Merge pull request #17 from josenimo/main

NatSorted samples, ignore hidden *.csv files, default upperbound marker, channel picker fixed

src/cell_gater/model/data_model.py

@@ -22,21 +22,32 @@ class DataModel:
     _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)
+    _markers_image_indices: Sequence[str] = field(default_factory=list, init=False)
     _marker_filter: str = field(default="dna,dapi", init=True)
     _validated: bool = field(default=False, init=True)
 
     _active_marker: str | None = field(default=None, init=False)
     _active_sample: str | None = field(default=None, init=False)
     _active_y_axis: str | None = field(default=None, init=False)
+    _active_ref_marker: str | None = field(default=None, init=False)
 
     _gates: pd.DataFrame = field(default_factory=pd.DataFrame, init=False)
     _current_gate: float = field(default_factory=float, init=False)
 
+    @property
+    def active_ref_marker(self):
+        """The reference marker for the gates."""
+        return self._active_ref_marker
+
+    @active_ref_marker.setter
+    def active_ref_marker(self, marker: str) -> None:
+        self._active_ref_marker = marker
+
     @property
     def gates(self):
         """The gates dataframe."""
         return self._gates
-    
+
     @gates.setter
     def gates(self, gates: pd.DataFrame) -> None:
         self._gates = gates
@@ -45,7 +56,7 @@ def gates(self, gates: pd.DataFrame) -> None:
     def current_gate(self) -> float:
         """The current gate value."""
         return self._current_gate
-    
+
     @current_gate.setter
     def current_gate(self, value: float) -> None:
         self._current_gate = value
@@ -132,6 +143,15 @@ def markers(self):
         """The markers included for gating."""
         return self._markers
 
+    @property
+    def markers_image_indices(self):
+        """The markers included for gating."""
+        return self._markers_image_indices
+
+    @markers_image_indices.setter
+    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

src/cell_gater/utils/csv_df.py

@@ -27,10 +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:
-        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")
+        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.")
 
     return df
 

src/cell_gater/widgets/sample_widget.py

@@ -21,6 +21,9 @@
 from cell_gater.utils.misc import napari_notification
 from cell_gater.widgets.scatter_widget import ScatterInputWidget
 
+#TODO still having problem with number of channels
+# if user picks a marker that is on the fifth position of the df.columns, then there is a shift
+
 class SampleWidget(QWidget):
     """Sample widget for loading required data."""
 
@@ -89,8 +92,8 @@ def __init__(self, viewer: Viewer, model: DataModel | None = None) -> None:
             placeholderText="Prefixes separated by commas.",
         )
         self.filter_field.editingFinished.connect(self._update_filter)
-        self.layout().addWidget(filter_label, 3, 0, 1 ,2)
-        self.layout().addWidget(self.filter_field, 3, 3)
+        self.layout().addWidget(filter_label,  3, 0, 1 ,1)
+        self.layout().addWidget(self.filter_field, 3, 1, 1, 1)
 
         # Button to start validating all the input
         self.validate_button = QPushButton("Validate input")
@@ -99,11 +102,10 @@ def __init__(self, viewer: Viewer, model: DataModel | None = None) -> None:
 
         self.model.events.regionprops_df.connect(self._set_dropdown_marker_lowerbound)
         self.model.events.regionprops_df.connect(self._set_dropdown_marker_upperbound)
-
-        #set default bounds
-
-
 
+    def update_ref_channel(self):
+        """Update the reference channel in the data model upon change of text in the reference channel column widget."""
+        self.model.ref_channel = self.ref_channel.currentText()
 
     @property
     def viewer(self) -> Viewer:
@@ -192,13 +194,13 @@ def _set_dropdown_marker_upperbound(self):
         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)
-
-        #TODO set default to column before "X_centroid"
-        # This does not work
-        # if "X_centroid" in list(self.model.regionprops_df.columns):
-        #     self.upper_bound_marker_col.setCurrentIndex(
-        #         self.model.regionprops_df.columns.index("X_centroid")-1 )
-
+            #set default to the last column before X_centroid
+            if "X_centroid" in region_props.columns:
+                default_index = self.model.regionprops_df.columns.tolist().index("X_centroid")
+                if default_index != -1:
+                    self.upper_bound_marker_col.setCurrentIndex(default_index-1)
+            else:
+                self.upper_bound_marker_col.setCurrentIndex(len(region_props.columns)-1)
 
     def _update_model_lowerbound(self):
         """Update the lowerbound marker in the data model upon change of text in the lowerbound marker column widget."""
@@ -229,6 +231,7 @@ def _validate(self):
         ), "Number of images and segmentation masks do not match."
 
