Merge branch 'master' into NoInstall

Author: dcoeurjo

.github/actions/dgtal-config/action.yml

@@ -31,7 +31,7 @@ runs:
       if: ${{ runner.os == 'Linux' && inputs.config-name == 'default' }}
       shell: bash
       run: |
-        echo "DGTAL_CMAKE_CONFIG=-DDGTAL_WITH_CGAL=true -DDGTAL_WITH_LIBIGL=true -DDGTAL_WITH_FFTW3=true -DDGTAL_WITH_HDF5=true -DDGTAL_WITH_OPENMP=true  -DDGTAL_WITH_POLYSCOPE_VIEWER=true  -DDGTAL_WITH_CAIRO=true -DDGTAL_WITH_ITK=true -DDGTAL_ENABLE_FLOATING_POINT_EXCEPTIONS=true -DDGTAL_WARNING_AS_ERROR=ON -G Ninja" >> "$GITHUB_ENV"
+        echo "DGTAL_CMAKE_CONFIG -DDGTAL_WITH_CGAL=true -DDGTAL_WITH_LIBIGL=true -DDGTAL_WITH_FFTW3=true -DDGTAL_WITH_HDF5=true -DDGTAL_WITH_OPENMP=true  -DDGTAL_WITH_POLYSCOPE_VIEWER=true  -DDGTAL_WITH_CAIRO=true -DDGTAL_WITH_ITK=true -DDGTAL_ENABLE_FLOATING_POINT_EXCEPTIONS=true -DDGTAL_WARNING_AS_ERROR=ON -G Ninja" >> "$GITHUB_ENV"
 
     - name: "Default MacOS"
       if: ${{ runner.os == 'macOS' && inputs.config-name == 'default' }}
@@ -72,5 +72,5 @@ runs:
       working-directory: ${{ inputs.dgtal }}
       run: |
         echo "cmake-config=$(echo $DGTAL_CMAKE_CONFIG)" >> "$GITHUB_OUTPUT"
-        echo "cmake-test-blacklist='(testLinearStructure|testIntegerConverter|testArithmeticalDSSComputerOnSurfels)'" >> "$GITHUB_OUTPUT"
+        echo "cmake-test-blacklist='(testLinearStructure|testIntegerConverter|testArithmeticalDSSComputerOnSurfels|testStern)'" >> "$GITHUB_OUTPUT"
         echo "cmake-test-whitelist='$( ${{ inputs.dgtal }}/.github/actions/dgtal-config/get_whitelist.sh )'" >> "$GITHUB_OUTPUT"

CMakeLists.txt

@@ -2,8 +2,21 @@
 # Project definition
 # -----------------------------------------------------------------------------
 cmake_minimum_required (VERSION 3.20)
-project (DGtal VERSION 2.1.0)
-set(DGTAL_VERSION 2.1.0) # TODO: Set version through VERSION file
+
+# Reading version 
+file(READ "VERSION" version_file_raw)
+string(REGEX REPLACE "[\r\n]" "" version_file "${version_file_raw}")
+string(REGEX MATCHALL "([0-9]+)" version_parts ${version_file})
+
+set(DGtal_VERSION ${version_file})
+list(GET version_parts 0 DGtal_VERSION_MAJOR)
+list(GET version_parts 1 DGtal_VERSION_MINOR)
+list(GET version_parts 2 DGtal_VERSION_PATCH)
+
+set(PROJECT_VERSION ${DGtal_VERSION})
+set(VERSION ${DGtal_VERSION})
+
+project (DGtal VERSION ${DGtal_VERSION})
 
 # Allow for cmake 3.5. This is required indirectly by polyscope (via glad)
 set(CMAKE_POLICY_VERSION_MINIMUM 3.5)

ChangeLog.md

@@ -5,6 +5,10 @@
 - *IO*
   - Polyscope viewer upgraded from 2.4 to 2.5 (David Coeurjolly,  [#1796](https://github.com/DGtal-team/DGtal/pull/1796)). Reverting to 2.4  due to build issues (David Coeurjolly,  [#1797](https://github.com/DGtal-team/DGtal/pull/1797))
 
