Example a4: Radius fields and cylinders, movies: heart and coronaries

Shows how cylinders, with radius defined by a field can be used to visualize the coronary mesh. Also demonstrates how to make movies with cmgui. NOTE: The coronary mesh is quite large and is slow to view on older workstations.

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For more information about running zinc see The Zinc web page.

The comfile run by this example is as follows:

#Example_a4: Radius fields, cylinders and movies: heart and coronaries
#
# The coronary model describes the network of arteries delivering blood to the
# heart. Starting with few, quite large vessels, the arteries bifurcate several
# times until they are very fine and numerous. Consequently, this mesh is quite
# large and takes some time to view. The elements in the mesh have a radius
# field that will be used to draw them into appropriately sized cylinders. Since
# it will be too slow to rotate the coronaries on most workstations, this
# example also shows how to make a movie of the model rotating, enabling a
# better appreciation of the 3-D layout of the arteries.
#
# Be sure to run the commands in this example in the order they are presented,
# and not all at once. Comments and instructions for things you can do are given
# between these commands.
#
#
#----------
#
# Create a few materials in addition to the default for use later.
gfx create material heart ambient 0.3 0 0.3 diffuse 1 0 0 specular 0.5 0.5 0.5 shininess 0.5
gfx cre mat bluey ambient 0 0.2 0.4 diffuse 0 0.5 1 specular 0.5 0.5 0.5 shininess 0.8
gfx cre mat gold ambient 1 0.7 0 diffuse 1 0.7 0 specular 0.5 0.5 0.5 shininess 0.8
#
# First read in the 120-element refined heart mesh (group heart) to show the
# coronaries against. Its node and element numbers are lower than those used in
# the coronary mesh and do not overlap.
# !!! CS 26/1/2001 The heart model used here predates a modification to the scale
# factors and the sheet angles in the current Auckland model. It has been left as
# is because the coronary solutions were calculated based on this model.

gfx read nodes example large_heart.exnode
gfx read elements example large_heart.exelem

# Clear the graphics for heart and set up increased surface quality:
gfx mod g_e heart general clear element_discretization "10*10*4";
#
# Draw the endo-cardial surfaces.
gfx mod g_e heart surfaces exterior face xi3_0 mat heart
#
# Read in the coronary mesh (group coro0) and hide the axes.
gfx read nodes example coro0.exnode
gfx read elements example coro0.exelem
#
# Open the graphics window and reorient the heart up the right way (since -x is
# "up" in the heart model). Also turn on perspective.
gfx cre win 1
gfx mod win 1 image rotate 0 1 0 -90
gfx mod win 1 view perspective
#
# Destroy the default lines
gfx modify g_element coro0 lines delete
#
# The coronary mesh has a very large number of nodes and elements. Since the
# elements are all lines, set minimal element discretization (of one segment per
# element curve) to reduce the memory requirements and increase rendering speed.
gfx modify g_element coro0 general element_discretization 1
#
# The radius of the coronary arteries is stored in component 1 of field
# 'general', defined over the elements in the coro0 group. Now draw cylinders
# using these radii with the following command, and note that it will take some
# time to appear on the window!
gfx mod g_e coro0 cylinders radius general.1 material gold
#
# Now we will make a movie of the coronaries rotating. The movie can be played
# in the program and will also be written to disk, so you can run it using the
# movieplayer program. Note that the movie file will be quite large and you
# should probably delete it once you have tried it. First we will set up the
# exact view we wish to see the object from.
#
# Set the resolution of the viewport in the window to 400x400.
gfx mod win 1 layout width 400 height 400
# Set the interest point, eye point and up vector that define the centre of
# what you are looking at, where you are viewing from and which way is up. CMGUI
# automatically makes sure the up_vector is orthogonal to the direction of view
# - unless you specify the 'allow_skew' options.
gfx mod win 1 view interest_point 10 0 0 eye_point 0 -300 0 up_vector -1 0 0
#
# Set the near and far clipping planes in distance from the view point.
gfx mod win 1 view near_clipping_plane 1 far_clipping_plane 600
#
# Set the view angle to mostly fill the screen.
gfx mod win 1 view view_angle 30
#
# Rotate the top of the heart slightly towards the viewer.
gfx mod win 1 image rotate 0 0 1 -15
#
# Set the number of segments used to draw the cylinders to 6. Increasing this
# number will make the movie look better, but rendering will be slower and
# smaller systems may run out of memory.
gfx mod g_e coro0 general circle_discretization 6
#
# If you wish to produce the best results, turn on "scene antialiasing"
# at the highest quality level of 8, using the command
gfx mod win 1 set antialias 8
#
for ($i = 0 ; $i < 6 ; $i++)
{
  # Rotate the coronaries about the -x axis by -10 degrees. Note that this angle
  # refers to the amount the viewer moves in the direction of a right hand screw
  # relative to the given axis.
  gfx modify window 1 image rotate -1 0 0 -10
  # Save the frame.  I am using sgi files as these are non lossy but compressed.
  # We probably could use jpg files but currently cmgui does not expose any way
  # of controlling the amount of compression and so defaults to a relatively low
  # value.
  gfx print window 1 file coronary_rotate$i.sgi
}
#
#
# If mpeg2enc is available build a movie.  Shell return codes need to inversed.
# Pipe output to /dev/null to hide it
if (!system("which convert >/dev/null") && !system("which mpeg2enc >/dev/null"))
{
  #convert images
  for ($i = 0 ; $i < 6 ; $i++)
  {
	 system("convert coronary_rotate$i.sgi coronary_rotate$i.jpg") and die "Unable to convert image.";
  }
  # Pipe output to /dev/null so that the example generates the same screen output whether
  # mpeg2enc is available or not.
  system("jpeg2yuv -f 25 -I p -b 0 -j coronary_rotate%d.jpg 2>/dev/null | mpeg2enc -f 3 -b 3800 -a 1 -4 2 -2 3 -s -F 3 -np -q 1 -v 1 -o coronary_rotate.m2v > /dev/null 2>&1") and die "Unable to generate movie.";
}
#----------
#
# FINAL NOTE: movies are extremely large files. To conserve disk space, make
# sure you delete the movie you just created after running this example!
#

