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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fix doc/conf.py |
files | doc/conf.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Change all http to https in doc/get-build-install.rst |
files | doc/get-build-install.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Disable building e/a/alphashapes2d-periodic |
files | examples/alphashapes/CMakeLists.txt |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fix a few compilation issues |
files | CMakeLists.txt bindings/python/CMakeLists.txt examples/homology-zigzags/CMakeLists.txt examples/homology-zigzags/rips-pairwise-zz.cpp examples/homology-zigzags/rips-pairwise.cpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Add .build.yml |
files | .build.yml |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Make dionysus-link depend on dionysus |
files | bindings/python/CMakeLists.txt |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Comment out explicit typedefs to make GCC happy |
files | include/utilities/consistencylist.h include/utilities/orderlist.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Use boost/next_prior.hpp with Boost >= 1.67 |
files | bindings/python/optional.h include/geometry/kinetic-sort.h include/topology/chain.hpp include/topology/cohomology-persistence.hpp include/topology/rips.hpp include/topology/static-persistence.hpp include/topology/zigzag-persistence.hpp include/utilities/boost.h include/utilities/consistencylist.h include/utilities/eventqueue.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Get rid of Boost.Signals dependency |
files | CMakeLists.txt examples/ar-vineyard/CMakeLists.txt examples/ar-vineyard/ar-vineyard.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Add CGAL pre-4.11 support back to e/a/alphashapes3d-periodic |
files | examples/alphashapes/alphashapes3d-periodic.hpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Vanessa's fix for e/a/alphashapes3d-periodic for CGAL 4.11 |
files | examples/alphashapes/alphashapes3d-periodic.hpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Add Vanessa Robins' periodic alpha shapes 2D code |
files | examples/alphashapes/CMakeLists.txt examples/alphashapes/alphashapes2d-periodic.cpp examples/alphashapes/alphashapes2d-periodic.h examples/alphashapes/alphashapes2d-periodic.hpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Add Vanessa Robins' periodic alpha shapes code |
files | examples/alphashapes/CMakeLists.txt examples/alphashapes/alphashapes3d-periodic.cpp examples/alphashapes/alphashapes3d-periodic.h examples/alphashapes/alphashapes3d-periodic.hpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Add a note about Dionysus 2 to the docs |
files | doc/index.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merge |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added a practical guide slides and examples to the docs |
files | doc/.static/dionysus-examples.tgz doc/.static/dionysus-slides.pdf doc/index.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Remove 'hg up tip' from doc/get-build-install.rst |
files | doc/get-build-install.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merge dev into default, to avoid the need for 'hg up tip' after clone |
files | FindCGAL.Makefile examples/grid/CMakeLists.txt examples/grid/combustion-vineyard.cpp examples/grid/grid2D.h examples/grid/grid2D.hpp examples/grid/grid2Dvineyard.h examples/grid/grid2Dvineyard.hpp examples/grid/pdbdistance-vineyard.cpp examples/grid/pdbdistance.h examples/grid/test-grid2D.cpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Add LICENSE + LEGAL |
files | LEGAL LICENSE |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Add register_ptr_to_python to PersistenceDiagram bindings to match changes in Boost.Python |
files | bindings/python/persistence-diagram.cpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fix compilation with Boost 1.58 (load_construct_data_adl error) |
files | include/topology/simplex.hpp |
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user | "Arnur Nigmetov <a.nigmetov@gmail.com>" |
description | Added executable to compute Wasserstein distance. Powering to 1/q is done in output. Maybe, should be changed in the function itself? |
files | examples/bottleneck-distance.cpp tools/matching/CMakeLists.txt tools/matching/bottleneck.cpp tools/matching/wasserstein.cpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Disabled glibcxx specific concept checks |
files | include/utilities/binaryheap.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Dave Millman's fix for and rlog problem |
files | include/utilities/log.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Increase template depth to fix a bug with XCode 5 |
files | CMakeLists.txt |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Brit Fasy's fix to compile with logging=on |
files | include/utilities/log.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | lscubes.py output infinite pairs + small bugfix |
files | examples/pl-functions/lscubes.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed non-POD array problem in homology-zigzags |
files | examples/homology-zigzags/M-ZZ.cpp examples/homology-zigzags/dM-ZZ.cpp examples/homology-zigzags/iR-ZZ.cpp examples/homology-zigzags/oR-ZZ.cpp examples/homology-zigzags/rips-pairwise.cpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added homology zigzags by Steve Oudot and Don Sheehy |
files | examples/CMakeLists.txt examples/homology-zigzags/CMakeLists.txt examples/homology-zigzags/M-ZZ.cpp examples/homology-zigzags/README examples/homology-zigzags/dM-ZZ.cpp examples/homology-zigzags/iR-ZZ.cpp examples/homology-zigzags/oR-ZZ.cpp examples/homology-zigzags/rips-pairwise.cpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added standalone bottleneck-distance.cpp |
files | examples/CMakeLists.txt examples/bottleneck-distance.cpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Dave Millman's fixes to compile with LLVM-based compilers |
files | CMakeLists.txt examples/alphashapes/alphashapes2d.hpp examples/alphashapes/alphashapes3d.hpp include/geometry/kinetic-sort.h include/geometry/kinetic-sort.hpp include/geometry/simulator.h include/geometry/simulator.hpp include/topology/dynamic-persistence.h include/topology/dynamic-persistence.hpp include/topology/filtration.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added CGAL_USE_FILE + added option use_cgal |
files | CMakeLists.txt bindings/python/CMakeLists.txt examples/alphashapes/CMakeLists.txt |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Bug in show_diagram() with empty diagrams |
files | bindings/python/dionysus/viewer/diagram.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | subcomplex in show_complex() + pan/zoom in ComplexViewer2D |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/complex2d.py bindings/python/dionysus/viewer/complex3d.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | DiagramViewer can show multiple diagrams at once |
files | bindings/python/dionysus/viewer/diagram.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | CohomologyPersistence returns dying cocycles + StaticCohomologyPersistence records them and normalizes coefficients + minor changes |
files | bindings/python/cohomology-persistence.cpp bindings/python/dionysus/adaptor.py bindings/python/dionysus/circular/__init__.py bindings/python/dionysus/viewer/PyGLWidget.py bindings/python/dionysus/viewer/complex3d.py doc/python/cohomology-persistence.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Display lists in ComplexViewer3D + circular.smooth() raises exceptions |
