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DGtalTools 1.5 (beta)

  • build
    • Fix DGtalTools doc deployement. (David Coeurjolly and Bertrand Kerautret #454)

DGtalTools 1.4

  • build

    • Remove STBimage preprocessor instruction used to fix MVSC that is no more usefull since DGtal PR 175 (Bertrand Kerautret #459)

  • visualisation

    • meshViewer: new options to change the default background color, to load camera settings at startup, to change at startup the light source mode attached or not to the camera and improve transparency process at startup rendering. It includes a fix of the -customColorMesh for obj mesh and add new possibilities to custom the color of each mesh given as input. It also includes a fix and some simplications of the option --doSnapShotAndExit. (Bertrand Kerautret #448)
    • meshViewer: new option to set alpha channel of the mesh color. (Bertrand Kerautret #451)
    • 3dSDPViewer: new option to set alpha channel of the mesh color. (Xun Gong #452)
    • meshViewer: Add colored SDP option in meshViewer when input texts is an alpha mesh and a colored SDP respectively. (Xun Gong #452)
    • volscope new vol visualization tool using polyscope (David Coeurjolly, #455)
    • volscope documentation enhanced (David Coeurjolly, #460)

  • volumetric

    • volReSample: fix the impossibility to export to vol when ITK is activated (Bertrand Kerautret #445)
    • volFillInterior: add new option to set the filling value.
      (Bertrand Kerautret #456)

  • converters

    • mesh2vol: small fix to read generic mesh. (Bertrand Kerautret #444)
    • mesh2vol: use the digitization space defined from bounding box of input mesh. (Bertrand Kerautret #450)

DGtalTools 1.3

  • build

    • New cmake option (DGTAL_RANDOMIZED_BUILD_THRESHOLD) to set the (approximated) % of tools build (Bertrand Kerautret #416)
    • Following DGtal C++17 is now required. (David Coeurjolly and Bertrand Kerautret, #449)

  • converters

    • heightfield2shading: new option to add a matcap rendering (from normal direction interpreted as HSV vector) (Bertrand Kerautret #399)
    • heightfield2shading: new option to generate a normal map. (Bertrand Kerautret #415)
    • mesh2heightfield: automatic object placement and improved usage. (Bertrand Kerautret & Florian Delconte #429)
    • vol2slice: fix infinite slices extraction. (Bertrand Kerautret #439)

  • generators

    • 2dSimplePolygonDigitizer: new tool compute the Gauss Digitization of a simple closed polyline. (Phuc Ngo #398)

  • visualisation

    • 3dImplicitSurfaceExtractorByThickening: adding OBJ export. (David Coeurjolly #413)
    • 3dVolViewer: adding new option to interprate intensity as transparency. (Bertrand Kerautret #425)
    • 3dCompSurfelData: fix --noWindows option (issue #427. (Bertrand Kerautret and Kacper Pluta #440)

  • volumetric

    • volSegment: adding new option to get long int images as output (for longvol exporting). (Bertrand Kerautret #420)
    • volInfo: get information from a volumetric file. (David Coeurjolly, #430)
    • criticalKernelsThinning3D: new option to keep the resulting image domain equal to the input image (instead using the resulting bouding box set). (Bertrand Kerautret #431)
    • criticalKernelsThinning3d: it can now export OBJ files for input surface and output skeletons (Jacques-Olivier Lachaud #414)

DGtalTools 1.2

  • global

    • Fix itk2vol and fix ITK cmake configuaration that was making issues with the ITK image read. (Bertrand Kerautret #393)
    • Travis: Fix old default osx_image with xcode12.2 and remove non used boost cmake references. (Bertrand Kerautret #394)
    • Uniform input/output option with previous use of CLI11 (issue #405). (Bertrand Kerautret #406)
    • Comply with cmake Policy CMP0115 "Source file extensions must be explicit". (Bertrand Kerautret and David Coeurjolly, #407)

  • visualisation

    • 3dVolViewer: improvement of the possibility to read input image of type double (with ITK). New possibility to select the voxel in order to display image intensity.
      (Bertrand Kerautret #402)
    • 3dVolBoundaryViewer: fix compilation issue (related to CLI11 change) when ITK is activated. (Bertrand Kerautret #395)

  • volumetric

    • volReSample: it can now export image including ITK image spacing. (Bertrand Kerautret #404)

