celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/viewers/base_viewer.py

@@ -0,0 +1,700 @@
+from collections import OrderedDict
+
+import numpy as np
+from PyQt5.QtCore import Qt
+from PyQt5.QtWidgets import QHBoxLayout, QAction, QLabel, QComboBox
+from fonticon_mdi6 import MDI6
+from superqt import QLabeledDoubleRangeSlider, QLabeledSlider
+from superqt.fonticon import icon
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+from celldetective.utils.image_loaders import auto_load_number_of_frames, _get_img_num_per_channel, load_frames
+from celldetective import get_logger
+
+logger = get_logger(__name__)
+
+class StackVisualizer(CelldetectiveWidget):
+    """
+    A widget for visualizing image stacks with interactive sliders and channel selection.
+
+    Parameters:
+    - stack (numpy.ndarray or None): The stack of images.
+    - stack_path (str or None): The path to the stack of images if provided as a file.
+    - frame_slider (bool): Enable frame navigation slider.
+    - contrast_slider (bool): Enable contrast adjustment slider.
+    - channel_cb (bool): Enable channel selection dropdown.
+    - channel_names (list or None): Names of the channels if `channel_cb` is True.
+    - n_channels (int): Number of channels.
+    - target_channel (int): Index of the target channel.
+    - window_title (str): Title of the window.
+    - PxToUm (float or None): Pixel to micrometer conversion factor.
+    - background_color (str): Background color of the widget.
+    - imshow_kwargs (dict): Additional keyword arguments for imshow function.
+
+    Methods:
+    - show(): Display the widget.
+    - load_stack(): Load the stack of images.
+    - locate_image_virtual(): Locate the stack of images if provided as a file.
+    - generate_figure_canvas(): Generate the figure canvas for displaying images.
+    - generate_channel_cb(): Generate the channel dropdown if enabled.
+    - generate_contrast_slider(): Generate the contrast slider if enabled.
+    - generate_frame_slider(): Generate the frame slider if enabled.
+    - set_target_channel(value): Set the target channel.
+    - change_contrast(value): Change contrast based on slider value.
+    - set_channel_index(value): Set the channel index based on dropdown value.
+    - change_frame(value): Change the displayed frame based on slider value.
+    - closeEvent(event): Event handler for closing the widget.
+
+    Notes:
+    - This class provides a convenient interface for visualizing image stacks with frame navigation,
+      contrast adjustment, and channel selection functionalities.
+    """
+
+    def __init__(
+        self,
+        stack=None,
+        stack_path=None,
+        frame_slider=True,
+        contrast_slider=True,
+        channel_cb=False,
+        channel_names=None,
+        n_channels=1,
+        target_channel=0,
+        window_title="View",
+        PxToUm=None,
+        background_color="transparent",
+        imshow_kwargs={},
+    ):
+        super().__init__()
+
+        # self.setWindowTitle(window_title)
+        self.window_title = window_title
+
+        # LRU Cache for virtual mode
+        self.frame_cache = OrderedDict()
+        self.max_cache_size = 128
+        self.current_time_index = 0
+
+        self.stack = stack
+        self.stack_path = stack_path
+        self.create_frame_slider = frame_slider
+        self.background_color = background_color
+        self.create_contrast_slider = contrast_slider
+        self.create_channel_cb = channel_cb
+        self.n_channels = n_channels
+        self.channel_names = channel_names
+        self.target_channel = target_channel
+        self.imshow_kwargs = imshow_kwargs
+        self.PxToUm = PxToUm
+        self.init_contrast = False
+        self.channel_trigger = False
+        self.roi_mode = False
+        self.line_mode = False
+        self.line_artist = None
+        self.ax_profile = None
+        self._min = 0
+        self._max = 0
+
+        self.load_stack()
+        self.generate_figure_canvas()
+        if self.create_channel_cb:
+            self.generate_channel_cb()
+        if self.create_contrast_slider:
+            self.generate_contrast_slider()
+        if self.create_frame_slider:
+            self.generate_frame_slider()
+
+        self.line_color = "orange"
+        self.line_artist = None
+        self.ax_profile = None
+        self.line_text = None
+        self.background = None
+        self.is_drawing_line = False
+        self.generate_custom_tools()
+
+        self.canvas.layout.setContentsMargins(15, 15, 15, 30)
+
+        center_window(self)
+
+    def generate_custom_tools(self):
+
+        tools_layout = QHBoxLayout()
+        tools_layout.setContentsMargins(15, 0, 15, 0)
+
+        actions = self.canvas.toolbar.actions()
+
+        # Create the action
+        self.line_action = QAction(
+            icon(MDI6.chart_line, color="black"), "Line Profile", self.canvas.toolbar
+        )
+        self.line_action.setCheckable(True)
+        self.line_action.setToolTip("Draw a line to plot intensity profile.")
