Finite Element Geometric Fitting To Epicardial Data

Example e43: Finite Element Geometric Fitting To Epicardial Data

Geometric data obtained from digitised ultrasound images are fitted using the finite element fitting technique. The data point are projected onto the intial mesh surface and this distance minimised.

Results can be view with draw.com.

Created by : Leo Cheng
On : 16 September 2000

The comfile run by this example is as follows:



$MODEL 	= "epi_ref0"
$OUTPUT = "epi_ref0c"
$FITNAME = "epi"





fem def para;r;fitting_lin;example
fem def coor 3,1


#
# Sets up three basis functions 
#   - 1 standard bicubic Hermite element
#   - 2 simplex element collapsed at x2=0
#   - 3 simplex element collapsed at x2=1
#
fem def base;r;bicubic_fit;example

#
# Reads in an initial mesh and calculates linear approximations
#  for the derivatives in xi=1 and 2 directions
#
fem def node;r;$MODEL;example
fem def elem;r;$MODEL;example
fem up node deriv 1 linear
fem up node deriv 2 linear

#
# The initial mesh
#
fem export node;${FITNAME}_init as ${FITNAME}_init offset 40000
fem export elem;${FITNAME}_init as ${FITNAME}_init offset_elem 40000


#
# Calculate the intial xi projections 
#   - alternatively the command fem def xi;c orthog can be used
#     it is slower but may produce better results in some cases
#
fem def data;r;$FITNAME;example
fem def xi;c close
fem li data err 
fem export data;${FITNAME}_data as ${FITNAME}_data error


#
# Setup the fitting problem - 
#  NOTE - alternatively it may be easier use the commands
#  "fem up field from geometry" to setup these fields automatically
#
fem def field;r;epi;example
fem def elem;r;epi;example field

#
# Defines the fitting problem by setting smoothing parameters
#  and setting some fixed nodes.
#
fem def fit;r;epi2;example geometry

Additional testing commands:


#
# First fit
#
fem fit
fem update node fit
fem update scale_factor normalise
# The `old' option on `def xi;c' means that the last projections are used as
# initial estimates for the non-linear projection calculation.
fem def xi;c close old
fem li data err 

#
# Second fit
#
fem fit
fem update node fit
fem update scale_factor normalise
fem def xi;c close old
fem li data err 

#
# Third fit
#
fem fit
fem update node fit
fem update scale_factor normalise
fem def xi;c close old
fem li data err 


#
# Export the fitted geometry
#
fem export data;${FITNAME}_data as ${FITNAME}_data error
fem export node;$FITNAME as $FITNAME offset 30000
fem export elem $FITNAME as $FITNAME offset_elem 30000

Files used by this example are:

Name                Modified     Size

example_e43.com     12-Dec-2000  1.3k
bicubic_fit.ipbase  16-Sep-2000  3.9k
epi.ipdata          16-Sep-2000  116k
epi.ipelfd          16-Sep-2000   18k
epi.ipfiel          16-Sep-2000  127k
epi2.ipfit          13-Apr-2007  3.0k
epi_ref0.ipelem     16-Sep-2000   23k
epi_ref0.ipnode     16-Sep-2000   45k
fitting_lin.ippara  12-Nov-2002  5.9k
test_output.com     08-Dec-2000  696

Download the entire example:

Name                      Modified     Size

examples_e_e4_e43.tar.gz  27-Aug-2010  224k

Testing status by version:

	Status	Tested	Real time (s)
cm_linux_optimised	Success	Tue Oct 8 03:47:08 2002	40
cmo_n32	Success	Tue Oct 8 14:20:19 2002	29
i686-linux
cm	Success	Sun Mar 6 00:03:17 2016	3
cm-debug	Success	Sat Mar 5 00:18:10 2016	9
mips-irix
cm	Success	Sun Aug 19 01:57:07 2007	27
cm-debug	Success	Wed Aug 15 02:02:17 2007	89
cm-debug-clear-malloc	Success	Sat Aug 18 02:19:55 2007	93
cm-debug-clear-malloc7	Success	Mon Aug 20 02:17:01 2007	93
cm64	Success	Sun Aug 19 01:59:17 2007	28
cm64-debug	Success	Tue Aug 21 02:05:03 2007	98
cm64-debug-clear-malloc	Success	Thu Apr 1 12:08:58 2004	40
rs6000-aix
cm	Success	Wed Mar 4 01:10:58 2009	3
cm-debug	Success	Mon Mar 2 01:14:36 2009	27
cm64	Success	Wed Mar 4 01:10:02 2009	3
cm64-debug	Success	Tue Mar 3 01:19:27 2009	28
x86_64-linux
cm	Success	Sun Mar 6 00:01:07 2016	1
cm-debug	Success	Sat Mar 5 00:01:56 2016	4

