Merge pull request #258 from schuhschuh/release-1.1.0

Release 1.1.0
BioMedIA · Apr 21, 2016 · e83cae4 · e83cae4
2 parents a33c2ef + 2deef40
commit e83cae4
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diff --git a/Applications/BasisProject.cmake b/Applications/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################

diff --git a/Applications/src/convert-dof.cc b/Applications/src/convert-dof.cc
@@ -51,7 +51,7 @@ void PrintHelp(const char *name)
   cout << "Description:\n";
   cout << "  Converts between different transformation file formats:\n";
   cout << "\n";
-  cout << "  =====================       =================================================================================\n";
+  cout << "  =========================   =========================================================================================\n";
   cout << "  unknown                     Unknown, try to guess it from file header/type.\n";
   cout << "  disp_world|disp|image       Dense displacement field image with world space displacement vectors [mm].\n";
   cout << "  disp_voxel                  Dense displacement field image with target space displacement vectors [voxel].\n";
@@ -88,7 +88,7 @@ void PrintHelp(const char *name)
   cout << "  star_ccm_table_xyz          Transformed points  as STAR CCM+ XYZ Table.\n";
   cout << "  table|csv|tsv               ASCII table of target point coordinates and displacement vectors.\n";
   cout << "  table_xyz|csv_xyz|tsv_xyz   ASCII table of transformed point coordinates.\n";
-  cout << "  =====================       =================================================================================\n";
+  cout << "  =========================   =========================================================================================\n";
 #if !MIRTK_IO_WITH_NIfTI
   cout << "\n";
   cout << "  Cannot convert from/to the following formats because the I/O module is missing NIfTI support:\n";

diff --git a/BasisProject.cmake b/BasisProject.cmake
@@ -1,8 +1,8 @@
 # ============================================================================
 # Medical Image Registration ToolKit (MIRTK)
 #
-# Copyright 2013-2015 Imperial College London
-# Copyright 2013-2015 Andreas Schuh
+# Copyright 2013-2016 Imperial College London
+# Copyright 2013-2016 Andreas Schuh
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -27,7 +27,7 @@
 # of another BASIS project, the dependencies to other modules have to be specified 
 # here such that the top-level project can analyze the inter-module dependencies.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # However, not only dependencies to other modules can be specified here,
 # but also dependencies on external packages. A more flexible alternative to
@@ -56,7 +56,7 @@ basis_project (
   SOVERSION    "0"     # API yet unstable
   AUTHORS      "Andreas Schuh"
   DESCRIPTION  "Medical Image Registration ToolKit"
-  COPYRIGHT    "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT    "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE      "Apache License Version 2.0"
   CONTACT      "Andreas Schuh <[email protected]>"
   TEMPLATE     "with-basis-submodule/1.0"

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -21,7 +21,7 @@
 # @file  CMakeLists.txt
 # @brief Root build configuration file.
 #
-# @sa <a href="http://opensource.andreasschuh.com/cmake-basis">CMake BASIS</a>
+# @sa <a href="https://cmake-basis.github.io">CMake BASIS</a>
 ##############################################################################
 
 # ----------------------------------------------------------------------------

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -24,14 +24,14 @@ this change is needed, what it does and how to check whether the code works as i
 If you intend to contribute your applications to the MIRTK distribution, develop your tools
 either in a fork of the MIRTK Git repository or a your own MIRTK Package
 with the common file organization for MIRTK Packages and the appropriate CMake_ configuration
-files. See some of the already available modules in the ``Packages/`` directory of the
+files. See some of the already available modules in the `Packages/` directory of the
 MIRTK source tree as reference. Examples of MIRTK Packages are the
 [Deformable](https://github.com/MIRTK/Deformable) and
 [Volumetric Mapping](https://github.com/MIRTK/VolumetricMapping) modules,
 each developed in their own respective GitHub repository.
 Template files for the creation of a new MIRTK Package can be found in the
 [Templates](Templates/mirtk-module) directory. These template files can be customized using
-the [basisproject](http://opensource.andreasschuh.com/cmake-basis/howto/use-and-customize-templates.html#use-a-template)
-tool of [CMake BASIS](http://opensource.andreasschuh.com/cmake-basis/), but can also
-simply be copied and edited by hand. But do not copy the ```_conf.py``` file from the
-```Templates/mirtk-module/v*/``` directory.
+the [basisproject](https://cmake-basis.github.io/howto/use-and-customize-templates.html#use-a-template)
+tool of [CMake BASIS](https://cmake-basis.github.io), but can also
+simply be copied and edited by hand. But do not copy the `_conf.py` file from the
+`Templates/mirtk-module/v*/` directory.
diff --git a/ChangeLog.txt b/ChangeLog.txt
@@ -6,13 +6,22 @@
 
