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doc 2009-06-06 tomduck [r61] Updated docs
examples 2009-06-06 tomduck [r60] Darwin-specific build modifications
gts 2009-06-06 tomduck [r59] Fixed vertex typecasting code and some cleanup ...
screenshots 2009-05-12 tomduck [r3] Added screenshots
test 2009-06-06 tomduck [r59] Fixed vertex typecasting code and some cleanup ...
web 2009-06-06 tomduck [r63] Small tweak to package description
AUTHORS 2009-06-03 tomduck [r57] Updated documentation
ChangeLog 2009-06-06 tomduck [r62] Updated ChangeLog
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MANIFEST 2009-06-06 tomduck [r62] Updated ChangeLog
MANIFEST.in 2009-06-02 tomduck [r55] Made isosurface a function and added more testi...
README 2009-06-03 tomduck [r57] Updated documentation
README.developers 2009-06-06 tomduck [r59] Fixed vertex typecasting code and some cleanup ...
setup.py 2009-06-06 tomduck [r63] Small tweak to package description

Read Me

PYGTS OVERVIEW FOR DEVELOPERS

  Copyright (C) 2009 Thomas J. Duck
  All rights reserved.

  Thomas J. Duck <tom.duck@dal.ca>
  Department of Physics and Atmospheric Science,
  Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5


CONTENTS

  1. INTRODUCTION
  2. GTS BINDING STATUS
  3. PREPARING A RELEASE


1. INTRODUCTION

  This overview assumes that you have some familiarity with GTS.  See

       http://gts.sourceforge.net/reference/book1.html

  for the GTS Library Reference Manual.  It would also help to understand 
  how extension types in python are defined and implemented.  See

       http://docs.python.org/extending/newtypes.html

  for a good tutorial on Defining New Types.

       The objective is to allow python to access GTS types in a 
  transparent fashion.  The programming is done in C, the language of 
  the standard python interpreter.  The GtsObject, GtsPoint, and GtsVertex 
  types etc are encapsujlated in corresponding PygtsObject, PygtsPoint and 
  PygtsVertex classes, etc.  Note that type and class mean the same thing 
  in python.

       Python and GTS have different approaches to the management of 
  object life-cycles.  Python uses reference counting: Once an object's 
  reference count is reduced to zero, it is freed.  In GTS, on the other 
  hand, each object such as GtsVertex, GtsEdge, and GtsFace, maintains a 
  list of objects it is attached to.  The object is freed when the last 
  object in its attachment list is freed.  This can be seen as an alternative 
  implementation of reference counting.  We need to merge the two approaches.

       Aside: GTS has intriniscally unattached objects, like 
       GtsPoint, GtsSegment, GtsTriangle, and GtsSurface.  These 
       are rather more straight-forward to handle.  It is also 
       possible under GTS to free an object that is attached to others, 
       in which case those others are all freed as well.  We will 
       deliberately avoid doing this in order to maintain a simple 
       approach to the reference-counting problem.

       The various python types are defined in object.h, point.h, vertex.h, 
  etc, and implemented in object.c, point.c, vertex.c, etc.  The inheritance 
  tree is as follows:
  
      PygtsObject +-- PygtsPoint -- PygtsVertex
                  |
                  +-- PygtsSegment -- PygtsEdge
                  |
                  +-- PygtsTriangle -- PygtsFace
                  |
                  +-- PygtsSurface

  The files are, for the most part, structured in the same way.  The top 
  section in each is titled "Methods exported python", and it ends with a 
  methods table.  This section is where most of the GTS functions are hooked 
  in.  Next comes the "Attributes exported to python" and its methods table, 
  and then the "Python type methods" section which ends with a table defining
  the python type.  The "Python type methods" section is where object
  allocation occurs for both the python and GTS objects.  Last comes the
  "PyGTS functions" section which is used to define protected functions
  used by PyGTS.  For example, there are the pygts_xxx_check() functions
  which are used for type-checking, and the pygts_xxx_is_ok() funtions
  which inspect the python and encapsulated GTS objects for correctness.

      This next bit is important.
  
