scShapeBench / data /synthetic /sample_00048.json
Joao Felipe Rocha
Added synthetic dataset and corrected croissant files
8f91d7b
raw
history blame
20.8 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": 0.08057231510574472,
"sampling_density_per_feature": 18.904563571566143,
"edge_length_jitter_ratio": 0.09043163918715937,
"branch_angle_spread": 0.978402632678696
},
"embedding_dimension": 3,
"requested_embedding_dimension": 3,
"feature_thickness_ratio": 0.6362316957101617,
"feature_thickness_budget": 0.6362316957101617,
"tube_sampling_mode": "solid",
"num_components": 1,
"component_gap_ratio": 5.646679318138688,
"component_node_ids": [
[
0,
1,
2,
3,
4,
5,
6,
7
]
],
"component_x_intervals": [
[
0.0,
2.60610884470718
]
],
"component_topology_classes": [
"tree"
],
"crowding_r": 0.17678125234848072,
"crowding_gamma": 0.8899329538600611,
"crowding_gamma_min": 0.37738281249999994,
"crowding_admissibility_epsilon_sep": 1.6803576222366432,
"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": 4,
"branch_nodes": [
2
],
"is_planar": true,
"max_edge_cycle_multiplicity": 0,
"branch_params": {
"num_initial_attachment_sites": 2,
"max_branch_depth": 2,
"promotion_prob": 0.5833263423099234,
"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": [
0
],
"branch_generation_nodes": {
"1": [
1,
2,
3,
4
],
"2": [
5,
6,
7
]
},
"branch_parent_map": {
"1": 0,
"2": 1,
"3": 2,
"4": 3,
"5": 2,
"6": 2,
"7": 6
},
"branch_root_map": {
"1": 0,
"2": 0,
"3": 0,
"4": 0,
"5": 0,
"6": 0,
"7": 0
},
"branch_depth_map": {
"1": 1,
"2": 1,
"3": 1,
"4": 1,
"5": 2,
"6": 2,
"7": 2
},
"num_leaves_after_branching": 4,
"num_branch_nodes_after_branching": 1,
"betti_1_after_branching": 0,
"embedding_valid": true,
"embedding_dimensions_attempted": [
3
],
"embedding_attempt_history": [
{
"dimension": 3,
"embedding_valid": true,
"global_embedding_attempts": 1,
"local_placement_rejections": 0,
"min_nonadjacent_node_distance": 2.62967448404681,
"min_nonincident_edge_distance": Infinity,
"min_nonincident_node_edge_distance": Infinity,
"failure_reason": null,
"refinement_applied": true,
"refinement_iterations": 24,
"refinement_objective_delta": -0.01793969957286229,
"refinement_clearance_delta": 0.046601587315074244
}
],
"embedding_constructive_success": true,
"embedding_rejected": false,
"min_nonadjacent_node_distance": 2.62967448404681,
"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": true,
"iterations": 24,
"objective_before": 0.38738148011720447,
"objective_after": 0.3694417805443422,
"objective_delta": -0.01793969957286229,
"clearance_before": 2.5830728967317356,
"clearance_after": 2.62967448404681,
"clearance_delta": 0.046601587315074244,
"accepted_steps": 24,
"reason": "accepted"
},
"topology_class": "tree",
"sampled_topology_spec": {
"topology_class": "tree",
"children_per_branch_point_range": [
1,
3
],
"branch_length_range": [
1,
4
],
"max_branch_depth_range": [
1,
2
],
"promotion_prob_range": [
0.2,
0.6
],
"max_degree": 4,
"num_cycles": 0,
"branch_attach_count": 2
},
"tube_embedding_separation_ratio": 6.0,
"realized_post_crowding_min_nonadjacent_node_distance": 2.43379403350144,
"realized_post_crowding_min_nonincident_edge_distance": Infinity,
"realized_post_crowding_min_nonincident_node_edge_distance": Infinity,
"realized_post_crowding_min_structural_distance": 2.43379403350144,
"realized_post_crowding_separation_to_feature_scale": 2.43379403350144,
"realized_post_crowding_separation_to_post_median_edge": 2.4922191569044134,
"realized_post_crowding_absolute_hardness": 0.41088111246674575,
"minimum_realized_component_gap": Infinity,
"feature_thickness_radius": 0.8301788111183216,
