"""Public measurement schema for the PhenoTypic library.
This subpackage is the canonical, public home for PhenoTypic's measurement
naming conventions: the :class:`MeasurementInfo` base class plus every
``MeasurementInfo`` subclass that names a column in an output DataFrame. Each
enum lives in its own module (``_<name>.py``) and is re-exported here, so the
public import surface stays stable:
from phenotypic.schema import MeasurementInfo, BBOX, GRID, SHAPE
It also hosts the metadata vocabulary: ``IMAGE`` (framework-populated image
bookkeeping) and eight semantic owners (``GENETIC``, ``SAMPLE``, ``PLATE``,
``CONDITION``, ``CULTURE``, ``ACQUISITION``, ``EXPERIMENT``, and ``STUDY``)
that standardize ``Metadata_*`` columns for the ``--metadata`` join and
``post/`` operations.
"""
import sys
import warnings
from ._measurement_info import (
Entry,
MeasurementInfo,
parse_qualified_header,
qualified_header,
)
from ._rembi import (
REMBI_MODULE as REMBI_MODULE,
header_to_module as header_to_module,
)
from ._tiers import (
DerivedMeasure as DerivedMeasure,
DescriptiveTrait as DescriptiveTrait,
DirectPhenotype as DirectPhenotype,
DiscriminativeFeature as DiscriminativeFeature,
IdentityInfo as IdentityInfo,
MetadataInfo as MetadataInfo,
PrimaryMeasure as PrimaryMeasure,
QualityInfo as QualityInfo,
)
from ._metadata import IMAGE
from ._experimental_tags import (
ACQUISITION,
CONDITION,
CULTURE,
EXPERIMENT,
GENETIC,
PLATE,
SAMPLE,
STUDY,
)
from ._bbox import BBOX
from ._color_composition import ColorComposition
from ._color_hsv import ColorHSV
from ._color_lab import ColorLab
from ._color_xy import Colorxy
from ._color_xyz import ColorXYZ
from ._edge_correction import EDGE_CORRECTION
from ._grid import GRID
from ._grid_linreg_stats import GRID_LINREG_STATS
from ._neighbor_dist import NEIGHBOR_DIST
from ._grid_spread import GRID_SPREAD
from ._linear_cap_and_lag_model import LINEAR_CAP_AND_LAG_MODEL
from ._intensity import INTENSITY
from ._linear_lag_model import LINEAR_LAG_MODEL
from ._log_growth_model import LOG_GROWTH_MODEL
from ._model_metrics import MODEL_METRICS
from ._object import OBJECT
from ._curation import CURATION
from ._error_category import ErrorCategory
from ._metadata_match import METADATA_MATCH
from ._quality_check import QUALITY_CHECK
from ._quality_count import QUALITY_COUNT
from ._quality_icc import QUALITY_ICC
from ._quality_mad import QUALITY_MAD
from ._quality_occupancy import QUALITY_OCCUPANCY
from ._quality_se import QUALITY_SE
from ._quality_tukey import QUALITY_TUKEY
from ._quality_zmax import QUALITY_ZMAX
from ._radial_expansion import RADIAL_EXPANSION
from ._orientation_zones import (
ORIENTATION_ZONE_DIAGNOSTIC,
ORIENTATION_ZONE_PRIMARY,
ORIENTATION_ZONES,
)
from ._shape import SHAPE
from ._size import SIZE
from ._symmetric_zones import SYMMETRIC_ZONES
from ._texture import TEXTURE
__all__ = [
"Entry",
"MeasurementInfo",
"MetadataInfo",
"parse_qualified_header",
"qualified_header",
"REMBI_MODULE",
"header_to_module",
"METADATA_MATCH",
"IMAGE",
"GENETIC",
"SAMPLE",
"PLATE",
"CONDITION",
"CULTURE",
"EXPERIMENT",
"STUDY",
"ACQUISITION",
"BBOX",
"ColorComposition",
"ColorHSV",
"ColorLab",
"Colorxy",
"ColorXYZ",
"CURATION",
"LINEAR_CAP_AND_LAG_MODEL",
"EDGE_CORRECTION",
"ErrorCategory",
"GRID",
"GRID_LINREG_STATS",
"NEIGHBOR_DIST",
"GRID_SPREAD",
"INTENSITY",
"LINEAR_LAG_MODEL",
"LOG_GROWTH_MODEL",
"MODEL_METRICS",
"OBJECT",
"QUALITY_CHECK",
"QUALITY_COUNT",
"QUALITY_ICC",
"QUALITY_MAD",
"QUALITY_OCCUPANCY",
"QUALITY_SE",
"QUALITY_TUKEY",
"QUALITY_ZMAX",
"RADIAL_EXPANSION",
"SHAPE",
"SIZE",
"ORIENTATION_ZONES",
"ORIENTATION_ZONE_DIAGNOSTIC",
"ORIENTATION_ZONE_PRIMARY",
"SYMMETRIC_ZONES",
"TEXTURE",
]
_LEGACY_METADATA_NAMES = {
"METADATA": IMAGE,
"GENETIC_METADATA": GENETIC,
"SAMPLE_METADATA": SAMPLE,
"PLATE_METADATA": PLATE,
"CONDITION_METADATA": CONDITION,
"CULTURE_METADATA": CULTURE,
"ACQUISITION_METADATA": ACQUISITION,
"EXPERIMENT_METADATA": EXPERIMENT,
"STUDY_METADATA": STUDY,
}
[docs]
def __getattr__(name: str):
"""Resolve one-release compatibility names for metadata enum owners."""
value = _LEGACY_METADATA_NAMES.get(name)
if value is None:
raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
caller = sys._getframe(1)
is_fromlist_probe = (
caller.f_code.co_name == "_handle_fromlist"
and caller.f_globals.get("__name__") == "importlib._bootstrap"
)
if not is_fromlist_probe:
warnings.warn(
f"phenotypic.schema.{name} is deprecated; use {value.__name__} instead",
DeprecationWarning,
stacklevel=2,
)
return value