+- *Documentation*
+  - Refactoring of the volumetric examples in the Shortcuts (David Coeurjolly,  [#1807](https://github.com/DGtal-team/DGtal/pull/1807)).
+
+
 ## Bug fixes
 
 - *Arithmetics*
@@ -14,6 +18,7 @@
   - Fix issue [#1797](https://github.com/DGtal-team/DGtal/pull/1797), assertions raised in testCellGeometry and testDigitalConvexity because of improper digital space extent (Jacques-Olivier Lachaud, [#1801](https://github.com/DGtal-team/DGtal/pull/1801))
 
 - *Build*
+  - Version is now extracted from the `VERSION` file for CMake and Python builds (Bastien Doignies, [#1810](https://github.com/DGtal-team/DGtal/pull/1810))
   - Replacing the global compilation flags when `DGTAL_WARNINGS_AS_ERRORS` is set, with per target `target_compile_options` to avoid errors on Boost warnings (David Coeurjolly,  [#1793](https://github.com/DGtal-team/DGtal/pull/1793))
   - Fixing the `make install` command for boost (issue #1794) (Bastien Doignies, [#1793](https://github.com/DGtal-team/DGtal/pull/1793))
   - Adding option not to install targets to avoid crashes when boost is fetched through multiple channels ([#1809](https://github.com/DGtal-team/DGtal/pull/1809))

VERSION

@@ -0,0 +1 @@
+2.1.0

examples/tutorial-examples/shortcuts-geometry.cpp

@@ -461,7 +461,7 @@ int main( int /* argc */, char** /* argv */ )
                  std::back_inserter(sites), 
                  *bimage);
 
-    // Compute VoronoiMap and get distances from sites
+    // Compute VoronoiMap and get distances from sites (L_1 and L_2 metrics)
     auto vmap1 = SHG3::getDistanceTransformation<1>(bimage->domain(), sites, params);
     auto vmap2 = SHG3::getDistanceTransformation<2>(bimage->domain(), sites, params);
 

pyproject.toml

@@ -4,7 +4,8 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "DGtal"
-version = "2.1.0"
+dynamic = ["version"]
+# version = "2.1.0"
 description = "DGtal is an open-source, cross-platform library providing Digital Geometry Tools and Algorithm"
 
 authors = [
@@ -27,6 +28,17 @@ classifiers = [
     "Operating System :: MacOS"
 ]
 
+[tool.scikit-build.metadata.version]
+provider = "scikit_build_core.metadata.regex"
+input = "VERSION"
+regex = '''(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)'''
+result = "{major}.{minor}.{patch}"
+
+
+[[tool.scikit-build.generate]]
+path = "VERSION"
+template = '''version = ${version}'''
+
 [project.urls]
 Homepage = "https://www.dgtal.org/"
 

src/DGtal/doc/packagePython.dox

@@ -39,6 +39,7 @@ namespace DGtal {
 @managers David Coeurjolly
 @since 1.2
 
+[TOC]
 
 @b Package @b Overview
 
@@ -75,7 +76,7 @@ import dgtal
 ....
 @endcode
 
-@section code_example Examples
+@section code_example_python Examples
 
 @subsection topology_example Topology example (Euler characteristics)
 
@@ -119,7 +120,7 @@ ccomplex.construct(mySet)
 print("Euler characteristic: "+str(ccomplex.euler()))
 @endcode
 
-@subsection shortcuts_examples Geometrical Estimators (Curvature and normals)
+@subsection shortcuts_examples_python Geometrical Estimators (Curvature and normals)
 
 This example loads a binary image and computes integral invariant estimators and displays them within an interactive viewer. It mostly follows Shortcuts examples with a one-to-one mapping. A few other utilities are provided not to loop over elements in python.
 
