dgtal-team / dgtal

Digital Geometry Tools and Algorithm Library

Main website: https://dgtal.org

Description

DGtal is a generic open source library for Digital Geometry programming for which the main objective is to structure different developments from the digital geometry and topology community. The aims are numerous: make easier the appropriation of our tools for a neophyte (new PhD students, researchers from other topics,...), permit better comparisons from new methods with already existing approaches and to construct a federative project. Another objective of DGtal is to simplify the construction of demonstration tools to share new results and potential efficiency of the proposed work.

Quick Install

• MacOS (using homebrew):

   brew tap DGtal-team/DGtal
   brew install dgtal
  

(brew options dgtal to enable optional features)

• Linux and windows: no binary package, please compile the library.

Additional instructions are available in the documentation.

Quick Build Instructions

More details are given in the documentation pages. We just sketch the main instructions on linux/unix-based systems:

git clone https://github.com/DGtal-team/DGtal.git
cd DGtal ; mkdir build ; cd build
cmake ..
make install

Minimum system requirements: C++11 enabled compiler, cmake, boost (>= 1.50).

DGtal can be compiled on Microsoft Windows system using Visual Studio 2014 (or newer): Generate the Visual Studio project using windows cmake tool and compile the DGtal solution (you may also need to set the cmake variable BUILD_SHARED_LIBS to false).

Docker

A Docker file is included in the repository in order to allow the users to build a docker image with the DGtal library installed. Inside the docker container, the library is installed with many optional dependencies (gmp, eigen, cgal, itk, cairo, qglviewer, openmp, fftw3) so the user can start developing without the need to install DGtal on the system.

To build the Docker image, Docker should have been installed in the system (to install Docker) download the Dockerfile inside the DGtal repository, in the same directory where the Dockerfile is located execute

docker build -t dgtal:lastest .

To run an interactive terminal inside the docker container and see the examples

docker run -it --user=digital dgtal:lastest bash
cd /home/digital/git/DGtal/build/examples

To enable Viewer3D/QGLViewer features, please check this discussion.

More Information

• Project homepage http://dgtal.org

• Related DGtalTools project: http://dgtal.org/dgtaltools, DGtalTools, DGtalTools-contrib

• Release 1.3

• Release 1.2

• Release 1.1

• Release 1.0

• Release 0.9.4

• Release 0.9.3

• Release 0.9.2

• Release 0.9.1

• Release 0.9

• Release 0.8

dgtal's Issues

Provide domain/image converters unBounded->Bounded

When computations are perfomed on an unbounded domain, we still would like to use an imagecontainer to export a cropped (and thus bounded domain)

updating test directory

Did we update test directory as src directory ?

Cairo3D->2D mode and camera as stream modifier

In other DGtal streams (DGtalBoard,..), modifications and mode are set via stream modifier, e.g.:

board << CustomStyle() << aObject

Could it be possible to convert CairoViewers modes into such "stream modes" (e.g. WireFrame, camera position, ...) ?

Prblms with Display3D

I'm trying to build DGtal on MSWindows and I'm doing code reviewing:

• Class documentation is missing
• why to you include Display3D.h in HyperRectDomains for instance ? do you agree that if neither Cairo nor VISU3D is defined, the class should never be loaded ?

Plenty of warnings on MS: https://gist.github.com/1167968

Z2i::DigitalSet does not valid the concept CDigitalSet

Problem:

There may be a problem with the CDigitalSet concept (probably due to the DefaulConstructible?)

Reproduce:

Try a BOOST_CONCEPT_ASSERT(( CDigitalSetZ2i::DigitalSet? ))

tips:

Cmake error and warning

It appears some warning and errors in the cmake configuration (on linux version) :

-- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work.
-- Configuring done
CMake Error: CMake can not determine linker language for target:dgtal-config
CMake Error: Cannot determine link language for target "dgtal-config".

Doc link to dox file

Did we link all the dox files in simply in the doc directory ?

Propagate "-WITH...." variable in DGtalConfig

e.g. "-WITH_CAIRO" , WIT3D......

Problem in DistanceTransformation when lowerBound has negative coord.

there is a strange propagation effect when the lowerBound is < (0,0,0..).

CMake: boost_program_options not found (by default) under Fedora

CMake Error at /usr/share/cmake/Modules/FindBoost.cmake:1128 (message):
Unable to find the requested Boost libraries.

