"""CLI settings set through command-line arguments and ``cli_config.json``.
Command-line arguments override the values in the JSON."""
from typing import Any
import NeuroRuler.utils.global_vars as global_vars
from NeuroRuler.utils.constants import ThresholdFilter
DEBUG: bool = False
"""Whether or not to print debugging information throughout execution."""
RAW: bool = False
"""Whether to print the \"raw\" circumference.
If false, it prints a \"pretty\", rounded output with units included."""
FILE: str = ""
"""The file path."""
THETA_X: int = global_vars.THETA_X
"""In degrees"""
THETA_Y: int = global_vars.THETA_Y
"""In degrees"""
THETA_Z: int = global_vars.THETA_Z
"""In degrees"""
SLICE: int = -1
"""0-indexed. Overwritten later."""
CONDUCTANCE_PARAMETER: float = global_vars.CONDUCTANCE_PARAMETER
"""Smoothing option. See global_vars.CONDUCTANCE_PARAMETER."""
SMOOTHING_ITERATIONS: int = global_vars.SMOOTHING_ITERATIONS
"""Smoothing option. See global_vars.SMOOTHING_ITERATIONS."""
TIME_STEP: float = global_vars.TIME_STEP
"""Smoothing option. See global_vars.TIME_STEP."""
THRESHOLD_FILTER: ThresholdFilter = ThresholdFilter.Otsu
"""Which threshold filter to use. Default is Otsu."""
LOWER_BINARY_THRESHOLD: float = global_vars.LOWER_BINARY_THRESHOLD
"""Required threshold option for binary threshold.
If ``THRESHOLD_FILTER`` is ``ThresholdFilter.Otsu``, then this field will not be updated by CLI args
or by ``cli_config.json``."""
UPPER_BINARY_THRESHOLD: float = global_vars.UPPER_BINARY_THRESHOLD
"""Required threshold option for binary threshold.
If ``THRESHOLD_FILTER`` is ``ThresholdFilter.Otsu``, then this field will not be updated by CLI args
or by ``cli_config.json``."""
[docs]
def get_settings() -> dict[str, Any]:
r"""Returns ``dict`` containing values of all variables in this file, used for debugging
:return: ``dict`` of all CLI settings
:rtype: ``dict[str, Any]``"""
return {
"DEBUG": DEBUG,
"RAW": RAW,
"FILE": FILE,
"THETA_X": THETA_X,
"THETA_Y": THETA_Y,
"THETA_Z": THETA_Z,
"SLICE": SLICE,
"CONDUCTANCE_PARAMETER": CONDUCTANCE_PARAMETER,
"SMOOTHING_ITERATIONS": SMOOTHING_ITERATIONS,
"TIME_STEP": TIME_STEP,
"THRESHOLD_FILTER": THRESHOLD_FILTER,
"LOWER_BINARY_THRESHOLD": LOWER_BINARY_THRESHOLD,
"UPPER_BINARY_THRESHOLD": UPPER_BINARY_THRESHOLD,
}