DGtalTools 1.1

  • global

    • New way to handle command line options of DGtalTools by using CLI11 instead boost program option. (Bertrand Kerautret and Phuc Ngo #373)
    • Fix issue of link with boost program option. (Bertrand Kerautret #356)
    • set cmake based CPP11 check instead the manual DGtal check. (Bertrand Kerautret #364)
    • Travis: Fix broken Eigen url. Update Eigen in travis to 3.3.7. (Pablo Hernandez and Bertrand Kerautret #373)

  • converters

    • itk2vol: change the type of the threshold parameter in order to be able to convert ITK images of type double, it also adds a new option to mask the source image using another image. (Bertrand Kerautret, #367)
    • volBoundary2obj improved using new Shortcuts helpers. (Bertrand Kerautret #370)

  • documentations

    • Fix doc link to the DGtal lib in the tool source (from new github website). (Bertrand Kerautret #372)
    • Fix missing title page and various small doc corrections. (Bertrand Kerautret #381)

  • estimators

    • volSurfaceRegularization now in the "make install" command. (David Coeurjolly, #376)
    • 3dLocalEstimators now included in the main build and fix compilation issues and documentation added. #382. (Bertrand Kerautret #383)

  • imageProcessing:

    • Add a variant of Ambrosio-Tortorelli functional for image restoration and inpainting, using Laplacian of discontinuity function instead of gradient and based on discrete calculus. (Jacques-Olivier Lachaud #363)

  • volumetric

    • fix ld boost program options macos warnings. (Bertrand Kerautret #366)
    • curvatureScaleSpaceBCC: better use of exportFile with template specialisation. (Bertrand Kerautret, #375)
    • Passing argument by const reference in (min|max|mean)Val of volSubSample. (Roland Denis, #359)
    • Using SourceForge to download doxygen sources during Travis CI jobs. (Roland Denis #360)
    • volMask: new tool to extract a new image from the a masked image. (Jonas Lamy and Bertrand Kerautret 374)
    • volAddBorder: Add an option that sets zero value to domain boundary voxels without changing the domain extent (Bertrand Kertautret #371)
    • volAddBorder: Fix VTKIMAGEDATA_CONTAINER_I (Phuc Ngo) #435)
    • Fix a wrong error message that appears when using the tool (wrong IO error) (Bertrand Kerautret #368)

DGtalTools 1.0

  • generators

    • 3dParametricCurveDigitizer - a tool for digitization of 3D parametric curves (Kacper Pluta, #341)

  • global

    • Continuous integration AppVeyor fix. (Bertrand Kerautret, #337).
    • Fix PointVector implicit conversion (in link to DGtal PR #1345) (Bertrand Kerautret and David Coeurjolly #347)
    • Fix Documentation nightly update on github website. (Bertrand Kerautret #348)
    • CMake exposes boost static option. (Bertrand Kerautret #351)
    • Fix compilation and execution with Visual Studio for volSurfaceRegularization. (Raphael Lenain #353)

  • volumetric

    • New tool to fill the interior of a voxel set (volFillInterior). (David Coeurjolly,#343).
    • Update Critical Kernels thinning using VoxelComplex, following recent changes in DGtal. (Pablo Hernandez, #345)

  • estimators

    • New option for 3dCurveTangentEstimator which allows to detect the principal curve direction (Kacper Pluta, #342)

DGtalTools 0.9.4

  • converters

    • mesh2vol: add option to add margin in the generated volume (to better extract the surfel boudary near domain limits).
      (Bertrand Kerautret, #322)
    • vol2vox/vox2vol: tools to convert vol file to a MagicaVoxel VOX file and conversly. (David Coeurjolly, #314)
    • volAddNoise moved to volumetric/. (David Coeurjolly, #300)
    • segfault fix in volBoundary2obj (David Coeurjolly, #317)
    • Fix the bad surfel display of volBoundary2obj (issue #320) (Bertrand Kerautret, #321)

  • volumetric

    • new option to volAddNoise to extract the largest 6-connected component. (David Coeurjolly, #300)
    • new option to 3dVolMarchingCubes to add some Kanungo noise to the input vol file. (David Coeurjolly, #300)
    • Add thinning based of Critical Kernels using VoxelComplex. Based on DGtal PR 1147 (Pablo Hernandez, #311)

  • visualisation:

    • New tool for mesh voxelization from a mesh in input (.off) to a volumetric output (vol, pgm3d) (Monir Hadji, #279

    • 2dCompImage : Computes and displays image comparisons (squared and absolute differences) (Bertrand Kerautret, #313)

    • Improve visualisation tools (vol2heightfield, vol2obj, vol2raw, vol2sdp, vol2slice,volBoundary2obj,3dImageViewer, 3dVolViewer, sliceViewer, Viewer3DImage) allowing to read longvol including rescaling. (Bertrand Kerautret, #296)