      Each python object encapsulates a pointer to a GTS object.  For GTS
  objects that can be attached, a private "parent" object is also
  encapsulated.  By doing this, we can make sure that an attachment always 
  exists, and so an object cannot be deallocated without our say-so.  We also 
  maintain a separate table of active python objects that are indexed using 
  their encapsulated GTS object.  This allows us to maintain a one-to-one
  correspondence between PyGTS and GTS objects.  The problem of one
  GTS object being encapsulated by more than one PyGTS object is 
  intentionally avoided.

       Sometimes it is necessary to differentiate encapsulated parent objects 
  from other attachments.  To do so, we can define special parent subtypes.  
  This is the approach taken, for example, with vertices, where the 
  complexities of the vertex replacement operation require such 
  differentiation.

       In general, the interface is made to be as "pythonic" as possible.
  GTS functions are combined into single python methods where it makes sense.
  In some cases a simpler version of the interface is provided.  Also, methods 
  are preferred over functions.  For example, the difference, union and
  intersection operations are provided as methods to PygtsSurface, and are
  composed from more general GTS functions.

      The main module file is pygts.c, and it handles binding the new
  types into python.  It also creates the "object table" described above,
  and contains the functions that PyGTS provides.  The C extensions 
  are compiled into _gts.so, and its types are imported into the main 
  module file gts.py.  This allows the incorporation of top-level 
  documentation and the inclusion of functions written in pure python.


2. GTS BINDING STATUS

  The categorized GTS functions and corresponding functions and methods 
  in python module gts, if implemented, are given below.  Not all of the 
  functions will be implemented in python.  Some are combined into a 
  single method (as appropriate), while others may be unnecessary or 
  irrelevant.  It should also be pointed out that PyGTS implements methods 
  that are not provided by GTS.

  The "Geometrical Object Hierarchy" API is mostly complete.  A few
  of the "Surface Operations" have also been implemented.  Additions
  from other categories will be completed on an "as-needed" basis,
  or more likely when there is a knowledgeable contributor who can help
  write meaningful units tests in these areas.


  Geometrical Object Hierarchy
  ----------------------------

    Points
    ~~~~~~

      gts_point_set():                      Point.set()
      gts_point_is_in_rectangle():          Point.is_in_rectangle()
      gts_segment_triangle_intersection():  Segment.intersection()
      gts_point_transform():                Point.rotate()
                                            Point.scale()
                                            Point.translate()
      gts_point_distance():                 Point.distance()
      gts_point_distance2():                Point.distance2()
      gts_point_orientation_3d():           Point.orientation_3d()
      gts_point_orientation_3d_sos():       Point.orientation_3d()
      gts_point_in_circle():                Point.is_in_circle()
      gts_point_in_triangle_circle():       Point.is_in_circle()
      gts_point_is_in_triangle():           Point.is_in()
      gts_point_orientation():              *** What should the signature be?
      gts_point_orientation_sos():          *** What should the signature be?
      gts_point_segment_distance2():        Point.distance2()
      gts_point_segment_distance():         Point.distance()
      gts_point_segment_closest():          Point.closest()
      gts_point_triangle_distance():        Point.distance()
      gts_point_triangle_closest():         Point.closest()
      gts_point_triangle_distance2():       Point.distance2()
      gts_point_is_inside_surface():        Point.is_inside()


    Vertices
    ~~~~~~~~

      gts_vertex_is_unattached():           Vertex.is_unattached()
      gts_vertex_is_boundary():             Vertex.is_boundary()
      gts_vertex_is_contact():              Vertex.is_contact()
      gts_vertices_are_connected():         Vertex.is_connected()
      gts_vertex_replace():                 Vertex.replace()
      gts_vertex_neighbors():               Vertex.neighbors()
      gts_vertex_triangles():               Vertex.triangles()
      gts_vertex_faces():                   Vertex.faces()
      gts_vertex_fan_oriented():            Surface.fan_oriented()
      gts_vertex_encroaches_edge():         Vertex.encroaches()
      gts_vertices_from_segments():         vertices()
      gts_vertices_merge():                 merge()


    Segments
    ~~~~~~~~

      gts_segments_are_identical():         N/A (duplicates are prevented)
      gts_segments_are_intersecting():      Segment.intersects()
      gts_segment_is_duplicate():           N/A (prevented using object table)
      gts_segment_is_ok():                  Segment.is_ok()
      gts_segment_connect():                Segment.connects()
      gts_segments_touch():                 Segment.touches()
      gts_segments_from_vertices():         segments()
      gts_segment_midvertex():              Segment.midvertex()


