scShapeBench / data /synthetic /sample_00031.json
Joao Felipe Rocha
Added synthetic dataset and corrected croissant files
8f91d7b
raw
history blame
24.7 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": 0.05563980845512021,
"sampling_density_per_feature": 23.615571403714146,
"edge_length_jitter_ratio": 0.003933106229303314,
"branch_angle_spread": 1.0751924960790853
},
"embedding_dimension": 5,
"requested_embedding_dimension": 5,
"feature_thickness_ratio": 0.7150133661003452,
"feature_thickness_budget": 0.7150133661003452,
"tube_sampling_mode": "solid",
"num_components": 1,
"component_gap_ratio": 5.836052854133409,
"component_node_ids": [
[
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12
]
],
"component_x_intervals": [
[
0.0,
2.8147496835310197
]
],
"component_topology_classes": [
"single_cycle"
],
"crowding_r": 0.0538842669291317,
"crowding_gamma": 0.9514473287010047,
"crowding_gamma_min": 0.0989453125,
"crowding_admissibility_epsilon_sep": 0.2686725640244242,
"thickness_aware_min_required_clearance": 0.02,
"thickness_crowding_order": "choose_tube_radius_then_apply_thickness_aware_crowding",
"cycle_tree_edges": [],
"cycle_lengths": {
"0": 6
},
"pair_separations": {},
"cycle_nodes": {
"0": [
0,
1,
2,
3,
4,
5
]
},
"cycle_motifs": {
"0": {
"cycle_id": 0,
"original_cycle_length": 6,
"original_motif_vertices": [
0,
1,
2,
3,
4,
5
],
"final_nodes": [
0,
1,
2,
3,
4,
5
]
}
},
"attachments": [],
"edge_cycle_membership": {
"(0, 1)": [
0
],
"(1, 2)": [
0
],
"(2, 3)": [
0
],
"(3, 4)": [
0
],
"(4, 5)": [
0
],
"(0, 5)": [
0
]
},
"num_cycles_ground_truth": 1,
"betti_1": 1,
"leaf_count": 2,
"branch_nodes": [
1
],
"is_planar": true,
"max_edge_cycle_multiplicity": 1,
"branch_params": {
"num_initial_attachment_sites": 1,
"max_branch_depth": 1,
"promotion_prob": 0.3141786463677987,
"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": [
1
],
"branch_generation_nodes": {
"1": [
6,
7,
8,
9,
10,
11,
12
]
},
"branch_parent_map": {
"6": 1,
"7": 6,
"8": 7,
"9": 1,
"10": 9,
"11": 10,
"12": 11
},
"branch_root_map": {
"6": 1,
"7": 1,
"8": 1,
"9": 1,
"10": 1,
"11": 1,
"12": 1
},
"branch_depth_map": {
"6": 1,
"7": 1,
"8": 1,
"9": 1,
"10": 1,
"11": 1,
"12": 1
},
"num_leaves_after_branching": 2,
"num_branch_nodes_after_branching": 1,
"betti_1_after_branching": 1,
"node_positions_5d": {
"0": [
2.1907861792951615,
0.371778105876272,
0.7482497953551905,
0.10364936355055687,
0.44068544606527577
],
"1": [
1.3506842063358397,
0.036537374436246994,
0.708518408194841,
0.3603940327747815,
0.16205121275974987
],
"2": [
1.0912728228893809,
-0.33107052292305394,
-0.023518272770315707,
0.2551211291900255,
-0.2657534134426992
],
"3": [
1.6583680505995193,
-0.3666145957107879,
-0.7017339009667379,
-0.0949106393331497,
-0.41043934569328316
],
"4": [
2.4912971530106454,
-0.030625197345382868,
-0.6532675694807119,
-0.35198269342105715,
-0.12410931944994967
],
"5": [
2.7562857528612223,
0.3385763546755719,
0.07173190969852294,
-0.25442208445294556,
0.3028168068420449
],
"6": [
1.2312213268792047,
0.2886436388635013,
1.138732034518973,
-0.15512045202660396,
0.8439804271131457
],
"7": [
0.9957419089273764,
0.46826082124430596,
1.4281376768175043,
-0.6432208533139722,
1.5930450286883084
],
"8": [
0.7697968606440213,
0.6208166061718208,
1.6447901959821052,
-1.2207527577543185,
2.3129048857086683
],
"9": [
1.0373964147410022,
-0.23942860839923694,
0.8226500936872186,
1.1595534990778733,
-0.29489689972536687
],
"10": [
0.7280709510804826,
-0.5261236856226084,
0.9038723484008977,
1.9443166104699792,
-0.7610368788489745
],
"11": [
0.4222507285458791,
-0.8089969917585433,
0.9938969828415656,
2.724653901730995,
-1.2225818150007293
],
"12": [
0.015624263495262802,