@@ -180,7 +181,7 @@ ps.show()
 # SH3.saveOBJ(surface, [], colors, "al.obj")
 @endcode
 
-@section documentation Documentation
+@section documentation_python Documentation
 
 @subsection base_topology_kernel Base, Topology and Kernel 
 
@@ -196,16 +197,16 @@ In this section, we provide a list of functions and classes that can be used in
 | DT4_8, DT8_4, DT6_16, DT18_6, DT6_26, DT26_6                            | DGtal::DigitalTopology                             | DigitalTopology(foreground, background)                          |
 | Object4_8, Object8_4,  Object6_18, Object18_6, Object6_26, Object26_6   | DGtal::Object                                      | Object(topology, domain, points, connectedness)                  |
 
-@subsection shortcuts Shortcuts
+@subsection shortcuts_python Python Shortcuts
 
-Most shortcuts (see. \subpage moduleShortcuts) also have their binding. These are available under:
+Most shortcuts (see. \ref moduleShortcuts) also have their binding. These are available under:
 
 @code
 from dgtal import SH3 #Import both shortcuts and geometry shortcuts
 SH3.a_function_or_classes..
 @endcode
 
-@subsubsection shortcuts_classes Classes
+@subsubsection shortcuts_classes_python Classes
 
 Objects within this module are not expected to be manipulated by the user. They are meant to be passed around to the next functions and are prefixed by two underscores. We reference them for completeness
 
@@ -223,7 +224,7 @@ Objects within this module are not expected to be manipulated by the user. They
 | SurfelRange                   | DGtal::Shortcuts::SurfelRange                                 |                                                                                                                                                                                                  | std::vector<SCell>. See documentation of kernel binding above. |
 | ScalarStatistic               | DGtal::Shortcuts::ScalarStatistic                             | samples(): number of samples / size(): number of samples / mean(): mean / variance(): biased variance / unbiasedVariance(): unbiased variance / min(): min / max(): max / values: list of values | Not to be created.                                             |
 
-@subsubsection shortcuts_functions Functions
+@subsubsection shortcuts_functions_python Functions
 
 Static functions are also bound. For overloads, we only indicate the main parameters, not the whole signature. Refer to the C++ functions for complete signature (1 to 1 match).
 
@@ -267,7 +268,7 @@ Static functions are also bound. For overloads, we only indicate the main parame
 | %SH3.getScalarsAbsoluteDifference  | ShortcutsGeometry::getScalarsAbsoluteDifference  | All.                                                                                                                                                                                                                             |
 | %SH3.getStatistic                  | ShortcutsGeometry::getStatistic                  | All.                                                                                                                                                                                                                             |
 
-@subsubsection shortcuts_helpers Helpers functions
+@subsubsection shortcuts_helpers_python Helpers functions
 
 Looping through objects is slow in python and digital objects may be large. For this reason, we also provide a few helper functions for ease of usage and faster code:
 

src/DGtal/doc/tutorials/moduleShortcuts.dox

@@ -6,9 +6,9 @@ namespace DGtal {
 
 /**
 
-@page moduleShortcuts  Shortcuts (for the impatient developper)
+@page moduleShortcuts  Shortcuts
 
-@writers Jacques-Olivier Lachaud
+@writers Jacques-Olivier Lachaud, Bastien Doignies, David Coeurjolly
 
 @since 1.0
 
@@ -465,38 +465,38 @@ Shortcuts::Point is Z3i::KSpace::Point.
 -# General methods
   - Shortcuts::defaultParameters: returns the set of all shorcut parameters.
 
--# ImplicitShape3D methods
+-# Shortcuts::ImplicitShape3D methods
   - Shortcuts::getPolynomialList: returns the list of polynomial shapes predefined for implicit shapes 
   - Shortcuts::parametersImplicitShape3D: parameters related to 3D implicit shapes (polynomial)
   - Shortcuts::makeImplicitShape3D: builds a 3D implicit shape
 
--# KSpace methods
+-# Shortcuts::KSpace methods
   - Shortcuts::parametersKSpace: parameters related to Khalimsky spaces (closed)
   - Shortcuts::getKSpace: overloaded methods for building a Khalimsky space from a domain or an image, from a bounding box, from a digitization process, or from a (indexed or not) digital surface.
   - Shortcuts::refKSpace: overloaded methods for referencing the Khalimsky space of a (indexed or not) digital surface.
   - Shortcuts::getCellEmbedder: returns the canonic cell embedder of the given space.
   - Shortcuts::getSCellEmbedder: returns the canonic signed cell embedder of the given space.
 
