from pydantic import BaseModel, Field, field_validator
from pathlib import Path
from enum import Enum
from .CellSegmenterConfig import ModelType
class GraphCreatorType(str, Enum):
knn = "knn"
radius = "radius"
delaunay_radius = "delaunay_radius"
dilate = "dilate"
similarity = "similarity"
@classmethod
def values(cls):
return [member.value for member in cls]
def __str__(self):
return self.value
class GraphCreatorCategory(str, Enum):
"""Type for feature extraction methods."""
Positional = ["knn", "radius", "delaunay_radius", "dilate"]
FeatureDependent = ["similarity"]
def __contains__(self, item: str) -> bool:
"""Check if the item is in the feature extraction type."""
return item in self.value
[docs]class GraphCreatorConfig(BaseModel):
"""Configuration for graph creation from segmented cells"""
method: GraphCreatorType = Field(..., description="Name of the graph creator to use")
gpu: int = Field(0, description="GPU device ID to use for processing")
patched_slide_path: Path = Field(..., description="Path to the patched slide image")
segmentation_model: ModelType = Field(..., description="Name of the segmentation model used to extract cells")
plot: bool = Field(True, description="Whether to plot the graph")
debug: bool = Field(default=False, description="Enable debug mode with interactive parameter tuning")
[docs] @field_validator('method')
def validate_model(cls, v: str) -> str:
if v not in GraphCreatorType.values():
raise ValueError(f"Unsupported graph creator type: {v}. Supported graph creators are: {GraphCreatorType.values()}")
return v
[docs] @field_validator('segmentation_model')
def validate_segmentation_model(cls, v: str) -> str:
if v not in ModelType.values():
raise ValueError(f"Unsupported segmentation model: {v}. Supported segmentation models are: {ModelType.values()}")
return v
[docs] class Config:
arbitrary_types_allowed = True