files | bindings/python/dionysus/circular/__init__.py bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/complex3d.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Set center and radius in ComplexViewer3D |
files | bindings/python/dionysus/viewer/complex3d.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Points at infinity in DiagramViewer |
files | bindings/python/dionysus/viewer/diagram.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed scale points in the diagram + noise filtering |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/diagram.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added pan + zoom to diagram viewer; show_diagram() didn't return; added PyQt, PyOpenGL, NumPy as dependencies in the docs |
files | bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/diagram.py doc/get-build-install.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Straightened out QApplication problems (made it global) |
files | bindings/python/dionysus/viewer/PyGLWidget.py bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/complex.py bindings/python/dionysus/viewer/complex2d.py bindings/python/dionysus/viewer/complex3d.py bindings/python/dionysus/viewer/diagram.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Started show_complex_3D() |
files | bindings/python/dionysus/viewer/PyGLWidget.py bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/complex3d.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed bugs in diagram.py and adaptor.py + added coloring of points in show_complex_2D(); Filtration can be initialized from iterator without comparison |
files | bindings/python/dionysus/adaptor.py bindings/python/dionysus/circular/__init__.py bindings/python/dionysus/viewer/complex.py bindings/python/dionysus/viewer/diagram.py bindings/python/filtration.cpp include/topology/filtration.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added viewer.show_complex_2D + center points in the persistence diagram |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/complex.py bindings/python/dionysus/viewer/diagram.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Moved dionysus.circular into its own subdirectory + added dionysus.viewer |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/circular.py bindings/python/dionysus/circular/__init__.py bindings/python/dionysus/circular/lsqr.py bindings/python/dionysus/lsqr.py bindings/python/dionysus/viewer/__init__.py bindings/python/dionysus/viewer/diagram.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added docs for StaticCohomologyPersistence + ImagePersistence + circular.smooth + minor fixes in adaptor.py |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/adaptor.py doc/python/cohomology-persistence.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added smooth() to Python binding + fixed a bug in adaptor.py |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/adaptor.py bindings/python/dionysus/circular.py bindings/python/dionysus/lsqr.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged upstream |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added adaptor for StaticCohomologyPersistence and ImagePersistence |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/adaptor.py bindings/python/zigzag-persistence.cpp include/topology/image-zigzag-persistence.h include/topology/zigzag-persistence.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added a note about reducing matrix Z in i/t/zigzag-persistence.hpp |
files | include/topology/zigzag-persistence.hpp |
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description | Merge |
files | tools/CMakeLists.txt |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added store_negative argument to StaticPersistence.pair_simpices() |
files | bindings/python/static-persistence.cpp doc/python/static-persistence.rst examples/triangle/triangle.py include/topology/static-persistence.h tools/CMakeLists.txt |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added a note about wasserstein_distance() to documentation + cleaned up docs for init_diagrams() |
files | doc/python/persistence-diagram.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Inlcuded munkres.cpp from munkres.h + matrix.cpp -> matrix.hpp |
files | bindings/python/CMakeLists.txt include/utilities/munkres/matrix.cpp include/utilities/munkres/matrix.hpp include/utilities/munkres/munkres.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added wasserstein_distance() |
files | bindings/python/CMakeLists.txt bindings/python/persistence-diagram.cpp include/topology/persistence-diagram.h include/topology/persistence-diagram.hpp include/utilities/munkres/matrix.cpp include/utilities/munkres/matrix.h include/utilities/munkres/munkres.cpp include/utilities/munkres/munkres.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Exposed init_diagrams() to Python |
files | bindings/python/dionysus/__init__.py bindings/python/filtration.h bindings/python/persistence-diagram.cpp bindings/python/static-persistence.cpp doc/python/alphashapes.rst doc/python/persistence-diagram.rst include/topology/persistence-diagram.h include/topology/persistence-diagram.hpp |
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description | Minor changes to compile with GCC 4.7 |
files | include/topology/simplex.hpp include/utilities/indirect.h tools/CMakeLists.txt |
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description | Added cohomology/candidates counter to i/t/cohomology-persistence.hpp |
files | include/topology/cohomology-persistence.hpp |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Minor fixes in tools/draw-diagram |
files | tools/draw-diagram/draw.py tools/draw-diagram/pd.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | alphashapes2d can handle degenerate inputs (thanks to Taras Galkovskyi for the bug report and the fix) |
files | examples/alphashapes/alphashapes2d.hpp |
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description | Fixed combinations in closure() for older versions of Python |
files | bindings/python/dionysus/__init__.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | closure() in Python can handle simplex data |
files | bindings/python/dionysus/__init__.py |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed a typo in b/p/persistence-diagram.cpp |
files | bindings/python/persistence-diagram.cpp |
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description | Added a note about GPL to the documentation |
files | doc/index.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Cleaned up CMake files to play nice with CGAL |
files | bindings/python/CMakeLists.txt examples/alphashapes/CMakeLists.txt examples/ar-vineyard/CMakeLists.txt examples/pl-functions/CMakeLists.txt |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Cleaned up PersistenceDiagram bindings |
files | bindings/python/persistence-diagram.cpp include/topology/persistence-diagram.h |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed a link to SYNAPS |
files | README |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged in Python bindings for DynamicPersistenceChains |
files |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added documentation for DynamicPersistenceChains |
