Initial import of the ultrasound tracking code (Field II) that
is integrated with the FEM models (LS-DYNA).

tags/ultratrack-1.0.0 - original code (Palmeri tracking paper)
tags/ultratrack-2.0.0 - URI code modified to accomodate parallel rx
(Dahl tracking paper)


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@2 57c3da9d-1720-0410-8437-ae526f62eb58
Added kasai_track.m to the trunk - based on sam_track_auto.m -
haven't tested yet!!


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@3 57c3da9d-1720-0410-8437-ae526f62eb58
Added matlabRun.pl to launch multiple tracking sims.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@4 57c3da9d-1720-0410-8437-ae526f62eb58
* Corrected matlabRun.pl email syntax.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@5 57c3da9d-1720-0410-8437-ae526f62eb58
I'm not sure what was going on with the TrackAx variable in the post-processing code... and I'm still not sure, but I've changed it to what I think it should be.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@6 57c3da9d-1720-0410-8437-ae526f62eb58
Corrected the Matlab system call email line in matlabRun.pl


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@7 57c3da9d-1720-0410-8437-ae526f62eb58
Modified matlabRun.pl to remove temporary run files.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@8 57c3da9d-1720-0410-8437-ae526f62eb58
The start of many changes to the tracking code structure.  I've added createtrackres.m that creates a res*.mat formatted file to be consistent w/ experimental (res_TIMESTAMP.mat) and new FEM result files (res_sim.mat).


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@9 57c3da9d-1720-0410-8437-ae526f62eb58
Added a documentation directory to the trunk (that still needs content!).


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@10 57c3da9d-1720-0410-8437-ae526f62eb58
testing phase for new sub-functions


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@11 57c3da9d-1720-0410-8437-ae526f62eb58
Removed the probe definitions that had different center frequencies - those shouldn't be used anymore.  Also renamed arfi_scans.m to arfi_scans_template.m to avoid name conflicts with local CWD copies.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@12 57c3da9d-1720-0410-8437-ae526f62eb58
added the ch41 and ch62 probes to the tracking probe definitions


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@13 57c3da9d-1720-0410-8437-ae526f62eb58
Fixed several errors in the result saving functions.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@14 57c3da9d-1720-0410-8437-ae526f62eb58
Fixing bugs in the displacement tracking portion of the code.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@15 57c3da9d-1720-0410-8437-ae526f62eb58
Correlation coefficients and displacements were switched - that makes a difference!


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@16 57c3da9d-1720-0410-8437-ae526f62eb58
Removed post-processing code that no longer works with the current trunk.

The post-code that was in place did jitter calculations by using axial running averages - that should be avoided, and instead the std over multiple speckle seeds should be used.  This is a product of the original version of the code.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@17 57c3da9d-1720-0410-8437-ae526f62eb58
Fixed the displacement to be positive instead of negative.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@18 57c3da9d-1720-0410-8437-ae526f62eb58
Fixed several additional displacement estimation bugs - several things still need to be done:
(1) The number of samples in the cross correlator needs to still be calculated by the number of wavelengths, but right now is still user-specified.
(2) Time index alignment corrected.
(3) Still need to implement the other tracking algorithms.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@19 57c3da9d-1720-0410-8437-ae526f62eb58
Deleted old "arfi_scan" templates that no longer work with the latest trunk.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@20 57c3da9d-1720-0410-8437-ae526f62eb58
Added the reference time step to 'arfidata' to sync with the time (t) variable.


git-svn-id: https://hogwarts.egr.duke.edu/svn/ultratrack@21 57c3da9d-1720-0410-8437-ae526f62eb58