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

celldetective/gui/settings/__init__.py

@@ -1,7 +0,0 @@
-from ._settings_measurements import SettingsMeasurements
-from ._settings_segmentation import SettingsSegmentation
-from ._settings_tracking import SettingsTracking
-from ._settings_segmentation_model_training import SettingsSegmentationModelTraining
-from ._settings_event_model_training import SettingsEventDetectionModelTraining
-from ._settings_signal_annotator import SettingsSignalAnnotator
-from ._settings_neighborhood import SettingsNeighborhood

celldetective/gui/settings/_cellpose_model_params.py

@@ -0,0 +1,181 @@
+from typing import List
+
+import numpy as np
+from PyQt5.QtCore import QSize, Qt
+from PyQt5.QtWidgets import QVBoxLayout, QPushButton, QComboBox, QHBoxLayout, QLabel
+from fonticon_mdi6 import MDI6
+from superqt import QLabeledDoubleSlider
+from superqt.fonticon import icon
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.gui_utils import ThresholdLineEdit
+from celldetective.gui.viewers.size_viewer import CellSizeViewer
+
+
+class CellposeParamsWidget(CelldetectiveWidget):
+    """
+    A widget to configure parameters for Cellpose segmentation, allowing users to set the cell diameter,
+    select imaging channels, and adjust flow and cell probability thresholds for cell detection.
+
+    This widget is designed for estimating cell diameters and configuring parameters for Cellpose,
+    a deep learning-based segmentation tool. It also provides functionality to preview the image stack with a scale bar.
+
+    Parameters
+    ----------
+    parent_window : QWidget, optional
+            The parent window that hosts the widget (default is None).
+    model_name : str, optional
+            The name of the Cellpose model being used, typically 'CP_cyto2' for cytoplasm or 'CP_nuclei' for nuclei segmentation
+            (default is 'CP_cyto2').
+
+    Notes
+    -----
+    - This widget assumes that the parent window or one of its ancestor windows has access to the experiment channels
+      and can locate the current image stack via `locate_image()`.
+    - This class integrates sliders for flow and cell probability thresholds, as well as a channel selection for running
+      Cellpose segmentation.
+    - The `view_current_stack_with_scale_bar()` method opens a new window where the user can visually inspect the
+      image stack with a superimposed scale bar, to better estimate the cell diameter.
+
+    """
+
+    view_diameter_btn: QPushButton = QPushButton()
+    diameter_le: ThresholdLineEdit
+    viewer: CellSizeViewer
+    cellpose_channel_cb: List[QComboBox]
+    cellpose_channel_template: List[str]
+    flow_slider: QLabeledDoubleSlider = QLabeledDoubleSlider()
+    set_cellpose_scale_btn: QPushButton = QPushButton("set")
+    cellprob_slider: QLabeledDoubleSlider = QLabeledDoubleSlider()
+
+    def __init__(self, parent_window=None, model_name="CP_cyto2", *args):
+
+        super().__init__(*args)
+        self.setWindowTitle("Estimate diameter")
+        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
+            )
+
+        # Layout and widgets setup
+        self.layout = QVBoxLayout()
+        self.populate_widgets()
+        self.setLayout(self.layout)
+        center_window(self)
+
+    def populate_widgets(self):
+        """
+        Populates the widget with UI elements such as buttons, sliders, and comboboxes to allow configuration
+        of Cellpose segmentation parameters.
+        """
+
+        # Button to view the current stack with a scale bar
+        self.view_diameter_btn.setStyleSheet(self.button_select_all)
+        self.view_diameter_btn.setIcon(icon(MDI6.image_check, color="black"))
+        self.view_diameter_btn.setToolTip("View stack.")
+        self.view_diameter_btn.setIconSize(QSize(20, 20))
+        self.view_diameter_btn.clicked.connect(self.view_current_stack_with_scale_bar)
+