-1.1472991494243,
1.0355936998186612,
3.4353614362142726,
-1.6762205907672778
]
},
"embedding_valid": true,
"embedding_dimensions_attempted": [
5
],
"embedding_attempt_history": [
{
"dimension": 5,
"embedding_valid": true,
"global_embedding_attempts": 1,
"local_placement_rejections": 0,
"min_nonadjacent_node_distance": 2.5476796437282703,
"min_nonincident_edge_distance": 2.7292717953002126,
"min_nonincident_node_edge_distance": 2.5476796437282703,
"failure_reason": null,
"refinement_applied": true,
"refinement_iterations": 24,
"refinement_objective_delta": -0.042416477029489474,
"refinement_clearance_delta": 0.055397220406408376
}
],
"embedding_constructive_success": true,
"embedding_rejected": false,
"min_nonadjacent_node_distance": 2.5476796437282703,
"min_nonincident_edge_distance": 2.7292717953002126,
"min_nonincident_node_edge_distance": 2.5476796437282703,
"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": 0.996233405158844,
"objective_after": 0.9538169281293545,
"objective_delta": -0.042416477029489474,
"clearance_before": 2.492282423321862,
"clearance_after": 2.5476796437282703,
"clearance_delta": 0.055397220406408376,
"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": 2.424239830874306,
"realized_post_crowding_min_nonincident_edge_distance": 2.602311018973834,
"realized_post_crowding_min_nonincident_node_edge_distance": 2.424239830874306,
"realized_post_crowding_min_structural_distance": 2.424239830874306,
"realized_post_crowding_separation_to_feature_scale": 2.424239830874306,
"realized_post_crowding_separation_to_post_median_edge": 2.4604177057760475,
"realized_post_crowding_absolute_hardness": 0.41250044127826596,
"minimum_realized_component_gap": Infinity,
"feature_thickness_radius": 0.1243362820122121,
"effective_max_tube_radius_for_sampling": 0.17389364717800634,
"cycle_hole_radius_cap": 0.17389364717800634,
"cycle_hole_radius_fraction": 0.2,
"crowding_applied": true,
"crowding_isotropy_epsilon": 0.05,
"crowding_axis": [
-0.2591002847400637,
-0.27859299039759383,
0.01542273595125495,
0.7474710172408687,
-0.5443364821042433
],
"crowding_centroid": [
1.2875997399465382,
-0.1019650653781688,
0.6244348770844396,
0.5586646532851106,
0.06926504186530098
],
"crowding_covariance_eigenvalues": [
3.0438521335898363,
1.0787611792510965,
0.1654838551247081,
0.0047691596026201285,
7.952268180476566e-05
],
"crowding_covariance_matrix": [
[
0.6329622843907673,
0.21211408925823788,
-0.37581042711043394,
-0.6217633540585654,
0.174565988814237
],
[
0.21211408925823788,
0.260521688226506,
0.06892031550750374,
-0.6034952507450525,
0.49679797488894667
],
[
-0.37581042711043394,
0.06892031550750374,
0.5534007195736012,
0.1615172274389285,
0.2948392196563821
],
[
-0.6217633540585654,
-0.6034952507450525,
0.1615172274389285,
1.7444914128308655,
-1.1748520529299673
],
[
0.174565988814237,
0.49679797488894667,
0.2948392196563821,
-1.1748520529299673,
1.1015697452283277
]
],
"crowding_isotropic_fallback_used": false,
"crowding_linear_operator": [
[
0.9547068131223749,
0.003504702872151985,
-0.00019401818727622853,
-0.009403193588021675,
0.006847758909961168
],
[
0.003504702872151985,
0.9552156983675506,
-0.0002086146182318225,
-0.010110617298636144,
0.007362931438542194
],
[
-0.00019401818727622853,
-0.0002086146182318225,
0.9514588774774759,
0.0005597175315808041,
-0.00040760733872653384
],
[
-0.009403193588021675,
-0.010110617298636144,
0.0005597175315808041,
0.9785743335346839,
-0.01975490425795523
],
[
0.006847758909961168,
0.007362931438542194,
-0.00040760733872653384,
-0.01975490425795523,
0.9658335923019334
]
],
"crowding_model_dimension": 5,
"feature_scale_nominal": 1.0,