 .. _v1.1.0:
 
-Release 1.1.0 (Apr 15)
+Release 1.1.0 (Apr 21)
 ~~~~~~~~~~~~~~~~~~~~~~
 
-- Enhanced basis_find_package of CMake BASIS Modules.
+- Use `CMake BASIS Modules 3.3.0 <http://cmake-basis.github.io/changelog.html#release-3-3-0-apr-19-2016>`_.
+- Fixed build with VTK 7.
+- Fixed Python scripts to run with both Python 2 and 3.
 - Fixed Visual Studio build warnings and errors.
 - Enabled build as shared libraries on Windows.
 - Renamed ``Image I/O`` module to :doc:`I/O </modules/io>`.
+- Read/Write both NIfTI-1 and NIfTI-2 image files.
+- Read/Write point sets and surfaces from GIFTI files.
+- Always save binary files in big-endian order.
+- Added Python package for execution of MIRTK commands.
+- Provide Docker image with MIRTK installation.
+- Refactored Applications module.
+- Various minor fixes of commands.
 
 
 .. _v1.0.0:

diff --git a/Documentation/commands/_descriptions/convert-dof.rst b/Documentation/commands/_descriptions/convert-dof.rst
@@ -3,7 +3,7 @@
 
 Converts between different transformation file formats:
 
-=====================       =================================================================================
+=========================   =========================================================================================
 unknown                     Unknown, try to guess it from file header/type.
 disp_world|disp|image       Dense displacement field image with world space displacement vectors [mm].
 disp_voxel                  Dense displacement field image with target space displacement vectors [voxel].
@@ -40,4 +40,4 @@ star_ccm_table              Point displacements as STAR CCM+ XYZ Table.
 star_ccm_table_xyz          Transformed points  as STAR CCM+ XYZ Table.
 table|csv|tsv               ASCII table of target point coordinates and displacement vectors.
 table_xyz|csv_xyz|tsv_xyz   ASCII table of transformed point coordinates.
-=====================       =================================================================================
+=========================   =========================================================================================
diff --git a/Documentation/commands/copy-pointset-attributes-from-mat.rst b/Documentation/commands/copy-pointset-attributes-from-mat.rst
@@ -34,7 +34,9 @@ Arguments
 
    File name of MAT file.
 
-.. option:: output  File name of output dataset.
+.. option:: output
+
+   File name of output dataset.
 
 
 

diff --git a/Documentation/download.rst b/Documentation/download.rst
@@ -112,4 +112,5 @@ with the MIRTK license. See the following links for details:
 - `ThirdParty/Boost <https://github.com/MIRTK/Boost>`__: `Boost Software License Version 1.0 <http://www.boost.org/users/license.html>`__
 - `ThirdParty/Eigen <https://github.com/MIRTK/Eigen>`__: `Mozilla Public License Version 2.0 <https://www.mozilla.org/en-US/MPL/2.0/>`__
 - `ThirdParty/LBFGS <https://github.com/BioMedIA/MIRTK/tree/master/ThirdParty/LBFGS>`__: `The MIT License <https://opensource.org/licenses/MIT>`__
-- `ThirdParty/NIfTI <https://github.com/BioMedIA/MIRTK/tree/master/ThirdParty/NIfTI>`__: `Public domain <https://en.wikipedia.org/wiki/Public_domain>`__
+- `NIfTI C library <https://www.nitrc.org/projects/nifti>`__: `Public domain <https://en.wikipedia.org/wiki/Public_domain>`__
+- `GIFTI C library <https://www.nitrc.org/projects/gifti/>`__: `Public domain <https://en.wikipedia.org/wiki/Public_domain>`__
diff --git a/Modules/Common/BasisProject.cmake b/Modules/Common/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################
@@ -46,7 +46,7 @@ basis_project (
   PACKAGE     "MIRTK"
   AUTHORS     "Andreas Schuh"
   DESCRIPTION "Common library of the Medical Image Registration ToolKit."
-  COPYRIGHT   "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT   "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE     "Apache License Version 2.0"
   CONTACT     "Andreas Schuh <[email protected]>"
   TEMPLATE    "mirtk-module/1.0"

