senoquant 1.0.0b1__py3-none-any.whl

senoquant/tabs/quantification/features/__init__.py

@@ -0,0 +1,80 @@
+"""Quantification feature UI components."""
+
+from __future__ import annotations
+
+import importlib
+import pkgutil
+from typing import Iterable
+
+from .base import FeatureConfig, FeatureData, SenoQuantFeature
+from .marker.config import MarkerFeatureData
+from .spots.config import SpotsFeatureData
+
+
+def _iter_subclasses(cls: type[SenoQuantFeature]) -> Iterable[type[SenoQuantFeature]]:
+    """Yield all subclasses of a feature class recursively.
+
+    Parameters
+    ----------
+    cls : type[SenoQuantFeature]
+        Base class whose subclasses should be discovered.
+
+    Yields
+    ------
+    type[SenoQuantFeature]
+        Feature subclass types.
+    """
+    for subclass in cls.__subclasses__():
+        yield subclass
+        yield from _iter_subclasses(subclass)
+
+
+def get_feature_registry() -> dict[str, type[SenoQuantFeature]]:
+    """Discover feature classes and return a registry by name."""
+    for module in pkgutil.walk_packages(__path__, f"{__name__}."):
+        importlib.import_module(module.name)
+
+    registry: dict[str, type[SenoQuantFeature]] = {}
+    for feature_cls in _iter_subclasses(SenoQuantFeature):
+        feature_type = getattr(feature_cls, "feature_type", "")
+        if not feature_type:
+            continue
+        registry[feature_type] = feature_cls
+
+    return dict(
+        sorted(
+            registry.items(),
+            key=lambda item: getattr(item[1], "order", 0),
+        )
+    )
+
+FEATURE_DATA_FACTORY: dict[str, type[FeatureData]] = {
+    "Markers": MarkerFeatureData,
+    "Spots": SpotsFeatureData,
+}
+
+
+def build_feature_data(feature_type: str) -> FeatureData:
+    """Create a feature data instance for the specified feature type.
+
+    Parameters
+    ----------
+    feature_type : str
+        Feature type name.
+
+    Returns
+    -------
+    FeatureData
+        Feature-specific configuration instance.
+    """
+    data_cls = FEATURE_DATA_FACTORY.get(feature_type, FeatureData)
+    return data_cls()
+
+
+__all__ = [
+    "FeatureConfig",
+    "FeatureData",
+    "SenoQuantFeature",
+    "build_feature_data",
+    "get_feature_registry",
+]

