phenotype
classes.phenotype
Runtime :class:Phenotype class.
Carries a cohort’s per-subject phenotype scores (cognitive, clinical, behavioral, demographic, physiological, derived) for multi-subject studies that correlate simulated quantities with empirical measurements. BIDS-aligned (BIDS phenotype/ directory standard).
Sidecar format mirrors the existing TVBO Network pattern:
::
<name>.yaml (descriptor: subjects, measures list, provenance)
<name>.h5
└── measures/
├── <measure_1> (1-D float array, length len(subjects))
├── <measure_2> ...
└── ...See tools/build_schirner2023_phenotype.py for an example writer.
Classes
| Name | Description |
|---|---|
| Phenotype | Runtime wrapper around the auto-generated Phenotype schema. |
Phenotype
classes.phenotype.Phenotype()Runtime wrapper around the auto-generated Phenotype schema.
The schema class carries the YAML-side descriptor (subjects, measures names, provenance, optional Cognitive Atlas IRIs via measure_specs); this subclass adds lazy h5 access via :attr:values plus from_file / to_file round-tripping.
Example
.. code-block:: python
from tvbo.classes.phenotype import Phenotype
ph = Phenotype.from_file("Schirner2023_HCPYA_phenotype.yaml")
print(ph.subjects[:5]) # ['100206', '100307', ...]
pmat_rt = ph.get("PMAT24_A_RTCR") # ndarray shape (50,)Attributes
| Name | Description |
|---|---|
| values | Dict of {measure_name: ndarray}, loaded lazily. |
Methods
| Name | Description |
|---|---|
| from_file | Load a Phenotype sidecar from a YAML descriptor. |
| get | Return one measure’s array. Raises KeyError if missing. |
| measure_spec | Return the optional MeasureSpec for name (or None). |
| subject_index | Return the row index of subject_id in every measure array. |
| to_file | Write the YAML descriptor + h5 companion to path. |
from_file
classes.phenotype.Phenotype.from_file(path)Load a Phenotype sidecar from a YAML descriptor.
Resolves data_file relative to the YAML’s directory so the h5 companion can sit next to it. Numeric arrays are NOT loaded eagerly — call :meth:get (or read :attr:values) to fault one in.
get
classes.phenotype.Phenotype.get(measure)Return one measure’s array. Raises KeyError if missing.
measure_spec
classes.phenotype.Phenotype.measure_spec(name)Return the optional MeasureSpec for name (or None).
subject_index
classes.phenotype.Phenotype.subject_index(subject_id)Return the row index of subject_id in every measure array.
to_file
classes.phenotype.Phenotype.to_file(path, values=None, provenance_comment=None)Write the YAML descriptor + h5 companion to path.
Parameters
path Target .yaml path. The .h5 companion is written next to it (named after self.data_file or the yaml basename). values {measure_name: 1-D array} mapping. Must cover every name listed in self.measures. Each array’s length must equal len(self.subjects). provenance_comment Optional block of #-prefixed lines prepended to the yaml for provenance.