Apr. 3, 2008: Amira, Cubit, AVS, and Control

Apr. 3, 2008: Amira, Cubit, AVS, and Control

Visualization

The AVS license server will be kept as is on Milagros. However, Milagros is expected to fail irreplaceably, and TACC will not be renewing the license and therefore AVS will no longer be available. This includes AVS on Maverick as well as offsite AVS installations that require TACC’s AVS license to run. Since AVS is at the heart of the visualization for this project, there are two options

  1. Attempt to work with AVS to get an individual license(s) for the group, so we can continue to use AVS for the project.
  2. Migrate the work to another visualization package such as EnSight, IDL, or VisIt.

Mesh Generation Pipeline

The following meshing pipeline (Figure 1) is now being considered.

Figure 1: Amira is used for 3D semi-automatic segmentation in the XY, XZ, and YZ planes of the anatomical data. The data is output as a facet file. The output facet file is then input into cubit to create a pillowed hexahedral mesh.

An intro to Amira tutorial may be found at http://www.amiravis.com/usersguide41/usersguide/first.html. The imaging data from M.D. Anderson should be ordered according to the slice orientation. Amira usually does this automatically, but on some data sets this must be done manually by dragging the slice orientation field to the far left of the image reader so that the image orientation has precedence.

The beta version of cubit is needed. The initial cubit commands from Jason Shepard at Sandia are:

set developer on
import facet ‘zpaf-Biotex-Prostate-Dog-7C243-labels.facet” feature_angle 0 make_elements
brick bounding box volume 1 extended percentage 10
volume 2 size 0.2
mesh volume 2
hexset hex in volume 2 separate tri all
hexset hex in group 4 nonman_edges
create mesh geometry hex in group 4 feature_angle 0
node in surface in volume 3 move onto surface 1 max_distance 0.1
node in surface in volume 3 move onto surface 1 max_distance 0.1
node in surface in volume 3 move onto surface 1 max_distance 0.1
reset genesis
block 1 volume 3
export mesh “fuentes1.g”
reset
import mesh geometry “fuentes1.g” feature_angle 0
surface in volume 1 smooth scheme centroid area pull
smooth surface in volume 1
export mesh “fuentes1.g” overwrite
reset
import mesh geometry “fuentes1.g” feature_angle 0
pillow hex in volume 1
surface all smooth scheme winslow
smooth face 451
volume all smooth scheme condition number
group “temp” equals hex in volume 1 scaled jacobian high 0.4
group “temp” equals quality volume 1 scaled jacobian high 0.4
smooth hex in temp
group “temp” equals quality volume 1 scaled jacobian high 0.5
smooth hex in temp
group “temp” equals quality volume 1 scaled jacobian high 0.5
export mesh “fuentes.g”


(a)

(b)
Figure 2: A sample mesh output from cubit is shown. (a) shows the full mesh of a canine prostate created from MRI data. (b) shows a section of the mesh

METIS is now being used for the domain decomposition. The serial version exploits the storage of the entire mesh on each mpi process.

Control

Development is under way to add to the dynamic capabilities of the control system. The planned capilities are:

  • Manual laser power override
  • Dynamic file manipulation
  • Dynamic filtering parameters

The data server and control task have been combined under a single mpi process but with different threads (Figure 3). This was done so that current power profile of the data server would be always available to the control task via shared memory. The control task may now broadcast a user input change in the power parameters to the compute drones.



Figure 3: Software Architecture.

The current treatment protocol is divided into four stages (Figure 4).

  1. MRTI thermal image data is acquired and used for model calibration
  2. The time span of actual calibration computations
  3. The time span for optimal temperature/damage/HSP computations
  4. The optimal laser control parameters are applied to the biological domain. In the event of the detection of an unexpectedly high temperature within the biological domain, a fail-safe shuts off the laser power.


Figure 4: Current Treatment Protocol.

Considering changing the protocol to make better use of stages 2 and 3.