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Fix examples by re-running with up-to-date sonata-generator #51

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joni-herttuainen merged 1 commit into from
May 13, 2024
Merged

Fix examples by re-running with up-to-date sonata-generator #51

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6 changes: 3 additions & 3 deletions source/usecases/usecase1/circuit_sonata.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@
"populations": {
"nodeA": {
"type": "biophysical",
"morphologies_dir": "/gpfs/bbp.cscs.ch/project/proj12/example_data/sonata/v2/components/CircuitA/morphologies/swc",
"biophysical_neuron_models_dir": "/gpfs/bbp.cscs.ch/project/proj12/example_data/sonata/v2/components/CircuitA/hoc",
"morphologies_dir": "/gpfs/bbp.cscs.ch/project/proj12/example_data/sonata/v3/components/CircuitA/morphologies/swc",
"biophysical_neuron_models_dir": "/gpfs/bbp.cscs.ch/project/proj12/example_data/sonata/v3/components/CircuitA/hoc",
"alternate_morphologies": {
"neurolucida-asc": "/gpfs/bbp.cscs.ch/project/proj12/example_data/sonata/v2/components/CircuitA/morphologies/asc"
"neurolucida-asc": "/gpfs/bbp.cscs.ch/project/proj12/example_data/sonata/v3/components/CircuitA/morphologies/asc"
}
}
}
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Binary file modified source/usecases/usecase1/edges.h5
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150 changes: 82 additions & 68 deletions source/usecases/usecase1/edges.h5.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -4,220 +4,234 @@ GROUP "/" {
GROUP "nodeA__nodeA__chemical" {
GROUP "0" {
DATASET "afferent_center_x" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
56.2096, 197.54, 40.0727, 422.442
446.137, 582.224, 56.2096, 40.0727
}
}
DATASET "afferent_center_y" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
198.723, 198.627, 209.624, 77.0581
98.7043, 55.5756, 198.723, 209.624
}
}
DATASET "afferent_center_z" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
-131.713, -165.373, -72.155, 293.07
302.396, 264.976, -131.713, -72.155
}
}
DATASET "afferent_section_id" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
303, 277, 319, 225
325, 310, 302, 318
}
}
DATASET "afferent_section_pos" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0.518639, 0.947377, 0.196576, 0.172505
}
}
DATASET "afferent_section_type" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
3, 3, 3, 4
2, 2, 2, 2
}
}
DATASET "afferent_segment_id" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
14, 36, 11, 0
11, 123, 14, 11
}
}
DATASET "afferent_segment_offset" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0.353905, 1.00072, 0.561802, 1.29577
0.160656, 0.16197, 0.353905, 0.5618
}
}
DATASET "afferent_surface_x" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
55.9272, 197.552, 40.0339, 422.69
446.03, 582.187, 56.805, 40.171
}
}
DATASET "afferent_surface_y" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
198.969, 198.478, 209.706, 77.0897
98.8763, 55.7313, 198.253, 209.463
}
}
DATASET "afferent_surface_z" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
-131.657, -165.422, -72.131, 293.118
302.396, 264.976, -131.713, -72.155
}
}
DATASET "conductance" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0.18662, 0.154087, 0.229656, 0.15987
0.107516, 0.347054, 0.344838, 0.346774
}
}
DATASET "conductance_scale_factor" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0.527228, 0.661159, 0.404207, 0.707277
0.687797, 0.327962, 0.51968, 0.319983
}
}
DATASET "decay_time" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
1.61116, 1.69324, 1.9513, 1.72497
1.97187, 1.84091, 1.67975, 1.71852
}
}
DATASET "delay" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
6.7366, 9.71945, 8.78193, 5.09624
8.20993, 0.971013, 8.37945, 0.960984
}
}
DATASET "depression_time" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
661.306, 690.235, 609.928, 696.981
669.763, 606.023, 666.677, 667.064
}
}
DATASET "efferent_center_x" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
841.042, 448.249, 253.156, -6.76278
17.2383, -333.916, 606.623, 608.067
}
}
DATASET "efferent_center_y" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
266.956, 53.8649, 202.412, 397.276
671.632, 687.578, 238.294, 240.563
}
}
DATASET "efferent_center_z" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
312.507, 242.043, 321.442, -66.7832
47.4607, -23.2959, 247.941, 256.943
}
}
DATASET "efferent_section_id" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
44, 131, 124, 228
201, 23, 227, 193
}
}
DATASET "efferent_section_pos" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0.943279, 0.13128, 0.0748085, 0.477509
}
}
DATASET "efferent_section_type" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
2, 2, 2, 2
1, 1, 1, 1
}
}
DATASET "efferent_segment_id" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
127, 121, 3, 0
15, 2, 0, 36
}
}
DATASET "efferent_segment_offset" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0.679841, 0.220142, 4.65528, 0.738516
0.122831, 1.77483, 0.738518, 2.39524
}
}
DATASET "efferent_surface_x" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
840.975, 448.333, 253.16, -6.58845
16.9363, -334.086, 606.25, 607.766
}
}
DATASET "efferent_surface_y" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
267.022, 53.7572, 202.22, 397.199
671.399, 687.237, 238.377, 240.798
}
}
DATASET "efferent_surface_z" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
312.467, 242.103, 321.512, -66.793
47.4607, -23.2959, 247.941, 256.943
}
}
DATASET "facilitation_time" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
18.0628, 8.41819, 12.163, 20.0137
9.20765, 7.57853, 11.3086, 12.2742
}
}
DATASET "n_rrp_vesicles" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
3, 1, 4, 4
4, 1, 4, 1
}
}
DATASET "spine_length" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
6350.63, 9953, 5818.55, 4143.74
759.732, 1149.71, 669.82, 657.177
}
}
DATASET "syn_type_id" {
DATATYPE H5T_STD_I64LE
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
94, 0, 113, 50
41, 35, 64, 95
}
}
DATASET "u_hill_coefficient" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
1.3172, 1.77835, 1.94957, 1.66253
1.15897, 1.11038, 1.65633, 1.13818
}
}
DATASET "u_syn" {
DATATYPE H5T_IEEE_F64LE
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0.530392, 0.516252, 0.501921, 0.531714
0.52851, 0.52193, 0.549419, 0.505102
}
}
}
Expand All @@ -242,8 +256,8 @@ GROUP "/" {
DATATYPE H5T_STD_U64LE
DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) }
DATA {
3, 4,
0, 3
0, 2,
2, 4
}
}
}
Expand All @@ -260,8 +274,8 @@ GROUP "/" {
DATATYPE H5T_STD_U64LE
DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) }
DATA {
0, 3,
3, 4
2, 4,
0, 2
}
}
}
Expand All @@ -270,7 +284,7 @@ GROUP "/" {
DATATYPE H5T_STD_U64LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
1, 1, 1, 0
0, 0, 1, 1
}
ATTRIBUTE "node_population" {
DATATYPE H5T_STRING {
Expand All @@ -289,7 +303,7 @@ GROUP "/" {
DATATYPE H5T_STD_U64LE
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
DATA {
0, 0, 0, 1
1, 1, 0, 0
}
ATTRIBUTE "node_population" {
DATATYPE H5T_STRING {
Expand Down
Binary file modified source/usecases/usecase1/nodes.h5
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