    Edges
    ~~~~~

      gts_edge_replace():                   N/A (causes broken triangles)
      gts_edge_is_unattached():             Edge.is_unattached()
      gts_edge_is_duplicate():              N/A (prevented using object table)
      gts_edge_has_parent_surface():        Surface.parent()
      gts_edge_has_any_parent_surface():    N/A (will interfere with PyGTS 
                                            parents)
      gts_edge_is_boundary():               Edge.is_boundary()
      gts_edge_is_contact():                Edge.contacts()
      gts_edge_belongs_to_tetrahedron():    Edge.belongs_to_tetrahedron()
      gts_edge_face_number():               Edge.face_number()
      gts_edge_manifold_faces():            Surface.manifold_faces()
      gts_edge_is_encroached():             *** Not clear how to implement
      gts_edges_merge():                    N/A (duplicate edges not allowed)
      gts_edges_from_vertices():            Surface.edges()
      gts_edge_swap():                      *** Not clear what this does,
                                            the consequences, or why you would 
                                            want it

    
    Triangles
    ~~~~~~~~~

      gts_triangle_set():                   N/A (could cause broken triangle)
      gts_triangle_area():                  Triangle.area()
      gts_triangle_perimeter():             Triangle.perimeter()
      gts_triangle_quality():               Triangle.quality()
      gts_triangle_normal():                Triangle.normal()
      gts_triangle_revert():                Triangle.revert()
      gts_triangle_orientation():           Triangle.orientation()
      gts_triangle_is_duplicate():          N/A (prevented using object table)
      gts_triangles_angle():                Triangle.angle()
      gts_triangles_are_compatible():       Triangle.is_compatible()
      gts_triangle_enclosing():             triangle_enclosing()
      gts_triangles_common_edge():          Triangle.common_edge()
      gts_triangle_neighbor_number():       Use face.neighbor_number()
      gts_triangle_neighbors():             Use face.neighbors()
      gts_triangle_vertices_edges():        N/A (redundant)
      gts_triangle_vertex_opposite():       Triangle.opposite()
      gts_triangle_edge_opposite():         Triangle.opposite()
      gts_triangle_vertices():              Triangle.vertices()
      gts_triangle_vertex():                Triangle.vertex()
      gts_triangle_is_ok():                 Triangle.is_ok()
      gts_triangle_use_edges():             N/A (duplicate triangles are
                                            already disallowed; creating
					    a new triangle with these
					    Edges will return the old one)
      gts_triangle_circumcircle_center():   Triangle.circumcenter()
      gts_triangle_is_stabbed():            Triangle.is_stabbed()
      gts_triangles_are_folded():           Use triangle.angle()
      gts_triangles_from_edges():           triangles()
      gts_triangle_interpolate_height():    Triangle.interpolate_height()


    Faces
    ~~~~~

      gts_face_has_parent_surface():        Face.is_on()
      gts_face_neighbor_number():           Face.neighbor_number()
      gts_face_neighbors():                 Face.neighbors()
      gts_face_foreach_neighbor():          Use Face.neighbors()
      gts_face_is_compatible():             Face.is_compatible()
      gts_faces_from_edges():               Surface.faces()


