Example 219c: Fitting a prolate spheroidal surface mesh to measured data of the endocardial and epicardial surfaces.

Fitting a prolate spheroidal surface mesh to measured data of the endocardial and epicardial surfaces. 38 nodes defines an ellipsoid. The first 19 nodes defines the endocardial surface while the last 19 defines the epicardial surface. By running through the executable example file twice, first with the variable $surface = 'endo' and then with $surface = 'epi', the initial nodes are fitted to the respective surfaces. The result will be written out in files called endo_fitted.ipnode and epi_fitted.ipnode. These two files can be merged by running the command "perl createMergedNodeFile.p" from the commandline (if you have perl installed). For each fit, the result can be viewed in CMGUI by running the draw.com file.

The comfile run by this example is as follows:

#Example_219c: Fitting of surface prolate spheroidal mesh to measured data of endocardial and epicardial surfaces.

fem define para;r;heart;example
fem define coor;r;ellipsoid;example       # prolate spheriodal coords
fem define nodes;r;;example               # 38 nodes, 19 per surface
fem define bases;r;2CubicHermite;example  # bicubic in lambda
fem define ;add bases;r;2Linear;example   # bilinear in mu and theta

$surface = 'endo'                         # choose what surface to fit
#$surface = 'epi' 
fem define elements;r;$surface;example    # 6 elem circumferentially, 3 longitudinally

# Export the initial geometry for viewing in CMGUI
$file = 'heart'
fem export nodes;$file as $file
fem export elements;$file as $file
# This command is temporary until bug in CMISS is fixed:
system "perl -p -i.bak -e 'if(/theta/){s/no modify/decreasing in xi1/}' $file.exelem"

fem define data;r;$surface;example        # read in data for specified surface
fem define xi;c orthog                    # calculate projection of datapoints onto surfacemesh
fem li data err                           # list the RMS of the projection error

# Export the data with error projections for viewing in CMGUI
$file = "${surface}1"
fem export data;$file as $file error
# This command is temporary until bug in CMISS is fixed:
system "perl -p -i.bak -e 'if(/coordinates,/){s/coordinates,/RC coordinates,/}' $file.exdata"

fem define field;r;$surface;example       # create list over nodes to fit including derivatives
fem define elements;r;;example field      # set up element file for field variable
fem define fit;r;surface;example geometry # specify fit problem

#
# First fit
fem fit
fem update node scale_factor
fem update node fit

# Have to read in data again because data is changed to prolate in memory.
# Shouldn't have to do this though. Might be changed in the future...
fem define data;r;$surface;example
fem def xi;c orthog
fem li data err 

# Export the data with error projections for viewing in CMGUI
$file = "${surface}2"
fem export data;$file as $file error offset 20000
# This command is temporary until bug in CMISS is fixed:
system "perl -p -i.bak -e 'if(/coordinates,/){s/coordinates,/RC coordinates,/}' $file.exdata"

# Export fittet geometry after first fit
$file = 'heart_fit1'
fem export node;$file fit as $file offset 1000          
fem export element;$file fit as $file offset_elem 1000
# This command is temporary until bug in CMISS is fixed:
system "perl -p -i.bak -e 'if(/theta/){s/no modify/decreasing in xi1/}' $file.exelem"

#
# Second fit (if not happy with first fit)
fem define fit;r;surface;example geometry
fem fit
fem update node scale_factor
fem update node fit

# Export fittet geometry after second fit
$file = 'heart_fit2'
fem export node;$file fit as $file offset 2000          
fem export element;$file fit as $file offset_elem 2000
# This command is temporary until bug in CMISS is fixed:
system "perl -p -i.bak -e 'if(/theta/){s/no modify/decreasing in xi1/}' $file.exelem"

# Write fitted nodes to file
fem define nodes;w;"${surface}_fitted"

Additional testing commands:

fem list nodes

Files used by this example are:

Name                    Modified     Size

example_219c.com        16-Nov-2000  3.0k
2CubicHermite.ipbase    14-Nov-2000  1.5k
2Linear.ipbase          14-Nov-2000  1.1k
createMergedNodeFile.p  14-Nov-2000  1.1k
draw.com                22-Nov-2001  903 
ellipsoid.ipcoor        14-Nov-2000  725 
ellipsoid.ipelem        14-Nov-2000   11k
ellipsoid.ipnode        14-Nov-2000   29k
endo.ipdata             14-Nov-2000   69k
endo.ipelem             14-Nov-2000  7.6k
endo.ipelfd             14-Nov-2000  2.5k
endo.ipfiel             14-Nov-2000  5.4k
endo_fitted.ipnode      14-Nov-2000   32k
endoepi_fitted.ipnode   14-Nov-2000   32k
epi.ipdata              14-Nov-2000   66k
epi.ipelem              14-Nov-2000  7.7k
epi.ipelfd              14-Nov-2000  2.5k
epi.ipfiel              14-Nov-2000  5.5k
epi_fitted.ipnode       14-Nov-2000   32k
heart.ippara            12-Nov-2002  5.9k
surface.ipfit           13-Apr-2007  1.6k
test_output.com         14-Nov-2000   15 

Download the entire example:

Name                           Modified     Size

examples_2_21_219_219c.tar.gz  14-Apr-2007   60k

Testing status by version:

Testing status by file:

• cmiss_test.log
  

  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
  

  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.

  
  

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Input last modified: Fri Apr 13 10:30:42 2007