New documentation

CodeContribution.md

@@ -0,0 +1,25 @@
+# Code contribution
+
+## Coding style
+
+RTK is based on ITK and aims at following its coding conventions. Any developer should follow these conventions when submitting new code or contributions to the existing one. We strongly recommend you to read thoroughly [ITK's style guide](http://www.itk.org/Wiki/ITK/Coding_Style_Guide).
+
+## Testing
+
+This section describes how to add/edit datasets for testing purposes for RTK. Datasets are not stored in the GIT repository for efficiency and also to avoid having large history due to binary files. Instead the files are stored on a [Girder](http://data.kitware.com) instance. Here's the recipe to add new datasets:
+
+1.  Register/Login to Girder hosted at Kitware: [http://data.kitware.com](http://data.kitware.com)
+2.  Locate the RTK collection: [https://data.kitware.com/#collection/5a7706878d777f0649e04776](https://data.kitware.com/#collection/5a7706878d777f0649e04776)
+3.  Upload the new datasets in the appropriate folder. If you don't have the necessary privileges please email the mailing list
+4.  In the GIT repository, add in testing/Data a file with the exact filename of the original file **but with the .md5 extension**. Inside that file put the md5sum of the file on Girder.
+5.  When adding a test use the new macro 'RTK_ADD_TEST' instead of 'ADD_TEST' and specify the datasets you want CTest to download by appending the data to 'DATA{}'. For example:
+
+```
+RTK_ADD_TEST(NAME rtkimagxtest
+    COMMAND ${EXECUTABLE\_OUTPUT\_PATH}/rtkimagxtest
+    DATA{Data/Input/ImagX/raw.xml,raw.raw}
+    DATA{Data/Baseline/ImagX/attenuation.mha})
+```
+## Dashboard
+
+*   The RTK dashboard is available at [RTK Dashboard](http://my.cdash.org/index.php?project=RTK)

GettingStarted.md

@@ -7,6 +7,6 @@ Here are suggested steps for the RTK beginner.
 
   2. If you are not already familiar with ITK, [get started with ITK](https://github.com/InsightSoftwareConsortium/ITK/blob/master/GettingStarted.md).
 
-  3. Check out the [FirstReconstruction](https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction) example (both the [CMake](https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/CMakeLists.txt) and the [C++](https://github.com/SimonRit/RTK/blob/master/examples/FirstReconstruction/FirstReconstruction.cxx) codes). Many other examples are on the wiki using the applications (corresponding source code in the [applications](https://github.com/SimonRit/RTK/blob/master/applications) subdirectory).
+  3. Check out the [FirstReconstruction](https://github.com/RTKConsortium/RTK/blob/master/examples/FirstReconstruction) example (both the [CMake](https://github.com/RTKConsortium/RTK/blob/master/examples/FirstReconstruction/CMakeLists.txt) and the [C++](https://github.com/RTKConsortium/RTK/blob/master/examples/FirstReconstruction/FirstReconstruction.cxx) codes). Many other examples are in the [documentation](https://docs.openrtk.org/) using the applications (corresponding source code in the [applications subdirectory](https://github.com/RTKConsortium/RTK/blob/master/applications)).
 
   4. Ask question to the [user mailing list](https://www.creatis.insa-lyon.fr/mailman/listinfo/rtk-users).

INSTALLATION.md

@@ -7,7 +7,7 @@ RTK is a module of [ITK](https://www.itk.org), the Insight Toolkit. Follow the i
 
 * `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](https://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 in the [documentation](http://docs.openrtk.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_VERSION`: Specifies an exact version of the CUDA toolkit which must be used. If unspecified, RTK only checks if the found version is recent enough.
 * `RTK_CUDA_PROJECTIONS_SLAB_SIZE`: Set the number of projections processed at once in CUDA processing. Default is 16.

README.md

@@ -18,7 +18,7 @@ Links
 * [Download](https://www.openrtk.org/RTK/resources/software.html)
 * [Mailing List](https://www.creatis.insa-lyon.fr/mailman/listinfo/rtk-users)
 * [Getting Started](GettingStarted.md)
-* [Help](https://wiki.openrtk.org)
+* [Help](https://docs.openrtk.org)
 * [Issue tracking](https://github.com/RTKConsortium/RTK/issues)
 
 

applications/rtksimulatedgeometry/rtksimulatedgeometry.ggo

@@ -1,5 +1,5 @@
 package "rtksimulatedgeometry"
-purpose "Creates an RTK geometry file from simulated/regular trajectory. See https://www.openrtk.org/Doxygen/DocGeo3D.html for more information."
+purpose "Creates an RTK geometry file from simulated/regular trajectory. See https://docs.openrtk.org/en/latest/documentation/docs/Geometry.html for more information."
 
 option "verbose"     v "Verbose execution"                                                    flag   off
 option "config"      - "Config file"                                                          string no

applications/rtksimulatedgeometry/rtksimulatedgeometry.py

@@ -6,7 +6,7 @@
 def main():
   # Argument parsing
   parser = argparse.ArgumentParser(description=
-    "Creates an RTK geometry file from simulated/regular trajectory. See https://www.openrtk.org/Doxygen/DocGeo3D.html for more information.")
+    "Creates an RTK geometry file from simulated/regular trajectory. See https://docs.openrtk.org/en/latest/documentation/docs/Geometry.html for more information.")
 
   parser.add_argument('--nproj', '-n', type=int, help='Number of projections')
   parser.add_argument('--output', '-o', help='Output file name')

conf.py

@@ -15,7 +15,7 @@ def setup(app):
 
 # -- Project information -----------------------------------------------------
 project = 'RTK'
-copyright = f'{date.today().year}, Simon Rit'
+copyright = f'{date.today().year}, RTK Consortium'
 author = 'RTK Consortium'
 
 # The full version, including alpha/beta/rc tags

documentation/Doxygen/rtkThreeDCirculationProjectionGeometry.dox

@@ -0,0 +1,7 @@
+/*!
+ * \page DocGeo3D RTK 3D circular projection geometry
+ *
+ * This documentation page has been moved to a <a
+ * href="https://docs.openrtk.org/en/latest/documentation/docs/Geometry.html">user
+ * documentation page</a>.
+ * */

documentation/docs/CMakeLists.txt

@@ -12,6 +12,7 @@ if(RTK_BUILD_SPHINX)
     COMMAND ${CMAKE_COMMAND} -E copy "${RTK_SOURCE_DIR}/index.md" "${RTK_DOC_OUTPUT_DIR}/index.md"
     COMMAND ${CMAKE_COMMAND} -E copy "${RTK_SOURCE_DIR}/GettingStarted.md" "${RTK_DOC_OUTPUT_DIR}/GettingStarted.md"
     COMMAND ${CMAKE_COMMAND} -E copy "${RTK_SOURCE_DIR}/INSTALLATION.md" "${RTK_DOC_OUTPUT_DIR}/INSTALLATION.md"
+    COMMAND ${CMAKE_COMMAND} -E copy "${RTK_SOURCE_DIR}/CodeContribution.md" "${RTK_DOC_OUTPUT_DIR}/CodeContribution.md"
     COMMENT "Copying documentation sources"
     )