         #TODO what happens when upperbound is before lowerbound?
+        #Should break and give error message
 
         # First check whether there is a difference between the file names without extension and then assign as samples
         image_paths_set = {i.stem if ".ome" not in i.stem else i.stem.rstrip(".ome") for i in self.model.image_paths}
@@ -252,6 +255,9 @@ def _validate(self):
         marker_columns = column_ls[lowerbound_index : upperbound_index + 1]
         self.model.markers = {marker: i for i, marker in enumerate(marker_columns)}
         n_markers = len(self.model.markers)
+        # ASSUMPTION: markers start at index 1 and finish before X_centroid
+        markers = column_ls[1:column_ls.index("X_centroid")-1]
+        self.model.markers_image_indices = {marker: i for i, marker in enumerate(markers)}
 
         for filter in self.model.marker_filter.split(","):
             # Do this because changing length would cause errors when deleting in loop.

src/cell_gater/widgets/scatter_widget.py

@@ -46,7 +46,6 @@
 logger.remove()
 logger.add(sys.stdout, format="<green>{time:HH:mm:ss.SS}</green> | <level>{level}</level> | {message}")
 
-
 #Good to have features
 #TODO Dynamic loading of markers, without reloading masks or DNA channel, so deprecate Load Sample and Marker button
 
@@ -79,7 +78,7 @@ def __init__(self, model: DataModel, viewer: Viewer) -> None:
         # Dropdown of samples once directory is loaded
         selection_label = QLabel("Select sample:")
         self.sample_selection_dropdown = QComboBox()
-        self.sample_selection_dropdown.addItems(self.model.samples)
+        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:")
@@ -96,27 +95,36 @@ def __init__(self, model: DataModel, viewer: Viewer) -> None:
         self.choose_y_axis_dropdown.setCurrentText("Area")
         self.choose_y_axis_dropdown.currentTextChanged.connect(self._on_y_axis_changed)
 
+        # Reference channel
+        DNA_to_show = QLabel("Select reference channel")
+        self.ref_channel_dropdown = QComboBox()
+        self.ref_channel_dropdown.addItems(self.model.markers_image_indices.keys())
+        self.ref_channel_dropdown.currentTextChanged.connect(self.update_ref_channel)
+
         self.layout().addWidget(selection_label, 0, 0)
         self.layout().addWidget(self.sample_selection_dropdown, 0, 1)
         self.layout().addWidget(marker_label, 0, 2)
         self.layout().addWidget(self.marker_selection_dropdown, 0, 3)
         self.layout().addWidget(apply_button, 1, 0, 1, 4)
-        self.layout().addWidget(choose_y_axis_label, 2, 0, 1, 2)
-        self.layout().addWidget(self.choose_y_axis_dropdown, 2, 2, 1, 2)
+        self.layout().addWidget(choose_y_axis_label, 2, 0, 1, 1)
+        self.layout().addWidget(self.choose_y_axis_dropdown, 2, 1, 1, 1)
+        self.layout().addWidget(DNA_to_show, 2, 2, 1, 1)
+        self.layout().addWidget(self.ref_channel_dropdown, 2, 3, 1, 1)
 
         # we have to do this because initially the dropdowns did not change texts yet so these variables are still None.
         self.model.active_sample = self.sample_selection_dropdown.currentText()
         self.model.active_marker = self.marker_selection_dropdown.currentText()
         self.model.active_y_axis = self.choose_y_axis_dropdown.currentText()
+        self.model.active_ref_marker = self.ref_channel_dropdown.currentText()
 
         self._read_data(self.model.active_sample)
-        self._load_layers(self.model.markers[self.model.active_marker])
+        self._load_layers(self.model.markers_image_indices[self.model.active_marker])
 
         # scatter plot
         self.scatter_canvas = PlotCanvas(self.model)
         self.layout().addWidget(self.scatter_canvas.fig, 3, 0, 1, 4)
 
-        # slider    
+        # slider
         self.slider_figure = Figure(figsize=(5, 1))
         self.slider_canvas = FigureCanvas(self.slider_figure)
         self.slider_ax = self.slider_figure.add_subplot(111)
@@ -130,11 +138,11 @@ def __init__(self, model: DataModel, viewer: Viewer) -> None:
 
         # Initialize gates dataframe 
         sample_marker_combinations = list(product(
-            self.model.regionprops_df['sample_id'].unique(), 
+            self.model.regionprops_df["sample_id"].unique(),
             self.model.markers
         ))
-        self.model.gates = pd.DataFrame(sample_marker_combinations, columns=['sample_id', 'marker_id'])
-        self.model.gates['gate_value'] = float(0)
+        self.model.gates = pd.DataFrame(sample_marker_combinations, columns=["sample_id", "marker_id"])
+        self.model.gates["gate_value"] = float(0)
 
         # gate buttons
         save_gate_button = QPushButton("Save Gate")
@@ -151,6 +159,10 @@ def __init__(self, model: DataModel, viewer: Viewer) -> None:
 
 
     ########################### FUNCTIONS ###########################
+
+    def update_ref_channel(self):
+        self.model.active_ref_marker = self.ref_channel_dropdown.currentText()
+        self._load_images_and_scatter_plot()
 
