Dionysus Changelog

[default] Fix doc/conf.py

Mon, 06 Mar 2023 12:54:27 -0800

changeset	47512d24f907
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fix doc/conf.py
files	doc/conf.py

Change all http to https in doc/get-build-install.rst

Mon, 06 Mar 2023 12:48:28 -0800

changeset	41d5aeb87565
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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

Disable building e/a/alphashapes2d-periodic

Mon, 06 Mar 2023 12:43:45 -0800

changeset	d24de31c84a6
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Disable building e/a/alphashapes2d-periodic
files	examples/alphashapes/CMakeLists.txt

Fix a few compilation issues

Mon, 06 Mar 2023 12:31:30 -0800

changeset	79789643a4cc
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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

Add .build.yml

Sun, 24 Nov 2019 13:35:45 -0800

changeset	02e680f6d987
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Add .build.yml
files	.build.yml

Make dionysus-link depend on dionysus

Sun, 24 Nov 2019 13:27:13 -0800

changeset	6a553ae00446
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Make dionysus-link depend on dionysus
files	bindings/python/CMakeLists.txt

Comment out explicit typedefs to make GCC happy

Sun, 24 Nov 2019 08:11:18 -0800

changeset	c328d7ecf6b8
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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

Use boost/next_prior.hpp with Boost >= 1.67

Sat, 23 Nov 2019 21:40:40 -0800

changeset	0beafc10719a
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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

Get rid of Boost.Signals dependency

Sat, 23 Nov 2019 21:29:50 -0800

changeset	5810d70ec967
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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

Add CGAL pre-4.11 support back to e/a/alphashapes3d-periodic

Mon, 27 Nov 2017 10:26:59 -0800

changeset	bc7bd0ac9af6
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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

Vanessa's fix for e/a/alphashapes3d-periodic for CGAL 4.11

Sun, 26 Nov 2017 18:42:36 -0800

changeset	b90319e7126f
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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

Add Vanessa Robins' periodic alpha shapes 2D code

Sun, 26 Nov 2017 12:07:49 -0800

changeset	5d387c35465b
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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

Add Vanessa Robins' periodic alpha shapes code

Thu, 07 Sep 2017 17:35:28 -0700

changeset	21b56c6c9512
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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

Add a note about Dionysus 2 to the docs

Fri, 14 Jul 2017 14:07:05 -0700

changeset	f7dbbfdac250
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Add a note about Dionysus 2 to the docs
files	doc/index.rst

Merge

Fri, 14 Jul 2017 14:04:13 -0700

changeset	e7ecdbf1e6e3
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merge
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[dev] Added a practical guide slides and examples to the docs

Sun, 27 Apr 2014 13:49:14 -0700

changeset	d3a10e66c6ab
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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

Remove 'hg up tip' from doc/get-build-install.rst

Tue, 27 Jun 2017 09:38:20 -0700

changeset	0496c5f88b2a
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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

Merge dev into default, to avoid the need for 'hg up tip' after clone

Tue, 27 Jun 2017 09:37:05 -0700

changeset	d9a79a28e3cc
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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

[dev] Add LICENSE + LEGAL

Sun, 16 Apr 2017 13:35:24 -0700

changeset	67644b9c7668
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Add LICENSE + LEGAL
files	LEGAL LICENSE

[dev] Add register_ptr_to_python to PersistenceDiagram bindings to match changes in Boost.Python

Mon, 22 Aug 2016 11:17:45 -0700

changeset	453eedc14be0
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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

[dev] Fix compilation with Boost 1.58 (load_construct_data_adl error)

Mon, 05 Oct 2015 09:02:38 -0700

changeset	c54290544583
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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

[dev] Added executable to compute Wasserstein distance.

Mon, 02 Mar 2015 13:20:51 +0100

changeset	6e883f004ebe
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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

[dev] Disabled glibcxx specific concept checks

Fri, 06 Dec 2013 19:09:12 -0800

changeset	668bf4bf1bfb
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Disabled glibcxx specific concept checks
files	include/utilities/binaryheap.h

[dev] Dave Millman's fix for and rlog problem

Fri, 06 Dec 2013 19:02:42 -0800

changeset	a125a3d9c723
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Dave Millman's fix for and rlog problem
files	include/utilities/log.h

[dev] Increase template depth to fix a bug with XCode 5

Wed, 16 Oct 2013 09:58:02 -0700

changeset	7479c3f0fc6b
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Increase template depth to fix a bug with XCode 5
files	CMakeLists.txt

[dev] Brit Fasy's fix to compile with logging=on

Fri, 09 Aug 2013 15:08:23 -0700

changeset	b4fd8880a09a
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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

[dev] lscubes.py output infinite pairs + small bugfix

Wed, 10 Jul 2013 14:39:29 -0700

changeset	4e136f6afbb5
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	lscubes.py output infinite pairs + small bugfix
files	examples/pl-functions/lscubes.py

