"""HCP tractography parameter extraction."""
from typing import TypedDict
from thesis.core.config import PipelineConfig
DEFAULT_N_SAMPLES = 5000
DEFAULT_N_STEPS = 2000
DEFAULT_STEP_LENGTH = 0.5
DEFAULT_CURVATURE_THRESHOLD = 0.2
DEFAULT_DIST_THRESH = 0.0
DEFAULT_FIBST = 1
DEFAULT_RAND_FIB = 0
DEFAULT_MEM_GB_GPU = 8.0
DEFAULT_MEM_GB_CPU = 4.0
[docs]
class TractographyParams(TypedDict):
"""Runtime tractography parameters for the ProbTrackX2 node."""
n_samples: int
n_steps: int
step_length: float
curvature_threshold: float
force_dir: bool
opd: bool
loop_check: bool
dist_thresh: float
fibst: int
rand_fib: int
mod_euler: bool
mem_gb_gpu: float
mem_gb_cpu: float
[docs]
def prepare_tractography_params(config: PipelineConfig) -> TractographyParams:
"""
Extract tractography parameters from config with sensible defaults.
Args:
config: PipelineConfig with tractography section
Returns:
Dict with tractography parameters: n_samples, n_steps, step_length,
curvature_threshold, force_dir, opd, loop_check, dist_thresh,
fibst, rand_fib, mod_euler, mem_gb_gpu, mem_gb_cpu
"""
tract_cfg = getattr(config, "tractography", None)
return {
"n_samples": getattr(tract_cfg, "n_samples", DEFAULT_N_SAMPLES),
"n_steps": getattr(tract_cfg, "n_steps", DEFAULT_N_STEPS),
"step_length": getattr(tract_cfg, "step_length", DEFAULT_STEP_LENGTH),
"curvature_threshold": getattr(
tract_cfg,
"curvature_threshold",
DEFAULT_CURVATURE_THRESHOLD,
),
"force_dir": getattr(tract_cfg, "force_dir", True),
"opd": getattr(tract_cfg, "opd", True),
"loop_check": getattr(tract_cfg, "loop_check", True),
"dist_thresh": getattr(tract_cfg, "dist_thresh", DEFAULT_DIST_THRESH),
"fibst": getattr(tract_cfg, "fibst", DEFAULT_FIBST),
"rand_fib": getattr(tract_cfg, "rand_fib", DEFAULT_RAND_FIB),
"mod_euler": getattr(tract_cfg, "mod_euler", False),
"mem_gb_gpu": getattr(tract_cfg, "mem_gb_gpu", DEFAULT_MEM_GB_GPU),
"mem_gb_cpu": getattr(tract_cfg, "mem_gb_cpu", DEFAULT_MEM_GB_CPU),
}