     ###################
     ### PLOT POINTS ###
@@ -187,14 +199,14 @@ def load_gates_dataframe(self):
         file_path, _ = self._file_dialog()
         if file_path:
             self.model.gates = pd.read_csv(file_path)
-        self.model.gates['sample_id'] = self.model.gates['sample_id'].astype(str)
+        self.model.gates["sample_id"] = self.model.gates["sample_id"].astype(str)
         # check if dataframe has samples and markers
-        assert 'sample_id' in self.model.gates.columns
-        assert 'marker_id' in self.model.gates.columns
-        assert 'gate_value' in self.model.gates.columns
+        assert "sample_id" in self.model.gates.columns
+        assert "marker_id" in self.model.gates.columns
+        assert "gate_value" in self.model.gates.columns
         # check if dataframe has the same samples and markers as the regionprops_df
-        assert set(self.model.gates['sample_id'].unique()) == set(self.model.regionprops_df['sample_id'].unique())
-        assert set(self.model.gates['marker_id'].unique()) == set(self.model.markers)
+        assert set(self.model.gates["sample_id"].unique()) == set(self.model.regionprops_df["sample_id"].unique())
+        assert set(self.model.gates["marker_id"].unique()) == set(self.model.markers)
 
     def save_gates_dataframe(self):
         options = QFileDialog.Options()
@@ -234,7 +246,7 @@ def access_gate(self):
     def get_min_max_median_step(self) -> tuple:
         df = self.model.regionprops_df
         df = df[df["sample_id"] == self.model.active_sample]
-        min = df[self.model.active_marker].min()
+        min = df[self.model.active_marker].min() + 1
         max = df[self.model.active_marker].max()
         init = df[self.model.active_marker].median()
         step = min / 100
@@ -264,8 +276,10 @@ def update_plot(self):
     def _load_images_and_scatter_plot(self):
         self._clear_layers(clear_all=True)
         self._read_data(self.model.active_sample)
-        self._load_layers(self.model.markers[self.model.active_marker])
-        logger.debug(f"loading index {self.model.markers[self.model.active_marker]}")
+        # active marker is a string
+        # markers is dict with marker_name_string:index (based on dropdowns)
+        self._load_layers(self.model.markers_image_indices[self.model.active_marker])
+        logger.debug(f"loading index {self.model.markers_image_indices[self.model.active_marker]}")
         self.update_plot()
         self.update_slider()
 
@@ -285,10 +299,9 @@ def _load_layers(self, marker_index):
         # if self.model.active_sample != self._current_sample:
         #     self._current_sample = copy(self.model.active_sample)
 
-        #TODO let user decide which is their DNA channel
         self.viewer.add_image(
-            self._image[0],
-            name="DNA_" + self.model.active_sample,
+            self._image[self.model.markers_image_indices[self.model.active_ref_marker]],
+            name="Reference" + self.model.active_sample,
             blending="additive",
             visible=False
         )
@@ -337,7 +350,7 @@ def _set_samples_dropdown(self) -> None:
             if len(self.model.samples) > 0:
                 self.sample_selection_dropdown.addItems([None])
                 self.sample_selection_dropdown.addItems(self.model.samples)
-    
+
     def _on_y_axis_changed(self):
         """Set active y-axis and update the scatter plot."""
         self.model.active_y_axis = self.choose_y_axis_dropdown.currentText()
@@ -356,7 +369,12 @@ def _file_dialog(self):
             "CSV Files (*.csv)",
             options=options,
         )
-
+
+    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
     def model(self) -> DataModel:
         """The dataclass model that stores information required for cell_gating."""
@@ -400,10 +418,10 @@ def model(self, model: DataModel) -> None:
     def plot_scatter_plot(self, model: DataModel) -> None:
         assert self.model.active_marker is not None
         assert self.model.active_sample is not None
-    
+
         df = self.model.regionprops_df
         df = df[df["sample_id"] == self.model.active_sample]
-        
+
         logger.debug(f"Plotting scatter plot for {self.model.active_sample} and {self.model.active_marker}.")
 
         self.ax.scatter(
@@ -419,13 +437,13 @@ def plot_scatter_plot(self, model: DataModel) -> None:
         self.ax.set_xlim(df[self.model.active_marker].min(), df[self.model.active_marker].max())
         self.ax.set_ylabel(self.model.active_y_axis)
         self.ax.set_xlabel(f"{self.model.active_marker} intensity")
-    
+
         logger.debug(f"The current gate is {self.model.current_gate}.")
         if self.model.current_gate > 0.0:
             self.ax.axvline(x=self.model.current_gate, color="red", linewidth=1.0, linestyle="--")
         else:
             self.ax.axvline(x=1, color="red", linewidth=1.0, linestyle="--")
-    
+
     def update_vertical_line(self, x_position):
         """Update the position of the vertical line."""
         self.ax.lines[0].set_xdata(x_position)