[dev] Fixed non-POD array problem in homology-zigzags

Mon, 10 Jun 2013 17:25:57 +0200

changeset	5f5f4cc70333
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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

[dev] Added homology zigzags by Steve Oudot and Don Sheehy

Mon, 10 Jun 2013 16:58:01 +0200

changeset	73d69c01ed6c
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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

[dev] Added standalone bottleneck-distance.cpp

Fri, 26 Apr 2013 22:31:58 -0700

changeset	815d6a978c6c
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added standalone bottleneck-distance.cpp
files	examples/CMakeLists.txt examples/bottleneck-distance.cpp

[dev] Dave Millman's fixes to compile with LLVM-based compilers

Thu, 28 Feb 2013 11:12:02 +0800

changeset	29306411272b
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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

[dev] Added CGAL_USE_FILE + added option use_cgal

Fri, 26 Oct 2012 11:45:58 -0700

changeset	0cdf9e9eed48
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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

[dev] Bug in show_diagram() with empty diagrams

Sun, 10 Jun 2012 18:54:26 -0700

changeset	91c35fefb54e
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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

[dev] subcomplex in show_complex() + pan/zoom in ComplexViewer2D

Sun, 10 Jun 2012 11:26:38 -0700

changeset	86a02dac0db2
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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

[dev] DiagramViewer can show multiple diagrams at once

Sat, 09 Jun 2012 12:56:36 -0700

changeset	9b0da55e5df0
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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

[dev] CohomologyPersistence returns dying cocycles + StaticCohomologyPersistence records them and normalizes coefficients + minor changes

Sat, 09 Jun 2012 12:17:17 -0700

changeset	2f02384a4d9b
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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

[dev] Display lists in ComplexViewer3D + circular.smooth() raises exceptions

Fri, 08 Jun 2012 15:40:09 -0700

changeset	38cf887cb139
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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

[dev] Set center and radius in ComplexViewer3D

Thu, 07 Jun 2012 21:36:53 -0700

changeset	66a311c0d597
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Set center and radius in ComplexViewer3D
files	bindings/python/dionysus/viewer/complex3d.py

[dev] Points at infinity in DiagramViewer

Thu, 07 Jun 2012 21:21:11 -0700

changeset	55700750a464
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Points at infinity in DiagramViewer
files	bindings/python/dionysus/viewer/diagram.py

[dev] Fixed scale points in the diagram + noise filtering

Thu, 07 Jun 2012 21:16:06 -0700

changeset	185923889ab4
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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

[dev] Added pan + zoom to diagram viewer; show_diagram() didn't return; added PyQt, PyOpenGL, NumPy as dependencies in the docs

Thu, 07 Jun 2012 11:57:33 -0700

changeset	ee064472dc1f
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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

[dev] Straightened out QApplication problems (made it global)

Thu, 07 Jun 2012 10:52:15 -0700

changeset	7b846a522bed
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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

[dev] Started show_complex_3D()

Thu, 07 Jun 2012 10:11:01 -0700

changeset	27c47fc33468
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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

[dev] Fixed bugs in diagram.py and adaptor.py + added coloring of points in show_complex_2D(); Filtration can be initialized from iterator without comparison

Wed, 06 Jun 2012 23:15:57 -0700

changeset	84c100980206
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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

[dev] Added viewer.show_complex_2D + center points in the persistence diagram

Tue, 05 Jun 2012 17:53:08 -0700

changeset	bb5bc5eff779
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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

[dev] Moved dionysus.circular into its own subdirectory + added dionysus.viewer

Tue, 05 Jun 2012 17:04:10 -0700

changeset	d69a9e11205e
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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

[dev] Added docs for StaticCohomologyPersistence + ImagePersistence + circular.smooth + minor fixes in adaptor.py

Tue, 05 Jun 2012 14:50:58 -0700

changeset	0f632dc3f53b
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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

[dev] Added smooth() to Python binding + fixed a bug in adaptor.py

Mon, 04 Jun 2012 09:05:45 -0700

changeset	a7e010314a03
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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

[dev] Merged upstream

Sun, 03 Jun 2012 16:39:18 -0700

changeset	fb0f9b4ca77a
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merged upstream
files

[dev] Added adaptor for StaticCohomologyPersistence and ImagePersistence

Sun, 03 Jun 2012 16:17:27 -0700

changeset	6dc64e820477
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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

[dev] Added a note about reducing matrix Z in i/t/zigzag-persistence.hpp

Mon, 14 May 2012 10:47:46 -0700

changeset	4de0bd5b4ae1
branch	dev
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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

[dev] Merge

Fri, 11 May 2012 17:06:55 -0700

changeset	870865d25958
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merge
files	tools/CMakeLists.txt

[dev] Added store_negative argument to StaticPersistence.pair_simpices()

Fri, 11 May 2012 10:25:57 -0700

changeset	021030a8f97c
branch	dev
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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

