Merge pull request #1569 from dcoeurjo/rel1.2

Release 1.2

Author: dcoeurjo

CMakeLists.txt

@@ -18,7 +18,7 @@ endif()
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake")
 set(DGtal_VERSION_MAJOR 1)
 set(DGtal_VERSION_MINOR 2)
-set(DGtal_VERSION_PATCH beta)
+set(DGtal_VERSION_PATCH 0)
 set(DGTAL_VERSION "${DGtal_VERSION_MAJOR}.${DGtal_VERSION_MINOR}.${DGtal_VERSION_PATCH}")
 set(PROJECT_VERSION "${DGtal_VERSION_MAJOR}.${DGtal_VERSION_MINOR}.${DGtal_VERSION_PATCH}")
 set(VERSION ${DGtal_VERSION_MAJOR}.${DGtal_VERSION_MINOR}.${DGtal_VERSION_PATCH})

ChangeLog.md

@@ -1,7 +1,12 @@
-# DGtal 1.2 (dev)
+# DGtal 1.2
 
 ## New Features / Critical Changes
 
+- *New Feature*
+  - DGtal now has a python binding `pip install dgtal`! For all
+    details on the list of classes available in python, you can have a
+    look to: Pablo Hernandez-Cerdan [#1528](https://github.com/DGtal-team/DGtal/pull/1528) 
+
 - *Geometry Package*
   - New normal vector estimation using plane-probing approaches.
     (Jocelyn Meyron, Tristan Roussillon,

README.md

@@ -19,10 +19,6 @@ results and potential efficiency of the proposed work.
 Quick Install
 =============
 
-* Linux: 
-    * [Arch, CentOS, Fedora, openSUSE, RHEL, SL](http://software.opensuse.org//download.html?project=home%3Acopyme%3ADGtal&package=libDGtal) 
-    * [Debian, Ubuntu, etc.](http://software.opensuse.org//download.html?project=home%3Acopyme%3ADGtal&package=dgtal) 
-
 * MacOS (using [homebrew](http://brew.sh)):
 
        brew tap DGtal-team/DGtal
@@ -31,7 +27,7 @@ Quick Install
 
 (```brew options dgtal``` to enable optional features)
 
-* Windows: no binary package, please compile the library.
+* Linux and windows: no binary package, please compile the library.
 
 
 Additional instructions are available in the
@@ -68,5 +64,5 @@ More Information
 * Release 0.9 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31884.svg)](http://dx.doi.org/10.5281/zenodo.31884)
 * Release 0.8 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11586.svg)](https://doi.org/10.5281/zenodo.11586)
 * Continuous Integration (Linux/MacOS) [![Build Status](https://travis-ci.org/DGtal-team/DGtal.svg?branch=master)](https://travis-ci.org/DGtal-team/DGtal)
-*  Continuous Integration (Windows) [![Build status](https://ci.appveyor.com/api/projects/status/7labe8ft0jf30ng7/branch/master?svg=true)](https://ci.appveyor.com/project/kerautret/dgtal-8op01/branch/master)
+* Continuous Integration (Windows) [![Build status](https://ci.appveyor.com/api/projects/status/7labe8ft0jf30ng7/branch/master?svg=true)](https://ci.appveyor.com/project/kerautret/dgtal-8op01/branch/master)
 

cmake/FetchExternalDeps.cmake

@@ -20,10 +20,10 @@ if (BUILD_TESTING)
   FetchContent_Declare(
     Catch2
     GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-    GIT_TAG        v2.13.3
+    GIT_TAG        v2.13.6
     )
 
-  message(STATUS "    Catch2 (v2.13.3)")
+  message(STATUS "    Catch2 (v2.13.6)")
   FetchContent_MakeAvailable(Catch2)
 
   list(APPEND CMAKE_MODULE_PATH ${catch2_SOURCE_DIR}/contrib)

examples/doc-examples/CMakeLists.txt

@@ -3,9 +3,15 @@ set(DGTAL_DOC_EX_SRC
   kernelDomain
   range
   labelledMapBestParameters
-  exampleCatch
   )
 
+
+if (BUILD_TESTING)
+  add_executable(exampleCatch exampleCatch.cpp)
+  target_link_libraries (exampleCatch DGtal)
+endif()
+
+
 if( WITH_VISU3D_QGLVIEWER  )
   set(DGTAL_DOC_EX_SRC_QGL
      )

examples/tutorial-examples/volDTGranulo-template.cpp

@@ -43,14 +43,13 @@
 #include "DGtal/io/readers/VolReader.h"
 #include "DGtal/io/writers/VolWriter.h"
 
