CHANGELOG.txt

CHANGE LOG: Zinc Library

v4.2.1
Update minimum version of CMake required to 3.18.
CI infrastructure fixes.

v4.2.0
Fix bug for export of single element line to webGL.
Fix undefined element field segfault.
Add docs target for building the documentation with Sphinx.
Rename Zinc_DEVELOPER_VERSION to Zinc_VERSION_DEVELOPER.
Upgrade numerical derivative test answers to a quartic interpolation.
Re-introduce viewing volume API.
Replace use of sprintf with snprintf.

v4.1.2
Fix bug with loading images with that have a depth that are not integrals of a byte.

v4.1.1
Fix empty classifiers for Python packaging.
Drop support for OS X Mountain Lion and below (last released 2015).

v4.1.0
Fix optimisation with conditional field applying partially to elements' nodes.
Region read with single time is ignored with a warning for field value types not supporting time sequence.
Add mesh group API to add adjacent elements sharing faces/lines/points with elements currently in mesh group.
Fix define faces to match faces with same nodes, centroid and orientation, and better detect collapsed elements.
Add API to selectively remove subobject and subregion groups from group field.

v4.0.1
Fix group remove nodes/elements conditional

v4.0.0
(Break) Rebrand as Zinc, using namespace 'cmlibs'.
(Break) Remove subobject groups. Group field directly owns mesh groups and nodeset groups.
(Break) Remove cmzn_mesh_match, cmzn_nodeset_match as can now use pointer comparison for these classes.
(Break) Remove deprecated elementtemplate define field simple nodal, element constant and associated API.
(Break) Remove deprecated Alias field. Use Apply field instead.
(Break) Remove deprecated Optimisation independent field APIs (use dependent field).
Add API to get owning group field from nodeset or mesh.
Add IO format ASCII STL and wavefront.

v2.10.2
Fix behaviour of get/create subregion groups, with get now able to discover subregion groups by name.
Fix scene set selection group so if not set, inherits subregion group of parent/ancestor scene selection group.
Destroy objects immediately on removal from manager to release objects they reference. Fixes invalid references from sub-object group to destroyed owner group.

v3.10.1
Fix serialisation of field types identity and if.

v3.10.0
Allow integrals over face and line meshes in optimisation objective fields.
Evaluate parameter and top-level/field element xi derivatives on faces and lines, and convert field element xi derivatives to face and line xi.
Support conditional field for NEWTON optimisation method.
Find mesh location field with lower dimensional search mesh restricts location to main mesh group if supplied.
Add API to get mixed mesh and parameter derivative operators.
Fix create field eigenvectors to take generic field argument.
Add API to get/set transpose field source number of rows.
Add API to get matrix multiply field number of rows.
Add API to define standard spectrums.
Fix serialisation of graphics line width and point size.
Fix wrapping of graphics vector fields where no coordinate field is set.
Fix Fieldassignment where source field is undefined.

v3.9.0
Add field evaluate range API.
Optimise find mesh location using pre-calculated element field range cache.
Improve find mesh location search mode nearest on 3-D elements.
Fix pre-merge checks of subregions when reading models.

v3.8.1
Fix read merge for embedded locations which corrupted element to embedded node map.
Fix write description for fields with NOT_APPLICABLE coordinate system type.

v3.8.0
Serialise mesh and nodeset operators fields to/from json description.
Add missing type-specific field API.

v3.7.0
Support optimisation at time for time-varying fields.
Add Region change notifier, for tree structure changes.
Add Sceneviewer incremental graphics build render timeout API.
Fix groups not immediately removing destoyed nodes or elements within begin/end change.
Fix enforce non-numeric fields have NOT_APPLICABLE coordinate system type.
Fix field assignment for embedding maps. Derivatives can now be mapped with finite difference node gradient of Apply field.

v3.6.0
Add material module change notifier.
Add Sceneviewer enum to/from string name APIs. Serialise transparency layers.
Add EX version 3 format supporting parameters with time sequence, node and element templates, compact group representation.
Fix conditional if field non-real value type reporting and use in field assignment.

v3.5.1
Fix const usage in C++ API.