[dev] Added a note about wasserstein_distance() to documentation + cleaned up docs for init_diagrams()

Thu, 10 May 2012 15:52:53 -0700

changeset	0c5c45ebbf97
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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

[dev] Inlcuded munkres.cpp from munkres.h + matrix.cpp -> matrix.hpp

Thu, 10 May 2012 15:46:52 -0700

changeset	45589223382c
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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

[dev] Added wasserstein_distance()

Thu, 10 May 2012 15:42:21 -0700

changeset	ad3aefb5a0e0
branch	dev
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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

[dev] Exposed init_diagrams() to Python

Thu, 10 May 2012 14:24:40 -0700

changeset	88f7806633e0
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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

[dev] Minor changes to compile with GCC 4.7

Tue, 08 May 2012 13:07:28 -0700

changeset	3a3dd22a98d9
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Minor changes to compile with GCC 4.7
files	include/topology/simplex.hpp include/utilities/indirect.h tools/CMakeLists.txt

[dev] Added cohomology/candidates counter to i/t/cohomology-persistence.hpp

Mon, 25 Jul 2011 23:21:29 -0700

changeset	66235db8d8b7
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user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added cohomology/candidates counter to i/t/cohomology-persistence.hpp
files	include/topology/cohomology-persistence.hpp

[dev] Minor fixes in tools/draw-diagram

Fri, 06 May 2011 10:38:06 -0700

changeset	c9b8c98187a8
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Minor fixes in tools/draw-diagram
files	tools/draw-diagram/draw.py tools/draw-diagram/pd.py

[dev] alphashapes2d can handle degenerate inputs (thanks to Taras Galkovskyi for the bug report and the fix)

Tue, 05 Apr 2011 18:29:50 -0700

changeset	a06b4b515476
branch	dev
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tag
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

[dev] Fixed combinations in closure() for older versions of Python

Fri, 28 Jan 2011 08:01:37 -0800

changeset	2ca64ce7d57c
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed combinations in closure() for older versions of Python
files	bindings/python/dionysus/__init__.py

[dev] closure() in Python can handle simplex data

Fri, 07 Jan 2011 23:11:46 -0800

changeset	ae6319bfb53d
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	closure() in Python can handle simplex data
files	bindings/python/dionysus/__init__.py

[dev] Fixed a typo in b/p/persistence-diagram.cpp

Mon, 20 Dec 2010 11:21:57 -0800

changeset	cda36c58ef98
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed a typo in b/p/persistence-diagram.cpp
files	bindings/python/persistence-diagram.cpp

[dev] Added a note about GPL to the documentation

Wed, 08 Dec 2010 10:29:26 -0800

changeset	79bf90c0200d
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added a note about GPL to the documentation
files	doc/index.rst

[dev] Cleaned up CMake files to play nice with CGAL

Fri, 03 Dec 2010 11:26:12 -0800

changeset	92b59e2e6fb3
branch	dev
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tag
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

[dev] Cleaned up PersistenceDiagram bindings

Sat, 09 Oct 2010 13:56:26 -0700

changeset	e90653a59fa6
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Cleaned up PersistenceDiagram bindings
files	bindings/python/persistence-diagram.cpp include/topology/persistence-diagram.h

[dev] Fixed a link to SYNAPS

Mon, 04 Oct 2010 18:03:35 -0700

changeset	07b3070cea74
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed a link to SYNAPS
files	README

[dev] Merged in Python bindings for DynamicPersistenceChains

Tue, 14 Sep 2010 15:36:13 -0700

changeset	7643a94222ae
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merged in Python bindings for DynamicPersistenceChains
files

[dev] Added documentation for DynamicPersistenceChains

Tue, 14 Sep 2010 15:00:34 -0700

changeset	ce6d679368c6
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added documentation for DynamicPersistenceChains
files	doc/python/static-persistence.rst

[dev] Added Python bindings for DynamicPersistenceChains

Sun, 12 Sep 2010 09:55:44 -0700

changeset	edbbf84fde9e
branch	dev
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tag
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

[dev] Added the ability to pickle Simplex class in Python

Tue, 14 Sep 2010 11:34:11 -0700

changeset	04a4629979da
branch	dev
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tag
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

[dev] Added ability to iterate over ZigzagPersistence cycles in Python

Tue, 14 Sep 2010 11:12:33 -0700

changeset	6a222607714c
branch	dev
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tag
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

[dev] Fixed a typo in the documentation of SPNode.cycle

Fri, 10 Sep 2010 21:21:27 -0700

changeset	ed3905be234f
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed a typo in the documentation of SPNode.cycle
files	doc/python/static-persistence.rst

[dev] Added Python closure function (for computing a k-skeleton of a closure of a list of simplices)

Tue, 07 Sep 2010 13:54:53 -0700

changeset	12e2daa0e03a
branch	dev
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tag
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

