extractDeformations

Description

SAENO find the best matching local shift for a set of positions. What set of positions it uses depends on the parameters SCATTEREDRFOUND and FINDBEADS according to the following table:

	SCATTEREDRFOUND = "0"	SCATTEREDRFOUND = "1"
FINDBEADS = "0"	The node positions of the tetrahedral mesh are used.	A set of positions is loaded from the VBEADS file
FINDBEADS = "1"	won't work	Local maxima in the relaxed stack are found and used.

For a given position the program maximizes the intensity cross-correlation of a section in the relaxed stack with voxelsize VB_SXxVB_SYxVB_SZ at the given position and the corresponding section in the alive stack shifted by the displacement vector that is subject to optimization. The method used for the optimization is the downhill-simplex method. If INITIALGUESS is set to "0" the optimization starts with the drift vector (computed in the loadStacks module) or 0 if the drift was not extracted. If INITIALGUESS is set to "1" SAENO loads displacements from the UGUESS file in the DATAIN directory and uses them as initial guess for the optimization. The specifications of the UGUESS file are the same as the ´UFOUND´ file in the loadDeformations module.

If SCATTEREDRFOUND is set to "1", SAENO also computes an interpolation matrix from the scattered points to the tetrahedral mesh, which is needed for the regularization procedure.

SAENO finally stores the measured set of displacements in the UFOUND file in the DATAOUT directory. For the structure of the UFOUND file see loadDeformations.

Table of Parameters

name	type	default	explanation
DATAIN	string	empty
DATAOUT	string	empty
UGUESS	string	Ugess.dat
VBEADS	string	vbeads.dat
SUBPIXEL	float	0.005	The optimization of the local displacement stops if the estimated accuracy in voxel falls below this value
VB_MINMATCH	float	0.7	Only if the final cross-correlation value is above this value the node is considered matched successfully. If the cross-correlation stays below this value the position is flaged as having unknown displacement
VB_N	integer	0	If chosen >0 SAENO will match not only one section per position but 2^(3*n) positions aranged in a cubic grid. It then averages all succesfull matchings.
VB_SX	int	12	Size of the matched sections in X-direction
VB_SY	int	12	Size of the matched sections in Y-direction
VB_SZ	int	12	Size of the matched sections in Z-direction
VB_REGPARA	float	0.01	To prevent the optmization algorithm to wander far away from the original position of the section the norm of the displacement times this value is substrated from the cross-correlation during optimization.

Console Output

Start:

EXTRACT DEFORMATIONS

During execution

                      1.▼    2.▼      3.▼
finding Displacements 19.4% S=0.789231 n=7

1. Percentage of allready matched positions (successfull or unsuccessfull)
2. Found cross-correlation value found for current position
3. Only present when VB_N is set >1. Displays number of successfully matched subsections

F.A.Q.