"""Contains Pydantic data models for the simulation
Several Pydantic data models are defined for different
root system architecture simulation procedures.
"""
from enum import Enum
from typing import Dict, List, Optional
from pydantic import BaseModel
class Config:
arbitrary_types_allowed = True
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class RootType(Enum):
STRUCTURAL = "structural"
FINE = "fine"
PRIMARY = "primary"
SECONDARY = "secondary"
OUTER = "outer"
INNER = "inner"
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class RootTypeModel(BaseModel):
"""The root type data model for classifying roots.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
root_type: str
order_type: str
position_type: str
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class RootNodeModel(BaseModel):
"""The node data model for the hierarchical graph representation of the root system.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
node_id: Optional[int] = 0
plant_id: Optional[int] = 1
parent_id: Optional[int] = -1
organ_id: Optional[int] = 0
x: Optional[float] = 0.0
y: Optional[float] = 0.0
z: Optional[float] = 0.0
order: Optional[int] = 0
segment_rank: Optional[int] = 0
diameter: Optional[float] = 0.0
length: Optional[float] = 0.0
root_tissue_density: Optional[float] = 0.0
root_type: Optional[str] = "base"
order_type: Optional[str] = "base"
position_type: Optional[str] = "base"
simulation_tag: Optional[str] = "default"
invalid_root: Optional[bool] = False
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class RootEdgeModel(BaseModel):
"""The edge data model for the hierarchical graph representation of the root system.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
parent_id: int
child_id: int
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class RootSimulationModel(BaseModel):
"""
The root system architecture simulation data model.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
random_seed: int | None
max_order: int
root_ratio: float
fine_root_threshold: float
outer_root_num: int
inner_root_num: int
min_primary_length: float
max_primary_length: float
base_diameter: float
diameter_reduction: float
apex_diameter: float
min_sec_root_num: int
max_sec_root_num: int
growth_sec_root: float
min_sec_root_length: float
max_sec_root_length: float
segments_per_root: int
length_reduction: float
root_vary: float
interbranch_distance: float
mechanical_constraints: float
root_tissue_density: float
gravitropism: float
origin_min: Optional[float] = 1e-3
origin_max: Optional[float] = 1e-2
enable_soil: Optional[bool] = False
soil_layer_height: Optional[float] = 0
soil_layer_width: Optional[float] = 0
soil_n_layers: Optional[int] = 0
soil_n_cols: Optional[int] = 0
max_val_attempts: Optional[int] = 50
simulation_tag: Optional[str] = "default"
no_root_zone: Optional[float] = 1e-4
floor_threshold: Optional[float] = 0.4
ceiling_threshold: Optional[float] = 0.9
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class ParameterIntervalModel(BaseModel):
"""The parameter specification data model.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
lower_bound: float
upper_bound: float
data_type: str
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class SummaryStatisticsModel(BaseModel):
"""The summary statistics data model.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
statistic_name: str
statistic_value: float
z_lower_bound: Optional[float] = 0.0
z_upper_bound: Optional[float] = 0.0
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class StatisticsComparisonModel(BaseModel):
"""The data model for comparing synthetic and observed data.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
summary_statistics: Optional[List[str]] = None
distance_metrics: Optional[List[str]] = None
stat_by_soil_layer: Optional[bool] = False
stat_by_soil_column: Optional[bool] = False
use_summary_statistics: Optional[bool] = True
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class RootCalibrationIntervals(BaseModel):
"""
The root system architecture calibration interval data model.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
max_order: ParameterIntervalModel
root_ratio: ParameterIntervalModel
fine_root_threshold: ParameterIntervalModel
outer_root_num: ParameterIntervalModel
inner_root_num: ParameterIntervalModel
min_primary_length: ParameterIntervalModel
max_primary_length: ParameterIntervalModel
base_diameter: ParameterIntervalModel
diameter_reduction: ParameterIntervalModel
apex_diameter: ParameterIntervalModel
min_sec_root_num: ParameterIntervalModel
max_sec_root_num: ParameterIntervalModel
growth_sec_root: ParameterIntervalModel
min_sec_root_length: ParameterIntervalModel
max_sec_root_length: ParameterIntervalModel
segments_per_root: ParameterIntervalModel
length_reduction: ParameterIntervalModel
root_vary: ParameterIntervalModel
interbranch_distance: ParameterIntervalModel
mechanical_constraints: ParameterIntervalModel
root_tissue_density: ParameterIntervalModel
gravitropism: ParameterIntervalModel
[docs]
class RootCalibrationModel(BaseModel):
"""
The root system architecture calibration data model.
Args:
BaseModel (BaseModel):
The Pydantic Base model class.
"""
random_seed: int | None
parameter_intervals: RootCalibrationIntervals
calibration_parameters: Dict[str, bool | float | int | str]
summary_statistics: Optional[List[SummaryStatisticsModel]] = None
observed_data: Optional[List[RootNodeModel]] = None
observed_data_content: Optional[str] = ""
raw_edge_content: Optional[str] = ""
statistics_comparison: Optional[StatisticsComparisonModel] = None
origin_min: Optional[float] = 1e-3
origin_max: Optional[float] = 1e-2
enable_soil: Optional[bool] = False
soil_layer_height: Optional[float] = 0
soil_layer_width: Optional[float] = 0
soil_n_layers: Optional[int] = 0
soil_n_cols: Optional[int] = 0
max_val_attempts: Optional[int] = 50
simulation_tag: Optional[str] = "default"
no_root_zone: Optional[float] = 1e-4
floor_threshold: Optional[float] = 0.4
ceiling_threshold: Optional[float] = 0.9