files | doc/python/static-persistence.rst |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added Python bindings for DynamicPersistenceChains |
files | bindings/python/CMakeLists.txt bindings/python/chain.cpp bindings/python/chain.h bindings/python/dionysus.cpp bindings/python/dynamic-persistence.cpp bindings/python/dynamic-persistence.h bindings/python/static-persistence.cpp bindings/python/static-persistence.h examples/triangle/triangle-chains.py |
changeset | 04a4629979da |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added the ability to pickle Simplex class in Python |
files | bindings/python/dionysus/__init__.py bindings/python/simplex.cpp |
changeset | 6a222607714c |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added ability to iterate over ZigzagPersistence cycles in Python |
files | bindings/python/zigzag-persistence.cpp doc/python/zigzag-persistence.rst include/topology/zigzag-persistence.h |
changeset | ed3905be234f |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed a typo in the documentation of SPNode.cycle |
files | doc/python/static-persistence.rst |
changeset | 12e2daa0e03a |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added Python closure function (for computing a k-skeleton of a closure of a list of simplices) |
files | bindings/python/dionysus/__init__.py |
changeset | c1e2626cde8f |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Removed the unnecessary typename in filtration-homology.cpp |
files | examples/filtration/filtration-homology.cpp |
changeset | 574a165c0a9c |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added output of essential cycles for any given input filtration |
files | examples/CMakeLists.txt examples/filtration/CMakeLists.txt examples/filtration/filtration-homology.cpp |
changeset | d4c3991a2462 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Minor touches in documentation |
files | doc/conf.py doc/python/persistence-diagram.rst |
changeset | 8f6fb2ad57f7 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged docs with upstream |
files |
changeset | 3d54247cbccf |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | CGAL is unncessary for vineyards (update in the documentation) |
files | doc/get-build-install.rst |
changeset | fdfde7291a0f |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged in Aravind's changes |
files |
changeset | 9ea8d4630907 |
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branch | dev |
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user | Aravindakshan Babu <akshan@stanford.edu> |
description | Changed the first iterator of PersistenceDiagram to accept dimension as well. Modified documentation. |
files | bindings/python/persistence-diagram.cpp doc/python/overview.rst doc/python/persistence-diagram.rst doc/python/point.rst |
changeset | d07d77561661 |
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user | Aravindakshan Babu <akshan@stanford.edu> |
description | Removed the points iterator in PersistenceDaigram; replaced it with a __iter__ method. Got rid of some python code in __init__.py, since it was not needed with the above change. Changed the docs to reflect this. |
files | bindings/python/dionysus/__init__.py bindings/python/persistence-diagram.cpp doc/python/persistence-diagram.rst |
changeset | 5311343eb2f5 |
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branch | dev |
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user | Aravindakshan Babu <akshan@stanford.edu> |
description | Added documentation for the python classes Point and PersistenceDiagram. Removed the __sub__ method for PersistenceDiagram. Minor renaming. Renamed BottleneckDistance to bottleneck_distance. Renamed intervals iterator for PersistenceDiagram to points. Seems in better conformance with usage. |
files | bindings/python/dionysus/__init__.py bindings/python/persistence-diagram.cpp doc/python/overview.rst doc/python/persistence-diagram.rst doc/python/point.rst |
changeset | 4f70a473e34b |
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branch | dev |
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tag | |
user | Aravindakshan Babu <akshan@stanford.edu> |
description | Added a __iter__ method to the PersistenceDiagram class in python. Renamed the points iterator to the intervals iterator. |
files | bindings/python/dionysus/__init__.py bindings/python/persistence-diagram.cpp |
changeset | 64a272a34cb2 |
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branch | dev |
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tag | |
user | Aravindakshan Babu <akshan@stanford.edu> |
description | Added extra functionality to Point class( an iterator ) and PersistenceDiagram( dimension property and __len__ func ). persistence-diagram.h: Added a new read-only dimension member and member function to access it. With a new constructor that that takes in an int type to initialize dimension. persistence-diagram.cpp: Added new bp::init constructor. Takes in an integer type to initialize the dimension. Exposed the dimension property. Exposed the size property via a __len__ method. __init__.py: Added an iterator for Point objects. This iterates over the coords and then the data( if present ). |
files | bindings/python/dionysus/__init__.py bindings/python/persistence-diagram.cpp include/topology/persistence-diagram.h |
changeset | 7aefb2d67203 |
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branch | dev |
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user | Aravindakshan Babu <akshan@stanford.edu> |
description | Made the data argument in Point's __init__method to be an optional argument by making it a boost::python::optional. |
files | bindings/python/persistence-diagram.cpp |
changeset | e94d521b72bb |
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branch | dev |
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tag | |
user | Aravindakshan Babu <akshan@stanford.edu> |
description | Added code to expose the persistence_diagram class, the bottleneck_distance function and the point class to python. Most of the commonly used methods for each class have been exported. The constructor for point now requires that a data argument be provided along with x and y coord. This needs to be made optional. The constructor for persistence_diagram could possibly be rewritten as well. |
files | bindings/python/CMakeLists.txt bindings/python/dionysus.cpp bindings/python/persistence-diagram.cpp |
changeset | ee0dca73ea47 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged docs with upstream |
files |
changeset | 3568e0bfe2cd |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Removed the warning about compiler versions (seems unnecessary after Andrew's fixes) |
files | doc/get-build-install.rst |
changeset | 291f6edf27b9 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed path for lsfiltration.py |
files | doc/examples/index.rst |
changeset | 347b3461965a |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Bug in the tutorial: simplices = [] -> simplices = Filtration() |
files | doc/tutorial.rst |
changeset | e84354d3a6c9 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | More typos in the docs |
files | doc/python/rips.rst |
changeset | 324354e0d3bf |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed a link: dionysis -> dionysus |
files | doc/python/simplex.rst |
changeset | 36ea2751f290 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Andrew Yarmola's fix to the in-class intialization syntax in OrderList<T> |