    • Add an option to filter vector displayed in 3dSDPViewer. (Bertrand Kerautret, #297)

    • meshViewer: add an option to set the ambient light source. (Bertrand Kerautret, #303)

    • 3dSDPViewer: new option to display vector field as unit vectors. (Bertrand Kerautret, #301)

  • converters:

    • sdp2vol: add the automatic set of the domain according to the bouding box of the set of points. (Bertrand Kerautret, #305)

  • global:

    • Fix travis Doxygen compilation for non Documention mode. (Bertrand Kerautret, #314)
    • Fix travis with boost installation which now use std package. (Bertrand Kerautret, #310)
    • Fix for the last QGLViewer version (2.7). (Bertrand Kerautret, #308)

DGtalTools 0.9.3

  • global:

    • Various fixes to enable the new Version3 (compressed) Vol/Longvol files. (David Coeurjolly, #287)
    • Fix Appveyor continuous integration with zlib installation and boost fix. (Bertrand Kerautret, #289)

  • imageProcessing:

    • Creates imageProcessing directory. Add tools for doing image restoration and inpainting with Ambrosio-Tortorelli functional and discrete calculus. (Jacques-Olivier Lachaud, Marion Foare #280)

  • converters:

    • fix tool itk2vol which was not able to read and convert int type image. (Bertrand Kerautret, #276)
    • add a CLOSURE export mode in volBoundary2obj. Default mode has been changed to "BDRY" (David Coeurjolly, #281)

  • visualisation:

    • Add SnapShot option for meshViewer and 3dVolViewer (useful to get visualisation without interaction like for scripting and/or online demonstration). It also contains a new option to display a mesh in 3DvolViewer. (Bertrand Kerautret, #282)
    • Add an option to display vector fields in displayContours (Bertrand Kerautret, #290)

  • estimators:

    • 2dlocalEstimators: add an option to export the generated contour. (Bertrand Kerautret, #285)
    • tangentBC: add an option to read sdp points as input. (Bertrand Kerautret, #285)
    • volSurfaceRegularization: a tool to compute a regularized quadrangulation from from a digital surface. (Pierre Gueth, David Coeurjolly, #306)

DGtalTools 0.9.2

  • global:

    • fix wrong Khalimsky space initialization in Freeman2Img. (Roland Denis, #271)
    • doxygen documentation added for all tools. (David Coeurjolly, Bertrand Kerautret, #258)
    • fix uses of temporaries when ConstAlias is needed. (Roland Denis, #253)
    • renaming of the shapeGenerator folder to generators (David Coeurjolly, #268))

  • visualisation:

  • meshViewer: add a key to display mesh information about number of vertex/faces. (Bertrand Kerautret, #273)

  • 3dSDPViewer: fix the mesh display which was not given with their original colors. (Bertrand Kerautret, #272)

  • 3dSDPViewer: add the possibility to display a set of point by using different sphere sizes (specified in the input sdp file). (Bertrand Kerautret, #252)

  • sliceViewer: fix bug when imported image domain doesn't contain (0,0,0) point. (Roland Denis, #256)

  • 3dSDPViewer: add an option to display on screen the selected voxel. (Bertrand Kerautret, #257)

  • volumetric:

    • fix reading options bug in volCComponentCounter and sdp2vol. (Bertrand Kerautret, #254)

DGtalTools 0.9.1

  • converters:

    • img2freeman: new option to sort the resulting contours by increasing size (B. Kerautret).

  • visualisation:

    • meshViewer: new possibility to display a vector field from a simple sdp file (B. Kerautret).

    • 3dImplicitSurfaceExtractorByThickening: a tool to visualize 3d polynomial implicit surface defined as some f(x,y,z)=0. Its principle is to thickened the set {f=0} as {|f|<=e}, to extract an associated cubical complex, then to collapse it to capture the correct topology of {f=0}. Afterwards, the complex is projected onto f=0 with Newton's method. (J.-O. Lachaud)

    • 3dImplicitSurfaceExtractorBy4DExtension: a tool to visualize 3d polynomial implicit surface defined as some f(x,y,z)=0. Its principle is to extend f as a 4D function F(x,y,z,t)=0 (for instance F=f-|nabla f|t). This 4d hypersurface is easier to detect. It is transformed into 4D cubical complex, that is then collapsed to capture the correct topology of {f=0}. Afterwards, the complex is projected in 3D onto f=0 with Newton's method. (J.-O. Lachaud)