senoquant/tabs/quantification/features/base.py

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+"""Feature UI base classes for quantification."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import TYPE_CHECKING, Iterable
+import uuid
+
+from qtpy.QtWidgets import QComboBox
+
+if TYPE_CHECKING:
+    from ..frontend import QuantificationTab
+    from ..frontend import FeatureUIContext
+
+
+class FeatureData:
+    """Base class for feature-specific configuration data.
+
+    Notes
+    -----
+    Concrete feature data classes should inherit from this class so they can
+    be stored on :class:`FeatureConfig`.
+    """
+
+
+@dataclass
+class FeatureConfig:
+    """Configuration for a single quantification feature.
+
+    Attributes
+    ----------
+    feature_id : str
+        Unique identifier for the feature instance.
+    name : str
+        User-facing name for the feature.
+    type_name : str
+        Feature type name (e.g., ``"Markers"``).
+    data : FeatureData
+        Feature-specific configuration payload.
+    """
+
+    feature_id: str = field(default_factory=lambda: uuid.uuid4().hex)
+    name: str = ""
+    type_name: str = ""
+    data: FeatureData = field(default_factory=FeatureData)
+
+
+class SenoQuantFeature:
+    """Base class for quantification feature UI."""
+
+    feature_type: str = ""
+    order: int = 0
+
+    def __init__(self, tab: "QuantificationTab", context: "FeatureUIContext") -> None:
+        """Initialize a feature with shared tab context.
+
+        Parameters
+        ----------
+        tab : QuantificationTab
+            Parent quantification tab instance.
+        context : FeatureUIContext
+            Feature UI context with configuration state.
+        """
+        self._tab = tab
+        self._context = context
+        self._state = context.state
+        self._ui: dict[str, object] = {}
+
+    def build(self) -> None:
+        """Build the UI for this feature."""
+        raise NotImplementedError
+
+    def export(self, temp_dir: Path, export_format: str) -> Iterable[Path]:
+        """Export feature outputs into a temporary directory.
+
+        Parameters
+        ----------
+        temp_dir : Path
+            Temporary directory where outputs should be written.
+        export_format : str
+            File format requested by the user (``"csv"`` or ``"xlsx"``).
+
+        Returns
+        -------
+        iterable of Path
+            Paths to files produced by the export routine.
+
+        Notes
+        -----
+        Implementations may either return explicit file paths or simply
+        write outputs into ``temp_dir`` and return an empty iterable.
+        """
+        return []
+
+    def on_features_changed(self, configs: list["FeatureUIContext"]) -> None:
+        """Handle updates when the feature list changes.
+
+        Parameters
+        ----------
+        configs : list of FeatureUIContext
+            Current feature contexts.
+        """
+        return
+
+    @classmethod
+    def update_type_options(
+        cls, tab: "QuantificationTab", configs: list["FeatureUIContext"]
+    ) -> None:
+        """Update type availability in feature selectors.
+
+        Parameters
+        ----------
+        tab : QuantificationTab
+            Parent quantification tab instance.
+        configs : list of FeatureUIContext
+            Current feature contexts.
+        """
+        return
+
+
+class RefreshingComboBox(QComboBox):
+    """Combo box that refreshes its items when opened."""
+
+    def __init__(self, refresh_callback=None, parent=None) -> None:
+        """Create a combo box that refreshes before showing its popup.
+
+        Parameters
+        ----------
+        refresh_callback : callable or None
+            Callback invoked before showing the popup.
+        parent : QWidget or None
+            Optional parent widget.
+        """
+        super().__init__(parent)
+        self._refresh_callback = refresh_callback
+
+    def showPopup(self) -> None:
+        """Refresh items before showing the popup."""
+        if self._refresh_callback is not None:
+            self._refresh_callback()
+        super().showPopup()

senoquant/tabs/quantification/features/marker/__init__.py

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+"""Marker feature UI package."""
+
+from .feature import MarkerFeature
+
+__all__ = ["MarkerFeature"]

senoquant/tabs/quantification/features/marker/config.py

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+"""Marker feature configuration models."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Optional
+
+from ..base import FeatureData
+from ..roi import ROIConfig
+
+
+@dataclass
+class MarkerSegmentationConfig:
+    """Configuration for a segmentation labels entry.
+
+    Attributes
+    ----------
+    label : str
+        Name of the labels layer selected for this segmentation entry.
+    """
+
+    label: str = ""
+
+
+@dataclass
+class MarkerChannelConfig:
+    """Configuration for a marker channel entry.
+
+    Attributes
+    ----------
+    name : str
+        User-friendly label for the channel entry.
+    channel : str
+        Selected image layer name.
+    threshold_enabled : bool
+        Whether threshold controls are active.
+    threshold_method : str
+        Automatic threshold method name.
+    threshold_min : float or None
+        Minimum threshold value.
+    threshold_max : float or None
+        Maximum threshold value.
+    """
+
+    name: str = ""
+    channel: str = ""
+    threshold_enabled: bool = False
+    threshold_method: str = "Manual"
+    threshold_min: Optional[float] = None
+    threshold_max: Optional[float] = None
+
+
+@dataclass
+class MarkerFeatureData(FeatureData):
+    """Configuration for marker feature inputs.
+
+    Attributes
+    ----------
+    segmentations : list of MarkerSegmentationConfig
+        Segmentation label selections.
+    channels : list of MarkerChannelConfig
+        Channel configurations used for marker measurement.
+    rois : list of ROIConfig
+        ROI entries applied to this feature.
+    """
+
+    segmentations: list[MarkerSegmentationConfig] = field(default_factory=list)
+    channels: list[MarkerChannelConfig] = field(default_factory=list)
+    rois: list[ROIConfig] = field(default_factory=list)