Datasets:

SubstrateCommons
/

test-fixtures

License:

Dataset Viewer

Split (1)

train

The dataset viewer is not available for this split.

Cannot load the dataset split (in streaming mode) to extract the first rows.

Error code:   StreamingRowsError
Exception:    CastError
Message:      Couldn't cast
tessera_manifest: int64
pack_id: string
spec: struct<kernel: string, pack: struct<id: string, license: string, citation: string>, substrate: struc (... 1196 chars omitted)
  child 0, kernel: string
  child 1, pack: struct<id: string, license: string, citation: string>
      child 0, id: string
      child 1, license: string
      child 2, citation: string
  child 2, substrate: struct<id: string, domain: struct<box_min: list<item: double>, box_max: list<item: double>, boundary (... 1006 chars omitted)
      child 0, id: string
      child 1, domain: struct<box_min: list<item: double>, box_max: list<item: double>, boundary: list<item: string>, surfa (... 22 chars omitted)
          child 0, box_min: list<item: double>
              child 0, item: double
          child 1, box_max: list<item: double>
              child 0, item: double
          child 2, boundary: list<item: string>
              child 0, item: string
          child 3, surface_relaxivity: double
      child 2, pools: list<item: struct<id: int64, name: string, D: double, water_fraction: double, T2: null, T1: null, su (... 20 chars omitted)
          child 0, item: struct<id: int64, name: string, D: double, water_fraction: double, T2: null, T1: null, susceptibilit (... 8 chars omitted)
              child 0, id: int64
              child 1, name: string
              child 2, D: double
              child 3, water_fraction: double
              child 4, T2: null
              child 5, T1: null
              child
...
er_fraction: double
packs: list<item: struct<id: string, path: string, sha256: string, bytes: int64, n_walkers: int64, T_max: d (... 368 chars omitted)
  child 0, item: struct<id: string, path: string, sha256: string, bytes: int64, n_walkers: int64, T_max: double, dt_t (... 356 chars omitted)
      child 0, id: string
      child 1, path: string
      child 2, sha256: string
      child 3, bytes: int64
      child 4, n_walkers: int64
      child 5, T_max: double
      child 6, dt_traj: double
      child 7, K: int64
      child 8, method: string
      child 9, temporal_bandwidth_hz: double
      child 10, channels: list<item: string>
          child 0, item: string
      child 11, floor_max: double
      child 12, err_max: double
      child 13, within_2x_floor: bool
      child 14, commit: null
      child 15, license: string
      child 16, citation: string
      child 17, substrate: string
      child 18, segments: struct<n: int64, n_t: int64, T: double, walks: list<item: struct<first: int64, last: int64, seed: li (... 18 chars omitted)
          child 0, n: int64
          child 1, n_t: int64
          child 2, T: double
          child 3, walks: list<item: struct<first: int64, last: int64, seed: list<item: int64>>>
              child 0, item: struct<first: int64, last: int64, seed: list<item: int64>>
                  child 0, first: int64
                  child 1, last: int64
                  child 2, seed: list<item: int64>
                      child 0, item: int64
to
{'schema': Value('string'), 'packs': List({'id': Value('string'), 'path': Value('string'), 'sha256': Value('string'), 'bytes': Value('int64'), 'n_walkers': Value('int64'), 'T_max': Value('float64'), 'dt_traj': Value('float64'), 'K': Value('int64'), 'method': Value('string'), 'temporal_bandwidth_hz': Value('float64'), 'channels': List(Value('string')), 'floor_max': Value('float64'), 'err_max': Value('float64'), 'within_2x_floor': Value('bool'), 'commit': Value('null'), 'license': Value('string'), 'citation': Value('string'), 'substrate': Value('string'), 'segments': {'n': Value('int64'), 'n_t': Value('int64'), 'T': Value('float64'), 'walks': List({'first': Value('int64'), 'last': Value('int64'), 'seed': List(Value('int64'))})}}), 'substrate': {'id': Value('string'), 'box_min': List(Value('float64')), 'box_max': List(Value('float64')), 'boundary': List(Value('string')), 'pools': List({'name': Value('string'), 'D': Value('float64'), 'water_fraction': Value('float64')})}}
because column names don't match
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/utils.py", line 147, in get_rows_or_raise
                  return get_rows(
                      dataset=dataset,
                  ...<4 lines>...
                      column_names=column_names,
                  )
                File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
                  return func(*args, **kwargs)
                File "/src/services/worker/src/worker/utils.py", line 127, in get_rows
                  rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
                File "/src/services/worker/src/worker/utils.py", line 483, in safe_iter
                  yield from ds.decode(False) if ds.features else ds
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2951, in __iter__
                  for key, example in ex_iterable:
                                      ^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2461, in __iter__
                  for key, pa_table in self._iter_arrow():
                                       ~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2486, in _iter_arrow
                  for key, pa_table in self.ex_iterable._iter_arrow():
                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 547, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 430, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 343, in _generate_tables
                  self._cast_table(pa_table, json_field_paths=json_field_paths),
                  ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 132, in _cast_table
                  pa_table = table_cast(pa_table, self.info.features.arrow_schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              tessera_manifest: int64
              pack_id: string
              spec: struct<kernel: string, pack: struct<id: string, license: string, citation: string>, substrate: struc (... 1196 chars omitted)
                child 0, kernel: string
                child 1, pack: struct<id: string, license: string, citation: string>
                    child 0, id: string
                    child 1, license: string
                    child 2, citation: string
                child 2, substrate: struct<id: string, domain: struct<box_min: list<item: double>, box_max: list<item: double>, boundary (... 1006 chars omitted)
                    child 0, id: string
                    child 1, domain: struct<box_min: list<item: double>, box_max: list<item: double>, boundary: list<item: string>, surfa (... 22 chars omitted)
                        child 0, box_min: list<item: double>
                            child 0, item: double
                        child 1, box_max: list<item: double>
                            child 0, item: double
                        child 2, boundary: list<item: string>
                            child 0, item: string
                        child 3, surface_relaxivity: double
                    child 2, pools: list<item: struct<id: int64, name: string, D: double, water_fraction: double, T2: null, T1: null, su (... 20 chars omitted)
                        child 0, item: struct<id: int64, name: string, D: double, water_fraction: double, T2: null, T1: null, susceptibilit (... 8 chars omitted)
                            child 0, id: int64
                            child 1, name: string
                            child 2, D: double
                            child 3, water_fraction: double
                            child 4, T2: null
                            child 5, T1: null
                            child
              ...
              er_fraction: double
              packs: list<item: struct<id: string, path: string, sha256: string, bytes: int64, n_walkers: int64, T_max: d (... 368 chars omitted)
                child 0, item: struct<id: string, path: string, sha256: string, bytes: int64, n_walkers: int64, T_max: double, dt_t (... 356 chars omitted)
                    child 0, id: string
                    child 1, path: string
                    child 2, sha256: string
                    child 3, bytes: int64
                    child 4, n_walkers: int64
                    child 5, T_max: double
                    child 6, dt_traj: double
                    child 7, K: int64
                    child 8, method: string
                    child 9, temporal_bandwidth_hz: double
                    child 10, channels: list<item: string>
                        child 0, item: string
                    child 11, floor_max: double
                    child 12, err_max: double
                    child 13, within_2x_floor: bool
                    child 14, commit: null
                    child 15, license: string
                    child 16, citation: string
                    child 17, substrate: string
                    child 18, segments: struct<n: int64, n_t: int64, T: double, walks: list<item: struct<first: int64, last: int64, seed: li (... 18 chars omitted)
                        child 0, n: int64
                        child 1, n_t: int64
                        child 2, T: double
                        child 3, walks: list<item: struct<first: int64, last: int64, seed: list<item: int64>>>
                            child 0, item: struct<first: int64, last: int64, seed: list<item: int64>>
                                child 0, first: int64
                                child 1, last: int64
                                child 2, seed: list<item: int64>
                                    child 0, item: int64
              to
              {'schema': Value('string'), 'packs': List({'id': Value('string'), 'path': Value('string'), 'sha256': Value('string'), 'bytes': Value('int64'), 'n_walkers': Value('int64'), 'T_max': Value('float64'), 'dt_traj': Value('float64'), 'K': Value('int64'), 'method': Value('string'), 'temporal_bandwidth_hz': Value('float64'), 'channels': List(Value('string')), 'floor_max': Value('float64'), 'err_max': Value('float64'), 'within_2x_floor': Value('bool'), 'commit': Value('null'), 'license': Value('string'), 'citation': Value('string'), 'substrate': Value('string'), 'segments': {'n': Value('int64'), 'n_t': Value('int64'), 'T': Value('float64'), 'walks': List({'first': Value('int64'), 'last': Value('int64'), 'seed': List(Value('int64'))})}}), 'substrate': {'id': Value('string'), 'box_min': List(Value('float64')), 'box_max': List(Value('float64')), 'boundary': List(Value('string')), 'pools': List({'name': Value('string'), 'D': Value('float64'), 'water_fraction': Value('float64')})}}
              because column names don't match

Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.

SubstrateCommons/test-fixtures

Replay packs (.rpk) built with dmipy_sim: one converged Monte-Carlo walk each, stored so any acquisition can be replayed on it. Load one with ReplayPack.load("hf://SubstrateCommons/test-fixtures/<path>"); the manifest (manifest.json) holds the sha256 every load is checked against. This file is rendered from the manifest by dmipy_sim.replay.publish.

Substrate

analytic/cylinder

box: 24 × 24 × 24 µm
boundary: open, open, open

pool	D (m²/s)	water fraction
extra	2e-09	0
intra	2e-09	1

Packs

id	duration	walkers	bands	channels	floor	size	commit	path
`cylinder-r3um-T60ms`	60 ms	80000	16	positions, boundary_local_time, compartment	0.018	19.6 MB	—	`packs/cylinder-r3um-T60ms.rpk`
`cylinder-r4um-T50ms`	50 ms	60000	16	positions, boundary_local_time, compartment	0.0158	14.7 MB	—	`packs/cylinder-r4um-T50ms.rpk`
`cylinder-r4p5um-T50ms`	50 ms	380000	16	positions, boundary_local_time, compartment	0.0199	93.1 MB	—	`packs/cylinder-r4p5um-T50ms.rpk`

Citation

Fick R., dmrai-lab. tessera test fixture: impermeable 3 um cylinder, D 2e-9 m^2/s, 60 ms walk (dmipy-sim de8590b).
Fick R., dmrai-lab. tessera test fixture: impermeable 4 um cylinder, D 2e-9 m^2/s, 50 ms walk (dmipy-sim de8590b).
Fick R., dmrai-lab. tessera test fixture: impermeable 4.5 um cylinder, D 2e-9 m^2/s, 50 ms walk (dmipy-sim de8590b).

Downloads last month: 24

Total file size:

128 MB