This examples illustrates a gait analysis using the host-mesh with volume conservation.
################ Host-mesh fitting with volume conservation ################
# This example deforms a host-mesh to conserve muscle attachment points, and
# in addition ensures that the jacobian at each Gauss point of the host-mesh
# is not changed (i.e. volume conservation). For the case of a tri-linear mesh
# illustrated here this was found to pass on the volume conservation to the slave.
# This example also illustrates the host-mesh approach to gait analysis.
################ parameters, regions, bases and coordinate system################
fem def para;r;volume_eg;example #parameter file
fem def region;r;volume_eg;example #define regions
fem def coord 3,1; #3D rectangular cartesian
fem def base;r;volume_eg;example #bases functions
$REG=1 #initialise region counter
$TOT_FITS=6 #initialiase no. of fits variable
################ muscle host MESHES ################
# host_list
@host_list = ('semimembranosus_host');
foreach $component(@host_list)
{
# Read in host
fem def node;r;$component;example region $REG
fem def element;r;$component;example region $REG
# Define fields
fem def field;r;$component;example reg 1;
fem def elem;r;$component;example field reg 1;
# Export host
#fem exp nodes;$component as $component region $REG
#fem exp elem;$component as $component region $REG
$REG=$REG+1;
}
################ bone MESHES ################
# bone_list
@bone_list = ('femur','tibia','hip');
foreach $component(@bone_list)
{
# Read in bone
fem def node;r;$component;example region $REG
fem def element;r;$component;example region $REG
# Export initial bone
#fem exp nodes;initial_$component as $component region $REG
#fem exp elem;initial_$component as $component region $REG
$REG=$REG+1;
}
################ SLAVE_muscles MESH ################
# muscle_list
@muscle_list = ('semimembranosus');
foreach $component(@muscle_list)
{
# Read in muscle
fem def node;r;$component;example region $REG
fem def element;r;$component;example region $REG
# Define fields
fem def field;r;$component;example reg $REG;
fem def elem;r;$component;example field reg $REG;
# Export initial muscle
#fem exp nodes;initial_$component as $component region $REG
#fem exp elem;initial_$component as $component region $REG
################ Define material coordinates of slave and control points ################
# Only performed once and then future runs can read in ipxi files.
## Define material positions of nodes in host
#fem def xi;c nodes contain of $REG in 1 loose
#fem def xi;w;nodes_$component nodes contain of $REG in 1
## Create landmark points attached at muscle ends.
## These are only generated once and stored as
## material coordinates for entire simulation
#fem def xi;c contact_tied XI_END points 4 reg $REG
## convert to spatial data point
#fem def data;c from_xi reg $REG
#fem def data;w;landmark
## check to see if correct
#fem exp data;landmark as landmark
## convert into material coordinates inside host (reg 1)
#fem def xi;c closest reg 1
## write out material coordinates
#fem def xi;w;landmark_$component reg 1
## Create target material points and store
## as material coordinates on hip and tibia bones
#fem def data;r;landmark
#fem def xi;c closest_face external reg 3,4
#fem def xi;w;target_$component
## check to see if correct
#fem def data;c from_xi
#fem exp data;target as target
$REG=$REG+1;