v3.5.0
Add support for relative paths in region find/create subregion; add get path, relative path, root.
Add Apply and Argument fields which apply real-valued field expressions with argument binding, including from another region.
Add Field dependsOnField API.
Deprecate Alias field. Now creates an equivalent Apply field.
Behaviour change: Automatically-named fields are automatically renamed to make way for different fields needing their names.
Behaviour change: Model read fails if any field is incompatible with existing field of same name. Previously renamed finite element fields.

v3.4.0
Fix crash in manager cleanup when change caching left active.
Fix defining fields from model files and respecting unmanaged status while change caching active.
Fix reading empty strings from EX files.
Evaluate gradient in lower dimensional elements.
Add exception-safe ChangeManager change caching template to C++ API.
Add Materialmodule description json serialisation API.
Add Materialmodule, Fieldmodule getContext API.
Add Context getName API.
Add Graphics BoundaryMode which generalises exterior flag.
Add enum to/from string name APIs. Fix some names to match unique part of enumeration constant.

v3.3.0
Add field parameters interface.
Add evaluation of field derivatives with respect to field parameters, fallback to finite difference.
Add NEWTON method to optimisation using field parameter derivatives and matrix assembly.
Add optimisation dependent field API
Deprecate optimisation independent field API (should have been called dependent).
Maintain map from element to nodes for stored mesh location fields at nodes.
Add optional map from nodes to elements in nodeset operators, to evaluate per-element.
Evaluate mesh integral field at elements to give element integral.
Evaluate exact higher field derivatives for many field operators, some to just second order.
(Break) Element field templates with unused scale factors now fail in validate check.

v3.2.0
Add support for cubic Hermite serendipity basis.
Add support for higher derivative evaluation w.r.t. element chart coordinates.

v3.1.2
API changes:
(Break) Split element API header into: element, elementbasis, elementfieldtemplate, elementtemplate, mesh
(Break) Split node API header into: node, nodeset, nodetemplate
Deprecated several element template methods.
Behaviour changes:
Now writes models in new EX and FieldML formats which cannot be read into older versions of Zinc.

v3.1.1
Deprecated API status headers and enums for result/error codes. Use result headers and enums instead.
Default behaviour changes:
Default ratio of diffuse to ambient light changed from 0.9:0.1 to 0.8:0.2.
Default tessellation refinement factors increased from 4 to 6.
2753 Incremental graphics build. Graphics build for approximately 1 second before display in scene viewer and triggering another build/redraw. Currently limited to whole elements or nodesets.

v3.0.1
API Changes:
(Break) 3490 Changed enumerator values in enum cmzn_node_value_label to permute in lowest s number fastest, matching cm/Iron. This is a binary break, not a source break.
(Break) 3490 New format for element fields written to EX file, mapping by derivatives and versions instead of node indices. Old files can still be read; new files can't be read by older versions.
(Break) 3288 Changed element face type enumeration: ALL replaces INVALID in matching any element, ANY_FACE replaces ALL in matching any element that is a face, NO_FACE option added. Binary enumeration values changed.

v3.0.0

API Changes:
3079 As part of branding as OpenCMISS-Zinc Library and eliminate name clashes, change C++ API namespace from zinc:: to CMLibs::Zinc::, and C API prefix from Cmiss_ to cmzn_.
3260 Move all enums into types/*id files. Removed interactive tool from external APIs. Removed all legacy Cmgui 'execute command' APIs. Replaced with direct APIs.
3360 Added isValid APIs for all C++ classes.
3361 Renamed iso_surfaces to contours.
3406 Change component field to use first component index = 1 (was 0).
3554 Removed rendition and merged its functions into scene, scene now is the
	graphical presentation of a region.
3574 Fix inconsistent API header names between C and C++.
3580 Dedicated APIs for get/set is_managed status replaced general attribute APIs.
3627 Replaced generic get/set_attribute functions with direct APIs.
3661 Removed graphics module APIs and moved the graphics related modules getter APIs to
	context and scene.
3662 Standardise API type names and enumerations in C and C++ APIs. Includes using full type names in create and other functions,	and multi-word type names are compounded into a single word e.g. 
	field_cache -> fieldcache (FieldCache -> Fieldcache in C++).
3668 Changed default projection mode to be perspective. Fly zoom mode is now the default right button drag behaviour. 

