public class SimulationParams
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
ALLCOMPS
flag for compartmental signal: output for each component
|
int |
buffsize
size of traj file output buffer (one meg by default)
|
static java.lang.String |
crossSectionFig
Name of file to output the cross section figure
|
static CylinderFactory.CylType |
cylinderType
type of cylinders
|
static double |
duration
duration of simulation in seconds
|
static int |
EXTRACELLULAR
flag for extracellular walkers only
|
static int |
EXTRAONLY
flag for compartmental signal: extracellular only
|
static int |
INTRACELLULAR
flag for intracellular walkers only
|
static int |
INTRAONLY
flag for compartmental signal: intracellular only
|
static int |
NOCOMPS
flag for compartmental signal: default (no compartmental segregation
|
static ScanFactory.ScanType |
scanType
scan type
|
static StepAmenderFactory.AmenderType |
sim_amender_type
type of step amender
|
static double |
sim_cAngle
angle between crossing fibres on crossing substrate.
|
static int |
sim_compartmentSignal
compartmental signal output? default no
|
static int |
sim_crossSectionImageSize
size of cross section image in pixels
|
static double |
sim_cyl_D1
core diffusivity of myelinated cylinders
|
static double |
sim_cyl_D2
sheath diffusivity in meylinated cyliners
|
static int |
sim_cyl_dist_size
number of cylinders along a side of square distributed
radius cylinder substrate
|
static double |
sim_cyl_max_r
distributed cylinder max radius (meters)
|
static double |
sim_cyl_min_r
distributed cylinder min radius (meters)
|
static int |
sim_cyl_pack
cylinder packing
|
static double |
sim_cyl_r
fixed cylinder radius (meters)
|
static double |
sim_cyl_R
fixed cylinder separation (meters)
|
static double |
sim_cyl_r1
outer radius of myelinated cylinders
|
static double |
sim_delta
simulation delta value
|
static double |
sim_DELTA
simulation diffusion time
|
static boolean |
sim_delta_set
has the simualtion set delta?
|
static boolean |
sim_DELTA_set
has the simulation set DELTA?
|
static boolean |
sim_drawCrossSection
flag to set drawing of cross section of cylinder substrate (TODO: squashy cyls only)
|
static double |
sim_G
simulation G value
|
static boolean |
sim_G_set
has the simulation set gradient strength?
|
static SubstrateFactory.SubstrateType |
sim_geomType
the default geometry type
|
static int |
sim_inflamm_increments |
static int |
sim_initial
initial conditions flag
|
static double |
sim_l
cell size for cellular lattice
|
static double |
sim_L
the substrate size
|
static int |
sim_N_walkers
number of walkers in the simulation
|
static int |
sim_num_cylinders
number of cylinders on substrate
|
static int |
sim_num_facets
number of facets on a facetted cylinder
|
static int |
sim_onlyRun
only run a single iteration of the substrate? -1 if no.
|
static double |
sim_p
membrane transition probability
|
static double |
sim_p_perc
percolation prob for perc lattic
|
static double |
sim_p_stick
probability for sticking to a membrane
|
static double |
sim_p_unstick
probability for a spin unsticking itself from a membrane
|
static java.lang.String |
sim_plyfile
name of PLY file to read
|
static java.lang.String |
sim_postproStatsFname
name of post-processing stats file
|
static boolean |
sim_separate_runs
indicates whether to run a separate simulation for
each voxel (true) or generate all voxels from the
same simulation
|
static int |
sim_spatial_grid_size
density of square grid used for sptial sorting
|
static java.lang.String |
sim_statsfile
name of stats output file
|
static StatisticsModuleFactory.StatsModuleType |
sim_StatsModType
type of statistics to generate
|
static StepGeneratorFactory.StepType |
sim_stepType
the type of step distibution
|
static int |
sim_stripethickness
stripe width for striped substrate
|
static double |
sim_surfaceDiffusivity
diffusivity on surface of an object for sticky walks
(default is one order of magnitude lower than free
diffusivity)
|
static double[] |
sim_T2
compartmental T2 in seconds
(default vals: 2.28s for bulk CSF, 10% of that on surface)
|
static int |
sim_tmax
number of timesteps in the diffusion simulation
|
static double |
sim_voxelSize
the size of the central voxel
|
static double |
sim_voxelSizeFrac
fraction of outer voxel voxel on mesh substrate used
to generate data
|
static int |
SPECIAL
flag for special (debug) initial conditions.