+        self.line_action.triggered.connect(self.toggle_line_mode)
+
+        # Lock Y-Axis Action
+        self.lock_y_action = QAction(
+            icon(MDI6.lock, color="black"), "Lock Y-Axis", self.canvas.toolbar
+        )
+        self.lock_y_action.setCheckable(True)
+        self.lock_y_action.setToolTip(
+            "Lock the Y-axis min/max values for the profile plot."
+        )
+        self.lock_y_action.setEnabled(False)  # Enable only when line mode is active
+
+        target_action = None
+        for action in actions:
+            if "Zoom" in action.text() or "Pan" in action.text():
+                target_action = action
+
+        if target_action:
+            insert_before = None
+            for action in actions:
+                if "Subplots" in action.text() or "Configure" in action.text():
+                    insert_before = action
+                    break
+
+            if insert_before:
+                self.canvas.toolbar.insertAction(insert_before, self.line_action)
+                self.canvas.toolbar.insertAction(insert_before, self.lock_y_action)
+            else:
+                if len(actions) > 5:
+                    self.canvas.toolbar.insertAction(actions[5], self.line_action)
+                    self.canvas.toolbar.insertAction(actions[5], self.line_action)
+                    self.canvas.toolbar.insertAction(actions[5], self.lock_y_action)
+                else:
+                    self.canvas.toolbar.addAction(self.line_action)
+                    self.canvas.toolbar.addAction(self.lock_y_action)
+
+        self.info_lbl = QLabel("")
+        tools_layout.addWidget(self.info_lbl)
+
+        self.canvas.layout.addLayout(tools_layout)
+
+    def toggle_line_mode(self):
+
+        if self.line_action.isChecked():
+
+            self.line_mode = True
+            self.lock_y_action.setEnabled(True)
+            self.canvas.toolbar.mode = ""
+
+            # Connect events
+            self.cid_press = self.fig.canvas.mpl_connect(
+                "button_press_event", self.on_line_press
+            )
+            self.cid_move = self.fig.canvas.mpl_connect(
+                "motion_notify_event", self.on_line_drag
+            )
+            self.cid_release = self.fig.canvas.mpl_connect(
+                "button_release_event", self.on_line_release
+            )
+
+            # Save original position if not saved
+            if not hasattr(self, "ax_original_pos"):
+                self.ax_original_pos = self.ax.get_position()
+
+            # Disable tight_layout/layout engine to prevent fighting manual positioning
+            if hasattr(self.fig, "set_layout_engine"):
+                self.fig.set_layout_engine("none")
+            else:
+                self.fig.set_tight_layout(False)
+
+            # Use GridSpec for robust layout
+            # 2 rows: Main Image (top, ~75%), Profile (bottom, ~25%)
+            # Add margins to ensure axis labels and text are visible
+            import matplotlib.gridspec as gridspec
+
+            gs = gridspec.GridSpec(
+                2,
+                1,
+                height_ratios=[3, 1],
+                hspace=0.05,
+                left=0.1,
+                right=0.9,
+                bottom=0.05,
+                top=1,
+            )
+
+            # Move main axes to top slot
+            self.ax.set_subplotspec(gs[0])
+            self.ax.set_position(gs[0].get_position(self.fig))
+
+            # create profile axes as a subplot in the bottom slot
+            if self.ax_profile is None:
+                self.ax_profile = self.fig.add_subplot(gs[1])
+            else:
+                self.ax_profile.set_subplotspec(gs[1])
+                self.ax_profile.set_position(gs[1].get_position(self.fig))
+
+            self.ax_profile.set_visible(True)
+            self.ax_profile.set_facecolor("none")
+            self.ax_profile.tick_params(axis="y", which="major", labelsize=8)
+            self.ax_profile.set_xticks([])
+            self.ax_profile.set_xlabel("")
+            self.ax_profile.set_ylabel("Intensity", fontsize=8)
+
+            # Hide spines initially
+            self.ax_profile.spines["top"].set_visible(False)
+            self.ax_profile.spines["right"].set_visible(False)
+            self.ax_profile.spines["bottom"].set_color("black")
+            self.ax_profile.spines["left"].set_color("black")
+
+            self.canvas.draw()
+        else:
+            self.line_mode = False
+            self.lock_y_action.setChecked(False)
+            self.lock_y_action.setEnabled(False)
+            # Disconnect events
