celldetective 1.4.2__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

celldetective/gui/settings/_stardist_model_params.py

@@ -0,0 +1,98 @@
+from PyQt5.QtWidgets import QVBoxLayout, QComboBox, QHBoxLayout, QLabel, QPushButton
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+
+
+class StarDistParamsWidget(CelldetectiveWidget):
+    """
+    A widget to configure parameters for StarDist segmentation.
+
+    This widget allows the user to select specific imaging channels for segmentation and adjust
+    parameters for StarDist, a neural network-based image segmentation tool designed to segment
+    star-convex shapes (typically nuclei).
+
+    Parameters
+    ----------
+    parent_window : QWidget, optional
+            The parent window hosting this widget (default is None).
+    model_name : str, optional
+            The name of the StarDist model being used, typically 'SD_versatile_fluo' for versatile
+            fluorescence or 'SD_versatile_he' for H&E-stained images (default is 'SD_versatile_fluo').
+    """
+
+    def __init__(
+        self, parent_window=None, model_name="SD_versatile_fluo", *args, **kwargs
+    ):
+
+        super().__init__(*args)
+        self.setWindowTitle("Channels")
+        self.parent_window = parent_window
+        self.model_name = model_name
+
+        # Setting up references to parent window attributes
+        if hasattr(self.parent_window.parent_window, "locate_image"):
+            self.attr_parent = self.parent_window.parent_window
+        elif hasattr(self.parent_window.parent_window.parent_window, "locate_image"):
+            self.attr_parent = self.parent_window.parent_window.parent_window
+        else:
+            self.attr_parent = (
+                self.parent_window.parent_window.parent_window.parent_window
+            )
+
+        # Set up layout and widgets
+        self.layout = QVBoxLayout()
+        self.populate_widgets()
+        self.setLayout(self.layout)
+        center_window(self)
+
+    def populate_widgets(self):
+        """
+        Populates the widget with channel selection comboboxes and a 'set' button to configure
+        the StarDist segmentation settings. Handles different models by adjusting the number of
+        available channels.
+        """
+
+        # Initialize comboboxes based on the selected model
+        self.stardist_channel_cb = [QComboBox() for i in range(1)]
+        self.stardist_channel_template = ["live_nuclei_channel"]
+        max_i = 1
+
+        # If the H&E model is selected, update the combobox configuration
+        if self.model_name == "SD_versatile_he":
+            self.stardist_channel_template = ["H&E_1", "H&E_2", "H&E_3"]
+            self.stardist_channel_cb = [QComboBox() for i in range(3)]
+            max_i = 3
+
+        # Populate the comboboxes with available channels from the experiment
+        for k in range(max_i):
+            hbox_channel = QHBoxLayout()
+            hbox_channel.addWidget(QLabel(f"channel {k+1}: "))
+            hbox_channel.addWidget(self.stardist_channel_cb[k])
+            if k == 1:
+                self.stardist_channel_cb[k].addItems(
+                    list(self.attr_parent.exp_channels) + ["None"]
+                )
+            else:
+                self.stardist_channel_cb[k].addItems(
+                    list(self.attr_parent.exp_channels)
+                )
+
+            # Set the default channel based on the template or fallback to the first option
+            idx = self.stardist_channel_cb[k].findText(
+                self.stardist_channel_template[k]
+            )
+            if idx > 0:
+                self.stardist_channel_cb[k].setCurrentIndex(idx)
+            else:
+                self.stardist_channel_cb[k].setCurrentIndex(0)
+
+            self.layout.addLayout(hbox_channel)
+
+        # Button to apply the StarDist settings
+        self.set_stardist_scale_btn = QPushButton("set")
+        self.set_stardist_scale_btn.setStyleSheet(self.button_style_sheet)
+        self.set_stardist_scale_btn.clicked.connect(
+            self.parent_window.set_stardist_scale
+        )
+        self.layout.addWidget(self.set_stardist_scale_btn)