+        # Line edit for entering cell diameter
+        self.diameter_le = ThresholdLineEdit(
+            init_value=40,
+            connected_buttons=[self.view_diameter_btn],
+            placeholder="cell diameter in pixels",
+            value_type="float",
+        )
+
+        # Comboboxes for selecting imaging channels
+        self.cellpose_channel_cb = [QComboBox() for _ in range(2)]
+        self.cellpose_channel_template = ["brightfield_channel", "live_nuclei_channel"]
+        if self.model_name == "CP_nuclei":
+            self.cellpose_channel_template = ["live_nuclei_channel", "None"]
+
+        for k in range(2):
+            hbox_channel = QHBoxLayout()
+            hbox_channel.addWidget(QLabel(f"channel {k+1}: "))
+            hbox_channel.addWidget(self.cellpose_channel_cb[k])
+            if k == 1:
+                self.cellpose_channel_cb[k].addItems(
+                    list(self.attr_parent.exp_channels) + ["None"]
+                )
+            else:
+                self.cellpose_channel_cb[k].addItems(
+                    list(self.attr_parent.exp_channels)
+                )
+            idx = self.cellpose_channel_cb[k].findText(
+                self.cellpose_channel_template[k]
+            )
+            if idx > 0:
+                self.cellpose_channel_cb[k].setCurrentIndex(idx)
+            else:
+                self.cellpose_channel_cb[k].setCurrentIndex(0)
+
+            if k == 1:
+                idx = self.cellpose_channel_cb[k].findText("None")
+                self.cellpose_channel_cb[k].setCurrentIndex(idx)
+
+            self.layout.addLayout(hbox_channel)
+
+        # Layout for diameter input and button
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("diameter [px]: "), 33)
+        hbox.addWidget(self.diameter_le, 61)
+        hbox.addWidget(self.view_diameter_btn)
+        self.layout.addLayout(hbox)
+
+        # Flow threshold slider
+        self.flow_slider.setOrientation(Qt.Horizontal)
+        self.flow_slider.setRange(-6, 6)
+        self.flow_slider.setValue(0.4)
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("flow threshold: "), 33)
+        hbox.addWidget(self.flow_slider, 66)
+        self.layout.addLayout(hbox)
+
+        # Cell probability threshold slider
+        self.cellprob_slider.setOrientation(Qt.Horizontal)
+        self.cellprob_slider.setRange(-6, 6)
+        self.cellprob_slider.setValue(0.0)
+        hbox = QHBoxLayout()
+        hbox.addWidget(QLabel("cellprob threshold: "), 33)
+        hbox.addWidget(self.cellprob_slider, 66)
+        self.layout.addLayout(hbox)
+
+        # Button to set the scale for Cellpose segmentation
+        self.set_cellpose_scale_btn.setStyleSheet(self.button_style_sheet)
+        self.set_cellpose_scale_btn.clicked.connect(
+            self.parent_window.set_cellpose_scale
+        )
+        self.layout.addWidget(self.set_cellpose_scale_btn)
+
+    def view_current_stack_with_scale_bar(self):
+        """
+        Displays the current image stack with a scale bar, allowing users to visually estimate cell diameters.
+        """
+
+        self.attr_parent.locate_image()
+        if self.attr_parent.current_stack is not None:
+            max_size = np.amax([self.attr_parent.shape_x, self.attr_parent.shape_y])
+            self.viewer = CellSizeViewer(
+                initial_diameter=float(self.diameter_le.text().replace(",", ".")),
+                parent_le=self.diameter_le,
+                stack_path=self.attr_parent.current_stack,
+                window_title=f"Position {self.attr_parent.position_list.currentText()}",
+                diameter_slider_range=(0, max_size),
+                frame_slider=True,
+                contrast_slider=True,
+                channel_cb=True,
+                channel_names=self.attr_parent.exp_channels,
+                n_channels=self.attr_parent.nbr_channels,
+                PxToUm=1,
+            )
+            self.viewer.show()