--# DigitizedImplicitShape3D methods
+-# Shortcuts::DigitizedImplicitShape3D methods
   - Shortcuts::parametersDigitizedImplicitShape3D: parameters related to shape digitization (bounding box, sampling)
   - Shortcuts::makeDigitizedImplicitShape3D: digitizes an implicit shape.
 
--# BinaryImage methods
+-# Shortcuts::BinaryImage methods
   - Shortcuts::parametersBinaryImage: parameters related to binary images (noise, threshold).
   - Shortcuts::makeBinaryImage: many overloaded methods for creating from scratch, vectorizing shape digitization, loading, copying/noisifying binary images, thresholding gray-scale images.
   - Shortcuts::saveBinaryImage: saves a binary image to a file.
 
--# GrayScaleImage methods
+-# Shortcuts::GrayScaleImage methods
   - Shortcuts::makeGrayScaleImage: overloaded methods for creating from scratch or from binary image, or for loading gray scale images, or for creating a gray-scale image from a float or double image.
   - Shortcuts::saveGrayScaleImage: saves a gray scale image to a file.
 
--# FloatImage methods
+-# Shortcuts::FloatImage methods
   - Shortcuts::makeFloatImage: overloaded methods for creating a float image from a domain or from an implicit shape.
 
--# DoubleImage methods
+-# Shortcuts::DoubleImage methods
   - Shortcuts::makeDoubleImage: overloaded methods for creating a double image from a domain or from an implicit shape.
 
--# DigitalSurface methods
+-# Shortcuts::DigitalSurface methods
   - Shortcuts::parametersDigitalSurface: parameters related to digital surfaces (surfel adjacency, components, internal heuristics)
   - Shortcuts::getCellEmbedder: returns the canonic cell embedder of the given (indexed or not) digital surface
   - Shortcuts::getSCellEmbedder: returns the canonic signed cell embedder of the given (indexed or not) digital surface.
@@ -510,10 +510,10 @@ Shortcuts::Point is Z3i::KSpace::Point.
   - Shortcuts::getPointelRange: returns the pointels of a digital surface in the default order and optionnaly the map Pointel -> Index giving the indices of each pointel, or simply the pointels around a surfel.
   - Shortcuts::saveOBJ: several overloaded functions that save geometric elements as an OBJ file. You may save a digital surface as an OBJ file, with optionally positions, normals and colors information
 
--# RealVectors methods
+-# Shortcuts::RealVectors methods
   - Shortcuts::saveVectorFieldOBJ: saves a vector field as an OBJ file (vectors are represented by tubes).
 
--# Mesh services
+-# Shortcuts::Mesh services
   - Shortcuts::parametersMesh: parameters related to mesh, triangulated or polygonal surfaces.
   - Shortcuts::makeTriangulatedSurface: builds the dual triangulated surface approximating an arbitrary digital surface, or the triangulated surface covering a given mesh, or subdivide a polygonal surface into a triangulated surface, or builds the marching cubes triangulated surface approximating an isosurface in a gray-scale image. 
   - Shortcuts::makePolygonalSurface: builds a polygonal surface from a mesh, or builds the marching cubes polygonal surface approximating an isosurface in a gray-scale image. 
@@ -523,7 +523,7 @@ Shortcuts::Point is Z3i::KSpace::Point.
   - Shortcuts::makeSurfaceMesh: load a surface mesh from file
   - Shortcuts::saveOBJ: saves a triangulated or polygonal surface or a mesh as an OBJ file, with optionnaly normals and colors information.
 
--# Utilities
+-# ShortcutsGeometry::Mesh utilities
   - Shortcuts::parametersUtilities: parameters related to colormaps.
   - Shortcuts::getColorMap: returns the specified colormap.
   - Shortcuts::getZeroTickedColorMap: returns the specified colormap with a tic around zero.
@@ -535,7 +535,7 @@ Shortcuts::Point is Z3i::KSpace::Point.
   - Shortcuts::outputPrimalIdxDigitalSurfaceAsObj: outputs any indexed digital surface in standard OBJ file format as its primal quadrangulated mesh.
   - Shortcuts::outputDualDigitalSurfaceAsObj: outputs any digital surface in standard OBJ file format as its dual polygonal or triangulated mesh.
 