Boost version: 1.46.0

Boost include path: /usr/include

The following Boost libraries could not be found:

      boost_program_options

No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the
directory containing Boost libraries or BOOST_ROOT to the location of
Boost.

Documentation for interpixel topology

A user-guide should be written.

BK: I have completed 2D/3D border tracking...

Main doc page empty

The first doc page is empty:
http://liris.cnrs.fr/dgtal/doc/nightly/
Same with the last version with mac config.

A Board mechanism for cells

To provide a mechanism for displaying cells with DGtalBoard.

(It seems ok, but Jaco you can check)

Fix build issues in MS VisuStudio

Change QColor by DGtal::Color

In 3D stream

DGtalCairo: fprintf -> trace mechanism

Change all the printf to C++ stream with the DGtal Trace mechanism (and remove unnecessary trace message or put them between #ifdef DEBUG_VERBOSE)

Doxygen doc required in DGtalCairo

Please comment all the classes and methods with appropriate doxygen macros

Problem with 2D contour tracker (from Surface.ih)

I've tried to use the surface tracker in shapeGEnerator (cf dcoeurjo/DGtal branch "shapeGenWitSignature") but I get an exception (out_of_range) during the contour construction (https://github.com/dcoeurjo/DGtal/blob/shapeGenWithSignature/tools/shapeGenerator/shapeGenerator.cpp#L232)

Can you confirm me the bug?

ascii PGM <-> binary PGM

shapeGenerator outputs ascii PGM (P2):
./tools/shapeGenerator/shapeGenerator -s flower -R 25 -r 5 -k 4 -o flower4
whereas pgm2freeman requieres binary PGM (P5):
./tools/2dContourTools/pgm2freeman -i flower4.pgm
gives the following error
PNMReader : No P5 format in flower4.pgm
terminate called after throwing an instance of 'DGtal::IOException'
what(): DGtal IO error
Abandon

Is it possible to only use ascii PGM (or binary PGM) or provides a tool for conversion ?

EPS export with CAIRO and alpha not equals to 1

When we export a figure with cairo in EPS format and if we use an alpha value different to 1, the export is no more vectorial.

For example:

./tools/2dContourTools/displayContours --FreemanChain? contours.fc --backgroundImage ../examples/samples/church.png

--outputEPS levelSetImage.eps --alphaBG 0.5

(the resulting file looks as a bitmap even but size=12Mo)

and

./tools/2dContourTools/displayContours --FreemanChain? contours.fc --backgroundImage ../examples/samples/church.png

--outputEPS levelSetImage.eps --alphaBG 1

(well vectorial size=2.8Mo)

If QT4 not present (but cairo is) DGtalCairo does not compile

because there is a dependency to QColor in DGtalCairo...

Add doc-example on 3d Khalimsky Surface Cell extraction

Like this example (http://liris.cnrs.fr/dgtal/gallery/fcextraction-2/) but in 3D with oriented surfels extraction.
And add a new simple mod to display Cell KS with basic classic surfel/pointel/voxel.

Enhance hyperRectDomain subRange with fast 1D subrange (aka SpanIterator)

Problem:

When performing intensive 1D subrange iterations, the generic subRange in HyperRectDomain? is a bit slow.

Aim:

That would be great to have a specialization of Subrange for 1D iteration.

tips:

seems to be similar to old SpanIterator?.

testLengthEstimators.cpp changed

I removed the typename and It works, Tristan can you check if it also works (just update the master) ?

[ 32%] Building CXX object tests/geometry/2d/CMakeFiles/testLengthEstimators.dir/testLengthEstimators.cpp.o
/Users/kerautre/EnCours/DGtal/tests/geometry/2d/testLengthEstimators.cpp: In function ‘bool testDisplay(double, double)’:
/Users/kerautre/EnCours/DGtal/tests/geometry/2d/testLengthEstimators.cpp:248: error: using ‘typename’ outside of template
/Users/kerautre/EnCours/DGtal/tests/geometry/2d/testLengthEstimators.cpp:257: error: using ‘typename’ outside of template
/Users/kerautre/EnCours/DGtal/tests/geometry/2d/testLengthEstimators.cpp:267: error: using ‘typename’ outside of template
make[2]: *** [tests/geometry/2d/CMakeFiles/testLengthEstimators.dir/testLengthEstimators.cpp.o] Error 1

Cmake error when Magick is not found

After doing a :
cmake -DWITH_ALL=true
I obtain:
.................
CMake Error at cmake/FindMagick.cmake:100 (MESSAGE):
GraphicsMagick required, please specify it's location with MAGICK_HOME,
MAGICK_LOCATION or MAGICK++_LOCATION
Call Stack (most recent call first):
cmake/CheckDGtalOptionalDependencies.cmake:53 (FIND_PACKAGE)
CMakeLists.txt:157 (INCLUDE)
............