"effective_max_tube_radius_for_sampling": 1.304837242023405,
"cycle_hole_radius_cap": Infinity,
"cycle_hole_radius_fraction": 0.2,
"crowding_applied": true,
"crowding_isotropy_epsilon": 0.05,
"crowding_axis": [
-0.4151561145749229,
0.5515885017502349,
0.7234607973262855
],
"crowding_centroid": [
1.436394228652521,
-1.2450528052756593,
-1.5059747193960344
],
"crowding_covariance_eigenvalues": [
1.2242535354488135,
0.7512205672489715,
0.00867244010214783
],
"crowding_covariance_matrix": [
[
0.75938485524196,
-0.302799892724442,
-0.035899852487140664
],
[
-0.302799892724442,
0.3796162905815576,
0.47021617027324264
],
[
-0.035899852487140664,
0.47021617027324264,
0.8451453969764148
]
],
"crowding_isotropic_fallback_used": false,
"crowding_linear_operator": [
[
0.9089035155122404,
-0.02520484056895079,
-0.033058546355906306
],
[
-0.02520484056895079,
0.923420838918712,
0.04392254724024844
],
[
-0.033058546355906306,
0.04392254724024844,
0.94754155328917
]
],
"crowding_model_dimension": 3,
"feature_scale_nominal": 1.0,
"feature_scale_pre_crowding": 0.9971184169095173,
"feature_scale_post_crowding_median_edge": 0.9765569880798352,
"pre_crowding_edge_length_summary": {
"min": 0.9622562417048331,
"median": 0.9971184169095173,
"mean": 1.025295218605982,
"max": 1.0964095755807812
},
"post_crowding_edge_length_summary": {
"min": 0.9610813636136434,
"median": 0.9765569880798352,
"mean": 0.9771789527599093,
"max": 0.9963183552570228
},
"pre_crowding_min_nonadjacent_node_distance": 2.62967448404681,
"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": false,
"realized_separation_ratio": 1.4697292269272815
},
{
"gamma": 1.0,
"admissible": true,
"realized_separation_ratio": 2.637274008233906
},
{
"gamma": 0.505,
"admissible": true,
"realized_separation_ratio": 1.839189962528903
},
{
"gamma": 0.2575,
"admissible": false,
"realized_separation_ratio": 1.574040029531852
},
{
"gamma": 0.38125,
"admissible": true,
"realized_separation_ratio": 1.6901688984288206
},
{
"gamma": 0.31937499999999996,
"admissible": false,
"realized_separation_ratio": 1.6275062118443433
},
{
"gamma": 0.35031249999999997,
"admissible": false,
"realized_separation_ratio": 1.65774958598363
},
{
"gamma": 0.36578124999999995,
"admissible": false,
"realized_separation_ratio": 1.673694953726251
},
{
"gamma": 0.37351562499999996,
"admissible": false,
"realized_separation_ratio": 1.6818668130455396
},
{
"gamma": 0.37738281249999994,
"admissible": true,
"realized_separation_ratio": 1.6860016970062386
}
],
"crowding_gamma_min_search_iterations": 10,
"crowding_gamma_min_search_bracket": [
0.37351562499999996,
0.37738281249999994
],
"crowding_relative_budget_definition": "gamma = 1 - r * (1 - gamma_min)",
"requested_noise_ratio": 0.08057231510574472,
"realized_noise_ratio": 0.08057231510574472,
"max_admissible_noise_ratio_after_crowding": 0.12557273521079948,
"requested_crowding_r": 0.17678125234848072,
"realized_crowding_r": 0.17678125234848072,
"staged_generation_order": "topology -> max-separation embedding -> admissible thickness -> thickness-constrained crowding -> clearance-capped noise -> sampling",
"tube_no_overlap_required_centerline_clearance": 2.002646882659622,
"tube_no_overlap_post_crowding_margin": 0.43114715084181787,
"tube_no_overlap_satisfied": true,
"tube_no_overlap_constraint_active": true,
"max_admissible_tube_radius_after_crowding": 1.0457523865392306,
"realized_tube_radius_budget_fraction": 0.7938579168493994,
"point_cloud_params": {
"feature_scale": 1.0,
"sampling_density_per_feature": 18.904563571566143,
"noise_ratio": 0.08057231510574472,
"sigma": 0.08057231510574472,