celldetective/gui/settings/_event_detection_model_params.py

@@ -0,0 +1,95 @@
+import json
+import os
+
+from PyQt5.QtCore import Qt
+from PyQt5.QtGui import QDoubleValidator
+from PyQt5.QtWidgets import QVBoxLayout, QComboBox, QHBoxLayout, QLabel, QPushButton
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+from celldetective.utils.model_loaders import locate_signal_model
+
+
+class SignalModelParamsWidget(CelldetectiveWidget):
+
+    def __init__(self, parent_window=None, model_name=None, *args, **kwargs):
+
+        super().__init__(*args)
+        self.setWindowTitle("Signals")
+        self.parent_window = parent_window
+        self.model_name = model_name
+        self.locate_model_path()
+        self.required_channels = self.input_config["channels"]
+        self.onlyFloat = QDoubleValidator()
+
+        # 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 locate_model_path(self):
+
+        self.model_complete_path = locate_signal_model(self.model_name)
+        if self.model_complete_path is None:
+            raise ValueError(f"Model {self.model_name} could not be found.")
+        else:
+            print(f"Model path: {self.model_complete_path}...")
+
+        config_path = os.path.join(self.model_complete_path, "config_input.json")
+        if not os.path.exists(config_path):
+            raise ValueError(
+                f"The configuration for the inputs to the model could not be located at {config_path}."
+            )
+
+        with open(config_path) as config_file:
+            self.input_config = json.load(config_file)
+
+    def populate_widgets(self):
+
+        self.n_channels = len(self.required_channels)
+        self.channel_cbs = [QComboBox() for i in range(self.n_channels)]
+
+        self.parent_window.load_available_tables()
+        available_channels = list(self.parent_window.signals) + ["None"]
+        # Populate the comboboxes with available channels from the experiment
+        for k in range(self.n_channels):
+            hbox_channel = QHBoxLayout()
+            hbox_channel.addWidget(QLabel(f"channel {k+1}: "), 33)
+
+            ch_vbox = QVBoxLayout()
+            ch_vbox.addWidget(
+                QLabel(f"Req: {self.required_channels[k]}"), alignment=Qt.AlignLeft
+            )
+            ch_vbox.addWidget(self.channel_cbs[k])
+
+            self.channel_cbs[k].addItems(
+                available_channels
+            )  # Give none option for more than one channel input
+            idx = self.channel_cbs[k].findText(self.required_channels[k])
+
+            if idx >= 0:
+                self.channel_cbs[k].setCurrentIndex(idx)
+            else:
+                self.channel_cbs[k].setCurrentIndex(len(available_channels) - 1)
+
+            hbox_channel.addLayout(ch_vbox, 66)
+            self.layout.addLayout(hbox_channel)
+
+        # Button to apply the StarDist settings
+        self.set_btn = QPushButton("set")
+        self.set_btn.setStyleSheet(self.button_style_sheet)
+        self.set_btn.clicked.connect(
+            self.parent_window.set_selected_signals_for_event_detection
+        )
+        self.layout.addWidget(self.set_btn)

