adjust sample widget

src/cell_gater/model/data_model.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Sequence
@@ -8,15 +10,21 @@
 
 @dataclass
 class DataModel:
+    """Model containing all necessary fields for gating."""
+
     events: EmitterGroup = field(init=False, default=None, repr=True)
     _samples: Sequence[str] = field(default_factory=list, init=False)
-    _regionprops_df: pd.DataFrame = field(
-        default_factory=pd.DataFrame, init=False
-    )
+    _regionprops_df: pd.DataFrame = field(default_factory=pd.DataFrame, init=False)
+    _regionprops_columns: Sequence[str] = field(default_factory=list, init=False)
     _image_paths: Sequence[Path] = field(default_factory=list, init=False)
     _mask_paths: Sequence[Path] = field(default_factory=list, init=False)
+    _lower_bound_marker: str | None = field(default=None, init=False)
+    _upper_bound_marker: str | None = field(default=None, init=False)
+    _markers: Sequence[str] = field(default_factory=list, init=False)
+    _active_marker: str | None = field(default=None, init=False)
 
     def __post_init__(self) -> None:
+        """Allow fields in the dataclass to emit events when changed."""
         self.events = EmitterGroup(
             source=self,
             samples=Event,
@@ -25,33 +33,77 @@ def __post_init__(self) -> None:
 
     @property
     def samples(self):
+        """Samples derived from the regionprops csv file names."""
         return self._samples
 
     @samples.setter
-    def samples(self, samples: Sequence[str]):
+    def samples(self, samples: Sequence[str]) -> None:
         self._samples = samples
 
     @property
     def regionprops_df(self):
+        """Regionprops dataframe derived from possibly multiple csv files."""
         return self._regionprops_df
 
     @regionprops_df.setter
-    def regionprops_df(self, regionprops: pd.DataFrame):
+    def regionprops_df(self, regionprops: pd.DataFrame) -> None:
         self._regionprops_df = regionprops
         self.events.regionprops_df()
 
     @property
     def image_paths(self):
+        """The paths to the images."""
         return self._image_paths
 
     @image_paths.setter
-    def image_paths(self, image_paths: Sequence[Path]):
+    def image_paths(self, image_paths: Sequence[Path]) -> None:
         self._image_paths = image_paths
 
     @property
     def mask_paths(self):
+        """The paths to the mask images."""
         return self._mask_paths
 
     @mask_paths.setter
-    def mask_paths(self, mask_paths: Sequence[Path]):
+    def mask_paths(self, mask_paths: Sequence[Path]) -> None:
         self._mask_paths = mask_paths
+
+    @property
+    def lower_bound_marker(self):
+        """The lower bound column name of the marker columns to be included from regionprops_df."""
+        return self._lower_bound_marker
+
+    @lower_bound_marker.setter
+    def lower_bound_marker(self, marker: str) -> None:
+        self._lower_bound_marker = marker
+
+    @property
+    def upper_bound_marker(self):
+        """The inclusive upper bound column name of the marker columns to be included from regionprops_df."""
+        return self._upper_bound_marker
+
+    @upper_bound_marker.setter
+    def upper_bound_marker(self, marker: str) -> None:
+        self._upper_bound_marker = marker
+
+    @property
+    def markers(self):
+        """The markers included for gating."""
+        return self._markers
+
+    @markers.setter
+    def markers(self, markers: Sequence[str]) -> None:
+        self._markers = markers
+
+    @property
+    def active_marker(self):
+        """The marker currently used on x-axis for gating."""
+        return self._active_marker
+
+    @active_marker.setter
+    def active_marker(self, marker: str) -> None:
+        self._active_marker = marker
+
+    def validate(self):
+        """Validate the input data from the user provided through the SampleWidget."""
+        pass

src/cell_gater/widgets/sample_widget.py

@@ -1,12 +1,10 @@
 from pathlib import Path
-from typing import Any
 
 from napari import Viewer
 from napari.utils.history import (
     get_open_history,
     update_open_history,
 )
-from qtpy.QtCore import Qt
 from qtpy.QtWidgets import (
     QComboBox,
     QFileDialog,
@@ -25,10 +23,25 @@
 class SampleWidget(QWidget):
     """Sample widget for loading required data."""
 
-    def __init__(self, viewer: Viewer) -> None:
+    def __init__(self, viewer: Viewer, model: DataModel | None = None) -> None:
+        """
+        Create the QWidget visuals.
+
+        This widget sets up the QtWidget elements used to determine what the input is that the user wants to use
+        for cell gating. It also connects these elements to their appropriate callback functions.
+
+        Parameters
+        ----------
+        viewer : napari.Viewer
+            The napari Viewer instance.
+        model : DataModel | None
+            The data model dataclass. If provided, this means that the plugin is used by means of a CLI to be
+            implemented.
+
+        """
         super().__init__()
         self._viewer = viewer
-        self._model = DataModel()
+        self._model = DataModel() if model is None else model
         self.setLayout(QGridLayout())
         self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
 
@@ -49,38 +62,30 @@ def __init__(self, viewer: Viewer) -> None:
         self.load_mask_dir_button.clicked.connect(self._open_mask_dir_dialog)
         self.layout().addWidget(self.load_mask_dir_button, 1, 2)
 
