scShapeBench / data /synthetic /sample_00038.json
Joao Felipe Rocha
Added synthetic dataset and corrected croissant files
8f91d7b
raw
history blame
11.8 kB
Invalid JSON: Unexpected token 'I', ..."istance": Infinity, "... is not valid JSON
{
"embedding_params": {
"feature_scale": 1.0,
"packing_ratio": 6.0,
"separation_ratio": 6.0,
"target_packing_distance": 6.0,
"hard_min_clearance_ratio": 0.2,
"hard_min_clearance": 0.2,
"target_min_separation": 0.2,
"preferred_min_separation": 0.95,
"preferred_min_separation_ratio": 0.95,
"noise_ratio": 0.025201966765471005,
"sampling_density_per_feature": 19.410804782938673,
"edge_length_jitter_ratio": 0.07599087817413673,
"branch_angle_spread": 1.1726603655535028
},
"embedding_dimension": 2,
"requested_embedding_dimension": 2,
"feature_thickness_ratio": 0.7304379358669497,
"feature_thickness_budget": 0.7304379358669497,
"tube_sampling_mode": "solid",
"num_components": 1,
"component_gap_ratio": 5.962504993384371,
"component_node_ids": [
[
0,
1
]
],
"component_x_intervals": [
[
0.0,
0.8520355086123008
]
],
"component_topology_classes": [
"single_edge"
],
"crowding_r": 0.034017082766491076,
"crowding_gamma": 0.9663230880611738,
"crowding_gamma_min": 0.01,
"crowding_admissibility_epsilon_sep": 1.4808758717338995,
"thickness_aware_min_required_clearance": 0.02,
"thickness_crowding_order": "choose_tube_radius_then_apply_thickness_aware_crowding",
"cycle_tree_edges": [],
"cycle_lengths": {},
"pair_separations": {},
"cycle_nodes": {},
"cycle_motifs": {},
"attachments": [],
"edge_cycle_membership": {},
"num_cycles_ground_truth": 0,
"betti_1": 0,
"leaf_count": 2,
"branch_nodes": [],
"is_planar": true,
"max_edge_cycle_multiplicity": 0,
"branch_params": {
"num_initial_attachment_sites": 1,
"max_branch_depth": 1,
"promotion_prob": 0.0,
"children_per_branch_point_range": [
1,
1
],
"branch_length_range": [
1,
1
],
"max_degree": 2,
"max_total_nodes": 80,
"max_total_edges": 88
},
"branch_attachment_nodes_initial": [
0
],
"branch_generation_nodes": {
"1": [
1
]
},
"branch_parent_map": {
"1": 0
},
"branch_root_map": {
"1": 0
},
"branch_depth_map": {
"1": 1
},
"num_leaves_after_branching": 2,
"num_branch_nodes_after_branching": 0,
"betti_1_after_branching": 0,
"embedding_valid": true,
"embedding_dimensions_attempted": [
2
],
"embedding_attempt_history": [
{
"dimension": 2,
"embedding_valid": true,
"global_embedding_attempts": 1,
"local_placement_rejections": 0,
"min_nonadjacent_node_distance": Infinity,
"min_nonincident_edge_distance": Infinity,
"min_nonincident_node_edge_distance": Infinity,
"failure_reason": null,
"refinement_applied": false,
"refinement_iterations": 1,
"refinement_objective_delta": 0.0,
"refinement_clearance_delta": NaN
}
],
"embedding_constructive_success": true,
"embedding_rejected": false,
"min_nonadjacent_node_distance": Infinity,
"min_nonincident_edge_distance": Infinity,
"min_nonincident_node_edge_distance": Infinity,
"global_embedding_attempts": 1,
"total_global_embedding_attempts": 1,
"local_placement_rejections": 0,
"embedding_fallback_used": false,
"embedding_fallback_mode": null,
"embedding_refinement": {
"enabled": true,
"applied": false,
"iterations": 1,
"objective_before": 0.0,
"objective_after": 0.0,
"objective_delta": 0.0,
"clearance_before": Infinity,
"clearance_after": Infinity,
"clearance_delta": NaN,
"accepted_steps": 0,
"reason": "no_admissible_improvement"
},
"topology_class": "single_edge",
