lnccbrown / lnccbrown/ssm-simulators

Types of data items in data object serialized in DataGenerator

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linear-ssm-simulators
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Description

@AlexanderFengler Check the boxes with objects to serialize below in data. Feel free to expand the discussion as needed.

  • ('cpn_data', <class 'numpy.ndarray'>),
  • ('cpn_labels', <class 'numpy.ndarray'>),
  • ('cpn_no_omission_data', <class 'numpy.ndarray'>),
  • ('cpn_no_omission_labels', <class 'numpy.ndarray'>),
  • ('opn_data', <class 'numpy.ndarray'>),
  • ('opn_labels', <class 'numpy.ndarray'>),
  • ('gonogo_data', <class 'numpy.ndarray'>),
  • ('gonogo_labels', <class 'numpy.ndarray'>),
  • ('theta', <class 'numpy.ndarray'>),
  • ('lan_data', <class 'numpy.ndarray'>),
  • ('lan_labels', <class 'numpy.ndarray'>),
  • ('binned_128', <class 'numpy.ndarray'>),
  • ('binned_256', <class 'numpy.ndarray'>),
  • ('generator_config', <class 'dict'>), # nested dict (see below)
  • ('model_config', <class 'dict'>) # nested dict (see below)

In data['generator_config']:

  • ('output_folder', <class 'str'>),
  • ('model', <class 'str'>),
  • ('nbins', <class 'int'>),
  • ('n_samples', <class 'int'>),
  • ('n_parameter_sets', <class 'int'>),
  • ('n_parameter_sets_rejected', <class 'int'>),
  • ('n_training_samples_by_parameter_set', <class 'int'>),
  • ('max_t', <class 'float'>),
  • ('delta_t', <class 'float'>),
  • ('pickleprotocol', <class 'int'>),
  • ('n_cpus', <class 'int'>),
  • ('kde_data_mixture_probabilities', <class 'list'>),
  • ('simulation_filters', <class 'dict'>), # nested dict (see below)
  • ('negative_rt_cutoff', <class 'float'>),
  • ('n_subruns', <class 'int'>),
  • ('bin_pointwise', <class 'bool'>),
  • ('separate_response_channels', <class 'bool'>),
  • ('smooth_unif', <class 'bool'>),
  • ('kde_displace_t', <class 'bool'>),
  • ('dgp_list', <class 'str'>)

In data['model_config']

  • ('name', <class 'str'>),
  • ('params', <class 'list'>),
  • ('param_bounds', <class 'list'>),
  • ('boundary_name', <class 'str'>),
  • ('boundary', <class 'function'>), # Serialize? If so, how?
  • ('n_params', <class 'int'>),
  • ('default_params', <class 'list'>),
  • ('nchoices', <class 'int'>),
  • ('choices', <class 'list'>),
  • ('n_particles', <class 'int'>),
  • ('simulator', <class '_cython_3_0_12.cython_function_or_method'>), # Serialize? If so, how?
  • ('constrained_param_space', <class 'dict'>) # nested dict (see below)

In data['generator_config']['simulation_filters']

  • ('mode', <class 'int'>),
  • ('choice_cnt', <class 'int'>),
  • ('mean_rt', <class 'int'>),
  • ('std', <class 'int'>),
  • ('mode_cnt_rel', <class 'float'>)

In data['model_config']['constrained_param_space'] [these are tuples of floats]

  • ('v', <class 'tuple'>),
  • ('a', <class 'tuple'>),
  • ('z', <class 'tuple'>),
  • ('t', <class 'tuple'>),
  • ('theta', <class 'tuple'>)

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating DataGenerator and the code that serializes the data object. Compare its behavior with the listed NumPy arrays, nested configuration values, tuples, and function or Cython callables. Done means the serializable items and treatment of unsupported callable values are decided and reflected in the relevant serialization behavior; no file or test is named in the issue.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
data-engineering
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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