"embedding_dimension": 3,
"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": 0.8301788111183216,
"feature_thickness_radius": 0.8301788111183216,
"tube_sampling_mode": "solid"
},
"num_clean_points": 439,
"num_edge_sampled_points": 431,
"num_node_sampled_points": 8,
"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,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
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,
334,
335,
336,
337,
338,
339,
340,
341,
342,
343,
344,
345,
346,
347,
348,
349,
350,
351,
352,
353,
354,
355,
356,
357,
358,
359,
360,
361,
362,
363,
364,
365,
366,
367,
368,
369,
370,
371,
372,
373,
374,
375,
376,
377,
378,
379,
380,
381,
382,
383,
384,
385,
386,
387,
388,
389,
390,
391,
392,
393,
394,
395,
396,
397,
398,
399,
400,
401,
402,
403,
404,
405,
406,
407,
408,
409,
410,
411,
412,
413,
414,
415,
416,
417,
418,
419,
420,
421,
422,
423,
424,
425,
426,
427,
428,
429,
430,
431,
432,
433,
434,
435,
436,
437,
438
]
],
"nearest_feature_changed_rate": 0.09567198177676538,
"nonincident_feature_confusion_rate": 0.24829157175398633,
"cross_component_confusion_rate": 0.0,
"noise_overlap_quality_pass": false,
"noise_overlap_quality_thresholds": {
"nonincident_feature_confusion_rate": 0.12,
"cross_component_confusion_rate": 0.03
},
"num_points_evaluated_for_noise_confusion": 439,
"num_nearest_feature_changes": 42,
"num_nonincident_feature_confusions": 109,
"num_cross_component_confusions": 0,
"sample_id": 48,
"difficulty": "full",
"difficulty_coordinate": {
"noise_ratio": 0.08057231510574472,
"crowding_r": 0.17678125234848072,
"sampling_density_per_feature": 18.904563571566143,
"feature_thickness_ratio": 0.6362316957101617,
"num_components": 1,
"requested_embedding_dimension": 3
},
"realized_geometry": {
"realized_separation_to_feature_scale": 2.43379403350144,
"realized_absolute_hardness": 0.41088111246674575,
"crowding_gamma": 0.8899329538600611,
"crowding_gamma_min": 0.37738281249999994,
"feature_thickness_radius": 0.8301788111183216,
"feature_thickness_budget": 0.6362316957101617,
"effective_max_tube_radius_for_sampling": 1.304837242023405,
"max_admissible_tube_radius_before_crowding": 1.304837242023405,
"cycle_hole_radius_cap": Infinity,
"cycle_hole_radius_fraction": 0.2,
"requested_noise_ratio": 0.08057231510574472,
"realized_noise_ratio": 0.08057231510574472,
"max_admissible_noise_ratio_after_crowding": 0.12557273521079948,
"requested_crowding_r": 0.17678125234848072,
"realized_crowding_r": 0.17678125234848072,
"thickness_aware_min_required_clearance": 1.6803576222366432,
"thickness_clearance_noise_margin": 0.3222892604229789,
"minimum_realized_component_gap": Infinity
},
"graph_summary": {
"num_nodes": 8,
"num_edges": 7,
"num_components": 1,
"num_clean_points": 439,
"topology_classes": [
"tree"
]
},
"seed_bundle": {
"point_cloud_seed": 548859110,
"component_seed_bundles": [
{
"topology_seed": 770219963,
"branch_seed": 955573409,
"embedding_seed": 795658115,
"topology_class": "tree"
}
]
},
"scheduled_normalized_axes": {
"noise_ratio": 0.3365128616985818,
"crowding_r": 0.2946354205808012,
"sampling_density_per_feature": 0.2835086710899467,
"feature_thickness_ratio": 0.3386030831093849
},
"scheduled_vector_magnitude": 0.3142770082362704,
"scheduled_sample_rank": 48,
"actual_normalized_axes": {
"noise_ratio": 0.3365128616985818,
"crowding_r": 0.2946354205808012,
"sampling_density_per_feature": 0.2835086710899467,
"feature_thickness_ratio": 0.3386030831093849
},
"actual_difficulty_coordinate": [
0.08057231510574472,
0.17678125234848072,
18.904563571566143,
0.6362316957101617
],
"difficulty_relaxation_factor": 1.0
}