16-bit OCTs and Intensity value correction

This release contains several major bug fixes with respect to the core of ORA.
Fixes:

• ORA can only accept 16-bit gray scale images now (Also known in Java as TYPE_USHORT_GRAY images). The reason is that the output of OCTs is now using 16-bit unsigned integers. A safety check has been added to ensure this rule is never broken.
• ORA can now process the 16-bit gray scale values correctly, returning intensity values correctly now. This means that intensity values are now on a scale of 0 (black) to 65,535 (white).
• Image processing techniques that only worked on 8-bit images were removed from the application

Updates:

• due to unforeseen changes in the Java ecosystem packaging of the application for use on Mac has changed now. Just download and unpack the ORA.zip file and drag the application to the application directory on your machine and you're good to go.

Foveal Pit Finding!

This release includes several bug fixes found during regular development as well as the initial implementation of assisted center of the foveal pit finding

• Fixed a bug that would crash the application if the LRP width was changed when a LRP selection was right at the edge of the OCT
• Fixed bug where the distance to foveal center calculation was not being displayed when an LRP existed at the center of the fovea
• Implemented assisted center of fovea finding algorithm, allow ORA to help determine the center of the foveal pit within a windowed region
  • assisted center of foveal pit finding is part of generating an anchor LRP
  • Instructions on it's usage are built into the tool once you activate it
  • Segmentation the ORA generates of the ILM will be drawn on top of the OCT but can be toggled on/off in the settings menu
  • the segmentation is highly dependent on how the selection window is drawn so make sure the distance between the top of the selection window drawn around the foveal pit is a decent distance into the vitrious from the ILM (~ 15 pixels or more)

Full Features implemented

This is the first official release of ORA. With this release comes numerous bug fixes and handling of edge cases and the application has been tested enough that it is prepared for full usage.

Install:

• Windows & Linux: Use the JAR file
• Mac OSX: Download the DMG and open it, copy ORA into your applications directory

Updates:

• Fixed issues with labels on peaks of LRPs
• Fixed issue with analysis buttons no functioning properly during analysis
• Freeform Multi-LRP analysis mode complete and working
• Removed Single freeform LRP mode because multi mode can handle single LRP case
• Packaging the application for distribution to Mac OSX
• Minor changes to test configurations and file names

Free form analysis and moving LRPs

This release has the following major changes:

• Free form analysis allows you to place a single LRP on the OCT, move it around with the arrow keys and change all of the settings and then you can export the analysis data for that LRP
• The anchor LRP for the preformatted analysis can now be moved with the arrow keys as well before running the analysis
• Added boundary checks for LRPs so they can't be generated outside of the boundaries of the OCT
• The preformatted and free form analysis modes are now working
• The exported data format has changed to now include the center Y position of the LRPs
• A testing OCT has been added (found under the file menu) that can be used for training/demo purposes

Analysis settings save/load

• added framework to support analysis modes and the saving and loading of analysis settings for sharing and reuse
  • save and loading of settings can be found under the settings menu
• .oasf files are the files with the settings save files and can be loaded back into version 0.3.0 and up of ORA
• support for analysis modes is available in beta state (really just use the regular analysis for now, buyer be warned)