-        # The lower bound marker column
+        # The lower bound marker column dropdown
         lower_col = QLabel("Select lowerbound marker column:")
         self.lower_bound_marker_col = QComboBox()
         if len(self.model.regionprops_df) > 0:
             self.lower_bound_marker_col.addItems([None] + self.model.regionprops_df.columns)
-        self.lower_bound_marker_col.currentTextChanged.connect(self._update_marker_widget)
+        self.lower_bound_marker_col.currentTextChanged.connect(self._update_model_lowerbound)
         self.layout().addWidget(lower_col, 2, 0)
         self.layout().addWidget(self.lower_bound_marker_col, 3, 0)
 
-        # The upper bound marker column
+        # The upper bound marker column dropdown
         upper_col = QLabel("Select upperbound marker column:")
         self.upper_bound_marker_col = QComboBox()
         if len(self.model.regionprops_df) > 0:
             self.upper_bound_marker_col.addItems([None] + self.model.regionprops_df.columns)
-        self.upper_bound_marker_col.currentTextChanged.connect(self._update_marker_widget)
+        self.upper_bound_marker_col.currentTextChanged.connect(self._update_model_upperbound)
         self.layout().addWidget(upper_col, 2, 1)
         self.layout().addWidget(self.upper_bound_marker_col, 3, 1)
 
-        # Dropdown of samples once directory is loaded
-        selection_label = QLabel("Select sample:")
-        self.sample_selection_dropdown = QComboBox()
-        if len(self.model.samples) > 0:
-            self.sample_selection_dropdown.addItems([None])
-            self.sample_selection_dropdown.addItems(self.model.samples)
-        self.sample_selection_dropdown.currentTextChanged.connect(self._on_sample_changed)
+        self.validate_button = QPushButton("Validate input")
+        self.validate_button.clicked.connect(self.model.validate)
+        self.layout().addWidget(self.validate_button, 4, 0)
 
-        self.layout().addWidget(selection_label, 4, 0, Qt.AlignCenter)
-        self.layout().addWidget(self.sample_selection_dropdown, 4, 1)
-
-        self.model.events.regionprops_df.connect(self._set_samples_dropdown)
-        self.model.events.regionprops_df.connect(self._set_marker_lowerbound)
-        self.model.events.regionprops_df.connect(self._set_marker_upperbound)
+        self.model.events.regionprops_df.connect(self._set_dropdown_marker_lowerbound)
+        self.model.events.regionprops_df.connect(self._set_dropdown_marker_upperbound)
 
     @property
     def viewer(self) -> Viewer:
@@ -92,10 +97,8 @@ def model(self) -> DataModel:
         """Data model of the widget."""
         return self._model
 
-    def _on_sample_changed(self):
-        pass
-
     def _dir_dialog(self):
+        """Open dialog for a user to pass on a directory."""
         dlg = QFileDialog()
         hist = get_open_history()
         dlg.setHistory(hist)
@@ -128,38 +131,36 @@ def _open_mask_dir_dialog(self):
         if folder not in {"", None}:
             self._set_mask_paths(folder)
 
-    def _set_image_paths(self, folder):
+    def _set_image_paths(self, folder: str) -> None:
+        """Set the image paths in the DataModel."""
         self.model.image_paths = list(Path(folder).glob("*tif"))
         napari_notification(f"{len(self.model.image_paths)} paths of images loaded.")
 
-    def _set_mask_paths(self, folder):
+    def _set_mask_paths(self, folder: str) -> None:
+        """Set the paths of the masks in the DataModel."""
         self.model.mask_paths = list(Path(folder).glob("*tif"))
         napari_notification(f"{len(self.model.mask_paths)} paths of masks loaded.")
 
-    def _assign_regionprops_to_model(self, folder):
-        self.model.regionprops_df = stack_csv_files(folder)
+    def _assign_regionprops_to_model(self, folder: str) -> None:
+        """Read the csv files in the directory and assign the resulting concatenated DataFrame in the DataModel."""
+        self.model.regionprops_df = stack_csv_files(Path(folder))
 
-    def _set_samples_dropdown(self, event: Any):
-        if (region_props := self.model.regionprops_df) is not None:
-            self.model.samples = list(region_props["sample_id"].cat.categories)
-
-            # New directory loaded so we reload the dropdown items
-            self.sample_selection_dropdown.clear()
-            if len(self.model.samples) > 0:
-                self.sample_selection_dropdown.addItems([None])
-                self.sample_selection_dropdown.addItems(self.model.samples)
-
-    def _update_marker_widget(self):
-        pass
-
-    def _set_marker_lowerbound(self):
+    def _set_dropdown_marker_lowerbound(self):
         self.lower_bound_marker_col.clear()
         region_props = self.model.regionprops_df
         if region_props is not None and len(region_props) > 0:
             self.lower_bound_marker_col.addItems(region_props.columns)
 
-    def _set_marker_upperbound(self):
+    def _set_dropdown_marker_upperbound(self):
         self.upper_bound_marker_col.clear()
         region_props = self.model.regionprops_df
         if region_props is not None and len(region_props) > 0:
             self.upper_bound_marker_col.addItems(region_props.columns)
+
+    def _update_model_lowerbound(self):
+        lower_bound_marker = self.lower_bound_marker_col.currentText()
+        self.model.lower_bound_marker = lower_bound_marker
+
+    def _update_model_upperbound(self):
+        upper_bound_marker = self.upper_bound_marker_col.currentText()
+        self.model.upper_bound_marker = upper_bound_marker