Added Features:
455 Added stream APIs to support compressed files.
2107 Added glyph APIs, custom glyphs can now be created from glyph module and set on point graphics.
3185 Improved region import/export APIs to support datapoints import and domain specific exports.
3260 Added setTextureField and setTextureCoordinateField APIs to materials.
3359 Implemented UI-independent OpenType fonts.
3360 Added field, scene filter and glyph cast-to-derived-type methods to C++ API.
3361 Completed graphics APIs, added graphics point attributes APIs for editing point graphics, added graphic line attributes APIs for editing line attributes. Points graphics type with separate field domain type (supersedes use_element_type) to replace point, node_points, data_points, element_points. Improved efficiency of changing spectrum.
3362 Added timekeeper module to support adding multiple timekeepers in future.
3425 Added field module notifier and field module event query for individual field changes. Added nodeset/mesh changes objects and API for enquiring about changes to nodes/elements from a field module event.
3454 Sceneviewerinput which handle inputs into libZinc scene viewer which is useful for transformation and zooming.
3492 Improved image field APIs.
3498 Adding analyze image format handling.
3528 Reintroduced timekeepers and timenotifier (previously known as time object).
3530 Adding API for creating derivative fields (derivative, curl, divergence, gradient).
3532 Adding new API to be able to compute nodeset minimum and maximum.
3550 Added scene picker which can be used for picking objects from scene with provided information.
3550 Added scene filter by graphics type.
3581 Added tessellation module for managing tessellation objects.
3583 Added font module for managing font objects.
3586 Added spectrum module for managing spectrum objects.
3589 Added material module for managing material objects.
3597 Added scenefilter module for managing scenefilter objects.
3609 Added scene API to render graphics to a point cloud.
3611 Added more image processing APIs to C++ interface.
3630 Added scene API to get spectrum data range.
3636 Greatly improved spectrum APIs.
3639 Added APIs to get and set wrap mode of image field.
3640 Improved Sceneviewer APIs.
3646 Added set identifier methods to node and element.
3647 Added new yellow, magenta, cyan, orange, brown, grey25, grey50 and grey75 default materials.
3678 Added functions in image resample field to specify input coordinates bounds and texture lookup coordinates, allowing image processing on images with texture coordinates outside of the 0 to 1 range.
3687 Added three new context APIs - get version, get_revision and get_version_string.

Bugs fixed:
Fixed several bugs causing occasional crashes and memory leaks.
3347 Fixed incorrect error message when creating a material.
3677 Fixed a bug causing libzinc unable to render selected elements/nodes 
	with selected material when display_lists is off.
3694 Fixed evaluation of derivatives for dot_product field.

Miscellaneous:
3079 Brand as OpenCMISS-Zinc Library.
3359 Separate Zinc Library from Cmgui source.
3439 Build Zinc using cmake, build and test with buildbot.
3558 Updated source code license to MPL2.0.

v2.9.0

API Changes:
(New) Add CMISS_SCENE_VIEWER_INPUT_MODIFIER_NONE mode
(New) Enable more field types for create/define fields APIs

Added Features (some incomplete):
3133 FieldML 0.5 import, replaces FieldML 0.4 import.
3184 Allowed reading data into a specific region.

Bugs fixed:
Fixed several bugs causing occasional crashes.
3115 Key presses now get sent to scene viewer callbacks
3160 Fixed crashes caused when passing a null field to cmzn_field_module_create_abs
3167 Fixed setting linear filter for image field has no effect
3181 Fixed crashes when passing null context to cmzn_context_get_default_region
3207 Fixed streamlines not showing on 2D models

Improvements:
2512 Remove group regions, replaced by group fields
3213 Improved field evaluation/assignment caching

Miscellaneous:
Removed cmgui-motif from current build

v2.8.0

API Changes:
(New) Optimisation API
(New) Graphics material API
(New) Field evaluation and assignment API
(New) Scene graphics filtering API
(New) Cmgui Input/Output (Stream) APIs for regions and image field
(New) Graphics tessellation API
(New)API to support external wx main loop
(New) Image field API
(Break) Remove cmiss_timer API
(Break) Remove texture API

