self_checkHOMCLOUD_USE_BUILTIN_BOOST_CGAL environmental variable
is set to 1 when HomCloud is installed.Volume.birth_position, Volume.death_position, Volume.points, Volume.boundary_points, Volume.boundary, Volume.boundary_points, Volume.cells, Volume.simplices, Volume.cubes, Volume.boundary_loop,Optimal1Cycle.path, Optimal1Cycle.boundary_pointsGraphOptimal1Cycle.boundary_pointsinterface.Volume.dump_to_dict and interface.Volume.restore_from_dictupper_valueinterface.Volume.boundary_loopinterface.Volume.boundary_loop_symbolsCPLEX_PY is now available from interface.Pair.optimal_volume and interface.Pair.stable_volumesolver_options of interface.Pair.optimal_volume and interface.Pair.stable_volumehomcloud.interface.Volume.to_pyvista_boundary_mesh and homcloud.interface.Volume.to_pyvista_volume_mesh have adjust_periodic_boundary parameterhomcloud.pict.show_volume2dhomcloud.interface.PDList.from_simplicial_levelset to create a filtration from a simplicial level function.diagram and .idiagram files loaderhomcloud.optimal_cycle moduleinterface.BitmapPHTrees.rootsinterface.PD.torch_tensor_tensor_birth_death (for bitmap and alpha)interface.PD.alpha_squaredsquared in interface.PDList.from_alpha_filtration. This paramter is equivalent to not no_square.save_cocycles argument to interface.PDList.from_rips_filtrationtorelance argument to interaface.Pair.optimal_1_cyclebgcolor in paraview_interface.show. We can specify the background color by this paramterinterface.PHTrees.all_nodes to get all nodes of the treeinterface.PHTrees.Node.stable_volume_informationresults field is renamed to resultinterface.Optimal1Cycle.to_pvnode is now available for alpha filtrationhomcloud.pict.pixel_levelset_nd.pdgm. This format is more recommended than .idiagram.optvol. This is the alternative module of optimal_volume for .pdgm format PD file.--no-dipha optionbuild_phtrees and phtrees. These are successors of full_ph_trees, query_pht, and query_full_phtrees.--save-phtrees option to pc_alphainterface.PDList.from_alpha_filtration accepts a new parameter save_phtrees to save PH-trees to .pdgm file.plot_PD and interface modules can plot essential pairs.pict.tree module can output .pdgm format fileload_indexed_pairs parameter to interface.PDList.dth_diagramHistoSpec.histogram_from_vectorinterface.Pair.ph0_componens and interface.PH0Componentsinterface.PDList.from_bitmap_levelset supports periodic boundary conditioninterface.distance_transform supports periodic boundary condition.diagram, .icomplex and .complex formatabstract_filtration module drops the support of .idiagram format
.pdgm for output formatrips modules drops the support of .idiagram format
.pdgm for output format-S option to off in dump_diagrampict.optimal_one_cycle drops the support of .idiagram format and only supports .pdgm formatinterface.Mesh is renamed to interface.HistoSpec
interface.Mesh is marked deprecated, but available nowinterface.PIVectorizerMesh is renamed to interface.PIVectorizeSpec
interface.PIVectorizerMesh is marked deprecated, but available nowinterface.PD.check_coefficient_problem
interface.PDList.check_coefficient_problem insteadinterface.Pair.tightened_volume is renamed to interface.Pair.stable_volumeinterface.Pair.tightened_subvolume is renamed to interface.Pair.stable_subvolumeinterface module now drops the support of .p2mt formatinterface.BitmapPHTreesPair
interface.BitmapPHTrees.for_bitmap_levelset instead to build bitmap ph-treesinterface.PDList.bitmap_phtrees instead to load bitmap ph-treespict.tree module does not supports .p2mt format. Use .pdgm format insteadinterface module, the default PD file format is changed from .idiagram to .pdgminterface module, the following functionalities only support .pdgm format and drop the support of .idiagram format
.idiagram from 3 to 4.--periodic option)--no-paraview optionpict.binarize, pict.binarize3d, pict.pixel_levelset are now marked as obsolete-u and -l options from pict.pixel_levelset_ndinterface.Pair.optimal_volume raises exception if an optimal volume is not
foundparaview_interface.PointCloudparaview_interface.PolyLine to draw polylinesparaview_interface.PipelineNode.set_colorparaview_interfaceoptimal_volume modulepict.slice3d-D option is strongly recommended by pc_alpha, binarize_nd,
and pixel_levelset_ndidiagram2diagram to convert a .idiagram file to
a .diagram file.abstract_filtration to construct a input directly
from boundary mapsinterface.show_slice3d to display voxel data by slicesinterface.Mesh accepts superclass parameter.plot_diagram and diagram_to_text are now obsolete.interface.Mesh class accepts "superlevel" parameter.scipy.misc.imread and imsave and use imageio insteadinterface.distance_transform is now available
interface.PDList.from_bitmap_distance_transform and
interface.BitmapPHTreesPair.from_bitmap_distance_transform are now obsolete.--tight-layout option to plot_PD module and you should useax parateter to interface.SlicedHistogram.plot()interface.PIVectorizerMesh.vector_size()
PIVectorizerMeshinterface.MaskHistogram.--dpi option to view_vecotrized_PD.pict.optimal_one_cycle and its interface to
interface module.marker_size parameter to interface.draw_volumes_on_2d_image.optimal_volume.homcloud.rips module.
