############################################################# #GENERAL PARAMETERS - leave no whitespace #Parameters that start with 'IN_' will be overridden by #command line options in the case of a conflict ############################################################# IN_ATLAS_PATH= IN_TARGET_PATH= IN_SERIES_PATH= IN_ATLAS_LMK_PATH= IN_TARGET_LMK_PATH= IN_OUTPUT_PATH= #Dimension, 2 or 3 IN_D=3 #Number of Simulations: 1000 SIMSTEPS=1000 #Number of timesteps in each simulation: 10 IN_TIMESTEPS=10 #If want to save subset of vtk files use parameter to specify interval to save #For example if IN_TIMESTEPS set to 10 and wish to save every 5th interval use IN_VTK_INTERVAL=5 IN_VTK_INTERVAL= #Integration delta: 0.1 DELTA=0.1 #Epsilon Energy: 0.0000000001 EPSILON=0.0000000001 #Number of Processors Z IN_PROCS_Z=1 #Number of Processors Y IN_PROCS_Y=1 #Number of Processors X IN_PROCS_X=1 #Alpha: 0.01 ALPHA=0.01 #Gamma: 1 GAMMA=1 #Power of Operator L: 1 POWERL=1 #PadI Supplied: 20 PADI=20 #PadH Supplied: 5 PADH=5 #normGradientToStopSimulation Supplied: 1000 NORM_GRAD=1000 #Restarting by reading existing velocity fields: 0 RESTART=0 #Noise Std. Deviation sigma: 1 SIGMA=1 #Fraction of Original Image Error To Reach Before Stop: 0.02 ERROR=0.02 #Simulation Steps after which to change Imge Matching Epsilon: 25 CH_EPSILON=25 #'true' for MPG movie file, blank otherwise CREATE_MPG= #'true' for TAR file, blank otherwise CREATE_TAR= ############################################################# #LANDMARK PARAMETERS #NO NEED TO CHANGE IF NOT USING [-l | --landmark | (-L & -M)] ############################################################# # 'true' for Landmark matching, blank otherwise USE_LMK_MATCHING= #First Apply Rigid LMK Matching (1 for yes, 0 for no ): 0 USE_RLM=0 #Operator Greens Function (1 for Gaussian, 2 for -a Laplacian + c): 1 OP_GREEN=1 #GreensParameter: for (1) GaussianSigma, (2) a/c: 5 GREEN_PARAM=5 #Noise associated with Landmark Placement: 1 LMK_NOISE=1 #Number of landmark simulations: 100 LMK_SIMS=100 #Gradient Step Epsilon for Landmark gradient update: 1e-4 LMK_EPSILON=1e-4 #GradientMethod (1-CamionSplines, 2-GradientV): 2 LMK_METHOD=2