Merge branch 'main' into stable

README.md

@@ -30,10 +30,16 @@ hook by running `pre-commit install` in the directory with the `.pre-commit-conf
 
 ## Installation
 
+Install napari (see https://napari.org/stable/tutorials/fundamentals/installation)
+
 You can install `napari-cell-gater` via [pip]:
 
     pip install napari-cell-gater
 
+or directly from github via [pip] with:
+
+    pip install git+https://github.com/melonora/napari-cell-gater.git@stable
+
 ## Visual Workflow 
 
 ![Image Alt Text](/docs/VisualWorkflow_highres.png)

src/cell_gater/_tests/_test_sample_widget.py

@@ -0,0 +1,41 @@
+import tempfile
+from typing import Any
+
+import numpy as np
+import pandas as pd
+
+from cell_gater.widgets.sample_widget import SampleWidget
+
+rng = np.random.default_rng(42)
+# if we get reports that with some column names there is a problem, we get it here to automatically test.
+MARKER_DF = pd.DataFrame(
+    {
+        "CellID": list(range(5)),
+        "DNA": rng.random(5),
+        "Rabbit IgG": rng.random(5),
+        "Goat IgG": rng.random(5),
+        "DNA2": rng.random(5),
+        "CD73": rng.random(5),
+        "Some.name.with.dots": rng.random(5),
+    }
+)
+
+
+def test_populate_markers_on_csv_load(make_napari_viewer: Any) -> None:
+    viewer = make_napari_viewer()
+    widget = SampleWidget(viewer)
+    with tempfile.TemporaryDirectory() as tmpdir:
+        MARKER_DF.to_csv(tmpdir + "/test1.csv", index=False)
+        MARKER_DF.to_csv(tmpdir + "/test12.csv", index=False)
+
+        widget._open_sample_dialog(folder=tmpdir)
+
+        lower_marker_cols = [
+            widget.lower_bound_marker_col.itemText(index) for index in range(widget.lower_bound_marker_col.count())
+        ]
+        upper_marker_cols = [
+            widget.upper_bound_marker_col.itemText(index) for index in range(widget.upper_bound_marker_col.count())
+        ]
+        reference_cols = list(MARKER_DF.columns)
+        reference_cols.append("sample_id")
+        assert lower_marker_cols == upper_marker_cols == reference_cols

src/cell_gater/model/data_model.py

@@ -7,6 +7,7 @@
 import pandas as pd
 from napari.utils.events import EmitterGroup, Event
 
+
 @dataclass
 class DataModel:
     """Model containing all necessary fields for gating."""
@@ -146,6 +147,10 @@ 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 markers_image_indices(self):
         """The markers included for gating."""
@@ -155,10 +160,6 @@ def markers_image_indices(self):
     def markers_image_indices(self, markers_image_indices: Sequence[str]) -> None:
         self._markers_image_indices = markers_image_indices
 
-    @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."""

src/cell_gater/utils/csv_df.py

@@ -27,13 +27,13 @@ def stack_csv_files(csv_dir: Path) -> pd.DataFrame | None:
     napari_notification(f"Loaded {len(csv_files)} regionprops csvs.")
     df = pd.DataFrame()
     for file in csv_files:
-        if not file.name.startswith('.'):
+        if not file.name.startswith("."):
             df_file = pd.read_csv(file)
             df_file["sample_id"] = file.stem
             df = pd.concat([df, df_file], ignore_index=True)
             df["sample_id"] = df.sample_id.astype("category")
         else:
-            print(f"Skipping file {file.name} as it is a hidden file.")
+            napari_notification(f"Skipping file {file.name} as it is a hidden file.")
 
     return df
 

src/cell_gater/utils/misc.py

@@ -5,6 +5,7 @@
 )
 
 
-def napari_notification(msg, severity=NotificationSeverity.INFO):
+def napari_notification(msg: str, severity: NotificationSeverity = NotificationSeverity.INFO) -> None:
+    """Display a napari notification within the napari viewer with a given severity."""
     notification_ = Notification(msg, severity=severity)
-    notification_manager.dispatch(notification_)
+    notification_manager.dispatch(notification_)

src/cell_gater/widgets/sample_widget.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 
 from napari import Viewer
@@ -125,11 +127,12 @@ def _dir_dialog(self):
             QFileDialog.Options(),
         )
 
-    def _open_sample_dialog(self):
+    def _open_sample_dialog(self, folder: str | None = None):
         """Open directory file dialog for regionprop directory."""
-        folder = self._dir_dialog()
+        if not folder:
+            folder = self._dir_dialog()
 
-        if folder not in {"", None}:
+        if isinstance(folder, str) and folder != "":
             self._assign_regionprops_to_model(folder)
             update_open_history(folder)
 

src/cell_gater/widgets/scatter_widget.py

@@ -3,6 +3,7 @@
 import sys
 from itertools import product
 
+
 import numpy as np
 import pandas as pd
 from dask_image.imread import imread
@@ -36,9 +37,10 @@
 
 #Good to have features
 
-#Ideas to maybe implement
-#TODO dynamic plotting of points on top of created polygons
-#TODO save plots as images for QC, perhaps when saving gates run plotting function to go through all samples and markers and save plots
+# Ideas to maybe implement
+# TODO dynamic plotting of points on top of created polygons
+# TODO save plots as images for QC, perhaps when saving gates run plotting function to go through all samples and markers and save plots
+
 
 class ScatterInputWidget(QWidget):
     """Widget for a scatter plot with markers on the x axis and any dtype column on the y axis."""
@@ -58,7 +60,7 @@ def __init__(self, model: DataModel, viewer: Viewer) -> None:
 
         selection_label = QLabel("Select sample:")
         self.sample_selection_dropdown = QComboBox()
-        self.sample_selection_dropdown.addItems(sorted(self.model.samples, key=self.natural_sort_key) )
+        self.sample_selection_dropdown.addItems(sorted(self.model.samples, key=self.natural_sort_key))
         self.sample_selection_dropdown.currentTextChanged.connect(self._on_sample_changed)
 
         marker_label = QLabel("Marker label:")
@@ -200,10 +202,13 @@ def update_plot(self):
         self.scatter_canvas.plot_scatter_plot(self.model)
         self.scatter_canvas.fig.draw()
 
+
     ###################
     ### PLOT POINTS ###
     ###################
 
+    # TODO dynamic plotting of points on top of created polygons
+
     def plot_points(self):
         """Plot positive cells in Napari."""
         df = self.model.regionprops_df
@@ -432,6 +437,7 @@ def _file_dialog(self):
     def natural_sort_key(self, s):
         """Key function for natural sorting."""
         import re
+
         return [int(text) if text.isdigit() else text.lower() for text in re.split(r"(\d+)", s)]
 
     @property