+            if hasattr(self, "cid_press"):
+                self.fig.canvas.mpl_disconnect(self.cid_press)
+                self.fig.canvas.mpl_disconnect(self.cid_move)
+                self.fig.canvas.mpl_disconnect(self.cid_release)
+
+            # Remove line artist
+            if self.line_artist:
+                self.line_artist.remove()
+                self.line_artist = None
+
+            if hasattr(self, "line_text") and self.line_text:
+                self.line_text.remove()
+                self.line_text = None
+
+            # Remove profile axes and restore space
+            if self.ax_profile is not None:
+                self.ax_profile.remove()
+                self.ax_profile = None
+
+            # Restore original layout
+            if hasattr(self, "ax_original_pos"):
+                # standard 1x1 GridSpec or manual restore
+                import matplotlib.gridspec as gridspec
+
+                gs = gridspec.GridSpec(1, 1)
+                self.ax.set_subplotspec(gs[0])
+                self.ax.set_position(gs[0].get_position(self.fig))
+                self.fig.subplots_adjust(
+                    top=1, bottom=0, right=1, left=0, hspace=0, wspace=0
+                )
+                # self.ax.set_position(self.ax_original_pos) # tight layout should fix it
+
+            self.canvas.draw()
+            self.info_lbl.setText("")
+
+    def on_line_press(self, event):
+        if event.inaxes != self.ax:
+            return
+        if self.canvas.toolbar.mode:
+            return
+
+        self.line_x = [event.xdata]
+        self.line_y = [event.ydata]
+        self.is_drawing_line = True
+
+        # Initialize line artist if needed
+        if self.line_artist is None:
+            (self.line_artist,) = self.ax.plot(
+                self.line_x,
+                self.line_y,
+                color=self.line_color,
+                linestyle="-",
+                linewidth=3,
+            )
+        else:
+            self.line_artist.set_data(self.line_x, self.line_y)
+            self.line_artist.set_visible(True)
+
+        # Blitting setup
+        self.line_artist.set_animated(True)
+        self.canvas.draw()
+        self.background = self.canvas.canvas.copy_from_bbox(self.ax.bbox)
+        self.ax.draw_artist(self.line_artist)
+        self.canvas.canvas.blit(self.ax.bbox)
+
+    def on_line_drag(self, event):
+        if not getattr(self, "is_drawing_line", False) or event.inaxes != self.ax:
+            return
+
+        self.line_x = [self.line_x[0], event.xdata]
+        self.line_y = [self.line_y[0], event.ydata]
+
+        # Blitting update
+        if self.background:
+            self.canvas.canvas.restore_region(self.background)
+
+        self.line_artist.set_data(self.line_x, self.line_y)
+        self.ax.draw_artist(self.line_artist)
+        self.canvas.canvas.blit(self.ax.bbox)
+
+    def update_profile(self):
+        if not self.line_mode or not hasattr(self, "line_x") or not self.line_x:
+            return
+
+        # Calculate profile
+        x0, y0 = self.line_x[0], self.line_y[0]
+        x1, y1 = self.line_x[1], self.line_y[1]
+        length_px = np.hypot(x1 - x0, y1 - y0)
+        if length_px == 0:
+            return
+
+        num_points = int(length_px)
+        if num_points < 2:
+            num_points = 2
+
+        x, y = np.linspace(x0, x1, num_points), np.linspace(y0, y1, num_points)
+
+        # Use self.init_frame as self.im.get_array() might be unreliable or cached
+        if hasattr(self, "init_frame") and self.init_frame is not None:
+            from scipy.ndimage import map_coordinates
+
+            profile = map_coordinates(
+                self.init_frame, np.vstack((y, x)), order=1, mode="nearest"
+            )
+        else:
+            return
+
+        if np.all(np.isnan(profile)):
+            # If profile is all NaNs, we can't plot meaningful data, but we should maintain the axes
+            profile = np.zeros_like(profile)
+            profile[:] = np.nan
+
+        # Distance in microns if available
+        dist_axis = np.arange(num_points)
+        x_label = "Distance (px)"
+
+        # Only show pixel length, rounded to integer
+        title_str = f"{round(length_px,2)} [px]"
+        if self.PxToUm is not None:
+            title_str += f" | {round(length_px*self.PxToUm,3)} [µm]"
+
+        # Handle Y-Axis Locking
+        current_ylim = None
+        if self.lock_y_action.isChecked():
+            current_ylim = self.ax_profile.get_ylim()
+
+        # Plot profile
+        self.ax_profile.clear()
+        self.ax_profile.set_facecolor("none")
