add sample widget

pyproject.toml

@@ -26,7 +26,7 @@ select = [
     "PIE", # flake8-pie
     "SIM", # flake8-simplify
 ]
-ignore = [
+lint.ignore = [
     "E501", # line too long. let black handle this
     "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
     "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9

src/cell_gater/widgets/sample_widget.py

@@ -0,0 +1,150 @@
+from pathlib import Path
+from typing import Any
+
+from Gating.src.gating.model.data_model import DataModel
+from Gating.src.gating.utils.csv_df import stack_csv_files
+from Gating.src.gating.utils.misc import napari_notification
+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,
+    QGridLayout,
+    QLabel,
+    QPushButton,
+    QWidget,
+)
+
+
+class SampleWidget(QWidget):
+    def __init__(self, viewer: Viewer) -> None:
+        super().__init__()
+        self._viewer = viewer
+        self._model = DataModel()
+        self.setLayout(QGridLayout())
+
+        # Open sample directory dialog
+        self.load_samples_button = QPushButton("Load regionprops dir")
+        self.load_samples_button.clicked.connect(self._open_sample_dialog)
+        self.layout().addWidget(self.load_samples_button, 0, 0)
+
+        # Open image directory dialog
+        self.load_image_dir_button = QPushButton("Load image dir")
+        self.load_image_dir_button.clicked.connect(self._open_image_dir_dialog)
+        self.layout().addWidget(self.load_image_dir_button, 0, 1)
+
+        # Open mask directory dialog
+        self.load_mask_dir_button = QPushButton("Load mask dir")
+        self.load_mask_dir_button.clicked.connect(self._open_mask_dir_dialog)
+        self.layout().addWidget(self.load_mask_dir_button, 0, 2)
+
+        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(
+                self.model.regionprops_df.columns
+            )
+        self.lower_bound_marker_col.currentTextChanged.connect(
+            self._update_marker_widget
+        )
+        self.layout().addWidget(lower_col, 2, 0)
+        self.layout().addWidget(self.lower_bound_marker_col, 3, 0)
+
+        # 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.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)
+
+    @property
+    def viewer(self) -> Viewer:
+        return self._viewer
+
+    @property
+    def model(self) -> DataModel:
+        """:mod:`napari` viewer."""
+        return self._model
+
+    def _on_sample_changed(self):
+        pass
+
+    def _dir_dialog(self):
+        dlg = QFileDialog()
+        hist = get_open_history()
+        dlg.setHistory(hist)
+        return dlg.getExistingDirectory(
+            self,
+            "select folder",
+            hist[0],
+            QFileDialog.Options(),
+        )
+
+    def _open_sample_dialog(self):
+        """Open directory file dialog for samples"""
+        folder = self._dir_dialog()
+
+        if folder not in {"", None}:
+            self._assign_regionprops_to_model(folder)
+            update_open_history(folder)
+
+    def _open_image_dir_dialog(self):
+        folder = self._dir_dialog()
+
+        if folder not in {"", None}:
+            self._set_image_paths(folder)
+
+    def _open_mask_dir_dialog(self):
+        folder = self._dir_dialog()
+
+        if folder not in {"", None}:
+            self._set_mask_paths(folder)
+
+    def _set_image_paths(self, folder):
+        self.model.image_paths = list(Path(folder).glob("*tif"))
+        napari_notification(
+            f"{len(self.model.mask_paths)} paths of images loaded."
+        )
+
+    def _set_mask_paths(self, folder):
+        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 _set_samples_dropdown(self, event: Any):
+        self.model.samples = list(
+            self.model.regionprops_df["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):
+        self.lower_bound_marker_col.clear()
+        if len(self.model.regionprops_df) > 0:
+            self.lower_bound_marker_col.addItems(
+                self.model.regionprops_df.columns
+            )