Added new labels and QLineEdits to the GUI.  Moved default log dosage value section from “Advanced Parameters” to “Parameters”.
Removed lines of code related to the saving and recalling of useDefaultOffset checkbox status.
Created a new RectangleCreator class.  In the process of stripping out any unneeded functionality.
Rectangle draws on the image.  Signal/slot hook-ups implemented.
Rectangle now transmits the correct coordinates, width/height measurements via signals and slots.
Created a BackgroundCalculation class to calculate the mean of the voxel values in the rectangle area.  If the user adds an image, a red rectangle automatically appears.  The user can then position the rectangle wherever on the image, and then press the Update button.  The calculations are done, and the mean is stored in the data field next to the Update button.
Removed unnecessary variables
Changed some API around to eliminate a few signals/slots implementations.
Changed the red box selection to a single tilt instead of all tilts.  Removed some unnecessary API.
The red rectangle now stays in the same position and shape when the tilt index is changed.
Added default dosage checkbox back into the GUI.
Renamed default dosage checkbox to useDefaultOffset.
Fixed default offset bug.  Changed outer iterations and inner iterations values to defaults of 600 and 100, respectively.
Fixed bug where red rectangle would not load correctly from the config file.
Fixed a bug where the red rectangle would disable movement after loading a config file and then changing the input file.
Fixed default placement of red rectangle.  The red rectangle will now appear in the middle of the image every time it is loaded.
The offset value from the GUI is now being used in the SigmaXEstimation class instead of the original #define value.  fixed #6.
Attempted fix for the “nan” bug
Adding more descriptive error message in order to better understand why files can not be written
Fixing GUI crashing issue due to some debugging code that was not doing adequate null pointer checking. The error would manifest itself if the user clicked in the empty image viewer on the right hand side.