"sampled_topology_spec": {
"topology_class": "single_edge",
"children_per_branch_point_range": [
1,
1
],
"branch_length_range": [
1,
1
],
"max_branch_depth_range": [
1,
1
],
"promotion_prob_range": [
0.0,
0.0
],
"max_degree": 2,
"num_cycles": 0,
"branch_attach_count": 1
},
"tube_embedding_separation_ratio": 6.0,
"realized_post_crowding_min_nonadjacent_node_distance": Infinity,
"realized_post_crowding_min_nonincident_edge_distance": Infinity,
"realized_post_crowding_min_nonincident_node_edge_distance": Infinity,
"realized_post_crowding_min_structural_distance": Infinity,
"realized_post_crowding_separation_to_feature_scale": Infinity,
"realized_post_crowding_separation_to_post_median_edge": Infinity,
"realized_post_crowding_absolute_hardness": Infinity,
"minimum_realized_component_gap": Infinity,
"feature_thickness_radius": 0.7304379358669497,
"effective_max_tube_radius_for_sampling": 1.0,
"cycle_hole_radius_cap": Infinity,
"cycle_hole_radius_fraction": 0.2,
"crowding_applied": true,
"crowding_isotropy_epsilon": 0.05,
"crowding_axis": [
-0.9096635787140881,
0.41534584813270764
],
"crowding_centroid": [
0.4260177543061504,
0.19451664288022913
],
"crowding_covariance_eigenvalues": [
0.2193278513414501,
6.938893903907228e-18
],
"crowding_covariance_matrix": [
[
0.18149112698405553,
-0.08286754337500665
],
[
-0.08286754337500665,
0.037836724357394595
]
],
"crowding_isotropic_fallback_used": false,
"crowding_linear_operator": [
[
0.9941903227226081,
-0.012723978937277568
],
[
-0.012723978937277568,
0.9721327653385657
]
],
"crowding_model_dimension": 2,
"feature_scale_nominal": 1.0,
"feature_scale_pre_crowding": 0.9366490299817752,
"feature_scale_post_crowding_median_edge": 0.9366490299817752,
"pre_crowding_edge_length_summary": {
"min": 0.9366490299817752,
"median": 0.9366490299817752,
"mean": 0.9366490299817752,
"max": 0.9366490299817752
},
"post_crowding_edge_length_summary": {
"min": 0.9366490299817752,
"median": 0.9366490299817752,
"mean": 0.9366490299817752,
"max": 0.9366490299817752
},
"pre_crowding_min_nonadjacent_node_distance": Infinity,
"pre_crowding_min_nonincident_edge_distance": Infinity,
"pre_crowding_min_nonincident_node_edge_distance": Infinity,
"crowding_gamma_min_search_tolerance": 0.005,
"crowding_gamma_min_search_history": [
{
"gamma": 0.01,
"admissible": true,
"realized_separation_ratio": Infinity
},
{
"gamma": 1.0,
"admissible": true,
"realized_separation_ratio": Infinity
}
],
"crowding_gamma_min_search_iterations": 2,
"crowding_gamma_min_search_bracket": [
0.01,
1.0
],
"crowding_relative_budget_definition": "gamma = 1 - r * (1 - gamma_min)",
"requested_noise_ratio": 0.025201966765471005,
"realized_noise_ratio": 0.025201966765471005,
"max_admissible_noise_ratio_after_crowding": 0.025201966765471005,
"requested_crowding_r": 0.034017082766491076,
"realized_crowding_r": 0.034017082766491076,
"staged_generation_order": "topology -> max-separation embedding -> admissible thickness -> thickness-constrained crowding -> clearance-capped noise -> sampling",
"tube_no_overlap_required_centerline_clearance": 1.5816837387957834,
"tube_no_overlap_post_crowding_margin": Infinity,
"tube_no_overlap_satisfied": true,
"tube_no_overlap_constraint_active": false,
"max_admissible_tube_radius_after_crowding": Infinity,
"realized_tube_radius_budget_fraction": 0.7304379358669497,
"point_cloud_params": {
"feature_scale": 1.0,
"sampling_density_per_feature": 19.410804782938673,