[dev] Removed the unnecessary typename in filtration-homology.cpp

Thu, 02 Sep 2010 09:13:42 -0700

changeset	c1e2626cde8f
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Removed the unnecessary typename in filtration-homology.cpp
files	examples/filtration/filtration-homology.cpp

[dev] Added output of essential cycles for any given input filtration

Mon, 30 Aug 2010 12:28:58 -0700

changeset	574a165c0a9c
branch	dev
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tag
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

[dev] Minor touches in documentation

Wed, 25 Aug 2010 14:36:11 -0700

changeset	d4c3991a2462
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Minor touches in documentation
files	doc/conf.py doc/python/persistence-diagram.rst

[dev] Merged docs with upstream

Wed, 25 Aug 2010 14:31:36 -0700

changeset	8f6fb2ad57f7
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merged docs with upstream
files

[dev] CGAL is unncessary for vineyards (update in the documentation)

Thu, 15 Jul 2010 10:25:08 -0700

changeset	3d54247cbccf
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

[dev] Merged in Aravind's changes

Wed, 25 Aug 2010 14:29:54 -0700

changeset	fdfde7291a0f
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merged in Aravind's changes
files

[dev] Changed the first iterator of PersistenceDiagram to accept dimension as well. Modified documentation.

Wed, 18 Aug 2010 15:35:48 -0700

changeset	9ea8d4630907
branch	dev
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tag
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

[dev] Removed the points iterator in PersistenceDaigram; replaced it with a iter method.

Wed, 18 Aug 2010 12:05:18 -0700

changeset	d07d77561661
branch	dev
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tag
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

[dev] Added documentation for the python classes Point and PersistenceDiagram. Removed the sub method for PersistenceDiagram. Minor renaming.

Tue, 17 Aug 2010 22:19:19 -0700

changeset	5311343eb2f5
branch	dev
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tag
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

[dev] Added a iter method to the PersistenceDiagram class in python. Renamed the points iterator to the intervals iterator.

Wed, 11 Aug 2010 17:07:09 -0700

changeset	4f70a473e34b
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

[dev] Added extra functionality to Point class( an iterator ) and PersistenceDiagram( dimension property and len func ).

Thu, 08 Jul 2010 23:50:39 -0700

changeset	64a272a34cb2
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

[dev] Made the data argument in Point's initmethod to be an optional argument by making it a boost::python::optional.

Fri, 02 Jul 2010 17:08:02 -0700

changeset	7aefb2d67203
branch	dev
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tag
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

[dev] Added code to expose the persistence_diagram class, the bottleneck_distance function and the point class to python.

Fri, 02 Jul 2010 04:19:29 -0700

changeset	e94d521b72bb
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

[dev] Merged docs with upstream

Thu, 15 Jul 2010 10:20:06 -0700

changeset	ee0dca73ea47
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merged docs with upstream
files

[dev] Removed the warning about compiler versions (seems unnecessary after Andrew's fixes)

Thu, 15 Jul 2010 10:19:18 -0700

changeset	3568e0bfe2cd
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

[dev] Fixed path for lsfiltration.py

Mon, 12 Jul 2010 09:53:30 -0700

changeset	291f6edf27b9
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed path for lsfiltration.py
files	doc/examples/index.rst

[dev] Bug in the tutorial: simplices = [] -> simplices = Filtration()

Mon, 05 Jul 2010 23:51:26 -0700

changeset	347b3461965a
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Bug in the tutorial: simplices = [] -> simplices = Filtration()
files	doc/tutorial.rst

[dev] More typos in the docs

Tue, 13 Apr 2010 09:09:04 -0700

changeset	e84354d3a6c9
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	More typos in the docs
files	doc/python/rips.rst

[dev] Fixed a link: dionysis -> dionysus

Mon, 12 Apr 2010 19:01:01 -0700

changeset	324354e0d3bf
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed a link: dionysis -> dionysus
files	doc/python/simplex.rst

[dev] Andrew Yarmola's fix to the in-class intialization syntax in OrderList

Tue, 20 Apr 2010 13:58:23 -0700

changeset	36ea2751f290
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
files	include/utilities/orderlist.h include/utilities/orderlist.hpp

[dev] Added Persistence::initialize(f) + fixed minor bug LinearKernel::sign_at_negative_infinity()

Tue, 09 Mar 2010 15:22:57 -0800

changeset	6f1ed27850c8
branch	dev
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tag
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

[dev] Added insert-at-the-end optimization for CohomologyPersistence::add_cocycle()

Sat, 06 Mar 2010 14:39:15 -0800

changeset	4a80392ab462
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added insert-at-the-end optimization for CohomologyPersistence::add_cocycle()
files	include/topology/cohomology-persistence.hpp

[dev] Count cocycles in CohomologyPersistence

Fri, 05 Mar 2010 09:26:54 -0800

changeset	f5d010aecc97
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Count cocycles in CohomologyPersistence
files	include/topology/cohomology-persistence.hpp

[dev] Andrew Yarmola's compilation fix for MacOSX.