Added Features (some incomplete):
1047 Merge scene and region hierarchies.
1699 Print out antialiasing images using cmgui-wx
1776 Region-capable selection and groups.
1844 Implement fitting and optimisation.
2549 FieldML 0.2 import.
2624 Scene graphics filtering           
2680 Added graphics coordinate system
2683 Export points with wavefront format
2684 Improve spectrum rainbow
2749 Graphics tessellation objects and editor
2775 Add xi discretization modes to streamlines
2842 Read fieldML 0.4 format into Cmgui

Bugs fixed:
Fixed numerous occasional crashes.
2769 gfx read elements generate option works for root region

Improvemnets:
2365 New mechanism for static graphics in scene
2702 Hierarchical transformation
2817 Visibility flag to work hierarchically
3026 Improved performance when rendering element points

Others:
2529: Simplify changes for buulding third_party on different windows platforms

v2.7.1 (In development)

Added Features (some incomplete):
1047 Merge scene and region hierarchies.
1776 Region-capable selection and groups.
1805 Use double precision for real fields. 
2549 FieldML 0.2 import.

v2.7.0
12 Apr 2010

This is an official release of cmgui.

API Changes:
(Break) Context API replaces command data. User interface must be enabled explicitly before using graphics, time and execute_command.
(Break) Region API. New methods for creating regions and finding subregions. New method to get field module. Removed obsolete cmzn_region_add_field.
(Break) Field API. New Field_module API has factory methods for creating fields owned by a region; no need to call cmzn_region_add_field. New get_name function.
(Break) Object persistence API. New ~set_persistent methods for field, material must be called for objects to persist in owning module when no external references held.
(New) Graphical material API.
(New) Time API. 

Added Features:
1037 Field API
1630 Time object and time keeper API
1788 Added information in about dialog
1854 Support write exnode function at specific time
1990 New isosurface code including tetrahedra support
1992 Surfaces made from exterior faces should now have outward normals 
2091 Support texture tiling on special case for orthogonal aligned texture coordinates
2096 Graphical material API
2105 Support per-element constant fields
2387 Region API
2417 Replaced command data with context as main object in API
2458 Added more discretization modes to simplex
2491 Object persistent API

Bugs fixed:
995 Remove CREATE and DESTROY macros from API
1023 Fixed missing geometry in tiled element
2037 Fixed crash when when closing the scene editor while the focus is on the isovalue text box
2092 Texture properties are no longer merged when a texture is modified by reading in a new image file 
2377 FixedIntel drivers incorrectly clip new graphics buffers
2427 Fixed image field API not working properly due to restriction on modifying number of components
2451 Fixed strange name when saving png file

Improvement:
2064 Rendering optimisation for picking, spectrum, glBegin/glEnd

v2.6.2
20 Jan 2010

This is an intermediate release of cmgui, parts of the software may or may 
not work.

Added Functions (selected list):
1626 Field dependent visibility
1837 Added glyphs that have texture coordinates
1917 Width option for isolines
1989 Triangular meshing
2050 Tetrahedral meshing

Bugs fixed:
949  Cmgui now prints out extra large images correctly
1789 Timekeeper's time has been tweak to work correctly
1791 Fixed cmgui does not evaluate field value at the right time in rare occasion
1833 Fixed antialiasing not applied to other scene viewer panels except the first one
     in rare occasion
1854 Allow user to output ex format file at a specified time

Improvement:
1738 Better CMake support.
1788 Added more information to the about box.
1990 New isosurface algorithem which should improve performance and it now handles tetrahedron
2012 Use 16bit storage for 16bit grey scale image when rendering using OpenGL

Others:
More api functions have been exposed for api user and have started work on the c++ api but note that the api functions are not yet finalised.


v2.6
5 May 2009

Breaks:
1609 Command "gfx write nodes/elements/data" 'fields' option now requires field names to be separated by ampersands (&)

