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ENH: Bump ITK and change http to https
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tbirdso committed May 31, 2022
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2 changes: 1 addition & 1 deletion .clang-format
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Expand Up @@ -4,7 +4,7 @@
## See: https://clang.llvm.org/docs/ClangFormatStyleOptions.html for details of each option
##
## The clang-format binaries can be downloaded as part of the clang binary distributions
## from http://releases.llvm.org/download.html
## from https://releases.llvm.org/download.html
##
## Use the script Utilities/Maintenance/clang-format.bash to faciliate
## maintaining a consistent code style.
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10 changes: 5 additions & 5 deletions .github/workflows/build-test-package.yml
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Expand Up @@ -13,27 +13,27 @@ jobs:
- os: self-hosted-linux
c-compiler: "gcc"
cxx-compiler: "g++"
itk-git-tag: "801370c025c7d296783481779a41c6d559c992c5"
itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
cmake-build-type: "MinSizeRel"
- os: self-hosted-windows
c-compiler: "cl.exe"
cxx-compiler: "cl.exe"
itk-git-tag: "801370c025c7d296783481779a41c6d559c992c5"
itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
cmake-build-type: "Release"
- os: ubuntu-20.04
c-compiler: "gcc"
cxx-compiler: "g++"
itk-git-tag: "801370c025c7d296783481779a41c6d559c992c5"
itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
cmake-build-type: "MinSizeRel"
- os: windows-2019
c-compiler: "cl.exe"
cxx-compiler: "cl.exe"
itk-git-tag: "801370c025c7d296783481779a41c6d559c992c5"
itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
cmake-build-type: "Release"
- os: macos-10.15
c-compiler: "clang"
cxx-compiler: "clang++"
itk-git-tag: "801370c025c7d296783481779a41c6d559c992c5"
itk-git-tag: "d6acfd26bfcdec606d605beb1301bddfb17c05a6"
cmake-build-type: "MinSizeRel"

steps:
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8 changes: 4 additions & 4 deletions COPYRIGHT.TXT
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Expand Up @@ -150,7 +150,7 @@ GNU General Public License for more details.
The included file 'COPYING' is a copy of the GNU General Public License.

------------------------------------------------------------------------
itkBinShrinkImageFilter has been taken from http://hdl.handle.net/10380/3450
itkBinShrinkImageFilter has been taken from https://hdl.handle.net/10380/3450
It uses the same Apache 2.0 license as RTK

------------------------------------------------------------------------
Expand All @@ -159,7 +159,7 @@ It uses the same Apache 2.0 license as RTK

------------------------------------------------------------------------
Some code is modified (a lot) from GIFT, the Generalized Image Fusion Toolkit
(http://hdl.handle.net/1926/216)
(https://hdl.handle.net/1926/216)
- rtkDaubechiesWaveletsKernelSource.h
- rtkDaubechiesWaveletsKernelSource.hxx
- rtkDeconstructImageFilter.h
Expand All @@ -172,7 +172,7 @@ Some code is modified (a lot) from GIFT, the Generalized Image Fusion Toolkit
- rtkUpsampleImageFilter.hxx

------------------------------------------------------------------------
Some code is modified from http://sourceforge.net/projects/niftyrec/:
Some code is modified from https://sourceforge.net/projects/niftyrec/:
- tt_project_ray_gpu_kernels.cu in rtkCudaForwardProjectionImageFilter.h

NIFTYREC TOMOGRAPHY TOOLBOX
Expand Down Expand Up @@ -207,7 +207,7 @@ THE POSSIBILITY OF SUCH DAMAGE.

------------------------------------------------------------------------
utilities/lpsolve has been taken from
http://sourceforge.net/projects/lpsolve/files/lpsolve/5.5.2.0/lp_solve_5.5.2.0_source.tar.gz/download
https://sourceforge.net/projects/lpsolve/files/lpsolve/5.5.2.0/lp_solve_5.5.2.0_source.tar.gz/download
and is distributed under the following license GNU lesser general public
license.

