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DGtalTools 1.4 (beta)

DGtalTools 1.3

  • build

    • New cmake option (DGTAL_RANDOMIZED_BUILD_THRESHOLD) to set the (approximated) % of tools build (Bertrand Kerautret #416)
  • 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).