Added Functions (selected list):
866 Added quadratic simplex (tetrahedron) element basis functions.
883 Implemented offscreen printing for cmgui-wx. (Anti-aliasing not supported yet)
901 Improved time dependent transformation interface.
948 Greater support of different DICOM formats using GDCM.
976 Rendering of full resolution textures about GPU supported sizes by tiling (in certain cases...)
990 Added scene chooser on graphics windows.
1019 Added transformation editor of scene objects.
1022 Added graphics font support in cmgui-wx.
1026 Added Opengl GLSL support.
1030 Added 'function' field type for reusing another field's function with a different source field.
1035 Optimized basis function calculations.
1037 (Ongoing) Introducing new field API.
1067 Fields owned by region - can now define computed fields in sub-regions.
1129 Complete wx interface
1130 Allowed user-defined shading programs.
1323 Enforced field ownership and relationships within region.
1447 (Ongoing) Using environment variable overrides for OpenGL extensions. 
1486 Added 'alias' field type for importing a field from another region.
1522 Added absolute value field.
1527 Beginnings of SWIG API support. 
1609 Added support for regions and comments in EX file format - read and write.
1630 Added time notifier and time keeper API.
1733 Windows support for the -example command line option
Added cmgui user documentation in docs folder and wiki including 1534 EX file format guide.

Bugs fixed (selected list)
844 Fixed sub-regions not supporting time
910 Fixed if a node is labelled with a field that is not defined for the node then it is not rendered.
1020 Fixed 'gfx destroy lines all' destroys elements too. 
1069 Fixed merging element fields with no scale factors crashes.
1580 Fixed set_values on composite field can lead to undefined values.
1623 Fixed time_keeper fails to notify clients when t = 0.
1643 Fixed file dialog title text is garbled for open com file dialog.
1654 Fixed CMGUI fails to continue playing time keeper.
1785 Fixed CMGUI fails to render all child scenes of a scene.

25 June 2008
API changes:
cmiss_scene_viewer.h
cmzn_scene_viewer_get_frame_pixels now takes a 
   enum cmzn_field_image_storage_pixel_format storage
   rather than a Texture_format enumerator.
cmiss_field_image.h New interface.

v2.5
17 Dec 2007

Third release of cmgui-wx.

Fixes:
Fixed user interface resizing issue.
Fixed a number of memoryleak.
Fixed a number of bugs.

Added interface components:
Element point viewer, Spectrum editor, Time editor, Material editor.

Added functions:
Time dependent transformation using quaternion.
Write out a total comfile.
Save all (reproduce the exnode, exelem and com file).
List all (List of commands used to construct the current model).
A number of image filters.
The ability to specify a sequence of iso values with a number, first and last value.
Added a new parameter for scaling the lit volume control.

Others:
cmgui-wx will use the best graphics settings available.
Offscreen buffering of cmgui-wx.
Enables order independent transparency in win32.

v2.4
11 May 2007
Releasing wx version.
Lots of new ITK filters.
Add support for a Graphics_library_tentative_check_extension which is true until we are sure whether
 or not an extension works.  This can be used for commands, which may be called before OpenGL is 
 initialised but we would like them to fail if they aren't working after it has been initialised.
Graphics_library_check_extension should be tested before actually using any extension, it will be 
 false unless we know the extension really works.  By now the display should have been initialised.
Use this new tentative check for bump_mapping and colour_lookup_spectra in materials.
Update perl modules to work with CMGUI without global variables.
Add image_resample computed field to commands.
No longer need to specify_width, specify_height, specify_depth or texture coordinate when working 
 using evaluate_image, the default values are retrieved from the source field.
Respect clear colour setting on spectrum when requesting rgb value.
Add support for bzip memory streams.
Each graphics window has its own interactive tools and settings of different interactive tools can now
 be triggered using commands and apply to all current graphics windows.
Add gfx define font to allow font objects to be created and most
 importantly to allow the default font to be redefined.
List the total number when nodes or elements are listed with gfx list node.
Allow the font to be specified when creating a colour_bar.
Allow a colour bar to be created for a specific data component.
Cmgui-wx now remember the directory where you previously open the file from.
Add a spectrum_settings that uses computed_fields to calculate the colour tranformation.
Add Option_table_add_help and try this function with the compose computed field.
Fix a bug passing the array of variables for matches and tidy up the regular expressions.
Fix a memory leak with the swizzle string for the material dependent texture program.
Node viewer now allows user to show variables from all fields at the same time.