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2 changes: 1 addition & 1 deletion GettingStarted.md
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Expand Up @@ -9,4 +9,4 @@ Here are suggested steps for the RTK beginner.

3. Check out the [FirstReconstruction](examples/FirstReconstruction) example (both the [CMake](examples/FirstReconstruction/CMakeLists.txt) and the [C++](examples/FirstReconstruction/FirstReconstruction.cxx) codes). Many other examples are on the wiki using the applications (corresponding source code in the [applications](applications) subdirectory).

4. Ask question to the [user mailing list](http://public.kitware.com/mailman/listinfo/rtk-users).
4. Ask question to the [user mailing list](https://public.kitware.com/mailman/listinfo/rtk-users).
2 changes: 1 addition & 1 deletion HEADER.TXT
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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4 changes: 2 additions & 2 deletions INSTALLATION.md
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Expand Up @@ -3,11 +3,11 @@ RTK installation

Configuration, compilation and installation with ITK
----------------------------------------------------
RTK is a module of [ITK](http://www.itk.org), the Insight Toolkit. Follow the instructions of the [ITK software guide](https://itk.org/ITKSoftwareGuide/html) ([chapter 2](https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch2.html) mainly) for configuring and compiling ITK. The following CMake options are RTK specific:
RTK is a module of [ITK](https://www.itk.org), the Insight Toolkit. Follow the instructions of the [ITK software guide](https://itk.org/ITKSoftwareGuide/html) ([chapter 2](https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch2.html) mainly) for configuring and compiling ITK. The following CMake options are RTK specific:

* `Module_RTK`: Activates RTK download and compilation. Default is `OFF`. Turn it `ON` to activate RTK or compile RTK independently (see below).
* `Module_RTK_GIT_TAG`: Git tag for the RTK download. By default, the RTK version which is downloaded and compiled is the one given in the [RTK.remote.cmake](https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Remote/RTK.remote.cmake). Change this option to build another version. For example, you can change it to `master` to build the latest RTK version. RTK is only maintained to be backward compatible with the latest ITK release and ITK master branch.
* `RTK_BUILD_APPLICATIONS`: Activates the compilation of RTK's command line tools. Although RTK is mainly a toolkit, we also provide several command line tools for doing most of the available processing. These command line tools use [gengetopt](https://www.gnu.org/software/gengetopt/gengetopt.html). Several examples are available on the [Applications](http://wiki.openrtk.org/index.php/RTK_wiki_help#Applications) section of the [wiki](http://wikiopenrtk.org).
* `RTK_BUILD_APPLICATIONS`: Activates the compilation of RTK's command line tools. Although RTK is mainly a toolkit, we also provide several command line tools for doing most of the available processing. These command line tools use [gengetopt](https://www.gnu.org/software/gengetopt/gengetopt.html). Several examples are available on the [Applications](https://wiki.openrtk.org/index.php/RTK_wiki_help#Applications) section of the [wiki](http://wikiopenrtk.org).
* `RTK_USE_CUDA`: Activates CUDA computation. Default is `ON` if CMake has automatically found the CUDA package and a CUDA-compatible GPU, and `OFF` otherwise.
* `RTK_CUDA_PROJECTIONS_SLAB_SIZE`: Set the number of projections processed at once in CUDA processing. Default is 16.
* `RTK_PROBE_EACH_FILTER`: Activates the timing, CPU and CUDA memory consumption of each filter. Defaults is `OFF`. When activated, each filter processing is probed and a summary can be displayed. All command line applications display the result with `--verbose`.
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14 changes: 7 additions & 7 deletions LICENSE.TXT
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@@ -1,7 +1,7 @@

Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
https://www.apache.org/licenses/

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

Expand Down Expand Up @@ -190,18 +190,18 @@
Copyright [2010-2012] [RTK Consortium]

