NEWS

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retistruct 0.8.2

NEW FEATURES

• Issue #79: Export spherical coordinates of points outwith flat outline https://github.com/davidcsterratt/retistruct/issues/79 dropna option added to ReconstructedOutline$mapFlatToSpherical(); TRUE by default

retistruct 0.8.1 (2025-06-08)

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.

retistruct 0.8.0 (2025-03-10)

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.

retistruct 0.7.4

BUG FIX

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

retistruct 0.7.3

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

retistruct 0.7.2

BUG FIXES

• Fix regression in v0.7.1 that caused some multi-fragment outlines to fail
• Improve image interpolation

retistruct 0.7.1

NEW FEATURE

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

retistruct 0.7.0

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

retistruct 0.6.4

BUG FIX

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

retistruct 0.6.3 (2020-04-04)

BUG FIX

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

retistruct 0.6.2 (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

retistruct 0.6.1 (2019-12-09)

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)

retistruct 0.6.0 (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

retistruct 0.5.12 (2017-08-09)

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)

retistruct 0.5.11 (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.

retistruct 0.5.10 (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.