  • converters:

    • homotopicThinning3D: the fixed points can be set from a file. (B. Kerautret)

DGtalTools 0.9

  • global:

    • Qt prog can now handle Qt5

  • visualisation:

    • meshViewer: fix to display mesh with colored faces (.off with colors).
    • 3dCurvatureViewer/Noise: can now be used without QGLViewer if exporting data.
    • 3dCurvatureViewer/Noise:
      • can now be used without QGLViewer if exporting data (Jérémy Levallois).
      • can now export II based normal vector field (Jérémy Levallois, David Coeurjolly).
    • 3dImageViewer: now display the current moving axis which was selected and display the slice numbers (can be disabled by key M).
    • sliceViewer: fix the bug when displaying vol with non 0 origin point.
    • itk2vol: convert any image of itk format (mhd, mha, ...) to vol (available with the itk option in DGtal).
    • sliceViewer: can now display 3d image with predefined color map (hue, gradient).

  • volumetric:

    • volIntensityScale: a simple tool to apply a linear scale of the intensity given in a volumetric file.

  • converters:

    • vol2heightfield: a new tool to transform volumetric file into 2D heightmap.
    • heightfield2vol: a new tool to transform 2D heightmap into volumetric file.
    • imgAddNoise: a new tool to add noise (Kanungo's) to a binary 2D object
    • volAddNoise: a new tool to add noise (Kanungo's) to a binary 3D object
    • heightfield2shading: a new tool to render a 2D heightfield image into a shading one.
    • mesh2heightfield: new tool to convert a mesh file into a 2D heightmap (from a normal direction N and from a starting point P).
    • freeman2img: (extended from previous freeman2pgm) fix options issues.

  • estimators:

    • 3dCurveTangentEstimator: a simple tool to estimate and visualize the tangent to a set of points approaching a 3D curve. Two estimators are implemented, one based on digital Voronoi Covariance Measure, the other based on 3D lambda-MST.

DGtalTools 0.8

  • visualisation:

    • 3dCompSurfelData: a tool to compare generic surfel data informations given from two data files.
    • 3dCurvatureViewer: can now display curvature on multiple connected components and can apply image re sampling for anisotropic grid.
    • 3dDisplaySurfelData: display surfel data from SDP file with color attributes given as scalar interpreted as color.
    • 3dHeightMapViewer: display a 2D image as heightmap by using QGLviewer.
    • 3dSDPViewer: basic display of a sequence of 3d points (as voxel or sphere) and vectors by using QGLviewer.
    • 3dVolBoundaryViewer: a simple viewer of the boundary of an object defined by thresholding a vol file.
    • sliceViewer: a new 2D and 3D slice viewer from 3D volumic files ( pgm3d, vol, longvol, and DICOM with ITK).

  • converters:

    • freeman2pgm: transform one or several freeman chains into a pgm file by filling their interior areas and renamed into freeman2img.
    • pgm2freeman: renamed to pgm2img.
    • vol2off: tool removed, see 3dVolMarchingCubes for the same tool.
    • volBoundary2obj: a simple tool to export the boundary of a an object in a volumetric file to OBJ

  • estimators:

    • curvatureScaleSpaceBCC: a tool to display the curvature scale space of a given contour with the Binomial Convolver Curvature Estimator.
    • eulerCharacteristic: bruteforce tool to extract (volumetric) Euler characteristic from volumetric binary object.
    • generic3dNormalEstimators: Computes a normal vector field over a digitized 3D implicit surface for several estimators (II|VCM|Trivial|True).

  • volumetric:

    • 3dVolMarchingCubes: speed-up by factor 10 simply by replacing the set predicate used in computations.
    • volCrop: crop an 3D vol image from to points.
    • volReSample: apply a basic re sampling of a 3D volumetric image (.vol, .longvol, .pgm3d) with a given grid size.
    • volSegment: Segment volumetric file from a simple threshold which can be set automatically from the Otsu's variance based estimation.
    • volTrValues: a basic tool to transform the voxel values from an input/output set.

DGtalTools 0.7

  • converters:

    • convertVol: a simple generic volume image converters (can process actually pgm3d, vol, longvol, raw (for writing)).
    • vol2sdp: a simple tools to extract digital points from 3d vol files.
    • vol2off: extract dual surface of a digital object (equiv. Marching Cubes)
    • vol2obj: convert a volume file into OBJ format (all voxels belonging to threshold interval)
    • vol2slice: tool to extract all slices from 3d volumic images.
    • slice2vol: tool to merge slices into one 3d volumic file.
    • sdp2vol: a simple tool to create a 3d vol image from 3d digital points.
    • longvol2vol: convert longvol to vol file using different conversion policies.
    • dicom2vol: convert dicom images into 3d volumic file (need itk option in DGtal).
    • pgm2freeman: add new possibility to set automatically a threshold from the otsu algorithm.
    • HDF52vol: convert HDF5 to vol file format.
    • raw2HDF5: convert raw image to HDF5.

