Example 9821: Generating supernumerary vessels for a pulmonary arterial mesh

This example demonstrates the use of an empirically based algorithm to generate pulmonary supernumerary blood vessels. "Supernumerary" vessels are extra pulmonary blood vessels (i.e. vessels which do not accompany the airways) which tend to branch off at right angles and quickly branch towards the closest respiratory unit. This example is illustrated for a portion of the arterial vessels in the left lower lobe (LLL) of the human lung. A series of data points are generated, each one represents a single acinar (gas exchange) unit. The supernumerary branches branch off the stem vessels and 'grow' towards the closest data point.

Created by Kelly Burrowes, 04/2004.

A branch of arteries (red)	Series of data points	Supernumerary vessels (gold)	Close in view of the arterial mesh

To create an image in order to visualise the results of this simulation, use draw.com.

The comfile run by this example is as follows:

# If the example path is not set, default to current directory
if (! defined $example) {
    $example = "./";
}
# Drop off the trailing / in the example path
$chopped = chop $example;
if ($chopped ne "/") {
    $example .= $chopped;
}

fem de param;r;$example/super; #define parameters
fem de coor 3,1;               #define coordinates
fem de base;r;$example/super;  #define 1D basis function

#reads in, then exports the data points for the left lower lobe (LLL)
fem de data;r;$example/lll_data;
fem export data;artery_data as artery_data;

#reads in the nodes and elements of a portion of the arterial mesh in the LLL
fem de node;r;$example/initial_arteries;
fem de elem;r;$example/initial_arteries;

#sets up field framework for radius only (not alveolar field)
fem de mesh;c lung field only_radius_field; 

#evaluates the generations and orders of the vessels
fem evaluate order;

#this inputs a constant value of 3.650 for the first mesh element
fem update mesh geometry radius_field 1 element 1 constant 3.650;

#defines the radius of each of the vessels, using a strahler diameter ratio of 1.5997
fem update mesh geometry radius_field 1 rd_strahler ratio_diameter 1.5997;

#adds the supernumerary vessels to the existing arterial mesh
#d_ratio:defines the diameter ratio of the supernumerary vessel to the stem vessel
#sv_freq=the supernumerary frequency from each stem vessel
#diam_ratio=the Strahler based diameter ratio -> used to define diameter of each vessel
#d_max_order=the diameter of the maximum order vessel (i.e. Strahler order 17)
fem de mesh;c lung add_super d_ratio 0.3 sv_freq 1.05 arteries diameter diam_ratio 1.5997 d_max_order 30;

#exports the nodes and elements on the mesh
fem export node;lll_arteries as lll_arteries;
fem export elem;lll_arteries as lll_arteries;

#exports the stem element group (containing all stem vessels before supernumerary addition)
fem export elem;stem as stem elem stem;

#an element group containing all the supernumerary elements (called supernumerary)
#gets created in the code, this is exported for viewing:
fem export elem;supernumeraries as supernumerary elem supernumerary;

Additional testing commands:

fem list nodes region all

Files used by this example are:

Name                     Modified     Size

example_9821.com         08-Jul-2004  2.1k
artery_data.exdata       11-Jun-2004  463k
convert.com              11-Jun-2004  128 
draw.com                 11-Jun-2004  1.8k
initial_arteries.ipelem  11-Jun-2004  254k
initial_arteries.ipnode  11-Jun-2004  174k
lll_arteries.exelem      11-Jun-2004  2.7M
lll_arteries.exnode      11-Jun-2004  807k
lll_data.ipdata          11-Jun-2004  886k
reorder.com              11-Jun-2004  1.0k
stem.exelem              11-Jun-2004  1.1M
super.ipbase             11-Jun-2004  893 
super.ippara             23-Jun-2005  5.9k
supernumeraries.exelem   11-Jun-2004  157k
test.com                 08-Jul-2004  2.2k
test_output.com          11-Jun-2004   26 

Download the entire example:

Name                           Modified     Size

examples_9_98_982_9821.tar.gz  19-Aug-2006  488k

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.
  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
  Failure	cm:	ndiff test: significant differences with generic answer.
  Failure	cm-debug:	ndiff test: 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.
  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
  Failure	cm:	ndiff test: significant differences with generic answer.
  Failure	cm-debug:	ndiff test: significant differences with generic answer.

  
  

Html last generated: Sun Mar 6 05:50:36 2016

Input last modified: Thu Jun 23 12:50:43 2005