Tue, 23 Feb 2010 17:39:15 -0800

changeset	7653574ff064
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

[dev] Removed unused instrumentation of cohomology and unnecessary includes

Mon, 22 Feb 2010 17:24:02 -0800

changeset	f31527c1f962
branch	dev
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tag
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

[dev] Removed reference to reference in ThreeOutcomeComparison

Tue, 09 Feb 2010 11:05:48 -0800

changeset	a91083de7386
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Removed reference to reference in ThreeOutcomeComparison
files	include/utilities/indirect.h

[dev] Made EventQueue into a binary heap (for efficiency and sanity)

Sun, 07 Feb 2010 21:10:54 -0800

changeset	4759535221ee
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

[dev] Replaced list with multi_index representation in EventQueue making it more efficient

Sun, 07 Feb 2010 10:46:23 -0800

changeset	73e8dce642be
branch	dev
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tag
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

[dev] Switched to internal KineticSort

Sat, 06 Feb 2010 23:22:43 -0800

changeset	2bde4c56101c
branch	dev
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tag
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

[dev] Added linear kernel for my own KineticSort

Fri, 05 Feb 2010 11:49:52 -0800

changeset	e95766342e5f
branch	dev
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tag
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

[dev] Commented out QField to get rid of the artifical dependence on GMP

Fri, 05 Feb 2010 11:07:42 -0800

changeset	29fbad86aff6
branch	dev
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tag
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

[dev] Fixed non-copyable temporary bug

Thu, 04 Feb 2010 23:43:36 -0800

changeset	5303ce3f1934
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed non-copyable temporary bug
files	include/topology/dynamic-persistence.hpp include/topology/static-persistence.hpp

[dev] Fixed the duplicates (degeneracy) and another assertion problem in LSVineyard

Wed, 03 Feb 2010 14:51:38 -0800

changeset	8a6f3ef2c42d
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Fixed the duplicates (degeneracy) and another assertion problem in LSVineyard
files	include/topology/lsvineyard.hpp

[dev] Removed a buggy assertion in LSVineard::transpose_vertices() (j points at the end() when moving the last simplex of the filtration)

Wed, 03 Feb 2010 11:20:40 -0800

changeset	6c2a98fb8990
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

[dev] StaticPersistence::pair_simplices() has an option to not display progress (LSVineyard uses it during consistency checking)

Tue, 02 Feb 2010 23:43:46 -0800

changeset	7198c9bf279d
branch	dev
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tag
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

[dev] Added rips-explicit-cohomology

Tue, 26 Jan 2010 11:14:50 -0800

changeset	19d35448c7c7
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added rips-explicit-cohomology
files	examples/cohomology/CMakeLists.txt examples/cohomology/rips-explicit-cohomology.cpp

[dev] Moved lsfiltration.py into examples/pl-functions + added lscubes.py example (cubical lower-star filtration)

Tue, 26 Jan 2010 11:00:51 -0800

changeset	2d8fba6d1d58
branch	dev
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tag
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

[dev] Fixed Python constructor of CohomologyPersistence + minor changes to cocycle.py

Tue, 12 Jan 2010 14:36:38 -0800

changeset	6edd7c861bc0
branch	dev
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tag
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

[dev] vertex_coface -> vertex_cofaces in Rips documentation (in Python)

Mon, 11 Jan 2010 10:21:37 -0800

changeset	e867c6cf02ef
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

[dev] Henry Adams' fixes to python/dionysus/zigzag.py + added CohomologyPersistence.show_cocycles method

Sat, 09 Jan 2010 15:03:52 -0800

changeset	23cb832e035d
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

[dev] CohomologyPersistence::add returns the dying cocycle

Thu, 07 Jan 2010 10:27:18 -0800

changeset	25e468323d77
branch	dev
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tag
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

[dev] Check Boost version in include/utilities/property-maps.h + minor changes to cocycle.py

Tue, 05 Jan 2010 11:02:07 -0800

changeset	6d81d6ae7a3b
branch	dev
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tag
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

[dev] Added pl-vineyard documentation

Thu, 31 Dec 2009 11:28:49 -0800

changeset	7241b887eabb
branch	dev
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tag
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

[dev] Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea:

Fri, 25 Dec 2009 06:56:27 -0800

changeset	a5e726461d3f
branch	dev
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tag
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

[dev] Moved files around: lsvineyard.h -> include/topology, examples/grid -> examples/pl-functions

Sun, 20 Dec 2009 10:43:00 -0800

changeset	0ca59b0ebc47
branch	dev
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tag
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

[dev] Merged Vineyards code changes with the main development line

Sun, 20 Dec 2009 08:27:01 -0800

changeset	451748b3c888
branch	dev
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tag
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

[dev] Python bindings work again

Sun, 20 Dec 2009 07:45:29 -0800

changeset	1ee6edc17cb6
branch	dev
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tag
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