    Surfaces
    ~~~~~~~~

      gts_surface_add_face():               Surface.add()
      gts_surface_remove_face():            Surface.remove()
      gts_surface_copy():                   Surface.copy()
      gts_surface_merge():                  Surface.add()
      gts_surface_read():                   Surface.read()
      gts_surface_is_manifold():            Surface.is_manifold()
      gts_surface_is_orientable():          Surface.is_orientable()
      gts_surface_is_closed():              Surface.is_closed()
      gts_surface_vertex_number():          Surface.Nvertices
      gts_surface_edge_number():            Surface.Nedges
      gts_surface_face_number():            Surface.Nfaces
      gts_surface_boundary():               Surface.boundary()
      gts_surface_area():                   Surface.area()
      gts_surface_volume():                 Surface.volume()
      gts_surface_center_of_mass():         Surface.center_of_mass()
      gts_surface_center_of_area():         Surface.center_of_area()
      gts_surface_stats():                  Surface.stats()
      gts_surface_quality_stats():          Surface.quality_stats()
      gts_surface_print_stats():            Seems unnecessary
      gts_surface_write():                  Surface.write()
      gts_surface_write_oogl():             Surface.write_oogl()
      gts_surface_write_oogl_boundary():    Surface.write_oogl_boundary()
      gts_surface_write_vtk():              Surface.write_vtk()
      gts_surface_foreach_vertex():         Use Surface.vertices()
      gts_surface_foreach_edge():           Use Surface.edges()
      gts_surface_foreach_face():           Use Surface iterator or 
                                            Surface.faces()
      gts_surface_foreach_face_remove():    N/A (can't implement)
      gts_surface_foreach_intersecting_face():  N/A (can't implement)
      gts_surface_traverse_next():          Use iteration over faces
      gts_surface_distance():               Surface.distance()
      gts_surface_strip():                  Surface.strip()
      gts_surface_tessellate():             Surface.tessellate()
      gts_surface_generate_sphere():        sphere()
      gts_surface_split():                  Surface.split()


  Surface Operations
  ------------------

    Boolean operations
    ~~~~~~~~~~~~~~~~~~

      gts_surface_inter_boolean():          Surface.difference()
                                            Surface.intersection()
                                            Surface.union()
      gts_surface_is_self_intersecting():   Surface.is_self_intersecting()


    Surface simplification and refinement
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      gts_surface_coarsen():                Surface.coarsen()
      gts_coarsen_stop_number():            N/A (used in coarsen operation)
      gts_coarsen_stop_cost():              N/A (used in coarsen operation)
      gts_volume_optimized_vertex():        N/A (used in coarsen operation)
      gts_volume_optimized_cost():          N/A (used in coarsen operation)
      gts_edge_collapse_is_valid():
      gts_edge_collapse_creates_fold():


    Out-of-core Simplification
    ~~~~~~~~~~~~~~~~~~~~~~~~~~

      gts_cluster_add():
      gts_cluster_update():
      gts_cluster_grid_add_triangle():
      gts_cluster_grid_update():


    Isosurfaces from 3D functions
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      gts_iso_slice_fill():
      gts_iso_slice_fill_cartesian():
      gts_isosurface_slice():
      gts_isosurface_cartesian():           isosurface()
      gts_isosurface_tetra():               isosurface()
      gts_isosurface_tetra_bounded():       isosurface()
      gts_isosurface_tetra_bcl():           isosurface()


    Delaunay and constrained Delaunay triangulations
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      gts_point_locate():
      gts_delaunay_add_vertex():
      gts_delaunay_add_vertex_to_face():
      gts_delaunay_remove_vertex():
      gts_delaunay_add_constraint():
      gts_delaunay_remove_hull():
      gts_delaunay_conform():
      gts_delaunay_refine():


    Differential geometry operators
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

      gts_vertex_gaussian_curvature():
      gts_vertex_mean_curvature_normal():
      gts_vertex_principal_curvatures():
      gts_vertex_principal_directions():


  Progressive and Hierarchical Surfaces
  -------------------------------------

    Vertex Split
    ~~~~~~~~~~~~

      gts_split_collapse():
      gts_split_expand():
      gts_split_height():
      gts_split_traverse():


    Progressive surfaces
    ~~~~~~~~~~~~~~~~~~~~

      gts_psurface_add_vertex():
      gts_psurface_remove_vertex():
      gts_psurface_set_vertex_number():
      gts_psurface_get_vertex_number():
      gts_psurface_min_vertex_number():
      gts_psurface_max_vertex_number():
      gts_psurface_foreach_vertex():
      gts_psurface_open():
      gts_psurface_read_vertex():
      gts_psurface_close():
      gts_psurface_write():


    Hierarchical vertex split
    ~~~~~~~~~~~~~~~~~~~~~~~~~

      gts_hsplit_collapse():
      gts_hsplit_expand():
      gts_hsplit_force_expand():

    
    Hierarchical surfaces
    ~~~~~~~~~~~~~~~~~~~~~

      gts_hsurface_traverse():
      gts_hsurface_height():
      gts_hsurface_foreach():


