scShapeBench / data /synthetic /sample_00026.json
Joao Felipe Rocha
Added synthetic dataset and corrected croissant files
8f91d7b
raw
history blame
18.6 kB
Invalid JSON: Unexpected token 'I', ..."ent_gap": 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": 0.025884376069883957,
"sampling_density_per_feature": 18.726358083183236,
"edge_length_jitter_ratio": 0.012142193150412872,
"branch_angle_spread": 1.1031866836736008
},
"embedding_dimension": 2,
"requested_embedding_dimension": 2,
"feature_thickness_ratio": 0.6032840345899628,
"feature_thickness_budget": 0.6032840345899628,
"tube_sampling_mode": "solid",
"num_components": 1,
"component_gap_ratio": 6.99447053488391,
"component_node_ids": [
[
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13
]
],
"component_x_intervals": [
[
0.0,
5.8757554490797155
]
],
"component_topology_classes": [
"single_cycle"
],
"crowding_r": 0.18463414553269253,
"crowding_gamma": 0.8379186268532735,
"crowding_gamma_min": 0.12214843750000001,
"crowding_admissibility_epsilon_sep": 0.3077085144674609,
"thickness_aware_min_required_clearance": 0.02,
"thickness_crowding_order": "choose_tube_radius_then_apply_thickness_aware_crowding",
"cycle_tree_edges": [],
"cycle_lengths": {
"0": 8
},
"pair_separations": {},
"cycle_nodes": {
"0": [
0,
1,
2,
3,
4,
5,
6,
7
]
},
"cycle_motifs": {
"0": {
"cycle_id": 0,
"original_cycle_length": 8,
"original_motif_vertices": [
0,
1,
2,
3,
4,
5,
6,
7
],
"final_nodes": [
0,
1,
2,
3,
4,
5,
6,
7
]
}
},
"attachments": [],
"edge_cycle_membership": {
"(0, 1)": [
0
],
"(1, 2)": [
0
],
"(2, 3)": [
0
],
"(3, 4)": [
0
],
"(4, 5)": [
0
],
"(5, 6)": [
0
],
"(6, 7)": [
0
],
"(0, 7)": [
0
]
},
"num_cycles_ground_truth": 1,
"betti_1": 1,
"leaf_count": 2,
"branch_nodes": [
6
],
"is_planar": true,
"max_edge_cycle_multiplicity": 1,
"branch_params": {
"num_initial_attachment_sites": 1,
"max_branch_depth": 1,
"promotion_prob": 0.4038628117951317,
"children_per_branch_point_range": [
1,
3
],
"branch_length_range": [
1,
4
],
"max_degree": 4,
"max_total_nodes": 80,
"max_total_edges": 88
},
"branch_attachment_nodes_initial": [
6
],
"branch_generation_nodes": {
"1": [
8,
9,
10,
11,
12,
13
]
},
"branch_parent_map": {
"8": 6,
"9": 8,
"10": 9,
"11": 6,
"12": 11,
"13": 12
},
"branch_root_map": {
"8": 6,
"9": 6,
"10": 6,
"11": 6,
"12": 6,
"13": 6
},
"branch_depth_map": {
"8": 1,
"9": 1,
"10": 1,
"11": 1,
"12": 1,
"13": 1
},
"num_leaves_after_branching": 2,
"num_branch_nodes_after_branching": 1,
"betti_1_after_branching": 1,
"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": 1.4137708856429736,
"min_nonincident_edge_distance": 1.4137708856429738,
"min_nonincident_node_edge_distance": 1.4137708856429736,
"failure_reason": null,
"refinement_applied": true,
"refinement_iterations": 24,
"refinement_objective_delta": -1.480403312228567,
"refinement_clearance_delta": 0.0928778230155003
}
],
"embedding_constructive_success": true,
"embedding_rejected": false,
"min_nonadjacent_node_distance": 1.4137708856429736,
"min_nonincident_edge_distance": 1.4137708856429738,
"min_nonincident_node_edge_distance": 1.4137708856429736,
"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": true,
"iterations": 24,
"objective_before": 4.873257194151378,
"objective_after": 3.3928538819228113,
"objective_delta": -1.480403312228567,
"clearance_before": 1.3208930626274733,
"clearance_after": 1.4137708856429736,
"clearance_delta": 0.0928778230155003,
"accepted_steps": 24,
"reason": "accepted"
},
"topology_class": "single_cycle",
"sampled_topology_spec": {
"topology_class": "single_cycle",
"children_per_branch_point_range": [
1,
3
],
"branch_length_range": [
1,
4
],
"max_branch_depth_range": [
1,
1
],
"promotion_prob_range": [
0.2,
0.6
],
"max_degree": 4,
"num_cycles": 1,
"branch_attach_count": 1
},
"tube_embedding_separation_ratio": 6.0,
"realized_post_crowding_min_nonadjacent_node_distance": 1.2222868409545546,
"realized_post_crowding_min_nonincident_edge_distance": 1.2222868409545546,
"realized_post_crowding_min_nonincident_node_edge_distance": 1.2222868409545546,