[dev] Created pl-vineyard.cpp to compute vineyards given a complex and a sequence of values at each vertex

Wed, 16 Dec 2009 15:39:38 -0800

changeset	27508309a680
branch	dev
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tag
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

[dev] Resurrected vineyard code:

Wed, 16 Dec 2009 15:39:06 -0800

changeset	d15c6d144645
branch	dev
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tag
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

[dev] Made storing negative simplices in StaticPersistence parameter-based, so that DynamicPersistence works again

Thu, 03 Dec 2009 13:21:23 -0800

changeset	cc0c26fba495
branch	dev
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tag
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

[dev] StaticPersistence operates on chains consisting of only positive simplices

Wed, 02 Dec 2009 14:03:54 -0800

changeset	b5f2e93fa75c
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	StaticPersistence operates on chains consisting of only positive simplices
files	include/topology/static-persistence.hpp

[dev] alphashapes3d.cpp measures persistence time

Tue, 01 Dec 2009 20:34:31 -0800

changeset	64177e8ef379
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	alphashapes3d.cpp measures persistence time
files	examples/alphashapes/alphashapes3d.cpp

[dev] Fixed DynamicPersistenceTrails::PairingTrailsVisitor to match the changes in StaticPersistence::PairVisitor

Sat, 28 Nov 2009 17:01:52 -0800

changeset	6a649c2bea0e
branch	dev
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tag
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

[dev] Instrumented code for counting:

Sat, 28 Nov 2009 16:45:42 -0800

changeset	3f1034dca432
branch	dev
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tag
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

[dev] Added arbitrary coefficients in boundaries (to C++ and Python) + cleaned up CohomologyPersistence.add overloading in Python

Fri, 06 Nov 2009 14:19:08 -0800

changeset	5fd3f43e6fbf
branch	dev
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tag
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

[dev] Added image persistence functionality to CohomologyPersistence

Wed, 28 Oct 2009 14:38:36 -0700

changeset	a6605dc232f2
branch	dev
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tag
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

[dev] Added draw.py under tools/draw-diagram

Fri, 23 Oct 2009 11:51:23 -0700

changeset	a172b960aaaa
branch	dev
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tag
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

[dev] Added link to CVXOPT in get-build-install documentation + progress bar to rips-pairwise-cohomology

Fri, 23 Oct 2009 09:36:55 -0700

changeset	e8b6706cedfc
branch	dev
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tag
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

[dev] Fixed a typo in documentation + added a warning and a tip about GCC 4.2 on a Mac

Tue, 20 Oct 2009 22:05:23 -0700

changeset	c0bf4675697c
branch	dev
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tag
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

[dev] The if-else cases in lsqr.py were not exhaustive. They become exhaustive by changing ab > aa to ab >= aa.

Mon, 31 Aug 2009 13:45:28 -0700

changeset	3b0665eb35bc
branch	dev
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tag
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

[dev] Removed Qt4 requirement + added link to download and tutorial to the front page of the documentation

Mon, 31 Aug 2009 10:51:56 -0700

changeset	5a5f3e1c466b
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

[dev] Exposed store argument to CohomologyPersistence.add() in Python

Fri, 21 Aug 2009 14:26:56 -0700

changeset	1f3d54b2315b
branch	dev
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tag
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

[dev] cocycle.py uses vertex list, and does not make any assumptions about the vertex-simplex order

Wed, 19 Aug 2009 12:01:47 -0700

changeset	c3c3c53dfc08
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

[dev] Consistency zigzag outputs intervals supported over a single complex

Thu, 13 Aug 2009 13:16:15 -0700

changeset	f7244460f21f
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

[dev] explicitely converts a Dimension (short int) into a size_t, for removing a warning

Wed, 12 Aug 2009 21:32:38 -0700

changeset	6cd50e622550
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

[dev] Removing unused parameter names in order to avoid warnings

Wed, 12 Aug 2009 07:16:35 -0700

changeset	eec482c29319
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

[dev] make-zigzag-subsamples.py doesn't output the union, rips-consistency-zigzag.cpp fixed show_progress

Wed, 12 Aug 2009 11:32:42 -0700

changeset	4bfb7c31ab28
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

[dev] Fixed bugs in cocycle.py introduced when rips-pairwise-cohomology.py was originally added

Mon, 10 Aug 2009 16:48:13 -0700

changeset	1b30e507e8aa
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

[dev] Fixed bugs in rips-pairwise-cohomology.py whose origin is unclear to me

Mon, 10 Aug 2009 15:22:32 -0700

changeset	92318b22ffa5
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

[dev] Merged in Chris' changes

Tue, 04 Aug 2009 17:12:47 -0700

changeset	ce2aa05994f0
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merged in Chris' changes
files

[dev] Modified cohomology code (unweighted and weighted) so that it doesn't use std::map for boundary computations, which should optimize memory usage.

Tue, 04 Aug 2009 16:58:44 -0700

changeset	700cbac5b23c
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

[dev] 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.