  Graph and Operations on Graphs
  ------------------------------

    Graph class
    ~~~~~~~~~~~

      gts_gnode_degree():
      gts_gnode_foreach_edge():
      gts_gnode_foreach_neighbor():
      gts_gnode_weight():
      gts_gnode_move_cost():

      gts_gedge_weight():
      gts_gedge_connects():

      gts_graph_read():
      gts_graph_read_jostle():
      gts_graph_write():
      gts_graph_write_dot():
      gts_graph_print_stats():
      gts_graph_foreach_edge():

      gts_graph_traverse_next():
      gts_graph_traverse_what_next():
      gts_graph_edges_cut():
      gts_graph_edges_cut_weight():
      gts_graph_distance_sum():
      gts_graph_farthest():
      gts_graph_weight():

      gts_surface_graph_surface():


    Weighted graph
    ~~~~~~~~~~~~~~

      gts_wgraph_weight_max():


    Progressive graph
    ~~~~~~~~~~~~~~~~~

      gts_gnode_split_collapse():
      gts_gnode_split_expand():

      gts_pgraph_add_node():
      gts_pgraph_remove_node():
      gts_pgraph_down():
      gts_pgraph_set_node_number():
      gts_pgraph_get_node_number():
      gts_pgraph_max_node_number():
      gts_pgraph_min_node_number():
      gts_pgraph_foreach_node():


    Graph partitioning
    ~~~~~~~~~~~~~~~~~~

      gts_graph_ggg_bisection():
      gts_graph_bfgg_bisection():
      gts_graph_bisection_kl_refine():
      gts_graph_bisection_bkl_refine():
      gts_graph_recursive_bisection():
      gts_graph_bubble_partition():
      gts_graph_edges_cut():
      gts_graph_edges_cut_weight():
      gts_graph_partition_edges_cut():
      gts_graph_partition_balance():
      gts_graph_partition_clone():
      gts_graph_partition_print_stats():
      gts_graph_partition_edges_cut_weight():


3. PREPARING A RELEASE

  Below are the steps used to prepare a PyGTS release.  This only of
  interest to the PyGTS Release Manager.

  1) Update the VERSION in setup.py and the ChangeLog.  Update the pydoc
     documentation.  Check everything into svn.

  2) Build the archive using

       $ python setup.py sdist

     The archive will be found in the dist directory.

  3) Install, build and unit test the distribution on different systems.  
     Note that different warning messages are found under Debian and 
     Mac OS X.  Eliminate whatever errors and warnings that are found, 
     and rebuild the archive.

  4) Login to SourceForge and upload the archive at

       https://frs.sourceforge.net/webupload

  5) Add a new release of PyGTS on SourceForge at

       https://sourceforge.net/project/admin/editpackages.php?group_id=262159

     Use the version number as the release name.

     Step 1: Paste in the Changelog entries since the last release, 
             choosing "Preserve my pre-formatted text".  Don't bother with 
	     the Notes -- that is what the News releases are for.

     Step 2: Add the file you just uploaded to the release.

     Step 3: Set "Processor" to "Platform-Independent" and "File Type"
             to "Source .gz".  Press "Update/Refresh".

  6) Update the Web site and upload it using

       $ sftp username,pygts@web.sourceforge.net

     to the htdocs directory.  The username should be replaced.

  7) Make a News announcement at

       https://sourceforge.net/news/?group_id=262159

     Here is a template announcement, with appropriate formatting for the
     Web page's text box:

PyGTS XX.XX.XX released

PyGTS (http://pygts.sourceforge.net/) is a python package used to construct, manipulate, and perform computations on 3D triangulated surfaces. It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library (http://gts.sourceforge.net/). 
 
This release fixes a number of issues with the install script.

See the SF project page (https://sourceforge.net/projects/pygts/), screenshots (https://sourceforge.net/project/screenshots.php?group_id=262159), or go straight to download (https://sourceforge.net/project/showfiles.php?group_id=262159).

  8) Update PyPI (the python package index) as follows:

       $ python setup.py register

  9) Make announcements on the mailing lists.

  10) Check the following primary locations that advertise PyGTS, to ensure 
      that they have up-to-date information:

        http://wiki.python.org/moin/NumericAndScientific
        http://www.scipy.org/Topical_Software
        http://freshmeat.net/projects/pygts
        http://pypi.python.org/pypi?%3Aaction=search&term=PyGTS