"realized_post_crowding_min_structural_distance": 1.2222868409545546,
"realized_post_crowding_separation_to_feature_scale": 1.2222868409545546,
"realized_post_crowding_separation_to_post_median_edge": 1.2378009061101842,
"realized_post_crowding_absolute_hardness": 0.8181385633007732,
"minimum_realized_component_gap": Infinity,
"feature_thickness_radius": 0.14385425723373044,
"effective_max_tube_radius_for_sampling": 0.23845195461123814,
"cycle_hole_radius_cap": 0.23845195461123814,
"cycle_hole_radius_fraction": 0.2,
"crowding_applied": true,
"crowding_isotropy_epsilon": 0.05,
"crowding_axis": [
-0.9803812805836533,
0.19711048851128182
],
"crowding_centroid": [
3.1493422087036484,
-0.5714586125711435
],
"crowding_covariance_eigenvalues": [
2.483825814176263,
1.0046186133710795
],
"crowding_covariance_matrix": [
[
2.4263548503142913,
-0.2858470778136772
],
[
-0.2858470778136772,
1.0620895772330508
]
],
"crowding_isotropic_fallback_used": false,
"crowding_linear_operator": [
[
0.9937027262078336,
-0.03132116099543101
],
[
-0.03132116099543101,
0.8442159006454398
]
],
"crowding_model_dimension": 2,
"feature_scale_nominal": 1.0,
"feature_scale_pre_crowding": 1.0126271536150333,
"feature_scale_post_crowding_median_edge": 0.9874664293110087,
"pre_crowding_edge_length_summary": {
"min": 0.9763857543476389,
"median": 1.0126271536150333,
"mean": 1.013275890261111,
"max": 1.0580176495489422
},
"post_crowding_edge_length_summary": {
"min": 0.8403379913041957,
"median": 0.9874664293110087,
"mean": 0.9637379329219123,
"max": 1.0529305583362452
},
"pre_crowding_min_nonadjacent_node_distance": 1.4137708856429736,
"pre_crowding_min_nonincident_edge_distance": 1.4137708856429738,
"pre_crowding_min_nonincident_node_edge_distance": 1.4137708856429736,
"crowding_gamma_min_search_tolerance": 0.005,
"crowding_gamma_min_search_history": [
{
"gamma": 0.01,
"admissible": false,
"realized_separation_ratio": 0.024998469847157735
},
{
"gamma": 1.0,
"admissible": true,
"realized_separation_ratio": 1.3961415913012754
},
{
"gamma": 0.505,
"admissible": true,
"realized_separation_ratio": 0.8474523827124816
},
{
"gamma": 0.2575,
"admissible": true,
"realized_separation_ratio": 0.6374376601094628
},
{
"gamma": 0.13375,
"admissible": true,
"realized_separation_ratio": 0.3340313104903998
},
{
"gamma": 0.07187500000000001,
"admissible": false,
"realized_separation_ratio": 0.1796269853712272
},
{
"gamma": 0.1028125,
"admissible": false,
"realized_separation_ratio": 0.2568691909098471
},
{
"gamma": 0.11828125,
"admissible": false,
"realized_separation_ratio": 0.2954617580419129
},
{
"gamma": 0.12601562500000002,
"admissible": true,
"realized_separation_ratio": 0.3147495977185483
},
{
"gamma": 0.12214843750000001,
"admissible": true,
"realized_separation_ratio": 0.3051064204384709
}
],
"crowding_gamma_min_search_iterations": 10,
"crowding_gamma_min_search_bracket": [
0.11828125,
0.12214843750000001
],
"crowding_relative_budget_definition": "gamma = 1 - r * (1 - gamma_min)",
"requested_noise_ratio": 0.025884376069883957,
"realized_noise_ratio": 0.025884376069883957,
"max_admissible_noise_ratio_after_crowding": 0.15242972108118227,
"requested_crowding_r": 0.18463414553269253,
"realized_crowding_r": 0.18463414553269253,
"staged_generation_order": "topology -> max-separation embedding -> admissible thickness -> thickness-constrained crowding -> clearance-capped noise -> sampling",
"tube_no_overlap_required_centerline_clearance": 0.41124601874699673,
"tube_no_overlap_post_crowding_margin": 0.8110408222075579,
"tube_no_overlap_satisfied": true,
"tube_no_overlap_constraint_active": true,
"max_admissible_tube_radius_after_crowding": 0.5493746683375094,
"realized_tube_radius_budget_fraction": 0.26185091072556205,
"point_cloud_params": {
"feature_scale": 1.0,
"sampling_density_per_feature": 18.726358083183236,
"noise_ratio": 0.025884376069883957,
"sigma": 0.025884376069883957,
"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": 0.14385425723373044,
"feature_thickness_radius": 0.14385425723373044,
"tube_sampling_mode": "solid"
},
"num_clean_points": 285,
"num_edge_sampled_points": 271,