Testing status by file:

cmiss_test.log

Success	cm_linux_optimised:	cmiss_test.log.retain.
Success	cmo_n32:	cmiss_test.log.retain.
i686-linux
Success	cm:	cmiss_test.log.retain.
Success	cm-debug:	cmiss_test.log.retain.
mips-irix
Success	cm:	cmiss_test.log.retain.
Success	cm-debug:	cmiss_test.log.retain.
Success	cm-debug-clear-malloc:	cmiss_test.log.retain.
Success	cm-debug-clear-malloc7:	cmiss_test.log.retain.
Success	cm64:	cmiss_test.log.retain.
Success	cm64-debug:	cmiss_test.log.retain.
Success	cm64-debug-clear-malloc:	cmiss_test.log.retain.
rs6000-aix
Success	cm:	cmiss_test.log.retain.
Success	cm-debug:	cmiss_test.log.retain.
Success	cm64:	cmiss_test.log.retain.
Success	cm64-debug:	cmiss_test.log.retain.
x86_64-linux
Success	cm:	cmiss_test.log.retain.
Success	cm-debug:	cmiss_test.log.retain.

cmiss_test.out

Success	cm_linux_optimised:	ndiff test: no significant differences with generic answer.
Success	cmo_n32:	ndiff test: no significant differences with generic answer.
i686-linux
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
mips-irix
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
Success	cm-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
Success	cm-debug-clear-malloc7:	ndiff test: no significant differences with generic answer.
Success	cm64:	ndiff test: no significant differences with generic answer.
Success	cm64-debug:	ndiff test: no significant differences with generic answer.
Success	cm64-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
rs6000-aix
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
Success	cm64:	ndiff test: no significant differences with generic answer.
Success	cm64-debug:	ndiff test: no significant differences with generic answer.
x86_64-linux
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.

epi.exelem

Success	cm_linux_optimised:	ndiff test: no significant differences with generic answer.
Success	cmo_n32:	ndiff test: no significant differences with generic answer.
i686-linux
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
mips-irix
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
Success	cm-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
Success	cm-debug-clear-malloc7:	ndiff test: no significant differences with generic answer.
Success	cm64:	ndiff test: no significant differences with generic answer.
Success	cm64-debug:	ndiff test: no significant differences with generic answer.
Success	cm64-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
rs6000-aix
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
Success	cm64:	ndiff test: no significant differences with generic answer.
Success	cm64-debug:	ndiff test: no significant differences with generic answer.
x86_64-linux
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.

epi.exnode

Success	cm_linux_optimised:	ndiff test: no significant differences with generic answer.
Success	cmo_n32:	ndiff test: no significant differences with irix_optimised answer.
i686-linux
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
mips-irix
Success	cm:	ndiff test: no significant differences with irix_optimised answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
Success	cm-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
Success	cm-debug-clear-malloc7:	ndiff test: no significant differences with generic answer.
Success	cm64:	ndiff test: no significant differences with generic answer.
Success	cm64-debug:	ndiff test: no significant differences with generic answer.
Success	cm64-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
rs6000-aix
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.
Success	cm64:	ndiff test: no significant differences with generic answer.
Success	cm64-debug:	ndiff test: no significant differences with generic answer.
x86_64-linux
Success	cm:	ndiff test: no significant differences with generic answer.
Success	cm-debug:	ndiff test: no significant differences with generic answer.

Graphical output from this problem is given here.

Html last generated: Sun Mar 6 05:51:27 2016

Input last modified: Thu Aug 26 14:53:07 2010

CMISS Help / Examples / e / e4 / e43