://www.spl.harvard.edu">SPL</a> and the <a href="https://slicer.readthedocs.io/en/latest/user_guide/about.html#acknowledgments">Slicer Community</a>. See <a href="https://www.slicer.org">https://www.slicer.org</a> for details.
+    <p align="justify">Development of 3D Slicer is supported by <a href="https://www.na-mic.org/">NA-MIC</a>, <a href="http://nac.spl.harvard.edu/">NAC</a>, <a href="http://www.ncigt.org/">NCIGT</a>, <a href="http://www.spl.harvard.edu">SPL</a> and the <a href="https://slicer.readthedocs.io/en/latest/user_guide/about.html#acknowledgments">Slicer Community</a>. See <a href="https://www.slicer.org">https://www.slicer.org</a> for details.
     </p>
     <p align="justify">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.
     </p>

diff --git a/Modules/Loadable/SlicerWelcome/Resources/HTML/Feedback.html b/Modules/Loadable/SlicerWelcome/Resources/HTML/Feedback.html
@@ -8,7 +8,7 @@
   <center>
     <table cellpadding="5" cellspacing="0" border="0"><tr>
       <td align="center" valign="middle">
-        <a href="http://www.na-mic.org/">
+        <a href="https://www.na-mic.org/">
           <img width="64" src="qrc:Icons/Chat.png"/>
         </a>
       </td>

diff --git a/Modules/Loadable/SubjectHierarchy/Testing/Python/SubjectHierarchyGenericSelfTest.py b/Modules/Loadable/SubjectHierarchy/Testing/Python/SubjectHierarchyGenericSelfTest.py
@@ -658,7 +658,7 @@ def createSampleModelNode(self, name, color, volumeNode=None):
       radius = 50
       x = y = z = 0
 
-    # Taken from: http://www.na-mic.org/Bug/view.php?id=1536
+    # Taken from: https://www.na-mic.org/Bug/view.php?id=1536
     sphere = vtk.vtkSphereSource()
     sphere.SetCenter(x, y, z)
     sphere.SetRadius(radius)

diff --git a/Modules/Scripted/DICOMLib/DICOMBrowser.py b/Modules/Scripted/DICOMLib/DICOMBrowser.py
@@ -244,7 +244,7 @@ def checkForExtensions(self):
     then return matches
 
     See
-    http://www.na-mic.org/Bug/view.php?id=4146
+    https://www.na-mic.org/Bug/view.php?id=4146
     """
 
     # 1 - load json

diff --git a/Modules/Scripted/Endoscopy/Endoscopy.py b/Modules/Scripted/Endoscopy/Endoscopy.py
@@ -34,7 +34,7 @@ def __init__(self, parent):
     self.parent.helpText += self.getDefaultModuleDocumentationLink()
     self.parent.acknowledgementText = """
 This work is supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy
-(See <a>http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy</a>)
+(See <a>https://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy</a>)
 NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community.
 """
 

diff --git a/Modules/Scripted/SelfTests/SelfTests.py b/Modules/Scripted/SelfTests/SelfTests.py
@@ -11,7 +11,7 @@
 #
 # This code includes the GUI for the slicer module.
 # The purpose is to provide a BIST (http://en.wikipedia.org/wiki/Built-in_self-test)
-# framework for slicer as discussed here: http://na-mic.org/Bug/view.php?id=1922
+# framework for slicer as discussed here: https://na-mic.org/Bug/view.php?id=1922
 #
 
 

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
@@ -43,7 +43,7 @@ if(EP_GIT_PROTOCOL STREQUAL "https")
 "adding 'git config' statement between the 'git checkout' and the 'submodule init', it is required "
 "to manually update your global git config to successfully build ${CMAKE_PROJECT_NAME} with "
 "option Slicer_USE_GIT_PROTOCOL set to FALSE. "
-"See http://na-mic.org/Mantis/view.php?id=2731"
+"See https://na-mic.org/Mantis/view.php?id=2731"
 "\nYou could do so by running the command:\n"
 "  ${GIT_EXECUTABLE} config --global url.${base}.insteadOf ${insteadof}\n")
     endif()

diff --git a/Utilities/Scripts/SEMToMediaWiki.py b/Utilities/Scripts/SEMToMediaWiki.py
@@ -246,11 +246,11 @@ def DumpSEMMediaWikiFooter(executableNode):
 
 Links to known bugs in the Slicer3 bug tracker
 
-* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000:description]
+* [https://www.na-mic.org/Bug/view.php?id=000 Bug 000:description]
 
 ===Usability issues===
 
-Follow this [http://na-mic.org/Mantis/main_page.php link] to
+Follow this [https://na-mic.org/Mantis/main_page.php link] to
 the Slicer3 bug tracker. Please select the '''usabilityissue category''' when browsing or contributing.
 
 ===Source code & documentation===
@@ -262,7 +262,7 @@ def DumpSEMMediaWikiFooter(executableNode):
 *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]
 
 Doxygen documentation:
-*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
+*[https://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
 
 == More Information ==
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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 https://www.slicer.org for details. Module implemented by Steve Pieper.
		This work is supported by PAR-07-249: R01CA131718 NA-MIC Virtual Colonoscopy (See https://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.