CHANGES IN VERSION 0.8.1 - Released 2025/06/07

BUG FIXES

* Issue #76: High resolution images not being output correctly
  https://github.com/davidcsterratt/retistruct/issues/76
  In the Shiny interface the "Maximum Width of Projection" option was
  not being respected.

* Issue #73: Bugs opening files due to Shiny JS not loading properly
  https://github.com/davidcsterratt/retistruct/issues/73
  Due to Shiny JS not loading properly and hard-coding directory names
  at compile-time, files would not open in the file chooser in the
  Windows and Mac binaries. Thanks to Jan Okul, who carried out this
  work as part of his undergraduate dissertation at the University of
  Edinburgh School of Informatics.

* Issue #74: Testing issues with at least one Mac M1 configuration
  https://github.com/davidcsterratt/retistruct/issues/74
  A floating point issue with Apple clang 17 on the Mac M1
  architecture caused RTriangle to give different triangulations on
  that architecture from other architectures. This triangulation
  caused a reproducibility test in Retistruct to fail. This issue was
  fixed in RTriangle 1.6-0.15
  (https://github.com/davidcsterratt/RTriangle/issues/23) and we
  increase the version of RTriangle required correspondingly. Thanks
  to the CRAN team for reporting.

CHANGES IN VERSION 0.8.0 - Released 2025/03/07

NEW FEATURES

* Issue #56: Port GUI to R shiny
  https://github.com/davidcsterratt/retistruct/issues/56
  This update removes the dependence on gWidgetsRGtk2, RGtk2 and the
  GTK library, which has made installation on Mac and Windows
  impossible, and has meant that Retistruct could not be hosted on
  CRAN. Thanks to Jan Okul, who carried out this work as part of his
  undergraduate dissertation at the University of Edinburgh School of
  Informatics.

BUG FIXES

* Issue #69: New CRAN submission: Writing in home filespace
  https://github.com/davidcsterratt/retistruct/issues/69
  Demos no longer write in home filespace
  Thanks to the CRAN team for reporting.

* Issue #70: New CRAN submission: options
  https://github.com/davidcsterratt/retistruct/issues/70
  Graphics parameters and options are saved and restored so that user
  options are not changed.
  Thanks to the CRAN team for reporting.

* Issue #71: New CRAN submission: Reset options in examples & demos
  https://github.com/davidcsterratt/retistruct/issues/71
  Graphics parameters and options are saved and restored so that user
  options are not changed.
  Thanks to the CRAN team for reporting.

* Issue #68: New CRAN submission: Make messages suppressible
  https://github.com/davidcsterratt/retistruct/issues/68
  Remove instances of print() in functions and replace with message
  (via the customisable report() function)
  Thanks to the CRAN team for reporting.

* Issue #67: New CRAN submission: dontrun
  https://github.com/davidcsterratt/retistruct/issues/67
  Currently inpoerational Magnifier code removed; future versions
  might use Plotly for viewing plots.
  Thanks to the CRAN team for reporting.

* Issue #66: New CRAN submission: TRUE/FALSE and T/F
  https://github.com/davidcsterratt/retistruct/issues/66
  All values of T relaced with Tr.
  Thanks to the CRAN team for reporting.

* Issue #65: New CRAN submission: Added references to Description
  https://github.com/davidcsterratt/retistruct/issues/65
  Thanks to the CRAN team for reporting.