The RTK consortium comprises:
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr/
- Massachusetts General Hospital http://www.mgh.harvard.edu/
- Université Catholique de Louvain http://www.uclouvain.be/
- IBA http://www.iba-protontherapy.com/
- Kitware http://www.kitware.com/
- CREATIS CNRS laboratory https://www.creatis.insa-lyon.fr/
- Massachusetts General Hospital https://www.mgh.harvard.edu/
- Université Catholique de Louvain https://www.uclouvain.be/
- IBA https://www.iba-protontherapy.com/
- Kitware https://www.kitware.com/
- radART http://www.open-radart.org/

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0
https://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
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18 changes: 9 additions & 9 deletions README.md
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Expand Up @@ -14,27 +14,27 @@ RTK: The Reconstruction ToolKit
Links
-----

* [Homepage](http://www.openrtk.org)
* [Download](http://www.openrtk.org/RTK/resources/software.html)
* [Mailing List](http://public.kitware.com/mailman/listinfo/rtk-users)
* [Homepage](https://www.openrtk.org)
* [Download](https://www.openrtk.org/RTK/resources/software.html)
* [Mailing List](https://public.kitware.com/mailman/listinfo/rtk-users)
* [Getting Started](GettingStarted.md)
* [Help](http://wiki.openrtk.org)
* [Help](https://wiki.openrtk.org)
* [Issue tracking](https://github.com/SimonRit/RTK/issues)


Copyright RTK Consortium
------------------------

Licensed under the Apache License, Version 2.0 (the
"[License](http://www.apache.org/licenses/LICENSE-2.0.txt)"); you may not use
"[License](https://www.apache.org/licenses/LICENSE-2.0.txt)"); you may not use
this file except in compliance with the
[License](http://www.apache.org/licenses/LICENSE-2.0.txt).
[License](https://www.apache.org/licenses/LICENSE-2.0.txt).

Unless required by applicable law or agreed to in writing, software
distributed under the
[License](http://www.apache.org/licenses/LICENSE-2.0.txt) is distributed on
[License](https://www.apache.org/licenses/LICENSE-2.0.txt) is distributed on
an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
express or implied. See the
[License](http://www.apache.org/licenses/LICENSE-2.0.txt) for the specific
[License](https://www.apache.org/licenses/LICENSE-2.0.txt) for the specific
language governing permissions and limitations under the
[License](http://www.apache.org/licenses/LICENSE-2.0.txt).
[License](https://www.apache.org/licenses/LICENSE-2.0.txt).
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkadmmwavelets/rtkadmmwavelets.cxx
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Expand Up @@ -6,7 +6,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkamsterdamshroud/rtkamsterdamshroud.cxx
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Expand Up @@ -6,7 +6,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkbackprojections/rtkbackprojections.cxx
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Expand Up @@ -6,7 +6,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkbioscangeometry/rtkbioscangeometry.cxx
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Expand Up @@ -6,7 +6,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkcheckimagequality/rtkcheckimagequality.cxx
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Expand Up @@ -6,7 +6,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkconjugategradient/rtkconjugategradient.cxx
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Expand Up @@ -6,7 +6,7 @@
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkdigisensgeometry/rtkdigisensgeometry.cxx
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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package "rtkdrawshepploganphantom"
purpose "Computes a 3D voxelized Shepp & Logan phantom with noise [http://www.slaney.org/pct/pct-errata.html]"
purpose "Computes a 3D voxelized Shepp & Logan phantom with noise [https://www.slaney.org/pct/pct-errata.html]"

option "verbose" v "Verbose execution" flag off
option "config" - "Config file" string no
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkfdk/rtkfdk.cxx
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkfdktwodweights/rtkfdktwodweights.cxx
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkfieldofview/rtkfieldofview.cxx
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkfourdfdk/rtkfourdfdk.cxx
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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2 changes: 1 addition & 1 deletion applications/rtkfourdrooster/rtkfourdrooster.cxx
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* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
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