"feature_scale_pre_crowding": 1.0060404401726002,
"feature_scale_post_crowding_median_edge": 0.9852960435064294,
"pre_crowding_edge_length_summary": {
"min": 0.9980492877333329,
"median": 1.0060404401726002,
"mean": 1.0073938529083797,
"max": 1.0184267615154352
},
"post_crowding_edge_length_summary": {
"min": 0.9612164057112892,
"median": 0.9852960435064294,
"mean": 0.9849072481390727,
"max": 1.0172462512900253
},
"pre_crowding_min_nonadjacent_node_distance": 2.5476796437282703,
"pre_crowding_min_nonincident_edge_distance": 2.7292717953002126,
"pre_crowding_min_nonincident_node_edge_distance": 2.5476796437282703,
"node_positions_5d_pre_crowding": {
"0": [
2.224891999196947,
0.3830677041725178,
0.7552814543655568,
0.1150023200635957,
0.43446213137804285
],
"1": [
1.3505669597036192,
0.04001772180231255,
0.7130078191068401,
0.359901498231838,
0.15977663061797795
],
"2": [
1.0820498291131835,
-0.3419063591094142,
-0.056630895376601494,
0.23733590222469794,
-0.2811779915898431
],
"3": [
1.6737159317088062,
-0.38396106775940175,
-0.7691960784821935,
-0.11795645996839212,
-0.4424242847171936
],
"4": [
2.540467039376401,
-0.04016187625443907,
-0.7177396668317079,
-0.36309868022662567,
-0.15972386008516307
],
"5": [
2.8147496835310197,
0.3433336283844858,
0.044508467912673114,
-0.2483610977070604,
0.280105097036374
],
"6": [
1.214573357334225,
0.29376954870214783,
1.1657964935984435,
-0.15181769061458247,
0.854583386361943
],
"7": [
0.957066356865684,
0.4717885154958457,
1.4705664974976886,
-0.635945596945962,
1.620841195093667
],
"8": [
0.7089587885152762,
0.6206968978806725,
1.698907755442443,
-1.2122758368505315,
2.3550982825842963
],
"9": [
1.034591937464836,
-0.23573036195801697,
0.8321720134405267,
1.1614736932242276,
-0.29254820752205823
],
"10": [
0.7227245540879697,
-0.5228162171222067,
0.9167507840889366,
1.9480789970573393,
-0.7546534906324106
],
"11": [
0.4144401824070305,
-0.8059939842130583,
1.0105871408850737,
2.730324298977156,
-1.2121416487408145
],
"12": [
0.0,
-1.1476499999376397,
1.0536416164500355,
3.4399791452407373,
-1.6617516955359053
]
},
"crowding_gamma_min_search_tolerance": 0.005,
"crowding_gamma_min_search_history": [
{
"gamma": 0.01,
"admissible": false,
"realized_separation_ratio": 0.11672636207842269
},
{
"gamma": 1.0,
"admissible": true,
"realized_separation_ratio": 2.5323829361085926
},
{
"gamma": 0.505,
"admissible": true,
"realized_separation_ratio": 1.2826299189589605
},
{
"gamma": 0.2575,
"admissible": true,
"realized_separation_ratio": 0.6613195946146455
},
{
"gamma": 0.13375,
"admissible": true,
"realized_separation_ratio": 0.3570359329134802
},
{
"gamma": 0.07187500000000001,
"admissible": false,
"realized_separation_ratio": 0.21458665759411294
},
{
"gamma": 0.1028125,
"admissible": true,
"realized_separation_ratio": 0.2839638027712803
},
{
"gamma": 0.08734375,
"admissible": false,
"realized_separation_ratio": 0.24861624322608128
},
{
"gamma": 0.095078125,
"admissible": false,
"realized_separation_ratio": 0.26615763858347813
},
{
"gamma": 0.0989453125,
"admissible": true,
"realized_separation_ratio": 0.27503082075358604
}
],
"crowding_gamma_min_search_iterations": 10,
"crowding_gamma_min_search_bracket": [
0.095078125,
0.0989453125
],
"crowding_relative_budget_definition": "gamma = 1 - r * (1 - gamma_min)",
"requested_noise_ratio": 0.05563980845512021,
"realized_noise_ratio": 0.05563980845512021,
"max_admissible_noise_ratio_after_crowding": 0.35926121114164694,
"requested_crowding_r": 0.0538842669291317,
"realized_crowding_r": 0.0538842669291317,
"staged_generation_order": "topology -> max-separation embedding -> admissible thickness -> thickness-constrained crowding -> clearance-capped noise -> sampling",