diff --git a/Modules/IO/BasisProject.cmake b/Modules/IO/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################
@@ -46,7 +46,7 @@ basis_project (
   PACKAGE     "MIRTK"
   AUTHORS     "Andreas Schuh"
   DESCRIPTION "I/O library of the Medical Image Registration ToolKit."
-  COPYRIGHT   "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT   "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE     "Apache License Version 2.0"
   CONTACT     "Andreas Schuh <[email protected]>"
   TEMPLATE    "mirtk-module/1.0"

diff --git a/Modules/Image/BasisProject.cmake b/Modules/Image/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################
@@ -46,7 +46,7 @@ basis_project (
   PACKAGE     "MIRTK"
   AUTHORS     "Andreas Schuh"
   DESCRIPTION "Image library of the Medical Image Registration ToolKit."
-  COPYRIGHT   "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT   "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE     "Apache License Version 2.0"
   CONTACT     "Andreas Schuh <[email protected]>"
   TEMPLATE    "mirtk-module/1.0"

diff --git a/Modules/Numerics/BasisProject.cmake b/Modules/Numerics/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################
@@ -46,7 +46,7 @@ basis_project (
   PACKAGE     "MIRTK"
   AUTHORS     "Andreas Schuh"
   DESCRIPTION "Numerics library of the Medical Image Registration ToolKit."
-  COPYRIGHT   "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT   "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE     "Apache License Version 2.0"
   CONTACT     "Andreas Schuh <[email protected]>"
   TEMPLATE    "mirtk-module/1.0"

diff --git a/Modules/PointSet/BasisProject.cmake b/Modules/PointSet/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################
@@ -46,7 +46,7 @@ basis_project (
   PACKAGE     "MIRTK"
   AUTHORS     "Andreas Schuh"
   DESCRIPTION "Point Set library of the Medical Image Registration ToolKit."
-  COPYRIGHT   "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT   "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE     "Apache License Version 2.0"
   CONTACT     "Andreas Schuh <[email protected]>"
   TEMPLATE    "mirtk-module/1.0"

diff --git a/Modules/Registration/BasisProject.cmake b/Modules/Registration/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################
@@ -46,7 +46,7 @@ basis_project (
   PACKAGE     "MIRTK"
   AUTHORS     "Andreas Schuh"
   DESCRIPTION "Registration library of the Medical Image Registration ToolKit."
-  COPYRIGHT   "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT   "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE     "Apache License Version 2.0"
   CONTACT     "Andreas Schuh <[email protected]>"
   TEMPLATE    "mirtk-module/1.0"

diff --git a/Modules/Transformation/BasisProject.cmake b/Modules/Transformation/BasisProject.cmake
@@ -27,7 +27,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################
@@ -46,7 +46,7 @@ basis_project (
   PACKAGE     "MIRTK"
   AUTHORS     "Andreas Schuh"
   DESCRIPTION "Transformation library of the Medical Image Registration ToolKit."
-  COPYRIGHT   "2013-2015 Imperial College London, Andreas Schuh"
+  COPYRIGHT   "2013-2016 Imperial College London, Andreas Schuh"
   LICENSE     "Apache License Version 2.0"
   CONTACT     "Andreas Schuh <[email protected]>"
   TEMPLATE    "mirtk-module/1.0"

diff --git a/Packages/Deformable b/Packages/Deformable
diff --git a/Packages/VolumetricMapping b/Packages/VolumetricMapping
diff --git a/Templates/mirtk-module/1.0/BasisProject.cmake b/Templates/mirtk-module/1.0/BasisProject.cmake
@@ -26,7 +26,7 @@
 # have to be specified here such that the top-level IRTK project can analyze the
 # inter-module dependencies, as well as dependencies on third-party libraries.
 #
-# @sa http://opensource.andreasschuh.com/cmake-basis/standard/modules.html
+# @sa https://cmake-basis.github.io/standard/modules.html
 #
 # @ingroup BasisSettings
 ################################################################################