Add expression template mecanisms to PointVector class

See WP : [[http://en.wikipedia.org/wiki/Expression_templates]]

PB in cmake for the generation of "ConfigExamples.h", ConfigTest.h" and "Config.h"

...
I added the generated file for simplify tests..

testArithDSS3d does not compile when libQGLViewer or Qt4 not found

Linking CXX executable testArithDSS3d
/usr/bin/ld: cannot find -lDGtal-visu3d
collect2: ld returned 1 exit status
make[2]: *** [tests/geometry/3d/testArithDSS3d] Erreur 1
make[1]: *** [tests/geometry/3d/CMakeFiles/testArithDSS3d.dir/all] Erreur 2

Check the cmakelists and allow the test file only when the dependency is fine.

Adapt the point size in QGLviewer

Adapt the scale for point size for the point visualisation as suggested by Martial.

Cleanup the FreemanChain class

Cleanup the FreemanChain class

Cleanup the FreemanChain class

Fast model of CCellularGridND

Backport class KnSpace from ImaGene in order to get a faster model of CCellularGridND.

help in shapeGenerator tool

When taping ./tools/shapeGenerator/shapeGenerator -l
we can see:
flower Flower with k petals.
Required parameter(s): --radius [-R], --smallradius [-r], --k [-k], --phi
But looking at the output shapes, I guess that -r is not the inner radius but the deviation between the outer and inner radii. This has to be checked for flower or other shapes like accFlower, etc.

Add doc-example on 3d Khalimsky Surface Cell extraction

Like this example (http://liris.cnrs.fr/dgtal/gallery/fcextraction-2/) but in 3D with oriented surfels extraction.

Update old INLINE version for all header files

Since it appears some problems when calling lib from ext program...

Renaming io-viewers to io ?

io-viewers does not make sense...I've assigned this issue to you just to be informed and to discuss about it;)

Correcting minor typos in doc on GIT

Small error a commit and chekout..

Backport Color for io/colormap

As done in ImaGene

Cellular Grid concept and other model

For now, the cellular grid space concept exists only through its first model : the KhalimskySpace. The concept should be written and another model should be proposed, We propose the integer coded model of cells of [http://gforge.liris.cnrs.fr/projects/imagene ImaGene] as another model of cellular grid space, especially for its efficiency.

Create parametric shapes in 3D

As in shapeGenerator (and srd/DGtal/helpers/*), create 3D parametric shapes with normal vector/curvature signature.

DGtal Cairo Code cleanup

• remove unnecessary commented code (e.g. dgtalcairo.cpp)
• remove all references to "GL" stuff in DGtalCairo

Gcc warnings to remove (ambiguous else)

/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp: In member function ‘virtual void LibBoard::Arrow::flushCairo(cairo_t_, const LibBoard::TransformCairo&) const’:
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp:912:10: warning: suggest explicit braces to avoid ambiguous ‘else’
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp: In member function ‘virtual void LibBoard::Ellipse::flushCairo(cairo_t_, const LibBoard::TransformCairo&) const’:
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp:1171:8: warning: suggest explicit braces to avoid ambiguous ‘else’
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp: In member function ‘virtual void LibBoard::Circle::flushCairo(cairo_t_, const LibBoard::TransformCairo&) const’:
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp:1349:5: warning: suggest explicit braces to avoid ambiguous ‘else’
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp: In member function ‘virtual void LibBoard::Arc::flushCairo(cairo_t_, const LibBoard::TransformCairo&) const’:
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp:1400:10: warning: suggest explicit braces to avoid ambiguous ‘else’
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp: In member function ‘virtual void LibBoard::Polyline::flushCairo(cairo_t_, const LibBoard::TransformCairo&) const’:
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp:1612:10: warning: suggest explicit braces to avoid ambiguous ‘else’
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp: In member function ‘virtual void LibBoard::Rectangle::flushCairo(cairo_t_, const LibBoard::TransformCairo&) const’:
/home/dcoeurjo/Sources/DGtal/src/Board/Shapes.cpp:1814:10: warning: suggest explicit braces to avoid ambiguous ‘else’

Add topological maps in DGtal

Enhance FreemanChain

• Create an CharIterator? that provides the chain code char by char
• Store the last point so that isClosed() may be performed in linear time,
• create extend and retract methods as if FreemanChain? is a primitive.