-#include "DGtal/images/imagesSetsUtils/SimpleThresholdForegroundPredicate.h"
+#include "DGtal/images/SimpleThresholdForegroundPredicate.h"
 #include "DGtal/geometry/volumes/distance/DistanceTransformation.h"
 #include "DGtal/shapes/implicit/ImplicitBall.h"
 #include "DGtal/base/BasicFunctors.h"
 //! [volGranulo-basicIncludes]
 
 //! [volGranulo-viewerIncludes]
-#include <QtGui/qapplication.h>
 #include "DGtal/io/viewers/Viewer3D.h"
 #include "DGtal/io/colormaps/GradientColorMap.h"
 //! [volGranulo-viewerIncludes]

src/DGtal/base/Common.h

@@ -43,6 +43,10 @@
 // Inclusions
 
 #ifdef WITH_VISU3D_QGLVIEWER
+#ifdef APPLE
+/* Defined before OpenGL and GLUT includes to avoid deprecation messages */
+#define GL_SILENCE_DEPRECATION
+#endif
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
 #pragma clang diagnostic push

src/DGtal/doc/mainpage.dox

@@ -46,7 +46,7 @@ at the [DGtalTools online
 documentation](https://dgtal-team.github.io/doctools-nightly) for additional 
 information.
 
-
+@note From release 1.2, DGtal has a (partial) python binding. For more information, cf \ref packagePython
 
 
 @section package_description DGtal Packages

src/DGtal/doc/packagePython.dox

@@ -0,0 +1,109 @@
+/**
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Lesser General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **/
+
+/**
+ * @file packagePython.dox
+ * @author David Coeurjolly (\c david.coeurjolly@liris.cnrs.fr )
+ * Laboratoire d'InfoRmatique en Image et Systèmes d'information - LIRIS (CNRS, UMR 5205), CNRS, France
+ *
+ * @date 2021/06/01
+ *
+ * Documentation file for feature Introduction
+ *
+ * This file is part of the DGtal library.
+ */
+
+/* 
+ * Useful to avoid writing DGtal:: in front of every class.
+ * Do not forget to add an entry in src/DGtal/base/Config.h.in !
+ */
+namespace DGtal {
+//----------------------------------------
+/*!
+@page packagePython DGtal python binding
+   
+
+@managers Pablo Hernandez-Cerdan, David Coeurjolly
+@since 1.2
+
+
+@b Package @b Overview
+
+Since release 1.2, DGtal has a partial python binding using
+[pybind11](https://github.com/pybind/pybind11). To install the python
+package, just use:
+@code
+pip install dgtal
+@endcode
+
+Then, you can import the module in python:
+
+@code
+import dgtal
+....
+@endcode
+
+At this point, only a partial support is available (some base, kernel,
+image, topology classes). For a complete review of the available
+tools, have a look to this
+[Pull-Request](https://github.com/DGtal-team/DGtal/pull/1528).
+
+Just a quick example (Euler characteristics and simple point detection on random sets):
+
+@code
+import dgtal
+import random
+
+Point  = dgtal.kernel.Point3D
+Domain = dgtal.kernel.DomainZ3i
+Set    = dgtal._dgtal.kernel.DigitalSetZ3i
+
+dom    = Domain( Point(0,0,0), Point(10,10,10))
+mySet  = Set(dom)
+
+# Random set
+for i in range(50*50):
+  mySet.insert(Point(random.randint(0,10),random.randint(0,10),random.randint(0,10)))
+
+# Digital Object (with topology)
+Object = dgtal.topology.Object26_6
+Topo   = Object.TDigitalTopology
+FAdj   = Topo.TForegroundAdjacency
+BAdj   = Topo.TBackgroundAdjacency
+fadj   = FAdj()
+badj   = BAdj()
+topo   = Topo(fadj, badj)
+obj    = Object(topo,mySet)
+
+#Counting the simple points
+cptSimple=0
+for p in mySet:
+    if obj.isSimple(p):
+        cptSimple += 1
+print("Number of simple points: "+str(cptSimple)+ " / " + str(mySet.size()))
+
+# Cubical Complex
+kspace   = dgtal.topology.KSpace3D()
+ccomplex = dgtal.topology.CubicalComplex3D(kspace)
+ccomplex.construct(mySet)
+
+print("Euler characteristic: "+str(ccomplex.euler()))
+@endcode
+
+
+*/
+
+}