* Issue #55: Windows 12 and R 4+ installation
  https://github.com/davidcsterratt/retistruct/issues/55
  Fixed by the port to Shiny (Issue #56)

* Issue #52: Retistruct GUI no longer works in R 4.2.0
  https://github.com/davidcsterratt/retistruct/issues/52
  Fixed by the port to Shiny (Issue #56)

* Issue #4: Running Retistruct GUI in MacOS X Mavericks and Yosemite
  https://github.com/davidcsterratt/retistruct/issues/4
  Fixed by the port to Shiny (Issue #56)

* Issue #53: Fix demos that are not working in 0.7
  https://github.com/davidcsterratt/retistruct/issues/53
  Left over work from the previous upgrade

* Issue #61: Plotting tears and cuts in sphericalplot is broken
  https://github.com/davidcsterratt/retistruct/issues/61
  Fix the plotting of tears and cuts

REGRESSIONS

* Issue #33: Make marking up retinae easier by enabling pan and zoom
  https://github.com/davidcsterratt/retistruct/issues/33
  Now that we have upgraded to Shiny, there may be better ways of
  achieving magnification and zooming of images

* Issue #60: Highlight points when marking up retina
  https://github.com/davidcsterratt/retistruct/issues/60
  In the move to Shiny we have lost the basic highlighting of points
  when marking up that used to work with identify(). We could
  reinstate the functionality in a basic way, but this involves
  redrawing the whole plot to highlight one point, which feels
  suboptimal. It may be that moving to Plotly or a method involving
  JavaScript would provide a better user experience.

CHANGES IN VERSION 0.7.4 - Released 2023/02/04

BUG FIX

* Renamed deprecated rgl.*functions,
  which were causing a crash in the GUI

CHANGES IN VERSION 0.7.3 - Released 2020/09/12

BUG FIXES

* Fix regression that caused the stitching to fail on some retinae with depthmaps

* Titration reinstated
  (https://github.com/davidcsterratt/retistruct/issues/29)

NEW FEATURES

* Determine the background value of depthmaps automatically

* Allow minimum and maximum size of window for inferring missing values
  in depthmaps to be specified

CHANGES IN VERSION 0.7.2 - Released 2020/08/31

BUG FIXES

* Fix regression in v0.7.1 that caused some multi-fragment outlines to fail

* Improve image interpolation

CHANGES IN VERSION 0.7.1 - Released 2020/08/28

NEW FEATURE

* Stitching together of fragments that contain a hole in the centre
  is now possible

CHANGES IN VERSION 0.7.0 - Released 2020/08/26

NEW FEATURES

* Stitching together separate petals or "fragments"

* Ability to magnify plots in the GUI

* Depthmaps, i.e. the ability to specify the depth at various points
  of the flatmount image, for more accurate reconstruction.

* Switch easily between 3D views of flatmount and reconstruction in
  GUI

CHANGES IN VERSION 0.6.4 - Released 2023/02/04

BUG FIX

* Renamed deprecated rgl.*functions,
  which were causing a crash in the GUI

CHANGES IN VERSION 0.6.3 - Released 2020/04/03

BUG FIX

* Error due to change in stringsAsFactors
  (https://github.com/davidcsterratt/retistruct/issues/49)

CHANGES IN VERSION 0.6.2 - Released 2019/12/13

NEW FEATURES

* Improved documentation of the API
  (https://github.com/davidcsterratt/retistruct/issues/47)
  Thanks to improvements in roxygen2, the class hierarchy can be viewed
  using help.start()

BUG FIXES

* Check problems on Debian systems
  (https://github.com/davidcsterratt/retistruct/issues/48)
  Thanks to the CRAN maintainers for reporting this problem

CHANGES IN VERSION 0.6.1 - Released 2019/12/08

NEW FEATURES

* Allow resizing of windows
  (https://github.com/davidcsterratt/retistruct/issues/34)

* Allow data counts to be read in using ijroi and csv formats
  (https://github.com/davidcsterratt/retistruct/issues/37)

* Expose the mapping from flat coordinates to spherical coordinates in
  reconstructed retina
  (https://github.com/davidcsterratt/retistruct/issues/20)
  This is achieved by the new member function mapFlatToSpherical() of
  a ReconstructedOutline object

BUG FIXES

* Reinstated saving reconstructed data
  (https://github.com/davidcsterratt/retistruct/issues/27)