files | include/utilities/orderlist.h include/utilities/orderlist.hpp |
changeset | 6f1ed27850c8 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added Persistence::initialize(f) + fixed minor bug LinearKernel::sign_at_negative_infinity() |
files | include/geometry/linear-kernel.h include/geometry/weighted-l2distance.h include/topology/dynamic-persistence.h include/topology/dynamic-persistence.hpp include/topology/static-persistence.h include/topology/static-persistence.hpp |
changeset | 4a80392ab462 |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added insert-at-the-end optimization for CohomologyPersistence::add_cocycle() |
files | include/topology/cohomology-persistence.hpp |
changeset | f5d010aecc97 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Count cocycles in CohomologyPersistence |
files | include/topology/cohomology-persistence.hpp |
changeset | 7653574ff064 |
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branch | dev |
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tag | |
user | Mikael Vejdemo Johansson <mik@math.stanford.edu> |
description | Andrew Yarmola's compilation fix for MacOSX. |
files | examples/consistency/rips-consistency-zigzag.cpp examples/rips/rips-image-zigzag.cpp examples/rips/rips-zigzag.cpp |
changeset | f31527c1f962 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Removed unused instrumentation of cohomology and unnecessary includes |
files | examples/cohomology/rips-explicit-cohomology.cpp examples/cohomology/rips-pairwise-cohomology.cpp |
changeset | a91083de7386 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Removed reference to reference in ThreeOutcomeComparison |
files | include/utilities/indirect.h |
changeset | 4759535221ee |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Made EventQueue into a binary heap (for efficiency and sanity) |
files | .issues/ebda8db3f9908e33/new/1265605942.M759644P4728Q1.vine include/geometry/kinetic-sort.hpp include/geometry/simulator.h include/geometry/simulator.hpp include/utilities/binaryheap.h include/utilities/eventqueue.h tests/geometry/test-eventqueue.cpp |
changeset | 73e8dce642be |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Replaced list with multi_index representation in EventQueue making it more efficient |
files | .issues/ebda8db3f9908e33/new/1221008555.M637662P30017Q16.cole .issues/ebda8db3f9908e33/new/1265568370.M269870P17954Q1.vine include/geometry/kinetic-sort.hpp include/geometry/simulator.h include/geometry/simulator.hpp include/topology/lsvineyard.h include/topology/lsvineyard.hpp include/utilities/eventqueue.h tests/geometry/test-eventqueue.cpp tests/geometry/test-ksort-linear.cpp |
changeset | 2bde4c56101c |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Switched to internal KineticSort |
files | examples/pl-functions/combustion-vineyard.cpp examples/pl-functions/pl-vineyard.cpp examples/pl-functions/test-grid2D-vineyard.cpp include/geometry/kinetic-sort.h include/geometry/kinetic-sort.hpp include/geometry/simulator.h include/geometry/simulator.hpp include/topology/lsvineyard.h include/topology/lsvineyard.hpp |
changeset | e95766342e5f |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added linear kernel for my own KineticSort |
files | include/geometry/linear-kernel.h tests/geometry/CMakeLists.txt tests/geometry/test-ksort-linear.cpp |
changeset | 29fbad86aff6 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Commented out QField to get rid of the artifical dependence on GMP |
files | include/topology/field-arithmetic.h |
changeset | 5303ce3f1934 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed non-copyable temporary bug |
files | include/topology/dynamic-persistence.hpp include/topology/static-persistence.hpp |
changeset | 8a6f3ef2c42d |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed the duplicates (degeneracy) and another assertion problem in LSVineyard |
files | include/topology/lsvineyard.hpp |
changeset | 6c2a98fb8990 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Removed a buggy assertion in LSVineard::transpose_vertices() (j points at the end() when moving the last simplex of the filtration) |
files | include/topology/lsvineyard.hpp |
changeset | 7198c9bf279d |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | StaticPersistence::pair_simplices() has an option to not display progress (LSVineyard uses it during consistency checking) |
files | bindings/python/static-persistence.cpp include/topology/lsvineyard.hpp include/topology/static-persistence.h include/topology/static-persistence.hpp |
changeset | 19d35448c7c7 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added rips-explicit-cohomology |
files | examples/cohomology/CMakeLists.txt examples/cohomology/rips-explicit-cohomology.cpp |
changeset | 2d8fba6d1d58 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Moved lsfiltration.py into examples/pl-functions + added lscubes.py example (cubical lower-star filtration) |
files | examples/lsfiltration.py examples/pl-functions/cube.py examples/pl-functions/lscubes.py examples/pl-functions/lsfiltration.py |
changeset | 6edd7c861bc0 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed Python constructor of CohomologyPersistence + minor changes to cocycle.py |
files | bindings/python/cohomology-persistence.cpp examples/cohomology/cocycle.py |
changeset | e867c6cf02ef |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | vertex_coface -> vertex_cofaces in Rips documentation (in Python) |
files | doc/python/rips.rst |
changeset | 23cb832e035d |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Henry Adams' fixes to python/dionysus/zigzag.py + added CohomologyPersistence.show_cocycles method |
files | bindings/python/cohomology-persistence.cpp bindings/python/dionysus/zigzag.py |
changeset | 25e468323d77 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | CohomologyPersistence::add returns the dying cocycle |
files | bindings/python/cohomology-persistence.cpp examples/alphashapes/alphashapes3d-cohomology.cpp examples/cohomology/output.h examples/cohomology/rips-cohomology.cpp examples/cohomology/rips-pairwise-cohomology.cpp examples/cohomology/rips-weighted-cohomology.cpp examples/cohomology/triangle-cohomology.cpp include/topology/cohomology-persistence.h include/topology/cohomology-persistence.hpp |
changeset | 6d81d6ae7a3b |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Check Boost version in include/utilities/property-maps.h + minor changes to cocycle.py |
files | examples/cohomology/cocycle.py include/utilities/property-maps.h |
changeset | 7241b887eabb |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added pl-vineyard documentation |
files | doc/examples/index.rst doc/examples/pl-vineyard.rst doc/get-build-install.rst doc/index.rst |
changeset | a5e726461d3f |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea: * added program options to pdbdistance-vineyard * pdbdistance-vineyard takes frame list in a file * more logging * verification of pairing after vertex transpositions (commented out) |
files | examples/pl-functions/CMakeLists.txt examples/pl-functions/pdbdistance-vineyard.cpp include/topology/dynamic-persistence.h include/topology/dynamic-persistence.hpp include/topology/filtration.h include/topology/lsvineyard.h include/topology/lsvineyard.hpp |
changeset | 0ca59b0ebc47 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Moved files around: lsvineyard.h -> include/topology, examples/grid -> examples/pl-functions |