"noise_ratio": 0.025201966765471005,
"sigma": 0.025201966765471005,
"embedding_dimension": 2,
"include_node_points": true,
"include_junction_points": true,
"node_tube_sampling_policy": "edge_tubes_only_except_isolated_nodes",
"min_points_per_edge": 2,
"density_jitter_ratio_range": [
0.0,
0.15
],
"endpoint_sampling_mode": "include",
"feature_thickness_ratio": 0.7304379358669497,
"feature_thickness_radius": 0.7304379358669497,
"tube_sampling_mode": "solid"
},
"num_clean_points": 44,
"num_edge_sampled_points": 42,
"num_node_sampled_points": 2,
"point_component_id": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0
],
"component_point_ids": [
[
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
23,
24,
25,
26,
27,
28,
29,
30,
31,
32,
33,
34,
35,
36,
37,
38,
39,
40,
41,
42,
43
]
],
"nearest_feature_changed_rate": 0.045454545454545456,
"nonincident_feature_confusion_rate": 0.0,
"cross_component_confusion_rate": 0.0,
"noise_overlap_quality_pass": true,
"noise_overlap_quality_thresholds": {
"nonincident_feature_confusion_rate": 0.12,
"cross_component_confusion_rate": 0.03
},
"num_points_evaluated_for_noise_confusion": 44,
"num_nearest_feature_changes": 2,
"num_nonincident_feature_confusions": 0,
"num_cross_component_confusions": 0,
"sample_id": 38,
"difficulty": "full",
"difficulty_coordinate": {
"noise_ratio": 0.025201966765471005,
"crowding_r": 0.034017082766491076,
"sampling_density_per_feature": 19.410804782938673,
"feature_thickness_ratio": 0.7304379358669497,
"num_components": 1,
"requested_embedding_dimension": 2
},
"realized_geometry": {
"realized_separation_to_feature_scale": Infinity,
"realized_absolute_hardness": Infinity,
"crowding_gamma": 0.9663230880611738,
"crowding_gamma_min": 0.01,
"feature_thickness_radius": 0.7304379358669497,
"feature_thickness_budget": 0.7304379358669497,
"effective_max_tube_radius_for_sampling": 1.0,
"max_admissible_tube_radius_before_crowding": 1.0,
"cycle_hole_radius_cap": Infinity,
"cycle_hole_radius_fraction": 0.2,
"requested_noise_ratio": 0.025201966765471005,
"realized_noise_ratio": 0.025201966765471005,
"max_admissible_noise_ratio_after_crowding": 0.025201966765471005,
"requested_crowding_r": 0.034017082766491076,
"realized_crowding_r": 0.034017082766491076,
"thickness_aware_min_required_clearance": 1.4808758717338995,
"thickness_clearance_noise_margin": 0.10080786706188402,
"minimum_realized_component_gap": Infinity
},
"graph_summary": {
"num_nodes": 2,
"num_edges": 1,
"num_components": 1,
"num_clean_points": 44,
"topology_classes": [
"single_edge"
]
},
"seed_bundle": {
"point_cloud_seed": 802215583,
"component_seed_bundles": [
{
"topology_seed": 789975782,
"branch_seed": 779601137,
"embedding_seed": 802659483,
"topology_class": "single_edge"
}
]
},
"scheduled_normalized_axes": {
"noise_ratio": 0.028899815363727797,
"crowding_r": 0.05669513794415179,
"sampling_density_per_feature": 0.25996256823541064,
"feature_thickness_ratio": 0.5098871561217267
},
"scheduled_vector_magnitude": 0.28793010734204955,
"scheduled_sample_rank": 38,
"actual_normalized_axes": {
"noise_ratio": 0.028899815363727797,
"crowding_r": 0.05669513794415179,
"sampling_density_per_feature": 0.25996256823541064,
"feature_thickness_ratio": 0.5098871561217267
},
"actual_difficulty_coordinate": [
0.025201966765471005,
0.034017082766491076,
19.410804782938673,
0.7304379358669497
],
"difficulty_relaxation_factor": 1.0
}