|
static int |
SPIKE
flag for delta-peaked initially posiitoned walkers
|
static boolean |
substrateInfo
flag to read out cylinder info
|
static boolean |
trajectories
are we generating trajectories?
|
static java.lang.String |
trajFile
name of trajectories file
|
static int |
UNIFORM
flag for uniformly distributed initial conditions
|
Constructor and Description |
---|
SimulationParams(int N_walkers,
int tmax,
double p,
int initial,
SubstrateFactory.SubstrateType geomType,
StepGeneratorFactory.StepType stepType,
double voxelSize,
double duration)
alternate constructor with no scheme object.
|
SimulationParams(int N_walkers,
int tmax,
double p,
int initial,
SubstrateFactory.SubstrateType geomType,
StepGeneratorFactory.StepType stepType,
double voxelSize,
SimulableScheme imPars) |
Modifier and Type | Method and Description |
---|---|
double |
getDt() |
SubstrateFactory.SubstrateType |
getGeometryType() |
int |
getInitialConditions() |
int |
getN_walkers() |
double |
getP() |
double[] |
getStepParams() |
StepGeneratorFactory.StepType |
getStepType() |
int |
getTmax() |
double |
getVoxelSize() |
static void |
main(java.lang.String[] args) |
void |
setStepParams(double[] stepParams)
sets the parameters for the step generator
|
public static boolean sim_separate_runs
public static int sim_inflamm_increments
public static int sim_N_walkers
public static int sim_tmax
public static double sim_p
public static int sim_initial
public static SubstrateFactory.SubstrateType sim_geomType
public static double sim_L
public static double sim_l
public static int sim_stripethickness
public static double sim_p_perc
public static double sim_voxelSize
public static StepGeneratorFactory.StepType sim_stepType
public static boolean sim_delta_set
public static double sim_delta
public static boolean sim_DELTA_set
public static double sim_DELTA
public static boolean sim_G_set
public static double sim_G
public static double sim_surfaceDiffusivity
public static double[] sim_T2
public static CylinderFactory.CylType cylinderType
public static int sim_cyl_pack
public static int sim_cyl_dist_size
public static double sim_cyl_min_r
public static double sim_cyl_max_r
public static double sim_cyl_r
public static double sim_cyl_R
public static double sim_cyl_r1
public static double sim_cyl_D1
public static double sim_cyl_D2
public static double sim_cAngle
public static int sim_num_cylinders
public static int sim_num_facets
public static java.lang.String sim_plyfile
public static double sim_voxelSizeFrac
public static java.lang.String sim_statsfile
public static StatisticsModuleFactory.StatsModuleType sim_StatsModType
public static int sim_spatial_grid_size
public static boolean sim_drawCrossSection
public static java.lang.String crossSectionFig
public static int sim_crossSectionImageSize
public static StepAmenderFactory.AmenderType sim_amender_type
public static double sim_p_stick
public static double sim_p_unstick
public static java.lang.String sim_postproStatsFname
public static ScanFactory.ScanType scanType
public static final int SPIKE
public static final int UNIFORM
public static final int SPECIAL
public static final int INTRACELLULAR
public static final int EXTRACELLULAR
public static final int NOCOMPS
public static final int EXTRAONLY
public static final int INTRAONLY
public static final int ALLCOMPS
public static java.lang.String trajFile
public int buffsize
public static double duration
public static boolean trajectories
public static boolean substrateInfo
public static int sim_onlyRun
public static int sim_compartmentSignal
public SimulationParams(int N_walkers, int tmax, double p, int initial, SubstrateFactory.SubstrateType geomType, StepGeneratorFactory.StepType stepType, double voxelSize, SimulableScheme imPars)
public SimulationParams(int N_walkers, int tmax, double p, int initial, SubstrateFactory.SubstrateType geomType, StepGeneratorFactory.StepType stepType, double voxelSize, double duration)
N_walkers
- number of walkerstmax
- number of timestepsp
- permeabilityinitial
- initial conditions flaggeomType
- substrate typestepType
- type of steps to generatevoxelSize
- size of voxelduration
- duration of simulated dynamics in secondspublic double getDt()
public int getN_walkers()
public int getTmax()
public static void main(java.lang.String[] args)
public double getP()
public SubstrateFactory.SubstrateType getGeometryType()
public int getInitialConditions()
public double[] getStepParams()
public void setStepParams(double[] stepParams)
steParams
- array of step generator parameterspublic StepGeneratorFactory.StepType getStepType()
public double getVoxelSize()