files | examples/CMakeLists.txt examples/grid/CMakeLists.txt examples/grid/combustion-vineyard.cpp examples/grid/grid2D.h examples/grid/grid2D.hpp examples/grid/lsvineyard.h examples/grid/lsvineyard.hpp examples/grid/pdbdistance-vineyard.cpp examples/grid/pdbdistance.h examples/grid/pl-vineyard.cpp |
changeset | 451748b3c888 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged Vineyards code changes with the main development line |
files | doc/tutorial.rst examples/alphashapes/alphashapes3d-cohomology.cpp examples/alphashapes/alphashapes3d.cpp examples/cohomology/rips-pairwise-cohomology.py examples/grid/grid2Dvineyard.h examples/grid/grid2Dvineyard.hpp examples/rips/rips-pairwise.cpp examples/rips/rips-weighted.cpp examples/triangle/triangle-zigzag.py include/topology/chain.hpp |
changeset | 1ee6edc17cb6 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Python bindings work again |
files | bindings/python/alphashapes2d.cpp bindings/python/alphashapes3d.cpp bindings/python/chain.cpp bindings/python/dionysus.cpp bindings/python/dionysus/__init__.py bindings/python/filtration.cpp bindings/python/filtration.h bindings/python/simplex.cpp bindings/python/simplex.h bindings/python/static-persistence.cpp |
changeset | 27508309a680 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Created pl-vineyard.cpp to compute vineyards given a complex and a sequence of values at each vertex |
files | examples/grid/CMakeLists.txt examples/grid/grid2D.h examples/grid/lsvineyard.h examples/grid/lsvineyard.hpp examples/grid/pl-vineyard.cpp include/topology/vineyard.h include/topology/vineyard.hpp |
changeset | d15c6d144645 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Resurrected vineyard code: * Switched StaticPersistence + (serializable) Filtration to Boost.MultiIndex * Updated DynamicPersistenceTrails to work with the new MultiIndex way * Created LSVineyard class, and fixed the grid examples |
files | examples/CMakeLists.txt examples/alphashapes/alphashapes2d.cpp examples/alphashapes/alphashapes2d.h examples/alphashapes/alphashapes2d.hpp examples/alphashapes/alphashapes3d.cpp examples/alphashapes/alphashapes3d.h examples/alphashapes/alphashapes3d.hpp examples/cech-complex/cech-complex.cpp examples/fitness/avida-distance.cpp examples/fitness/avida-rips-distance.cpp |
changeset | cc0c26fba495 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Made storing negative simplices in StaticPersistence parameter-based, so that DynamicPersistence works again |
files | include/topology/dynamic-persistence.hpp include/topology/static-persistence.h include/topology/static-persistence.hpp |
changeset | b5f2e93fa75c |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | StaticPersistence operates on chains consisting of only positive simplices |
files | include/topology/static-persistence.hpp |
changeset | 64177e8ef379 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | alphashapes3d.cpp measures persistence time |
files | examples/alphashapes/alphashapes3d.cpp |
changeset | 6a649c2bea0e |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed DynamicPersistenceTrails::PairingTrailsVisitor to match the changes in StaticPersistence::PairVisitor |
files | include/topology/dynamic-persistence.h include/topology/dynamic-persistence.hpp |
changeset | 3f1034dca432 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Instrumented code for counting: * added counters to addition in cohomology and ChainWrapper * rips-pairwise-cohomology counts the maximum elements stored in the cycles * added alphashapes3d-cohomology * moved progress_display from DynamicPersistence to StaticPersistence |
files | examples/alphashapes/CMakeLists.txt examples/alphashapes/alphashapes3d-cohomology.cpp examples/alphashapes/alphashapes3d.cpp examples/cohomology/rips-pairwise-cohomology.cpp examples/rips/rips-pairwise.cpp include/topology/chain.hpp include/topology/cohomology-persistence.hpp include/topology/dynamic-persistence.h include/topology/static-persistence.h include/utilities/counter.h |
changeset | 5fd3f43e6fbf |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added arbitrary coefficients in boundaries (to C++ and Python) + cleaned up CohomologyPersistence.add overloading in Python |
files | bindings/python/cohomology-persistence.cpp doc/python/cohomology-persistence.rst examples/cohomology/rips-pairwise-cohomology.py include/topology/cohomology-persistence.h include/topology/cohomology-persistence.hpp include/topology/field-arithmetic.h |
changeset | a6605dc232f2 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added image persistence functionality to CohomologyPersistence |
files | bindings/python/cohomology-persistence.cpp doc/python/cohomology-persistence.rst include/topology/cohomology-persistence.h include/topology/cohomology-persistence.hpp |
changeset | a172b960aaaa |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added draw.py under tools/draw-diagram |
files | doc/get-build-install.rst tools/draw-diagram/draw.py tools/draw-diagram/pd.py |
changeset | e8b6706cedfc |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added link to CVXOPT in get-build-install documentation + progress bar to rips-pairwise-cohomology |
files | doc/get-build-install.rst doc/index.rst examples/cohomology/rips-pairwise-cohomology.cpp |
changeset | c0bf4675697c |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed a typo in documentation + added a warning and a tip about GCC 4.2 on a Mac |
files | doc/get-build-install.rst doc/tutorial.rst |
changeset | 3b0665eb35bc |
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branch | dev |
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user | mridul@ramrod.Stanford.EDU |
description | The if-else cases in lsqr.py were not exhaustive. They become exhaustive by changing ab > aa to ab >= aa. |
files | examples/cohomology/lsqr.py |
changeset | 5a5f3e1c466b |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Removed Qt4 requirement + added link to download and tutorial to the front page of the documentation |
files | doc/get-build-install.rst doc/index.rst doc/tutorial.rst tools/CMakeLists.txt |
changeset | 1f3d54b2315b |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Exposed store argument to CohomologyPersistence.add() in Python |
files | bindings/python/cohomology-persistence.cpp doc/python/cohomology-persistence.rst |
changeset | c3c3c53dfc08 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | cocycle.py uses vertex list, and does not make any assumptions about the vertex-simplex order |
files | examples/cohomology/cocycle.py |
changeset | f7244460f21f |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Consistency zigzag outputs intervals supported over a single complex |
files | examples/consistency/rips-consistency-zigzag.cpp |
changeset | 6cd50e622550 |
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branch | dev |
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tag | |
user | Camille Wormser <camille.wormser@normalesup.org> |
description | explicitely converts a Dimension (short int) into a size_t, for removing a warning |
files | include/topology/rips.hpp |
changeset | eec482c29319 |
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branch | dev |
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tag | |
user | Camille Wormser <camille.wormser@normalesup.org> |
description | Removing unused parameter names in order to avoid warnings -> no warning anymore in zigzag-persistence |
