Todo.txt

* Make file should be defaulted to release 
* Enable saving the latest reconstruction at time of cancellation.
*Change the Advanced parameter -> Noise_Model to Noise_Esimation
* Streamline progress feedback to the GUI
* Add more "Cancel" checks in the code
* Turn doubles to floats to save memory. 
* Need to enable a quick load option to continue the reconstruction for a few 
more iterations. This will need reading the final rec, offset, gain and var.
*Enable data sets in which max tilt is 90 degrees - there is a divide by cos(max angle) which will break if this occurs 

Stuff Completed

* Memory calculate routines need to be dynamically computed
* Display image with lowerleft as default and make the y go from 0 - ? from bottom to top 
* Allow user to define the XZ Plane that is shown during the reconstruction
* Implement Target Gain estimation based on input data file.- Done. Venkat 6/14
* Bug in name of the final sinogram file - Done.Venkat/Mike 6/13/2012
* While choosing a region to recons. for multi-resolution need subvolume
to be a proper multiple of xz size at all resolutions - Done. Venkat 6/14/2012
* Parallelize the code - Done by Mike 6/12/2012
* Enable Bright-Field .mrc input to GUI - Done. Venkat. 
* Implement reconstruction when Bright-Field is available - Done. Venkat 5/30
* Do more tests of the automatic SigmaX calculation based on TargetGain - is it robust? - Done. Venkat 6/14/2012
* Make a command line version of the code so that user can run multiple instances using script files if needed. - Done. Venkat 6/24/2012
* The shape parameter can only take values from 1 to 2. Right now it goes right to zero.
*Fix the smoothness and SigmaX calculation. SigmaX needs to be computed and multiplied by 1/smoothness internally. - Done. Venkat 
*Code fails if the extension .bin is not given in OutputReconstructionFile  - Done Mike?
* When in single slice mode we need to FORCE the num resolutions to 1 - Seems to be done by Mike. 
* Move : Target Gain, Stop Threshold, Outer, Inner Iterations, Default OFfset, Default variance, Default Initial Recon value, Num Resolutions to a Advanced Params Tab - done by Mike. 
* The check box for default offset is being placed near Stop threshold incorrectly - fixed. Venkat
* Do we allow the user to set the SigmaX or do we always calculate it 
internally.- taken care of with smoothness. Venkat
* Add an option to switch off #define for Joint_Estimation and #Noise estimation - done by Mike.
I just noticed. In the data load section I think we should rename MRC File -> HAADF Data File. - Done

Would it be possible to put a zoom capability on the single slice reconstruction? - Done. Mike.