Tue, 04 Aug 2009 13:23:16 -0700

changeset	f75fb57d2831
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

[dev] Added rips-weighted-cohomology, and channeled WeightedRips logging to the same channel as Rips

Tue, 28 Jul 2009 15:04:06 -0700

changeset	1dde8a05fcd7
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

[dev] Merged upstream

Tue, 28 Jul 2009 11:42:03 -0700

changeset	8af75817ecbc
branch	dev
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tag
user	Christos Mantoulidis <cmad@stanford.edu>
description	Merged upstream
files

[dev] 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())

Tue, 28 Jul 2009 10:58:53 -0700

changeset	7731c42892de
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

[dev] added logging to WeightedRips (still needs debugging)

Mon, 27 Jul 2009 21:42:51 -0700

changeset	fdc2835b3e88
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

[dev] Updated weighted rips libraries to make use of OOP--now WeightedRips inherits from Rips. It is possible that logging for WeightedRips does not work.

Mon, 13 Jul 2009 19:44:04 -0700

changeset	104ea146b9bc
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

[dev] Added weighted rips code and libraries

Thu, 02 Jul 2009 15:42:44 -0700

changeset	eb629d8f00bf
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

[dev] Simplices are deleted from the complex after removal in triangle-zigzag.py + touched up documentation (to mention CohomologyPersistence better)

Tue, 04 Aug 2009 14:28:17 -0700

changeset	3d15aca95dfb
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

[dev] Consistency zigzag outputs intervals for dimensions less than the skeleton dimension only

Tue, 28 Jul 2009 13:27:13 -0700

changeset	a99fdaafa31a
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

[dev] Switched PairwiseDistances in Python bindings to C++

Thu, 30 Jul 2009 10:35:49 -0700

changeset	d39a20acb253
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

[dev] Added Python bindings for CohomologyPersistence (+ example + documentation)

Thu, 30 Jul 2009 10:23:31 -0700

changeset	4e27f1f7c169
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

[dev] Minor changes in distances.py + rips-pairwise.py wrapped into a main() function

Fri, 24 Jul 2009 14:18:16 -0700

changeset	ee096f207dfb
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

[dev] Disable alphashapes in Python bindings if no CGAL

Wed, 17 Jun 2009 16:02:52 -0700

changeset	baa53970eb88
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

[dev] Made ListRandomAccessIterator generic with respect to value, and moved it to utils.h

Sun, 17 May 2009 20:05:26 -0700

changeset	b555e6587908
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

[dev] Cleaner output in rips-pairwise.cpp + added make-zigzag-subsamples.py + added lsfiltration.py

Fri, 24 Jul 2009 11:08:48 -0700

changeset	ae2b1702c936
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

[dev] Fixed plot.py in tools/plot-values

Thu, 09 Jul 2009 07:47:22 -0700

changeset	cda0b85ffc50
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

[dev] In documentation put contents into sidebar

Thu, 14 May 2009 17:43:19 -0700

changeset	9851fee5a33b
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	In documentation put contents into sidebar
files	doc/index.rst

[dev] Documentation for parametrization using persistent cohomology

Thu, 09 Jul 2009 02:46:53 -0700

changeset	656ec2838fb8
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

[dev] Rips pairwise cohomology produces output necessary for 1-cocycle parametrization

Thu, 09 Jul 2009 02:42:47 -0700

changeset	96030f8d2f2c
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

[dev] Added field arithmetic to CohomologyPersistence (Zp + Q)

Thu, 09 Jul 2009 00:59:32 -0700

changeset	069596c71902
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

[dev] Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h

Thu, 14 May 2009 14:04:43 -0700

changeset	beff535b53ff
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

[dev] read_points() does not need ambient dimension and ignores lines starting with '#'

Thu, 14 May 2009 13:09:06 -0700

changeset	fc8ebbae62e2
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

[dev] Added documentation; for now mostly for the Python bindings

Mon, 11 May 2009 12:45:49 -0700

changeset	c270826fd4a8
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

[dev] Touch up to compile with GCC 4.4

Thu, 07 May 2009 14:53:13 -0700

changeset	7ccecc57688d
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

[dev] Cleaned up simplex comparison functions, rip-pairwise.py outputs a diagram, auxilliary add_simplices() + remove_simplices() for zigzags

Wed, 29 Apr 2009 10:16:03 -0700

changeset	2a737609b8bf
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

[dev] Alphashapes and Python bindings

Thu, 16 Apr 2009 00:23:01 -0700

changeset	d9e050258358
branch	dev
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tag
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

[dev] Placed all Python bindings code into dionysus::python namespace

Wed, 15 Apr 2009 14:17:21 -0700

changeset	580eaa850c4f
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

[dev] Cleaned up Python bindings to restore functionality:

Tue, 14 Apr 2009 14:38:08 -0700

changeset	95454ea3f9c0
branch	dev
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tag
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