files | include/topology/zigzag-persistence.h include/topology/zigzag-persistence.hpp include/utilities/containers.h |
changeset | 4bfb7c31ab28 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | make-zigzag-subsamples.py doesn't output the union, rips-consistency-zigzag.cpp fixed show_progress |
files | examples/consistency/make-zigzag-subsamples.py examples/consistency/rips-consistency-zigzag.cpp |
changeset | 1b30e507e8aa |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed bugs in cocycle.py introduced when rips-pairwise-cohomology.py was originally added |
files | examples/cohomology/cocycle.py |
changeset | 92318b22ffa5 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed bugs in rips-pairwise-cohomology.py whose origin is unclear to me |
files | examples/cohomology/rips-pairwise-cohomology.py |
changeset | ce2aa05994f0 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged in Chris' changes |
files |
changeset | 700cbac5b23c |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | Modified cohomology code (unweighted and weighted) so that it doesn't use std::map for boundary computations, which should optimize memory usage. |
files | examples/cohomology/CMakeLists.txt examples/cohomology/output.h examples/cohomology/rips-pairwise-cohomology.cpp examples/cohomology/rips-weighted-cohomology.cpp examples/cohomology/wrappers.h |
changeset | f75fb57d2831 |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | Changed implementation of WeightedRips to store simplex values (max distance between simplices' vertices) as an invisible layer on top of each simplex object, so that the data() field of WeightedRips has been freed for use by the users again. |
files | examples/cohomology/rips-weighted-cohomology.cpp examples/rips/rips-weighted.cpp include/topology/simplex.h include/topology/weighted-rips.h |
changeset | 1dde8a05fcd7 |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | Added rips-weighted-cohomology, and channeled WeightedRips logging to the same channel as Rips |
files | examples/cohomology/CMakeLists.txt examples/cohomology/rips-weighted-cohomology.cpp include/topology/weighted-rips.h include/topology/weighted-rips.hpp |
changeset | 8af75817ecbc |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | Merged upstream |
files |
changeset | 7731c42892de |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | Modified WeightedRips::generate() to incorporate the simplex-appearance-value computation (before it would have to be done explicitly by the user by a for-loop after the call to generate()) |
files | examples/rips/rips-weighted.cpp include/topology/weighted-rips.h |
changeset | fdc2835b3e88 |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | added logging to WeightedRips (still needs debugging) |
files | examples/rips/rips-weighted.cpp include/topology/weighted-rips.h include/topology/weighted-rips.hpp |
changeset | 104ea146b9bc |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | Updated weighted rips libraries to make use of OOP--now WeightedRips inherits from Rips. It is possible that logging for WeightedRips does not work. |
files | include/topology/rips.h include/topology/weighted-rips.h include/topology/weighted-rips.hpp |
changeset | eb629d8f00bf |
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branch | dev |
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tag | |
user | Christos Mantoulidis <cmad@stanford.edu> |
description | Added weighted rips code and libraries |
files | examples/rips/CMakeLists.txt examples/rips/rips-weighted.cpp include/geometry/weighted-cechdistance.h include/geometry/weighted-l2distance.h include/topology/weighted-rips.h include/topology/weighted-rips.hpp |
changeset | 3d15aca95dfb |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Simplices are deleted from the complex after removal in triangle-zigzag.py + touched up documentation (to mention CohomologyPersistence better) |
files | doc/ext/__init__.py doc/tutorial.rst examples/triangle/triangle-zigzag.py |
changeset | a99fdaafa31a |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Consistency zigzag outputs intervals for dimensions less than the skeleton dimension only |
files | examples/consistency/rips-consistency-zigzag.cpp |
changeset | d39a20acb253 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Switched PairwiseDistances in Python bindings to C++ |
files | bindings/python/CMakeLists.txt bindings/python/dionysus.cpp bindings/python/dionysus/__init__.py bindings/python/distances.cpp bindings/python/distances.h doc/python/rips.rst doc/tutorial.rst examples/rips/rips-pairwise.py include/geometry/distances.h |
changeset | 4e27f1f7c169 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added Python bindings for CohomologyPersistence (+ example + documentation) |
files | bindings/python/CMakeLists.txt bindings/python/birthid.cpp bindings/python/birthid.h bindings/python/cohomology-persistence.cpp bindings/python/cohomology-persistence.h bindings/python/dionysus.cpp bindings/python/optional.h bindings/python/zigzag-persistence.cpp bindings/python/zigzag-persistence.h doc/examples/cohomology.rst |
changeset | ee096f207dfb |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Minor changes in distances.py + rips-pairwise.py wrapped into a main() function |
files | bindings/python/dionysus/distances.py examples/rips/rips-pairwise.py |
changeset | baa53970eb88 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Disable alphashapes in Python bindings if no CGAL |
files | bindings/python/CMakeLists.txt bindings/python/dionysus.cpp |
changeset | b555e6587908 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Made ListRandomAccessIterator generic with respect to value, and moved it to utils.h |
files | bindings/python/filtration.cpp bindings/python/filtration.h bindings/python/utils.h |
changeset | ae2b1702c936 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Cleaner output in rips-pairwise.cpp + added make-zigzag-subsamples.py + added lsfiltration.py |
files | doc/examples/index.rst examples/consistency/make-zigzag-subsamples.py examples/lsfiltration.py examples/rips/rips-pairwise.cpp include/geometry/l2distance.h |
changeset | cda0b85ffc50 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed plot.py in tools/plot-values |
files | tools/plot-values/plot.py tools/plot-values/scatter.py |
changeset | 9851fee5a33b |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | In documentation put contents into sidebar |
files | doc/index.rst |
changeset | 656ec2838fb8 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Documentation for parametrization using persistent cohomology |
files | doc/examples/cohomology.rst doc/examples/index.rst doc/index.rst |
changeset | 96030f8d2f2c |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Rips pairwise cohomology produces output necessary for 1-cocycle parametrization |
files | examples/cohomology/cocycle.py examples/cohomology/lsqr.py examples/cohomology/output.h examples/cohomology/rips-pairwise-cohomology.cpp tools/plot-values/plot.py tools/plot-values/scatter.py |
changeset | 069596c71902 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added field arithmetic to CohomologyPersistence (Zp + Q) |
files | examples/cohomology/rips-pairwise-cohomology.cpp examples/cohomology/triangle-cohomology.cpp include/topology/cohomology-persistence.h include/topology/cohomology-persistence.hpp include/topology/field-arithmetic.h include/utilities/indirect.h |