homcloud.interface also supports VR filtrations--vertex-symbols option of homcloud.pc_alphahomcloud.dump_diagram by
-s optionhomcloud.optimal_volume and homcloud.query_pht
now contains symbolic representations of points, simplices,
boundary, boundary-points. The names are points-symbols,
simplices-symbols, boundary-symbols, and boundary-points-symbols.homcloud.view_index_pict3d. This program is useful by combining
other visualization program homcloud.pict.pict3d_vtkoptimal_volume supports --threads option to specify the number of threads
for LP solver.homcloud-pc-alpha modulehomcloud-pc-alpha moduleoptimal_cycle module
--owned-volume--tightened-volume--tightened-subvolumeplot_PD_gui--no-optimal-volume option to optimal_cycle modulepict.slice3d to show the 3D npy data by 2d slice images.-S option in pict.show_volume_2dplot_PD_gui suuports the folloiwng options: --power, -l, --loglog,
-m, --colormapplot_PD_gui correctly treats -y and -Y optionsplot_PD_guihomcloud-base package and homcloud-advanced packagepc2diphacomplex to pc_alpha (pc2diphacomplex is now also available for
backward compatibility)-p (--periodic) option for pict.binarize_nd and pict.pixel_levelset_ndview_birth_death_simplices moduleoptimal_cycle module, you should compute a .idiagram file
with -M option to compute a volume optimal cycle-n option in pc2diphacomplexHOMCLOUD_USE_CUBICALRIPSER to 1 if you want to use
them.-E (--show-essential-pairs) optionplot_PD_guifull_ph_treepict.show_volume_2dplot_PD_sliceplot_diagrampict.show_volume_2dview_index_pict_gui to use the same color as other programsview_index_pict:
--birth-color, --death-color, and --line-color.view_index_pict, the default value of -s option is changed from 3 to 1HOMCLOUD_PARAVIEW_PROGRAMNAMEoptimal_cycleoptimal_cycle--optimal-cycle-options option to plot_PD_gui--reorder-process option to vectorized_PDfull_ph_tree and pict.treepict.tree--text-output option to plot_PD_sliceoptimal_cycleoptimal_cycleplot_PD_slice--aspect option to plot_PD and plot_PD_guiph_tree and birth_death_area modules
--optimal-cycle option to plot_PD_gui__init__.py and use PEP-420-j option to full_ph_treepc2diphacomplexvectorize_PDwrite-volume-simplices-in-rectangle command to query_full_ph_treequery_full_ph_treewrite-volume-points-in-rectangle command to query_full_ph_treemerge_tree_levelset module to compute persistence-merge-tree--vmin to plot_PDplot_PD_GUIfull_ph_treeplot_PD_gui can browse an output by full_ph_treeph_tree and birth_death_area are now obsolete. Please use full_ph_tree and query_full_ph_tree.plot_PD_gui--font-size option to plot_PDplot_PD accept empty titlepict.binarize_nd and pict.pixel_levelset_nd accept npy foramt file-M option to view_index_pictview_index_pict_gui (Thanks for Ichinomiya's bug report)-S option to view_index_pictpict.pixel_levelset_nd and pict.binarize_ndplot_PD_guiph_tree, full_ph_tree, and query_full_ph_tree programsplot_PD program to show some addition information
on the diagramview_vectorized_PD program. This program shows the vectorized PD by
vectorize_PD.view_birth_death_simplices. This program shows the birth/death simplices
computed from a 3D point cloud.-V|--version option to show version-v and -H option into view_index_pict--no-label option to view_index_pict not to draw birth/death values labelsChange the commandline optionss of plot_PD
Add the following options instead
-x|--x-range X_RANGE-X|--xbins XBINS-y|--y-range Y_RANGE-Y|--ybins YBINS