celldetective/gui/settings/_segmentation_model_params.py

@@ -0,0 +1,159 @@
+import json
+import os
+
+import numpy as np
+from PyQt5.QtCore import QSize, Qt
+from PyQt5.QtGui import QDoubleValidator
+from PyQt5.QtWidgets import QVBoxLayout, QComboBox, QPushButton, QHBoxLayout, QLabel
+from fonticon_mdi6 import MDI6
+from superqt.fonticon import icon
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.gui_utils import ThresholdLineEdit
+from celldetective.gui.viewers.size_viewer import CellSizeViewer
+from celldetective.utils.model_loaders import locate_segmentation_model
+
+
+class SegModelParamsWidget(CelldetectiveWidget):
+
+    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
+        self.locate_model_path()
+        self.required_channels = self.input_config["channels"]
+        self.onlyFloat = QDoubleValidator()
+
+        # 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 locate_model_path(self):
+
+        self.model_complete_path = locate_segmentation_model(self.model_name)
+        if self.model_complete_path is None:
+            print("Model could not be found. Abort.")
+            self.abort_process()
+        else:
+            print(f"Model path: {self.model_complete_path}...")
+
+        if not os.path.exists(self.model_complete_path + "config_input.json"):
+            print(
+                "The configuration for the inputs to the model could not be located. Abort."
+            )
+            self.abort_process()
+
+        with open(self.model_complete_path + "config_input.json") as config_file:
+            self.input_config = json.load(config_file)
+
+    def populate_widgets(self):
+
+        self.n_channels = len(self.required_channels)
+        self.channel_cbs = [QComboBox() for i in range(self.n_channels)]
+
+        # Button to view the current stack with a scale bar
+        self.view_diameter_btn = QPushButton()
+        self.view_diameter_btn.setStyleSheet(self.button_select_all)
+        self.view_diameter_btn.setIcon(icon(MDI6.image_check, color="black"))
+        self.view_diameter_btn.setToolTip("View stack.")
+        self.view_diameter_btn.setIconSize(QSize(20, 20))
+        self.view_diameter_btn.clicked.connect(self.view_current_stack_with_scale_bar)
+
+        # Line edit for entering cell diameter
+        self.diameter_le = ThresholdLineEdit(
+            init_value=40,
+            connected_buttons=[self.view_diameter_btn],
+            placeholder="cell diameter in µm",
+            value_type="float",
+        )
+
+        available_channels = list(self.attr_parent.exp_channels) + ["None"]
+        # Populate the comboboxes with available channels from the experiment
+        for k in range(self.n_channels):
+            hbox_channel = QHBoxLayout()
+            hbox_channel.addWidget(QLabel(f"channel {k+1}: "), 33)
+
+            ch_vbox = QVBoxLayout()
+            ch_vbox.addWidget(
+                QLabel(f"Req: {self.required_channels[k]}"), alignment=Qt.AlignLeft
+            )
+            ch_vbox.addWidget(self.channel_cbs[k])
+
+            self.channel_cbs[k].addItems(
+                available_channels
+            )  # Give none option for more than one channel input
+            idx = self.channel_cbs[k].findText(self.required_channels[k])
+
+            if idx >= 0:
+                self.channel_cbs[k].setCurrentIndex(idx)
+            else:
+                self.channel_cbs[k].setCurrentIndex(len(available_channels) - 1)
+
+            hbox_channel.addLayout(ch_vbox, 66)
+            self.layout.addLayout(hbox_channel)
+
+        if "cell_size_um" in self.input_config:
+
+            # Layout for diameter input and button
+            hbox = QHBoxLayout()
+            hbox.addWidget(QLabel("cell size [µm]: "), 33)
+            hbox.addWidget(self.diameter_le, 61)
+            hbox.addWidget(self.view_diameter_btn)
+            self.layout.addLayout(hbox)
+
+            self.diameter_le.set_threshold(self.input_config["cell_size_um"])
+
+            # size_hbox = QHBoxLayout()
+            # size_hbox.addWidget(QLabel('cell size [µm]: '), 33)
+            # self.size_le = QLineEdit(str(self.input_config['cell_size_um']).replace('.',','))
+            # self.size_le.setValidator(self.onlyFloat)
+            # size_hbox.addWidget(self.size_le, 66)
+            # self.layout.addLayout(size_hbox)
+
+        # Button to apply the StarDist settings
+        self.set_btn = QPushButton("set")
+        self.set_btn.setStyleSheet(self.button_style_sheet)
+        self.set_btn.clicked.connect(
+            self.parent_window.set_selected_channels_for_segmentation
+        )
+        self.layout.addWidget(self.set_btn)
+
+    def view_current_stack_with_scale_bar(self):
+        """
+        Displays the current image stack with a scale bar, allowing users to visually estimate cell diameters.
+        """
+
+        self.attr_parent.locate_image()
+        if self.attr_parent.current_stack is not None:
+            max_size = np.amax([self.attr_parent.shape_x, self.attr_parent.shape_y])
+            self.viewer = CellSizeViewer(
+                initial_diameter=float(self.diameter_le.text().replace(",", ".")),
+                parent_le=self.diameter_le,
+                stack_path=self.attr_parent.current_stack,
+                window_title=f"Position {self.attr_parent.position_list.currentText()}",
+                diameter_slider_range=(0, max_size * self.attr_parent.PxToUm),
+                frame_slider=True,
+                contrast_slider=True,
+                channel_cb=True,
+                channel_names=self.attr_parent.exp_channels,
+                n_channels=self.attr_parent.nbr_channels,
+                PxToUm=self.attr_parent.PxToUm,
+            )
+            self.viewer.show()

celldetective/gui/settings/_settings_base.py

@@ -1,70 +1,82 @@
 from abc import abstractmethod
-from PyQt5.QtWidgets import QApplication, QScrollArea, QSizePolicy, QVBoxLayout, QPushButton
+from PyQt5.QtWidgets import (
+    QApplication,
+    QScrollArea,
+    QSizePolicy,
+    QVBoxLayout,
+    QPushButton,
+)
 from PyQt5.QtCore import Qt
-from celldetective.utils import get_software_location
-from celldetective.gui.gui_utils import center_window
-from celldetective.gui import CelldetectiveMainWindow, CelldetectiveWidget
+from celldetective import get_software_location
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.base.components import (
+    CelldetectiveMainWindow,
+    CelldetectiveWidget,
+)
 from PyQt5.QtGui import QDoubleValidator, QIntValidator
 