  • volumetric:

    • homotopicThinning3D exploits now the GenericReader class and is no more limited to vol format.
    • volFlip: tool to flip all volume slice images according a given dimension.
    • volImageMetrics: apply basic measures from two volumetric images: RMSE and PSNR.
    • volShapeMetrics: Apply shape measures for comparing two volumetric images A and B (shape defined from thresholds):
      • Measures from voxel partition (true/false+-, precision recall, f-measure)
      • Measures bases on euclidean distance between the two Shape A and B.

  • estimators:

    • 2dLocalEstimators: Improvement of 2dLocalEstimators + possibility to compare with noised data.
    • 3dLocalEstimators: Adding possibility to compare curvature (mean, gaussian and principal curvatures) with Integral Invariant and Monge via Jet Fitting + possibility to compare with noised data.

  • volumetric:

    • volTools directory moved into volumetric.

  • visualisation:

    • 3dCurveViewer: A tool for visualizing the tangential cover of 3d curves.
    • 3dVolViewer: new option to limit the number of displayed voxels (can open dicom format if WITH_ITK is set to true).
    • 3dImageViewer: new tool to display slice image with interactive translatations or rotations (can open dicom format if WITH_ITK is set to true).
    • patternTriangulation: a new tool that draws with Board2D the convex hull, the closest-point Delaunay triangulation or the farthest-point Delaunay triangulation of a pattern.
    • 3dCurvatureViewer: Now allow to draw principal curvature directions on objets.
    • 3dCurvatureViewerNoise: Same as 3dCurvatureViewer, but allow to add some noise to objects.

  • distanceTransform:

    • LUTBasedNSDistanceTransform: Compute the 2D translated neighborhood-sequence distance transform of a binary image.
    • CumulativeSequenceTest and RationalBeattySequenceTest: tests from LUTBasedNSDistanceTransform.

DGtalTools 0.6

  • estimators:

    • 2dLocalEstimators: program to compare local curvature/tangent estimators on implicit shapes:
      • Maximal DSS based estimators
      • Maximal DCA based estimators
      • Binomial convolver based estimators
      • Integral Invariants based estimators -3dLocalEstimators: program to compare 3D local curvature (mean or gaussian) estimators on 3D implicit shapes.

  • visualisation:

    • 3dCurvatureViewer: computes and displays mean or gaussian curvature of vol binary shapes.
    • Various updates for 0.6 DGtal compatibility.

DGtalTools 0.1

  • converters: utilities to convert various simple file formats:

    • freeman2sdp: convert freeman chain towards a Sequence of Discrete Points.
    • pgm2freeman: to extract a freeman chain contour from a grayscale image.
    • raw2vol and vol2raw: transform 3D volumes files from (resp. to) raw to vol.
    • ofs2off: convert OFS mesh format towards a OFF variant.

  • estimators:

    • lengthEstimator: program to generate multigrid analysis of length estimators.
    • tangentBC: tangent estimator using the Binomial convolver.
    • curvatureBC: curvature estimator using the Binomial convolver.
    • curvatureMCMS: curvature estimator using the maximal segments cover (to be updated for current DGtal version).
    • estimatorComparator: program to perform comparison of local quantity estimators (to be updated for current DGtal version).
    • vol2normalField: compute the normal vector field of a given vol file .

  • shapeGenerator:

    • shapeGenerator: generate multigrid shape
    • contourGenerator: generate multigrid shape contours

  • visualization:

    • 3dVolViewer: volume file (.vol and .pgm3d) viewer with QGLViewer.
    • displayContours: display discrete contours from various format (.fc (freemanchain), .sdp).
    • meshViewer: display 3D mesh from OFS or OFF format.

  • volumetric:

    • 3dVolMarchingCubes: marching cubes form a Vol file
    • homotopicThinning3D: ultimate skeleton from vol file

  • *volumetric:

    • volAddBorder: add a 1 voxel boundary with value 0 to a vol file.
    • volCComponentCounter: a simple program to count the number of connected components in a 3D image.
    • volSubSample: sub sample a vol file (division by 2 in each direction).