}
#################Rigid body rotations from motion capture######################
# Adjustments to static position (orthotrak motion capture system)
fem change nodes scale by 1.2,1.2,1.2 reg 4
fem change nodes rotate by -8 axis 1,0,0 reg 2
fem change nodes rotate by -6 axis 0,1,0 reg 2
fem change nodes rotate by -180 axis 0,0,1 reg 2
fem change nodes translate by 689,-154,-76 reg 2
fem change nodes rotate by -6 axis 1,0,0 reg 3
fem change nodes rotate by 6 axis 0,1,0 reg 3
fem change nodes rotate by 180 axis 0,0,1 reg 3
fem change nodes translate by 790,-170,10 reg 3
fem change nodes rotate by 8 axis 1,0,0 reg 4
fem change nodes rotate by 8 axis 0,1,0 reg 4
fem change nodes rotate by 172 axis 0,0,1 reg 4
fem change nodes translate by 864,-545,-9 reg 4
# Bone transformation (to a random dynamic position).
fem change nodes rotate by -3.621821 axis 1,0,0 reg 2
fem change nodes rotate by -30.46 axis 0,1,0 reg 2
fem change nodes rotate by 172.25 axis 0,0,1 reg 2
fem change nodes translate by -619.76,439.90,-111.15 reg 2
fem change nodes rotate by -12.065170 axis 1,0,0 reg 3
fem change nodes rotate by -15.52 axis 0,1,0 reg 3
fem change nodes rotate by 170.17 axis 0,0,1 reg 3
fem change nodes translate by -447.84,466.63,-9.61 reg 3
fem change nodes rotate by 3.380810 axis 1,0,0 reg 4
fem change nodes rotate by -1.93 axis 0,1,0 reg 4
fem change nodes rotate by 176.87 axis 0,0,1 reg 4
fem change nodes translate by -201.99,316.14,-28.25 reg 4
# Export transformed bone
#fem exp nodes;transformed_femur as femur region 2
#fem exp nodes;transformed_tibia as tibia region 3
#fem exp nodes;transformed_hip as hip region 4
# Rigid body rotation of semimembranosus and host (same as femur)
# to account for global motion
# Adjustments to static position (orthotrak motion capture system)
fem change nodes rotate by -8 axis 1,0,0 reg 1,5
fem change nodes rotate by -6 axis 0,1,0 reg 1,5
fem change nodes rotate by -180 axis 0,0,1 reg 1,5
fem change nodes translate by 689,-154,-76 reg 1,5
# Bone transformation (to a random dynamic position).
fem change nodes rotate by -3.621821 axis 1,0,0 reg 1,5
fem change nodes rotate by -30.46 axis 0,1,0 reg 1,5
fem change nodes rotate by 172.25 axis 0,0,1 reg 1,5
fem change nodes translate by -619.76,439.90,-111.15 reg 1,5
# Export transformed host
#fem exp nodes;transformed_semimembranosus_host as semimembranosus_host region 1
#fem exp nodes;transformed_semimembranosus as semimembranosus region 5
############# HOST MESH FITTING ############
# put initial host geometry into fields 4,5,6
fem update field 4 reg 1 subst geometry x reg 1;
fem update field 5 reg 1 subst geometry y reg 1;
fem update field 6 reg 1 subst geometry z reg 1;
# target xi points
fem def xi;r;target_semimembranosus;example reg 1
# convert to spatial data points
fem def data;c from_xi
# check
#fem exp data;check as check
# landmark xi points
fem def xi;r;landmark_semimembranosus;example reg 1
fem list data error reg 1; #outputs initial error
fem def fit;r;volume_eg;example geometry reg 1;
for ($fit_itt=1; $fit_itt<=$TOT_FITS; $fit_itt=$fit_itt+1)
{
fem fit reg 1;
fem update node fit reg 1
system "echo ' ======================================================' "
system "echo ' FIT ${fit_itt} DONE' "
system "echo ' ======================================================' "
}
############# SLAVE MESH UPDATE ############
# put back undeformed geometry from fields 4,5,6 to geometry x,y,z
fem update geometry x reg 1 subst field 4 reg 1;
fem update geometry y reg 1 subst field 5 reg 1;
fem update geometry z reg 1 subst field 6 reg 1;
# check initial volume of muscle slave
#fem list elem reg 5
fem def xi;r;nodes_semimembranosus;example nodes contain of 5 in 1
fem update mesh position fit of 5 in 1;
# check final volume of muscle slave
#fem list elem reg 5
# Export transformed bone
#fem exp nodes;deformed_semimembranosus as semimembranosus region 5
############# HOST MESH UPDATE #############
# check initial volume of host mesh
#fem list elem reg 1
fem update node fit reg 1;
#fem export node;deformed_semimembranosus_host as semimembranosus_host reg 1;
# check final volume of host mesh
#fem list elem reg 1