--# ShapeGeometry services
+-#  Shape Geometry services
   - ShortcutsGeometry::parametersShapeGeometry: parameters related to implicit shape geometry. 
   - ShortcutsGeometry::getPositions: returns the positions on the 3D implicit shape close to the specified surfels.
   - ShortcutsGeometry::getNormalVectors: returns the vectors normal to the 3D implicit shape close to the specified surfels.
@@ -547,7 +547,7 @@ Shortcuts::Point is Z3i::KSpace::Point.
   - ShortcutsGeometry::getSecondPrincipalDirections: returns the second principal directions along the 3D implicit shape close to the specified surfels.
   - ShortcutsGeometry::getPrincipalCurvaturesAndDirections: returns the first and second principal curvatures and directions along the 3D implicit shape close to the specified surfels.
 
--# GeometryEstimation services
+-# Geometry Estimation services
   - ShortcutsGeometry::parametersGeometryEstimation: parameters related to geometric estimators.
   - ShortcutsGeometry::getTrivialNormalVectors: returns the trivial (Trivial) normal vectors to the given surfel range  
   - ShortcutsGeometry::getCTrivialNormalVectors: returns the convolved trivial (CTrivial) normal vectors to the given surfel range
@@ -560,18 +560,25 @@ Shortcuts::Point is Z3i::KSpace::Point.
   - ShortcutsGeometry::getCNCGaussianCurvatures: returns the Corrected Normal Current (CNC) gaussian curvatures onto the given faces (as ids of the mesh).
   - ShortcutsGeometry::getCNCPrincipalCurvaturesAndDirections: returns the Corrected Normal Current (CNC) principal curvatures values and directions for the given face range (as ids of the mesh).
   - ShortcutsGeometry::orientVectors: reorient a range of vectors so as to point in the same half-space as another range of vectors.
-  - ShortcutsGeometry::getScalarsAbsoluteDifference: return the range of scalars that is the difference of two range of scalars
-  - ShortcutsGeometry::getVectorsAngleDeviation: return the range of scalars that form the angle deviations between two range of vectors
-  - ShortcutsGeometry::getStatistic: return the statistic of the given range of values.
-  - ShortcutsGeometry::getVoronoiMap: return the voronoi map on a domain from a list of sites
-  - ShortcutsGeometry::getDistanceTransformation: return the distance to the closest voronoi site on a domain from a list of sites
-  - ShortcutsGeometry::getDirectionToClosestSite: return the list of vector to the closest site
+
+-# Volumetric services
+  - ShortcutsGeometry::getVoronoiMap: return the Voronoi map on a domain from a list of sites
+  - ShortcutsGeometry::getDistanceTransformation: return the distance transformation on a domain from a list of sites
+  - ShortcutsGeometry::getDirectionToClosestSite: return the list of vectors to the closest site
   - ShortcutsGeometry::getDistanceToClosestSite: return the distance to the closest site
+  - ShortcutsGeometry::getRAwDistanceToClosestSite: return the (raw) distance to the closest site. Raw distance means an exact representation of the distance value from integers dropping the 1/p exponent for Lp metrics (i.e. squared distance for the Euclidean L2 metric)
 
--# ATApproximation services
+-# AT Approximation services
   - ShortcutsGeometry::parametersATApproximation: parameters related to piecewise-smooth AT approximation.
   - ShortcutsGeometry::getATVectorFieldApproximation: returns the piecewise-smooth approximation of the given vector field, and optionnaly returns the locii of discontinuity
 
+-# Misc. services
+  - ShortcutsGeometry::getScalarsAbsoluteDifference: return the range of scalars that is the difference of two range of scalars
+  - ShortcutsGeometry::getVectorsAngleDeviation: return the range of scalars that form the angle deviations between two range of vectors
+  - ShortcutsGeometry::getStatistic: return the statistic of the given range of values.
+
+
+
 
 @subsection dgtal_shortcuts_ssec3_4 Parameters