revise.config.runner_conf.BenchmarkSegConf

class revise.config.runner_conf.BenchmarkSegConf(sample_name: 'str', raw_data_path: 'str', result_root_path: 'str', cell_type_col: 'str', confidence_col: 'str', unknown_key: 'str', st_file: 'str', gt_svc_file: 'str', sc_ref_file: 'str', seg_method: 'str', annotate_mode: 'str', case_subdir: 'Optional[str]' = None, annotate_pot_reg: 'float' = 0.1, annotate_pot_reg_m: 'float' = 0.0, annotate_pot_reg_type: 'str' = 'entropy', dropout_total_counts: 'int' = 60, swapping_total_counts: 'int' = 300, lower_ts: 'float' = 0.2, upper_ts: 'float' = 0.8, rec_graph_n_neighbors: 'int' = 50, rec_graph_exp_neighbor_num: 'int' = 30, rec_graph_spatial_neighbor_num: 'int' = 30, rec_graph_method: 'str' = 'joint', rec_graph_alpha: 'float' = 0.8, rec_pot_reg: 'float' = 1.0, rec_pot_reg_m: 'float' = 0.0, rec_pot_reg_type: 'str' = 'kl', rec_alpha: 'float' = 1.0)[source]

Bases: BaseConf

__init__(sample_name: str, raw_data_path: str, result_root_path: str, cell_type_col: str, confidence_col: str, unknown_key: str, st_file: str, gt_svc_file: str, sc_ref_file: str, seg_method: str, annotate_mode: str, case_subdir: str | None = None, annotate_pot_reg: float = 0.1, annotate_pot_reg_m: float = 0.0, annotate_pot_reg_type: str = 'entropy', dropout_total_counts: int = 60, swapping_total_counts: int = 300, lower_ts: float = 0.2, upper_ts: float = 0.8, rec_graph_n_neighbors: int = 50, rec_graph_exp_neighbor_num: int = 30, rec_graph_spatial_neighbor_num: int = 30, rec_graph_method: str = 'joint', rec_graph_alpha: float = 0.8, rec_pot_reg: float = 1.0, rec_pot_reg_m: float = 0.0, rec_pot_reg_type: str = 'kl', rec_alpha: float = 1.0) → None

Methods

__init__(sample_name, raw_data_path, ...[, ...])

Attributes

`annotate_pot_reg`
`annotate_pot_reg_m`
`annotate_pot_reg_type`
`case_subdir`
`dropout_total_counts`
`gt_svc_file_path`
`lower_ts`
`rec_alpha`
`rec_graph_alpha`
`rec_graph_exp_neighbor_num`
`rec_graph_method`
`rec_graph_n_neighbors`
`rec_graph_spatial_neighbor_num`
`rec_pot_reg`
`rec_pot_reg_m`
`rec_pot_reg_type`
`result_dir`
`sc_ref_file_path`
`st_file_path`
`swapping_total_counts`
`upper_ts`
`st_file`
`gt_svc_file`
`sc_ref_file`
`seg_method`
`annotate_mode`
`sample_name`
`raw_data_path`
`result_root_path`
`cell_type_col`
`confidence_col`
`unknown_key`

st_file: str

gt_svc_file: str

sc_ref_file: str

seg_method: str

annotate_mode: str

case_subdir: str | None = None

annotate_pot_reg: float = 0.1

annotate_pot_reg_m: float = 0.0

annotate_pot_reg_type: str = 'entropy'

dropout_total_counts: int = 60

swapping_total_counts: int = 300

lower_ts: float = 0.2

upper_ts: float = 0.8

rec_graph_n_neighbors: int = 50

rec_graph_exp_neighbor_num: int = 30

rec_graph_spatial_neighbor_num: int = 30

rec_graph_method: str = 'joint'

rec_graph_alpha: float = 0.8

rec_pot_reg: float = 1.0

rec_pot_reg_m: float = 0.0

rec_pot_reg_type: str = 'kl'

rec_alpha: float = 1.0

property result_dir

property st_file_path

property gt_svc_file_path

property sc_ref_file_path