Files used by this example are:

Name                      Modified     Size

example_a4.com            17-Mar-2014  5.9k
COPYRIGHT                 17-Mar-2014  504 
coro.rgb                  17-Mar-2014  587k
coro0.exelem              17-Mar-2014  1.1M
coro0.exnode              17-Mar-2014  1.9M
coronary_rotate.com       17-Mar-2014  296 
coronary_rotate.com_save  17-Mar-2014  292 
large_heart.exelem        17-Mar-2014  432k
large_heart.exnode        30-Mar-2015   71k

Download the entire example:

Name                  Modified     Size

examples_a_a4.tar.gz  09-Mar-2016  3.5M

Testing status by version:

Testing status by file:

• status
  

  x86_64-linux
  139	cmgui-wx:	error exit status 139.
  139	cmgui-wx-debug:	error exit status 139.
  139	cmgui-wx-debug-memorycheck:	error exit status 139.
  139	cmgui-wx-debug-valgrind:	error exit status 139.

  
  
• cmiss_test.log
  

  i686-linux
  Failure	cmgui-wx:	diff test: differences with generic answer; Test output.
  Failure	cmgui-wx-debug:	diff test: differences with generic answer; Test output.
  Failure	cmgui-wx-debug-memorycheck:	diff test: differences with generic answer; Test output.
  Failure	cmgui-wx-debug-valgrind:	diff test: differences with generic answer; Test output.
  x86_64-linux
  Failure	cmgui-wx:	diff test: differences with generic answer; Test output.
  Failure	cmgui-wx-debug:	diff test: differences with generic answer; Test output.
  Failure	cmgui-wx-debug-memorycheck:	diff test: differences with generic answer; Test output.
  Failure	cmgui-wx-debug-valgrind:	diff test: differences with generic answer; Test output.

  
  
• coronary_rotate5.sgi
  

  i686-linux
  Failure	cmgui-wx:	idiff test: Test output; wx answer.
  Failure	cmgui-wx-debug:	idiff test: Test output; wx answer.
  Failure	cmgui-wx-debug-memorycheck:	idiff test: Test output; wx answer.
  Failure	cmgui-wx-debug-valgrind:	idiff test: Test output; wx answer.
  x86_64-linux
  Missing	cmgui-wx:	output file not generated for idiff; wx answer.
  Missing	cmgui-wx-debug:	output file not generated for idiff; wx answer.
  Missing	cmgui-wx-debug-memorycheck:	output file not generated for idiff; wx answer.
  Missing	cmgui-wx-debug-valgrind:	output file not generated for idiff; wx answer.

  
  

Html last generated: Wed Mar 9 16:01:13 2016

Input last modified: Wed Mar 9 15:49:38 2016