v2.3.3
18 December 2006
Shifted to externally visible subversion server.
Added cmzn_scene_viewer_set_depth_of_field and cmzn_scene_viewer_get_depth_of_field.
Add cmzn_scene_viewer_set_background_texture_info.
Fix bug calling get_FE_element_dimension when there is no element.
Fix bug in derivative computed field.
Stop segfault if source field not specified for derivative computed field.
Add a natural logarithm computed field "log".
Registered command for threshold filter computed field
Changes for initial support for WX_USER_INTERFACE and conversion of files to C++.
Enable element_tool and element_point_tool without dialog in all versions.

v2.3.2
5 October 2006
Added colour_lookup_spectrums to materials for doing colour space transformations
in the graphics hardware.

v2.3.1
30 August 2006
Started adding in ITK.

v2.3.0
29 August 2006
Changed internal structure of Computed_fields to use a C++ class rather than 
imitating this in C with function pointers.  Reduced the number of virtual methods by
consolidating the set/get functions with a generic location rather than separate
functions for nodes and elements.
Removed legacy image processing computed fields as we plan to replace them with ITK.
Fix some typos where data groups propogated incorrectly to the node parent.

v2.2.3
Enabled emoter to work without motif gui and enabled command only version for all non
motif builds.
Internally renamed Control_curve to just Curve.

v2.2.2
Support the OpenGL extension GL_ARB_texture_non_power_of_two and delay the 
expansion of textures that are not power of two till render time so it can be
avoided when not required.
Add support for conversion of lines (isolines) to node points in "gfx convert graphics".
Fix for reading in of wavefront obj files.

v2.2.1
Added node_offset/data_offset to gfx read nodes and data respectively.
Added node_offset, element_offset, face_offset and line offset to gfx read elements.
Added generate_faces_and_lines to gfx read elements.
Calculate winding order left or right handed at element centres for isosurfaces.
Added string_constant computed field.
Change equal_to computed_field so that it can operate on string values if either
field is defined but does not have numerical components.
Use CMISS_EXAMPLES environment variable to determine where the example tree is
rather than the Cmgui motif/X setting file.

v2.2
Removed computed variables by default.  To put it back in change USE_COMPUTED_VARIABLES to true in the makefile or by specifying it on the make command line.
Added new texture wrap modes edge_clamp_wrap, border_clamp_wrap and
mirrored_repeat_wrap from recent versions of OpenGL.
Fixed problems with methods not being fully set correctly for some computed fields.
Changes to support streamlines in tetrahedral meshes.
Changes to support isosurface generation in tetrahedral meshes.
Added code so that triangles for isosurfaces are generated with a consistent winding
order even in meshes which have inconsistent lefthanded and righthanded coordinate systems.
Fixed to grid point evaluation.
Allowing streamlines to be seeded from the nodes in a region.

v2.1.1
Large speed improvements for "gfx select nodes" and "gfx select elements".
Get regions to cache get_next_element_id so that it can be kept over multiple commands.
Image resampling improvements.
Started 'gfx export cm'
Reenabled automatic monochrome storage of images.
Added a weighting field to "gfx create snake".
Added a few more logical operators for less_than, greater_than and equal_to in computed fields. 

v2.1
Fix comfile script: cmgui-2.1/fixcom.pl
Added support for fitting multiple fields with "gfx create snake"
Began "gfx export cm" to write files for the old cm.
Added gfx convert elements (and changed the old gfx convert to be gfx convert graphics) which converts one form of elements to another. The only conversion I have implemented so far is the conversion of any 2D element surfaces to true toplevel 2D bicubic hermite elements. The cross-derivatives are not correct and need to think about how to fix this.

v2.0.2
Fixed gfx unselect data.
Fixed contour bands on iso_surfaces.
Fixed code for allocation of large arrays to use long ints where necessary.
Added code so that node changes propogate through a nodal_lookup computed field to a computed_field change.
Fixed a couple of bugs in cmgui with the scene editor and an iso_values list.
Many minor fixes of leaks or use of uninitialised values as detected by the new valgrind testing.

v2.0.1
Added glyph functionality to create graph axes
Added first pass at iso_surface_decimation.
Added a new coordinate system where objects are displayed relative to screen coordinates.

v2.0.0
First open source release.  License updated to Mozilla Public License.
Lots of tidying up.
Added README, INSTALL, RELEASE_NOTES and CHANGELOG.