[dev] Renamed header files in bindings/python to get rid of the "python-" prefix

Mon, 13 Apr 2009 20:44:31 -0700

changeset	a5fd0c2a1c88
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

[dev] Changes in Python Bindings:

Mon, 13 Apr 2009 20:38:46 -0700

changeset	406c6cc00b9c
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

[dev] Added Python bindings for the Rips complex + an example

Sat, 11 Apr 2009 10:29:53 -0700

changeset	3c3e77ac43d2
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

[dev] Cleaned up traits (chain and container) for static- and dynamic-persistence

Fri, 01 May 2009 15:09:38 -0700

changeset	0a2c2283e4a8
branch	dev
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tag
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

[dev] Added tools/extract-diagram + minor fixes

Fri, 01 May 2009 15:36:25 -0700

changeset	af54138b98fd
branch	dev
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tag
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

[dev] Added intrusive containers issue and issue filters

Fri, 10 Apr 2009 14:35:43 -0700

changeset	c50e7020a1e4
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added intrusive containers issue and issue filters
files	.issues/.filters .issues/e6f52c44ef26f4a7/new/1239399291.M841173P26652Q1.cole

[dev] Moved l2distance.h into include/geometry

Thu, 09 Apr 2009 14:43:37 -0700

changeset	51a7ed5b51f0
branch	dev
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tag
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

[dev] Added categories to some of the issues

Thu, 09 Apr 2009 14:39:12 -0700

changeset	b2103b289f06
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

[dev] Fixed distance to diagonal calculation + added stand-alone bottleneck distance tool

Thu, 09 Apr 2009 12:58:10 -0700

changeset	3c830b15d694
branch	dev
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tag
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

[dev] Added ZigzagPersistence::is_alive() + consistency zigzag outputs betti 1 at each stage

Wed, 25 Mar 2009 09:56:52 -0700

changeset	505b3795d239
branch	dev
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tag
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

[dev] Added consistency zigzag

Tue, 24 Mar 2009 15:17:39 -0700

changeset	c4e25fb4082c
branch	dev
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tag
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

[dev] Merged in cohomology branch

Mon, 23 Mar 2009 11:40:29 -0700

changeset	06a4361bddaa
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Merged in cohomology branch
files	examples/rips/rips-pairwise.cpp

[dev] Added CohomologyPersistence and Rips pairwise distances computation

Fri, 27 Feb 2009 10:14:26 -0800

changeset	5095771715ab
branch	dev
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tag
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

[dev] Added DynamicPersistenceChains (no dynamic part yet)

Sun, 22 Mar 2009 11:18:07 -0700

changeset	a3410b6ba79c
branch	dev
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tag
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

[dev] Updated Rips zigzags

Tue, 03 Feb 2009 11:31:10 -0800

changeset	374f94f92e50
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

[dev] Switched Rips complex computation to Bron-Kerbosch algorithm

Sat, 31 Jan 2009 23:02:22 -0800

changeset	3e8bebb5d857
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

[dev] Added python bindings for ZigzagPersistence (as well as ImageZigzagPersistence)

Thu, 29 Jan 2009 10:16:56 -0800

changeset	f209958b5c17
branch	dev
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tag
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

[dev] Switched to CGAL 3.4 (native CMake configuration): for now only alphashapes

Wed, 28 Jan 2009 14:57:17 -0800

changeset	958dec48d946
branch	dev
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tag
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

[dev] Implemented ImageZigzagPersistence

Tue, 20 Jan 2009 10:53:35 -0800

changeset	430d9e71e921
branch	dev
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tag
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

[dev] Debugged ZigzagPersistence (having added heavier consistency checking)

Mon, 12 Jan 2009 15:33:04 -0800

changeset	75eb7a4628f2
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 * 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

[dev] Added rips-zigzag; in the process caught a number of bugs in ZigzagPersistence (added check_consistency() to it)

Fri, 02 Jan 2009 14:54:15 -0800

changeset	e096f8892a04
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

[dev] Added DequeChains (for ZigzagPersistence)

Wed, 31 Dec 2008 11:54:34 -0800

changeset	a5debdc35559
branch	dev
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tag
user	Dmitriy Morozov <dmitriy@mrzv.org>
description	Added DequeChains (for ZigzagPersistence)
files	include/topology/cycles.h include/topology/zigzag-persistence.h

[dev] Added ZigzagPersistence

Wed, 31 Dec 2008 11:51:14 -0800

changeset	dfa74f2f2a76
branch	dev
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tag
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

[dev] Merged in Python branch

Sat, 27 Dec 2008 14:51:38 -0800

changeset	051af83fba4c
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

[dev] Initial commit of Python bindings

Thu, 25 Dec 2008 13:09:00 -0800

changeset	2cc1db3b98c6
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

[dev] Empty is now a template, replaced RecursiveIterator with boost::counting_iterator

Thu, 25 Dec 2008 13:08:41 -0800

changeset	2ac129839e02
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