"num_node_sampled_points": 14,
"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,
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,
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,
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,
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,
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,
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,
44,
45,
46,
47,
48,
49,
50,
51,
52,
53,
54,
55,
56,
57,
58,
59,
60,
61,
62,
63,
64,
65,
66,
67,
68,
69,
70,
71,
72,
73,
74,
75,
76,
77,
78,
79,
80,
81,
82,
83,
84,
85,
86,
87,
88,
89,
90,
91,
92,
93,
94,
95,
96,
97,
98,
99,
100,
101,
102,
103,
104,
105,
106,
107,
108,
109,
110,
111,
112,
113,
114,
115,
116,
117,
118,
119,
120,
121,
122,
123,
124,
125,
126,
127,
128,
129,
130,
131,
132,
133,
134,
135,
136,
137,
138,
139,
140,
141,
142,
143,
144,
145,
146,
147,
148,
149,
150,
151,
152,
153,
154,
155,
156,
157,
158,
159,
160,
161,
162,
163,
164,
165,
166,
167,
168,
169,
170,
171,
172,
173,
174,
175,
176,
177,
178,
179,
180,
181,
182,
183,
184,
185,
186,
187,
188,
189,
190,
191,
192,
193,
194,
195,
196,
197,
198,
199,
200,
201,
202,
203,
204,
205,
206,
207,
208,
209,
210,
211,
212,
213,
214,
215,
216,
217,
218,
219,
220,
221,
222,
223,
224,
225,
226,
227,
228,
229,
230,
231,
232,
233,
234,
235,
236,
237,
238,
239,
240,
241,
242,
243,
244,
245,
246,
247,
248,
249,
250,
251,
252,
253,
254,
255,
256,
257,
258,
259,
260,
261,
262,
263,
264,
265,
266,
267,
268,
269,
270,
271,
272,
273,
274,
275,
276,
277,
278,
279,
280,
281,
282,
283,
284
]
],
"nearest_feature_changed_rate": 0.11929824561403508,
"nonincident_feature_confusion_rate": 0.07719298245614035,
"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": 285,
"num_nearest_feature_changes": 34,
"num_nonincident_feature_confusions": 22,
"num_cross_component_confusions": 0,
"sample_id": 26,
"difficulty": "full",
"difficulty_coordinate": {
"noise_ratio": 0.025884376069883957,
"crowding_r": 0.18463414553269253,
"sampling_density_per_feature": 18.726358083183236,
"feature_thickness_ratio": 0.6032840345899628,
"num_components": 1,
"requested_embedding_dimension": 2
},
"realized_geometry": {
"realized_separation_to_feature_scale": 1.2222868409545546,
"realized_absolute_hardness": 0.8181385633007732,
"crowding_gamma": 0.8379186268532735,
"crowding_gamma_min": 0.12214843750000001,
"feature_thickness_radius": 0.14385425723373044,
"feature_thickness_budget": 0.6032840345899628,
"effective_max_tube_radius_for_sampling": 0.23845195461123814,
"max_admissible_tube_radius_before_crowding": 0.23845195461123814,
"cycle_hole_radius_cap": 0.23845195461123814,
"cycle_hole_radius_fraction": 0.2,
"requested_noise_ratio": 0.025884376069883957,
"realized_noise_ratio": 0.025884376069883957,
"max_admissible_noise_ratio_after_crowding": 0.15242972108118227,
"requested_crowding_r": 0.18463414553269253,
"realized_crowding_r": 0.18463414553269253,
"thickness_aware_min_required_clearance": 0.3077085144674609,
"thickness_clearance_noise_margin": 0.10353750427953583,
"minimum_realized_component_gap": Infinity
},
"graph_summary": {
"num_nodes": 14,
"num_edges": 14,
"num_components": 1,
"num_clean_points": 285,
"topology_classes": [
"single_cycle"
]
},
"seed_bundle": {
"point_cloud_seed": 760555280,
"component_seed_bundles": [
{
"topology_seed": 354693440,
"branch_seed": 409922384,
"embedding_seed": 831814640,
"topology_class": "single_cycle"
}
]
},
"scheduled_normalized_axes": {
"noise_ratio": 0.03269097816602197,
"crowding_r": 0.3077235758878209,
"sampling_density_per_feature": 0.29179729845659363,
"feature_thickness_ratio": 0.27869824470902327
},
"scheduled_vector_magnitude": 0.2542542399848505,
"scheduled_sample_rank": 26,
"actual_normalized_axes": {
"noise_ratio": 0.03269097816602197,
"crowding_r": 0.3077235758878209,
"sampling_density_per_feature": 0.29179729845659363,
"feature_thickness_ratio": 0.27869824470902327
},
"actual_difficulty_coordinate": [
0.025884376069883957,
0.18463414553269253,
18.726358083183236,
0.6032840345899628
],
"difficulty_relaxation_factor": 1.0
}