changeset | beff535b53ff |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h |
files | examples/cohomology/rips-pairwise-cohomology.cpp examples/consistency/rips-consistency-zigzag.cpp examples/fitness/avida-rips-distance.cpp examples/rips/rips-image-zigzag.cpp examples/rips/rips-pairwise.cpp examples/rips/rips-zigzag.cpp include/geometry/distances.h include/geometry/distances.hpp include/topology/rips.h include/topology/rips.hpp |
changeset | fc8ebbae62e2 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | read_points() does not need ambient dimension and ignores lines starting with '#' |
files | examples/cohomology/rips-pairwise-cohomology.cpp examples/consistency/rips-consistency-zigzag.cpp examples/rips/rips-image-zigzag.cpp examples/rips/rips-pairwise.cpp examples/rips/rips-zigzag.cpp include/geometry/l2distance.h |
changeset | c270826fd4a8 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added documentation; for now mostly for the Python bindings |
files | .hgignore doc/Makefile doc/bibliography.rst doc/conf.py doc/examples/alphashape.rst doc/examples/index.rst doc/examples/rips.rst doc/examples/triangle-zigzag.rst doc/examples/triangle.rst doc/ext/cppdocs.py |
changeset | 7ccecc57688d |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Touch up to compile with GCC 4.4 |
files | include/topology/chain.h include/topology/chain.hpp include/topology/dynamic-persistence.hpp include/topology/static-persistence.hpp |
changeset | 2a737609b8bf |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Cleaned up simplex comparison functions, rip-pairwise.py outputs a diagram, auxilliary add_simplices() + remove_simplices() for zigzags |
files | bindings/python/dionysus/__init__.py bindings/python/dionysus/distances.py bindings/python/dionysus/zigzag.py examples/rips/rips-pairwise.py |
changeset | d9e050258358 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Alphashapes and Python bindings * converted alphashapes2d to the new format * added Python bindings for alphashapes * added sample alphashapes.py that dynamically distinguishes between 2D and 3D |
files | bindings/python/CMakeLists.txt bindings/python/alphashapes2d.cpp bindings/python/alphashapes3d.cpp bindings/python/dionysus.cpp examples/alphashapes/CMakeLists.txt examples/alphashapes/alphashapes.py examples/alphashapes/alphashapes2d.cpp examples/alphashapes/alphashapes2d.h examples/alphashapes/alphashapes2d.hpp examples/alphashapes/alphashapes3d.cpp |
changeset | 580eaa850c4f |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Placed all Python bindings code into dionysus::python namespace |
files | bindings/python/chain.cpp bindings/python/chain.h bindings/python/filtration.cpp bindings/python/filtration.h bindings/python/rips.cpp bindings/python/rips.h bindings/python/simplex.cpp bindings/python/simplex.h bindings/python/static-persistence.cpp bindings/python/static-persistence.h |
changeset | 95454ea3f9c0 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Cleaned up Python bindings to restore functionality: * StaticPersistence is iterable, its nodes are usable (sign, pair, cycle) * StaticPersistence knows how to map its nodes into Filtration indices * moved PythonCmp into utils.h * minor cosmetic changes |
files | bindings/python/chain.cpp bindings/python/chain.h bindings/python/dionysus/__init__.py bindings/python/filtration.cpp bindings/python/filtration.h bindings/python/static-persistence.cpp bindings/python/static-persistence.h bindings/python/utils.h examples/triangle/triangle.py |
changeset | a5fd0c2a1c88 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Renamed header files in bindings/python to get rid of the "python-" prefix |
files | bindings/python/chain.cpp bindings/python/filtration.cpp bindings/python/filtration.h bindings/python/optional.h bindings/python/python-filtration.h bindings/python/python-optional.h bindings/python/python-rips.h bindings/python/python-simplex.h bindings/python/python-static-persistence.h bindings/python/python-zigzag-persistence.h |
changeset | 406c6cc00b9c |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Changes in Python Bindings: * the exposed C++ simplex has Empty data * Python Simplex constructor with data as well as data-based comparison functions are implemented in pure Python |
files | bindings/python/dionysus/__init__.py bindings/python/python-filtration.h bindings/python/python-rips.h bindings/python/python-simplex.h bindings/python/rips.cpp bindings/python/simplex.cpp bindings/python/static-persistence.cpp include/topology/simplex.hpp |
changeset | 3c3e77ac43d2 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added Python bindings for the Rips complex + an example |
files | bindings/python/CMakeLists.txt bindings/python/chain.cpp bindings/python/dionysus.cpp bindings/python/dionysus/__init__.py bindings/python/dionysus/distances.py bindings/python/python-rips.h bindings/python/rips.cpp examples/rips/CMakeLists.txt examples/rips/rips-pairwise.py examples/rips/rips.py |
changeset | 0a2c2283e4a8 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Cleaned up traits (chain and container) for static- and dynamic-persistence |
files | examples/rips/rips-pairwise.cpp examples/rips/rips.cpp include/topology/cycles.h include/topology/dynamic-persistence.h include/topology/dynamic-persistence.hpp include/topology/order.h include/topology/static-persistence.h include/topology/static-persistence.hpp include/utilities/types.h |
changeset | af54138b98fd |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added tools/extract-diagram + minor fixes |
files | examples/rips/rips-pairwise.cpp include/topology/simplex.h tools/CMakeLists.txt tools/extract-diagram.cpp |
changeset | c50e7020a1e4 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added intrusive containers issue and issue filters |
files | .issues/.filters .issues/e6f52c44ef26f4a7/new/1239399291.M841173P26652Q1.cole |
changeset | 51a7ed5b51f0 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Moved l2distance.h into include/geometry |
files | examples/cohomology/rips-pairwise-cohomology.cpp examples/consistency/rips-consistency-zigzag.cpp examples/rips/l2distance.h examples/rips/rips-pairwise.cpp examples/rips/rips-zigzag.cpp include/geometry/l2distance.h |
changeset | b2103b289f06 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added categories to some of the issues |
files | .issues/957a589d7c6c3fa8/new/1230356422.M300560P11955Q1.rufus .issues/957a589d7c6c3fa8/new/1239235561.M108369P10645Q1.cole .issues/cd79223a108d3900/new/1221008555.M511949P30017Q2.cole .issues/cd79223a108d3900/new/1239235469.M178107P10641Q1.cole .issues/de674a2ac5f6c18c/new/1229837097.M859247P31105Q1.rufus .issues/de674a2ac5f6c18c/new/1239235533.M711045P10644Q1.cole .issues/ebda8db3f9908e33/new/1221008555.M637662P30017Q16.cole .issues/ebda8db3f9908e33/new/1239235517.M200551P10643Q1.cole .issues/f6496b3e37275888/new/1229837161.M623187P31203Q1.rufus .issues/f6496b3e37275888/new/1239235438.M855747P10635Q1.cole |
changeset | 3c830b15d694 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Fixed distance to diagonal calculation + added stand-alone bottleneck distance tool |
files | include/topology/persistence-diagram.h tools/CMakeLists.txt tools/matching/CMakeLists.txt tools/matching/bottleneck.cpp |
changeset | 505b3795d239 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added ZigzagPersistence::is_alive() + consistency zigzag outputs betti 1 at each stage |