+
 class CelldetectiveSettingsPanel(CelldetectiveMainWindow):
-	
-	def __init__(self, title=""):
-		
-		super().__init__()
-		self.setWindowTitle(title)
-		
-		self._get_screen_height()
-		#self.setMinimumWidth(500)
-		self.setMaximumHeight(int(0.8 * self._screen_height))
-		self._scroll_area = QScrollArea(self)
-		self._floatValidator = QDoubleValidator()
-		self._intValidator = QIntValidator()
-		self._software_path = get_software_location()
-
-		self._create_widgets()
-		self._build_layouts()
-		self.center_window()
-	
-	def _create_widgets(self):
-		self.submit_btn: QPushButton = QPushButton("Save")
-		self.submit_btn.setStyleSheet(self.button_style_sheet)
-		self.submit_btn.clicked.connect(self._write_instructions)
-	
-	def center_window(self):
-		return center_window(self)
-	
-	def _get_screen_height(self):
-		app = QApplication.instance()
-		screen = app.primaryScreen()
-		geometry = screen.availableGeometry()
-		self._screen_width, self._screen_height = geometry.getRect()[-2:]
-	
-	def _adjustSize(self):
-		self._widget.adjustSize()
-		self._scroll_area.adjustSize()
-		self.adjustSize()
-	
-	def _build_layouts(self):
-		
-		self._layout: QVBoxLayout = QVBoxLayout()
-		self._widget: CelldetectiveWidget = CelldetectiveWidget()
-		self._widget.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
-		
-		# Create button widget and layout
-		self._widget.setLayout(self._layout)
-		self._layout.setContentsMargins(30, 30, 30, 30)
-		
-		self._scroll_area.setAlignment(Qt.AlignCenter)
-		self._scroll_area.setWidget(self._widget)
-		self._scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self._scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
-		self._scroll_area.setWidgetResizable(True)
-		self.setCentralWidget(self._scroll_area)
-		
-		QApplication.processEvents()
-	
-	@abstractmethod
-	def _load_previous_instructions(self): pass
-	
-	@abstractmethod
-	def _write_instructions(self): pass
+
+    def __init__(self, title=""):
+
+        super().__init__()
+        self.setWindowTitle(title)
+
+        self._get_screen_height()
+        # self.setMinimumWidth(500)
+        self.setMaximumHeight(int(0.8 * self._screen_height))
+        self._scroll_area = QScrollArea(self)
+        self._floatValidator = QDoubleValidator()
+        self._intValidator = QIntValidator()
+        self._software_path = get_software_location()
+
+        self._create_widgets()
+        self._build_layouts()
+        self.center_window()
+
+    def _create_widgets(self):
+        self.submit_btn: QPushButton = QPushButton("Save")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.clicked.connect(self._write_instructions)
+
+    def center_window(self):
+        return center_window(self)
+
+    def _get_screen_height(self):
+        app = QApplication.instance()
+        screen = app.primaryScreen()
+        geometry = screen.availableGeometry()
+        self._screen_width, self._screen_height = geometry.getRect()[-2:]
+
+    def _adjust_size(self):
+        self._widget.adjustSize()
+        self._scroll_area.adjustSize()
+        self.adjustSize()
+
+    def _build_layouts(self):
+
+        self._layout: QVBoxLayout = QVBoxLayout()
+        self._widget: CelldetectiveWidget = CelldetectiveWidget()
+        self._widget.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+
+        # Create button widget and layout
+        self._widget.setLayout(self._layout)
+        self._layout.setContentsMargins(30, 30, 30, 30)
+
+        self._scroll_area.setAlignment(Qt.AlignCenter)
+        self._scroll_area.setWidget(self._widget)
+        self._scroll_area.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+        self._scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
+        self._scroll_area.setWidgetResizable(True)
+        self.setCentralWidget(self._scroll_area)
+
+        QApplication.processEvents()
+
+    @abstractmethod
+    def _load_previous_instructions(self):
+        pass
+
+    @abstractmethod
+    def _write_instructions(self):
+        pass