* Reinstated sphericalplot
  (https://github.com/davidcsterratt/retistruct/issues/28)

* retistruct.batch.summary() fails on retinae without CountSets
  (https://github.com/davidcsterratt/retistruct/issues/30)

CHANGES IN VERSION 0.6.0 - Released 2019/07/10

BUG FIXES

* Error unclear with infinite determinant in retistruct.reconstruct
  (https://github.com/davidcsterratt/retistruct/issues/21)
  Thanks to Brian Cohn for reporting this, and to Inmaculada Soldado
  and Klaudia Szatko for reporting the same problem and contributing
  an example that gave the same error.

CODE IMPROVEMENTS

* Major refactor of code to use R6 classes
  (https://github.com/davidcsterratt/retistruct/issues/25)

* Stitching algorithm changed so it only creates new points when they
  lie outwith tolerance a of an existing one. This prevents very short
  lengths in triangulated outlines.
  (https://github.com/davidcsterratt/retistruct/issues/21) This work
  arose from the bug with the indefinite determinant (see above).

NEW FEATURES

* It is now possible to have completely silent operation
  (https://github.com/davidcsterratt/retistruct/issues/22)
  Thanks to Brian Cohn for the suggestion

CHANGES IN VERSION 0.5.12 - Released 2017/08/08

NEW FEATURES

* AnnotatedOutline() and Outline() are exported to allow use with
  external packages
  (https://github.com/davidcsterratt/retistruct/issues/17)
  Thanks to Brian Cohn for the report and the patch.

BUG FIXES

* Documentation has been spell checked using devtools::spell_check()
  (https://github.com/davidcsterratt/retistruct/issues/19)

CHANGES IN VERSION 0.5.11 - Released 2017/07/15

RELEASE NOTES

* R 3.4.0 is required to run the graphical user interface (GUI),
  because there is no version of the RGtk2 package that works with
  earlier versions of R available on CRAN.

* There is a bug in version 1.0.5 of gWidgets2RGtk that prevents the GUI
  working. If you encounter this problem, work around it by typing

    install.packages("gWidgets2RGtk2")

  in the R console and then running retistruct() again. (You may need
  to quit R before being able to run this command.) More information
  at: https://github.com/davidcsterratt/retistruct/issues/13

NEW FEATURES

* The CSV input format can now take a file of counts (or "grouped") data
  (https://github.com/davidcsterratt/retistruct/issues/7)
  Thanks to Nicolas Nagoo for the report.

BUG FIXES

* 3D (RGL) plot now appears after reconstruction
  (https://github.com/davidcsterratt/retistruct/issues/5)
  Thanks to Nicolas Nagoo for the report.

* gWidgets2RGtk not found and package.dependencies() is deprecated
  (https://github.com/davidcsterratt/retistruct/issues/12)

* gWidgets2::gdroplist is deprecated
  (https://github.com/davidcsterratt/retistruct/issues/10)

* Test failed building on Windows i386
  (https://github.com/davidcsterratt/retistruct/issues/14)

* Issue with adding tears in retistruct
  (https://github.com/davidcsterratt/retistruct/issues/11)
  Thanks to https://github.com/sagewiltse for the report.

CODE IMPROVEMENTS

* gWidgets2 is now used instead of gWidgets. Thanks to John Verzani
  for fixing bugs in gWidgets2.

CHANGES IN VERSION 0.5.10 - Released 2015/02/16

CODE IMPROVEMENTS

* retistruct:::bary.to.sphere.cart() and
  retistruct:::sphere.cart.to.sphere.spherical() are exported.
  (https://github.com/davidcsterratt/retistruct/issues/2) 
  Thanks to Brian Cohn for the request.

BUG FIXES

* The message produced by delaunayn() in geometry package 0.3-5 has
  been suppressed.
  (https://github.com/davidcsterratt/retistruct/issues/3)
  Thanks to Brian Cohn for the report.