files | examples/consistency/rips-consistency-zigzag.cpp include/topology/zigzag-persistence.h |
changeset | c4e25fb4082c |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added consistency zigzag |
files | examples/CMakeLists.txt examples/consistency/CMakeLists.txt examples/consistency/rips-consistency-zigzag.cpp examples/rips/l2distance.h examples/rips/rips-zigzag.cpp include/topology/rips.h include/topology/rips.hpp |
changeset | 06a4361bddaa |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged in cohomology branch |
files | examples/rips/rips-pairwise.cpp |
changeset | 5095771715ab |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added CohomologyPersistence and Rips pairwise distances computation |
files | examples/CMakeLists.txt examples/cohomology/CMakeLists.txt examples/cohomology/rips-cohomology.cpp examples/cohomology/rips-pairwise-cohomology.cpp examples/cohomology/triangle-cohomology.cpp examples/rips/CMakeLists.txt examples/rips/l2distance.h examples/rips/rips-pairwise.cpp examples/rips/rips-zigzag.cpp include/topology/cohomology-persistence.h |
changeset | a3410b6ba79c |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added DynamicPersistenceChains (no dynamic part yet) |
files | README examples/rips/rips.cpp include/topology/dynamic-persistence.h include/topology/dynamic-persistence.hpp |
changeset | 374f94f92e50 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Updated Rips zigzags * Updated to use Bron-Kerbosch * Compute in the order of increasing epsilon, and decreasing point sizes * Split into plain zigzag (rips-zigzag) and image zigzag (rips-image-zigzag) * Added minor enhancements (show_progress and timers) |
files | examples/rips/CMakeLists.txt examples/rips/rips-image-zigzag.cpp examples/rips/rips-zigzag.cpp include/topology/zigzag-persistence.h include/topology/zigzag-persistence.hpp include/utilities/timer.h |
changeset | 3e8bebb5d857 |
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branch | dev |
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tag | |
user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Switched Rips complex computation to Bron-Kerbosch algorithm |
files | bindings/python/CMakeLists.txt examples/fitness/avida-rips-distance.cpp examples/rips/CMakeLists.txt examples/rips/rips-zigzag.cpp examples/rips/rips.cpp include/topology/rips.h include/topology/rips.hpp include/topology/simplex.h include/utilities/containers.h |
changeset | f209958b5c17 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added python bindings for ZigzagPersistence (as well as ImageZigzagPersistence) |
files | bindings/python/CMakeLists.txt bindings/python/dionysus.cpp bindings/python/dionysus/__init__.py bindings/python/python-optional.h bindings/python/python-zigzag-persistence.h bindings/python/simplex.cpp bindings/python/zigzag-persistence.cpp examples/triangle/triangle-zigzag.py include/topology/zigzag-persistence.hpp |
changeset | 958dec48d946 |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Switched to CGAL 3.4 (native CMake configuration): for now only alphashapes |
files | CMakeLists.txt FindCGAL.Makefile README examples/alphashapes/CMakeLists.txt tests/utilities/CMakeLists.txt |
changeset | 430d9e71e921 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Implemented ImageZigzagPersistence * Changed ZigzagPersistence to support a visitor, and implemented ImageZigzagPersistence * examples/rips/rips-zigzag now computes using ImageZigzagPersistence * PersistenceDiagram no longer records zero persistence pairs * Added utilities/memory.h with report_memory() function |
files | examples/rips/rips-zigzag.cpp include/topology/image-zigzag-persistence.h include/topology/image-zigzag-persistence.hpp include/topology/persistence-diagram.h include/topology/persistence-diagram.hpp include/topology/zigzag-persistence.h include/topology/zigzag-persistence.hpp include/utilities/memory.h |
changeset | 75eb7a4628f2 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Debugged ZigzagPersistence (having added heavier consistency checking) * Added DEBUG_CONTAINERS option (uses std::__debug::* containers for chains and in ZigzagPersistence) * Added SizeStorage specialization for std::deque<T> * ZigzagPersistence got a lot more consistency checking (in debug mode only, which now crawls); as a result it's been debugged (running on non-trivial examples) * examples/rips/rips-zigzag takes command-line options * added ChainWrapper::clear() * added Simplex::VertexDimensionComparison * added PairwiseDistances class (for computing distances between points in a container according to a distance functor) |
files | examples/rips/CMakeLists.txt examples/rips/rips-zigzag.cpp examples/rips/rips.cpp include/topology/chain.h include/topology/chain.hpp include/topology/cycles.h include/topology/rips.h include/topology/simplex.h include/topology/zigzag-persistence.h include/topology/zigzag-persistence.hpp |
changeset | e096f8892a04 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added rips-zigzag; in the process caught a number of bugs in ZigzagPersistence (added check_consistency() to it) |
files | examples/rips/CMakeLists.txt examples/rips/rips-zigzag.cpp include/topology/chain.hpp include/topology/zigzag-persistence.h include/topology/zigzag-persistence.hpp |
changeset | a5debdc35559 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added DequeChains (for ZigzagPersistence) |
files | include/topology/cycles.h include/topology/zigzag-persistence.h |
changeset | dfa74f2f2a76 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Added ZigzagPersistence |
files | examples/triangle/CMakeLists.txt examples/triangle/triangle-zigzag.cpp include/topology/chain.h include/topology/chain.hpp include/topology/filtration.hpp include/topology/order.h include/topology/zigzag-persistence.h include/topology/zigzag-persistence.hpp include/utilities/containers.h include/utilities/indirect.h |
changeset | 051af83fba4c |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Merged in Python branch |
files | CMakeLists.txt bindings/python/simplex.cpp include/topology/filtration.h include/topology/lowerstarfiltration.hpp include/topology/persistence-diagram.h include/topology/persistence-diagram.hpp include/topology/simplex.h include/topology/simplex.hpp include/utilities/counter.h include/utilities/types.h |
changeset | 2cc1db3b98c6 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Initial commit of Python bindings |
files | CMakeLists.txt bindings/CMakeLists.txt bindings/python/CMakeLists.txt bindings/python/chain.cpp bindings/python/dionysus.cpp bindings/python/filtration.cpp bindings/python/python-filtration.h bindings/python/python-simplex.h bindings/python/python-static-persistence.h bindings/python/simplex.cpp |
changeset | 2ac129839e02 |
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branch | dev |
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user | Dmitriy Morozov <dmitriy@mrzv.org> |
description | Empty is now a template, replaced RecursiveIterator with boost::counting_iterator |
files | include/topology/dynamic-persistence.h include/topology/filtration.hpp include/topology/order.h include/topology/persistence-diagram.h include/topology/persistence-diagram.hpp include/topology/simplex.h include/topology/static-persistence.h include/utilities/counter.h include/utilities/indirect.h include/utilities/types.h |