src/DGtal/geometry/surfaces/ArithmeticalDSSComputerOnSurfels.ih

@@ -512,7 +512,7 @@ DGtal::ArithmeticalDSSComputerOnSurfels<TKSpace,TIterator,TInteger,adjacency>::g
     }
     else if (p1 == linel2)
     {
-        aPoint == p2;
+        aPoint = p2;
     }
     else if (p2 == linel1)
     {

src/DGtal/io/viewers/Viewer3D.h

@@ -48,7 +48,10 @@
 #ifdef WIN32
 #include <windows.h>
 #endif
+
 #ifdef APPLE
+/* Defined before OpenGL and GLUT includes to avoid deprecation messages */
+#define GL_SILENCE_DEPRECATION
 #include <OpenGL/gl.h>
 #include <OpenGL/glu.h>
 #else

tests/kernel/testIntegerConverter.cpp

@@ -61,15 +61,21 @@ SCENARIO( "IntegerConverter< 1, int32 >", "[integer_conversions]" )
   typedef IntegerConverter< 1, DGtal::int32_t > Converter;
   DGtal::int32_t    small_int32   = 0x12345678;
   DGtal::int64_t    small_int64   = 0x12345678L;
+#ifdef WITH_BIGINTEGER
   DGtal::BigInteger small_bigint  = 0x12345678;
+#endif
   WHEN( "Converting small integers" ) {
     DGtal::int32_t a = Converter::cast( small_int32 );
     DGtal::int32_t b = Converter::cast( small_int64 );
+#ifdef WITH_BIGINTEGER
     DGtal::int32_t c = Converter::cast( small_bigint );
+#endif
     THEN( "Their values are all identical" ) {
       REQUIRE( a == small_int32 );
       REQUIRE( a == b );
+#ifdef WITH_BIGINTEGER
       REQUIRE( a == c );
+#endif
     }
   }
   WHEN( "Converting medium integers" ) {
@@ -86,28 +92,40 @@ SCENARIO( "IntegerConverter< 1, int64 >", "[integer_conversions]" )
   typedef IntegerConverter< 1, DGtal::int64_t > Converter;
   DGtal::int32_t    medium_int32  = DGtal::int32_t( 0x123456789ABCDEFL );
   DGtal::int64_t    medium_int64  = 0x123456789ABCDEFL;
-  DGtal::BigInteger medium_bigint = 0x123456789ABCDEFL;
+ #ifdef WITH_BIGINTEGER
+ DGtal::BigInteger medium_bigint = 0x123456789ABCDEFL;
+ #endif
   WHEN( "Converting 64bits integers" ) {
     DGtal::int64_t a = Converter::cast( medium_int32 );
     DGtal::int64_t b = Converter::cast( medium_int64 );
-    DGtal::int64_t c = Converter::cast( medium_bigint );
-    THEN( "Only bigger integers are identical" ) {
+ #ifdef WITH_BIGINTEGER
+   DGtal::int64_t c = Converter::cast( medium_bigint );
+ #endif
+   THEN( "Only bigger integers are identical" ) {
       REQUIRE( a == medium_int32 );
       REQUIRE( a != b );
       REQUIRE( b == medium_int64 );
-      REQUIRE( b == c );
-    }
+#ifdef WITH_BIGINTEGER
+    REQUIRE( b == c );
+ #endif
+   }
     THEN( "It gives the same results with NumberTraits" ) {
       DGtal::int64_t ap = NumberTraits<DGtal::int32_t>::castToInt64_t( medium_int32 );
       DGtal::int64_t bp = NumberTraits<DGtal::int64_t>::castToInt64_t( medium_int64 );
+#ifdef WITH_BIGINTEGER
       DGtal::int64_t cp = NumberTraits<DGtal::BigInteger>::castToInt64_t( medium_bigint );
+#endif
       REQUIRE( a == ap );
       REQUIRE( b == bp );
+#ifdef WITH_BIGINTEGER
       REQUIRE( c == cp );
+#endif
     }
   }
 }
 
+
+#ifdef WITH_BIGINTEGER
 SCENARIO( "IntegerConverter< 1, BigInteger >", "[integer_conversions]" )
 {
   typedef IntegerConverter< 1, DGtal::BigInteger > Converter;
@@ -132,3 +150,4 @@ SCENARIO( "IntegerConverter< 1, BigInteger >", "[integer_conversions]" )
     }
   }
 }
+#endif