Convert SpaceND into a pure "type/static only" struct

In spaceND, there are plenty of typdefs and a few methods: (selfdisplay, subspace, subcospace)

The methods make sense only if we create instances of SpaceND. In the current DGtal dev, SpaceND is just use as a template parameter (and never instantiated).

I suggest to remove the constructor and the methods.

Export in PDF 3D: format U3D

A great feature for the 3D visualisation should be to have an export with the format U3D which allows to display interactive 3D view in pdf format.
See for instance this example: http://www.loria.fr/~kerautre/lobster.pdf
You just need to read the pdf file with acroread for instance.
It can be generated simply from latex file and/or in a beamer presentation!

It could be a great feature for the next potential demo/tutorial session...
Perhaps Martial it could be included with the cairo related framework ?

Remove ConstRange in HyperRectDomain

Because an HyperRectDomain is a range, we don't need the inner class.

compile pb with new build directory...

I don't why but after the new directory "build" I obtain this error:

Scanning dependencies of target testReverseDT
[ 41%] Building CXX object tests/geometry/nd/CMakeFiles/testReverseDT.dir/testReverseDT.cpp.o
In file included from /Users/kerautre/EnCours/DGtal/tests/geometry/nd/testReverseDT.cpp:36:
/Users/kerautre/EnCours/DGtal/src/DGtal/geometry/nd/volumetric/ReverseDistanceTransformation.h:211: error: ‘Vector’ does not name a type
In file included from /Users/kerautre/EnCours/DGtal/src/DGtal/geometry/nd/volumetric/ReverseDistanceTransformation.h:226,
from /Users/kerautre/EnCours/DGtal/tests/geometry/nd/testReverseDT.cpp:36:
/Users/kerautre/EnCours/DGtal/src/DGtal/geometry/nd/volumetric/ReverseDistanceTransformation.ih: In member function ‘typename DGtal::ReverseDistanceTransformation<Image, p, IntegerShort>::OutputImage DGtal::ReverseDistanceTransformation<Image, p, IntegerShort>::reconstruction(const I&)’:
/Users/kerautre/EnCours/DGtal/src/DGtal/geometry/nd/volumetric/ReverseDistanceTransformation.ih:73: error: ‘myDisplacementVector’ was not declared in this scope
/Users/kerautre/EnCours/DGtal/src/DGtal/geometry/nd/volumetric/ReverseDistanceTransformation.ih: In member function ‘void DGtal::ReverseDistanceTransformation<Image, p, IntegerShort>::reconstructionAsSet(Set&, const I&)’:
/Users/kerautre/EnCours/DGtal/src/DGtal/geometry/nd/volumetric/ReverseDistanceTransformation.ih:105: error: ‘myDisplacementVector’ was not declared in this scope
make[2]: *** [tests/geometry/nd/CMakeFiles/testReverseDT.dir/testReverseDT.cpp.o] Error 1
make[1]: *** [tests/geometry/nd/CMakeFiles/testReverseDT.dir/all] Error 2
make: *** [all] Error 2

Specific display for Signed Cell (SCell)

Define a specific display for Signed Cell, by using for instance:

• triangle like shape instead quad for dim 2
• cone instead cylinder for dim1

PB in cmake:

When trying to compile on linux from the master of main remote I get the following pb:
(pershpas the cmake version 2.6-patch 4 since it works on mac with version 2.8.4 ?)

---

CMake Error at cmake/DGtalConfigGenerator.cmake:7 (export):
export Unknown arguments.
Call Stack (most recent call first):
CMakeLists.txt:176 (INCLUDE)

-- Configuring incomplete, errors occurred!

"Generic" Image Reader

Specs:

Provide a mechanism to load a file image with the bestloader according to an image filename (parsing the extension).

Some readers may not be relevant. E.g. for RAW reader, there are ambiguities: dimension, Raw8 vs. Raw16, size,...

Interface:

e.g.:

typname ImageContainer... MyImage

MyImage image = GenericReader::import("glop.png");
MyImage image2= GenericReader::import("glop.vol");

introspection (to return/display the best loader used for this filename):

trace.info() << GenericReader::getReaderName("glop.png") <<std::endl;