Shows how to create embedded Element Xi nodes in the front end. Then error vectors showing the distance from the embedded point to element_xi point can be generated. These will interactively update whenever the host mesh is adjusted.
#Example_ap: Element Xi Coordinates : Fitting a face to a fox
#
# This example shows how to convert ipxi to cmgui elementxi, an example of
# converting exnode and exelem to ipnode and ipelem (this is not generic
# unfortunately), some fitting with cmiss,
#
#----------
#
set dir example ap
#
gfx create material aqua_blue ambient 0.1 0.9 1 diffuse 0.1 0.9 1 emission 0 0 0 specular 0.8 0.8 0.8 alpha 1 shininess 0.8
gfx create material jade ambient 0.1 0.56 0 diffuse 0.1 0.39 0 emission 0 0 0 specular 0.8 0.8 0.8 alpha 1 shininess 0.8
gfx create material purple ambient 0.72 0 1 diffuse 0.5 0 1 emission 0 0 0 specular 1 1 1 alpha 1 shininess 0.8
gfx create material red ambient 1 0 0 diffuse 1 0 0 emission 0 0 0 specular 0.8 0.8 0.8 alpha 1 shininess 0.8
if (!$TESTING)
{
gfx create window 1;
gfx modify window 1 view parallel eye_point 360.515 -98.2134 593.377 interest_point 27.6929 18.9214 48.7295 up_vector 0.0456354 0.981996 0.183306 view_angle 41.4883 near_clipping_plane 6.48947 far_clipping_plane 2319.12 relative_viewport ndc_placement -1 1 2 2 viewport_coordinates 0 0 1 1;
}
#
# Read in the four cubic elements in which we will embed our mesh
gfx read nodes example host.exnode
gfx read elements example host.exelem
#
gfx modify g_element host general clear;
gfx modify g_element host lines coordinate coordinates material default;
#
# Read in the embedded face mesh in its original position.
gfx read nodes example new_source.exnode
gfx read elements example new_mesh.exelem
gfx modify g_element mesh general clear;
gfx modify g_element mesh lines coordinate coordinates material default;
gfx modify g_element mesh surfaces coordinate coordinates material jade;
gfx modify g_element mesh node_points coordinate coordinates glyph sphere size "5*5*5" centre 0,0,0 no_select material purple;
#
# Calculate xi positions for each of these embedded nodes.
# This will be done in cm. The host mesh was converted to ipnode
# and ipelem using the fortran program ex2ip. This program is available
# here but makes many assumptions about the file structure, specifically
# the number of derivatives and where some of the spaces are.
# It can usually be modified to work with other exnode and exelem files.
# The new_source nodes must be converted to ipdata. This was done with the
# fortran program ex2ipdata.
# Now we can run cmiss to calculate the xi points.
gfx create cmiss
set dir example ap
open comfile example anthro_xi.com exec
# This generates a file called face.ipxi
#
# By converting this file to element xi we can graphically visualise the
# error between the xi positions and the data positions. An awk script
# is available here to convert ipxi to and exnode or exdata file which
# can be read in.
system "awk -f $example/ipxi2ex.awk < face.ipxi > face_xi.exnode"
#
gfx read nodes face_xi.exnode
# Now each of the embedded nodes has two 3D coordinates. An explicit
# original coordinate and an element_xi_coordinate. By drawing a line
# between these positions we get to see the error. Because we just
# calculated the xi's there shouldn't be any error at this point.
#
# In addition, read in a third coordinate at the target positions, then we can
# interactively see the error in the fit represented as red lines.
gfx read nodes example new_target.exnode
gfx define field error coordinate_system rectangular_cartesian add fields target_coordinates element_xi_coordinate scale_factors 1 -1
gfx modify g_element mesh node_points glyph line size "0*1.8*1.8" centre 0,0,0 orientation error scale_factors "1*0*0" no_select material red
#
# If we edit the positions of the host mesh the error vectors update.
gfx modify g_element host node_points glyph sphere size "5*5*5" centre 0,0,0 select_on material aqua_blue
# Now choose select mode in the graphics window and drag the host mesh nodes.
#
# We can use cmiss to calculate an optimal host mesh.
gfx create cmiss
set dir example ap
open comfile example anthro_fit.com exec
gfx read node host_fit.exnode
#
# The error vectors update with the host mesh. You can see how difficult it was
# to fit around the snout. Element_xi coordinates cannot be interpolated by
# elements like normal nodes, to draw the lines and elements at the fitted
# positions the actual coordinates of the element_xi nodes must be explicitly
# calculated and stored as real numbers.
gfx evaluate ngroup mesh source element_xi_coordinate destination coordinates
#
# So what? Wasn't that a very complicated way to move the nodes?
# True but now we have a mapping from the first face to the second so
# can update a high res version of the first face to approximate the second,
# or if we had a standard human body model we can fit some important markers
# measured on a specific individual, fit to those and then update the whole
# model to approximate that individual.
#
gfx
Name Modified Size
example_ap.com 17-Mar-2014 4.7k COPYRIGHT 17-Mar-2014 504 anthro_fit.com 17-Mar-2014 833 anthro_xi.com 17-Mar-2014 479 ex2ip 17-Mar-2014 21k ex2ip.f 17-Mar-2014 5.5k ex2ip2.f 17-Mar-2014 5.5k ex2ipdata 17-Mar-2014 16k ex2ipdata.f 17-Mar-2014 2.7k face.exdata 17-Mar-2014 8.4k face.ipxi 17-Mar-2014 7.8k face_xi.exnode 17-Mar-2014 8.5k host.com 17-Mar-2014 298 host.exelem 17-Mar-2014 9.2k host.exnode 17-Mar-2014 5.9k host.ipbase 17-Mar-2014 6.0k host.ipcoor 17-Mar-2014 588 host.ipelem 17-Mar-2014 1.5k host.ipelfd 17-Mar-2014 1.1k host.ipfiel 17-Mar-2014 16k host.ipmesh 17-Mar-2014 1.0k host.ipnode 17-Mar-2014 3.9k host_fit.exelem 17-Mar-2014 12k host_fit.exnode 17-Mar-2014 11k host_fit.ipfit 17-Mar-2014 1.9k ipxi2ex.awk 17-Mar-2014 314 new_mesh.exelem 17-Mar-2014 18k new_source.exnode 17-Mar-2014 4.1k new_source.ipdata 17-Mar-2014 4.7k new_target.exnode 17-Mar-2014 4.1k new_target.ipdata 17-Mar-2014 4.7k
Name Modified Size
examples_a_ap.tar.gz 09-Mar-2016 176k
Html last generated: Wed Mar 9 16:01:27 2016
Input last modified: Wed Mar 9 15:49:43 2016