"tube_no_overlap_required_centerline_clearance": 0.49123179784490506,
"tube_no_overlap_post_crowding_margin": 1.9330080330294008,
"tube_no_overlap_satisfied": true,
"tube_no_overlap_constraint_active": true,
"max_admissible_tube_radius_after_crowding": 1.0908402985269126,
"realized_tube_radius_budget_fraction": 0.11398211285384095,
"point_cloud_params": {
"feature_scale": 1.0,
"sampling_density_per_feature": 23.615571403714146,
"noise_ratio": 0.05563980845512021,
"sigma": 0.05563980845512021,
"embedding_dimension": 5,
"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": 0.1243362820122121,
"feature_thickness_radius": 0.1243362820122121,
"tube_sampling_mode": "solid"
},
"num_clean_points": 334,
"num_edge_sampled_points": 321,
"num_node_sampled_points": 13,
"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,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
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,
285,
286,
287,
288,
289,
290,
291,
292,
293,
294,
295,
296,
297,
298,
299,
300,
301,
302,
303,
304,
305,
306,
307,
308,
309,
310,
311,
312,
313,
314,
315,
316,
317,
318,
319,
320,
321,
322,
323,
324,
325,
326,
327,
328,
329,
330,
331,
332,
333
]
],
"nearest_feature_changed_rate": 0.10778443113772455,
"nonincident_feature_confusion_rate": 0.0718562874251497,
"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": 334,
"num_nearest_feature_changes": 36,
"num_nonincident_feature_confusions": 24,
"num_cross_component_confusions": 0,
"sample_id": 31,
"difficulty": "full",
"difficulty_coordinate": {
"noise_ratio": 0.05563980845512021,
"crowding_r": 0.0538842669291317,
"sampling_density_per_feature": 23.615571403714146,
"feature_thickness_ratio": 0.7150133661003452,
"num_components": 1,
"requested_embedding_dimension": 5
},
"realized_geometry": {
"realized_separation_to_feature_scale": 2.424239830874306,
"realized_absolute_hardness": 0.41250044127826596,
"crowding_gamma": 0.9514473287010047,
"crowding_gamma_min": 0.0989453125,
"feature_thickness_radius": 0.1243362820122121,
"feature_thickness_budget": 0.7150133661003452,
"effective_max_tube_radius_for_sampling": 0.17389364717800634,
"max_admissible_tube_radius_before_crowding": 0.17389364717800634,
"cycle_hole_radius_cap": 0.17389364717800634,
"cycle_hole_radius_fraction": 0.2,
"requested_noise_ratio": 0.05563980845512021,
"realized_noise_ratio": 0.05563980845512021,
"max_admissible_noise_ratio_after_crowding": 0.35926121114164694,
"requested_crowding_r": 0.0538842669291317,
"realized_crowding_r": 0.0538842669291317,
"thickness_aware_min_required_clearance": 0.2686725640244242,
"thickness_clearance_noise_margin": 0.22255923382048085,
"minimum_realized_component_gap": Infinity
},
"graph_summary": {
"num_nodes": 13,
"num_edges": 13,
"num_components": 1,
"num_clean_points": 334,
"topology_classes": [
"single_cycle"
]
},
"seed_bundle": {
"point_cloud_seed": 959085582,
"component_seed_bundles": [
{
"topology_seed": 691217824,
"branch_seed": 449301264,
"embedding_seed": 567224568,
"topology_class": "single_cycle"
}
]
},
"scheduled_normalized_axes": {
"noise_ratio": 0.1979989358617789,
"crowding_r": 0.08980711154855284,
"sampling_density_per_feature": 0.06439202773422578,
"feature_thickness_ratio": 0.4818424838188094
},
"scheduled_vector_magnitude": 0.26626462792469074,
"scheduled_sample_rank": 31,
"actual_normalized_axes": {
"noise_ratio": 0.1979989358617789,
"crowding_r": 0.08980711154855284,
"sampling_density_per_feature": 0.06439202773422578,
"feature_thickness_ratio": 0.4818424838188094
},
"actual_difficulty_coordinate": [
0.05563980845512021,
0.0538842669291317,
23.615571403714146,
0.7150133661003452
],
"difficulty_relaxation_factor": 1.0
}