[visualase]
visualase_file = mlat.dat
override = False
visualase_dir = /tmp
override_power = 0.0

[probe]
z_0 = -.0247
domain = 2;10
x_0 = .209
y_0 = .2625

[perfusion]
w_0_probe = 48.35e0
w_2_lb =  1.0e-1
w_i = 0.0e0
w_i_ub =  1.0e2 
w_d_ub =  4.0e0 
w_ni = 305.0e0
w_n = 0.0e0
w_d_lb =  0.0e0 
w_0_ub =  50.0e0
w_0_healthy = 0.0;3.0;6.0;12.0
w_0_lb =  6.0e0 
w_nid_md = 315.0e0
w_id = 315.0e0
w_i_lb = 20.0e0 
w_nid_ub = 335.0e0
w_nid_lb = 300.0e0
w_d = 0.0e0
w_n_lb =  4.0e0 
w_2_ub =  10.0e0
w_n_ub = 20.0e0 
w_2 = 0.0e0

[kalman]
modelcov = 6.25
meascov = 2.0
roi = [0,255,0,255]
statecov = 1.5
method = 2
magiy = 65
magix = 65

[thermal_conductivity]
k_2 = 0.0e0
k_3_lb = 305.0e0
k_1_lb = 0.0e0  
k_0_ub = 0.72e0 
k_1 = 0.0e0
k_0_lb = 0.40e0 
k_3 = 0.0e0
k_0_healthy = .527e0
k_2_lb = 1.0e-2 
k_0_probe = .5e0
k_1_ub = 0.33e0 
k_2_ub = 10.0e0 
k_3_ub = 325.0e0

[timestep]
isteps_per_ideal = 6
ideal_dt = 6.0e0

[bc]
u_dirichletid = 1
newton_coeff = 0.0
newton_coeff_ub = 112.0e0
u_flux_lb = 0.1e0
u_flux = 0.0
u_flux_ub = 112.0e0
newton_coeff_lb = 0.1e0

[mrti]
img_sizefile = mrtiimg.size
ixlo = 132
dictionary = $ITK_SOURCE/Utilities/gdcm/Dicts/GEMS.dic
iyhi = 142
nzero = 0
ixhi = 152
exampath = /FUS4/data2/BioTex/Brain_PhaseII/070205_BrainDog3_Treat/e126515
filein = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog3_980/dog3_98000/mrivis/temperature.%04d.vtk
uncertaintyin = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog3_980/dog3_98000/mrivis/tmapstd.%04d.vtk
dirid = 128475
ntime = 74
iylo = 118

[qoi_0]
init_time_window = [0,74]
noptsteps = 1
optimize_k_2 = False
optimize_k_3 = False
optimize_k_0 = False
optimize_k_1 = False
noffset = 0
plotoptsolve = true
numideal = 0
optimize_w_0 = False
optimize_pow = False
optimize_mu_a = False
optimize_mu_s = False

[avs]
femvis_sizefile = ucdvis.size
mrtivis_sizefile = mrtivis.size

[field]
w_0_field = False
k_0_field = False

[optical]
mu_a_healthy = 5.0e2
mu_a_tumor = 2.38e2
mu_a_probe = 0.0195e0
mu_s_probe = 100.0e0
mu_s_healthy = 140.0e2
anfact = 0.88e0
mu_s_tumor = 3.5e2

[compexec]
a21 = 1.0
executable = image
comphost = dip_stafford
a11 = 0.0
a10 = 0.13917310096006544
solver = superlu_dist
a02 = 0.13917310096006544
a00 = 0.99026806874157036
a12 = -0.99026806874157036
a22 = 0.0
jobid = dog3_980
execcode = cd /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat/dog3_980/dog3_98000 ; mpirun -n 1 $WORK/exec/image_$COMPILER-$MPI_VERSION-cxx-$METHOD   /FUS4/data2/BioTex/Brain_PhaseII/070205_BrainDog3_Treat/e126515 128475 $ITK_SOURCE/Utilities/gdcm/Dicts/GEMS.dic mrivis -snes_ls basic -info  -info_exclude null,vec,mat,pc,ksp,snes -ksp_rtol 1.e-9 -pc_type bjacobi  -snes_monitor -snes_rtol 1.e-6 -snes_converged_reason -tao_max_funcs 0 -magIx 65 -magIy 65 -nzero 0 -ntime 74  -X_0 0.209000 -Y_0 0.262500 -Z_0 -0.024700 -meascov 2.000000 -statecov 1.500000  -ix 0 -nx 255 -iy 0 -ny 255 -bodytemp 33.900000 -method 2 -solver superlu_dist
workdir = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/980brainStat
b0 = .209
b1 = .2625
b2 = -.0247
powerdata = [9,13,17,22,23,24,39,46,74]@[0.0,4.2,0.0,14.54,0.0,14.54,0.0,12.0,0.0]
numproc = 1
runtime_options = -snes_ls basic -info  -info_exclude null,vec,mat,pc,ksp,snes -ksp_rtol 1.e-9 -pc_type bjacobi  -snes_monitor -snes_rtol 1.e-6 -snes_converged_reason -tao_max_funcs 0
method = opt
meshdata = /home/dfuentes/DDDAS/data/mdacc/canine_feb07/generic-mesh/meshTemplate.e

[registration]
createbackupmesh = createboxmesh.py
transform_script = LBIE_2_hp3d.py 1 1
subsamplefactorx = 2
subsamplefactorz = 1
registration_exe = RigidRegistration
dicomconvert = DicomSeriesConvert
subsamplevolume = SubsampleNoFilter
registration = False
subsamplefactory = 2
interop_dicom_dir = 

[output]
femgmv = False
compwritefem = femvis/
mrtiavs = False
fem_filename = fem
computefinalobjective = false
mriavs = False
femraw = False
femavs = False
compwritemri = mrivis/
mrirawiv = False
mrtirawiv = False

[source_laser]
mu_s_ub = 2820.0e+2
pow_ub = 15.0e0
pow_lb = -0.1e0
mu_s_lb = 2.0e+2
anfact_ub = 1.0e0
mu_a_ub = 0.60e+2
mu_a_lb = 0.30e+2
anfact_lb = 0.6e0
anfact = 0.71e0

[method]
pde = 1
qoi = 4

[initial_condition]
u_init = 33.9
probe_init = 21.0;34.3
z_init = 7.431e4