+        if hasattr(self, "profile_line") and self.profile_line:
+            try:
+                self.profile_line.remove()
+            except:
+                pass
+
+        # Distance in microns if available
+        dist_axis = np.arange(num_points)
+
+        (self.profile_line,) = self.ax_profile.plot(
+            dist_axis, profile, color="black", linestyle="-"
+        )
+        self.ax_profile.set_xticks([])
+        self.ax_profile.set_ylabel("Intensity", fontsize=8)
+        self.ax_profile.set_xlabel(title_str, fontsize=8)
+        self.ax_profile.tick_params(axis="y", which="major", labelsize=6)
+        # self.ax_profile.grid(True)
+
+        # Hide spines
+        self.ax_profile.spines["top"].set_visible(False)
+        self.ax_profile.spines["right"].set_visible(False)
+        self.ax_profile.spines["bottom"].set_color("black")
+        self.ax_profile.spines["left"].set_color("black")
+
+        self.fig.set_facecolor("none")
+
+        if current_ylim:
+            self.ax_profile.set_ylim(current_ylim)
+
+        self.fig.canvas.draw_idle()
+
+    def on_line_release(self, event):
+        if not getattr(self, "is_drawing_line", False):
+            return
+        self.is_drawing_line = False
+
+        if event.inaxes != self.ax:
+            return
+
+        # Final update
+        self.line_x = [self.line_x[0], event.xdata]
+        self.line_y = [self.line_y[0], event.ydata]
+        self.line_artist.set_data(self.line_x, self.line_y)
+
+        # Finalize drawing (disable animation for persistence)
+        self.line_artist.set_animated(False)
+        self.background = None
+
+        self.update_profile()
+        self.canvas.canvas.draw_idle()
+
+    def show(self):
+        # Display the widget
+        self.canvas.show()
+
+    def load_stack(self):
+        # Load the stack of images
+        if self.stack is not None:
+            if isinstance(self.stack, list):
+                self.stack = np.asarray(self.stack)
+
+            if self.stack.ndim == 3:
+                # Assuming stack is (T, Y, X) -> convert to (T, Y, X, 1) for consistent 4D handling
+                logger.info(
+                    "StackVisualizer: 3D stack detected (T, Y, X). Adding channel axis."
+                )
+                self.stack = self.stack[:, :, :, np.newaxis]
+                self.target_channel = 0
+
+            self.mode = "direct"
+            self.stack_length = len(self.stack)
+            self.mid_time = self.stack_length // 2
+            self.init_frame = self.stack[self.mid_time, :, :, self.target_channel]
+            self.last_frame = self.stack[-1, :, :, self.target_channel]
+        else:
+            self.mode = "virtual"
+            assert isinstance(self.stack_path, str)
+            assert self.stack_path.endswith(".tif")
+            self.locate_image_virtual()
+
+    def locate_image_virtual(self):
+        # Locate the stack of images if provided as a file
+
+        self.stack_length = auto_load_number_of_frames(self.stack_path)
+        self.mid_time = self.stack_length // 2
+        self.img_num_per_channel = _get_img_num_per_channel(
+            np.arange(self.n_channels), self.stack_length, self.n_channels
+        )
+
+        self.init_frame = load_frames(
+            self.img_num_per_channel[self.target_channel, self.mid_time],
+            self.stack_path,
+            normalize_input=False,
+        )[:, :, 0]
+        self.last_frame = load_frames(
+            self.img_num_per_channel[self.target_channel, self.stack_length - 1],
+            self.stack_path,
+            normalize_input=False,
+        )[:, :, 0]
+
+    def generate_figure_canvas(self):
+
+        if np.all(np.isnan(self.init_frame)):
+            p01, p99 = 0, 1
+        else:
+            p01 = np.nanpercentile(self.init_frame, 0.1)
+            p99 = np.nanpercentile(self.init_frame, 99.9)
+
+        if np.isnan(p01):
+            p01 = 0
+        if np.isnan(p99):
+            p99 = 1
+
+        import matplotlib.pyplot as plt
+        from celldetective.gui.base.figure_canvas import FigureCanvas
+
+        self.fig, self.ax = plt.subplots(figsize=(5, 5))
+
+        self.fig.subplots_adjust(top=1, bottom=0, right=1, left=0, hspace=0, wspace=0)
+        self.ax.margins(0)
+        self.fig.patch.set_alpha(0)
+        self.canvas = FigureCanvas(self.fig, title=self.window_title, interactive=True)
+        self.ax.clear()
+        self.im = self.ax.imshow(
+            self.init_frame,
+            cmap="gray",
+            interpolation="none",
+            zorder=0,
+            vmin=p01,
+            vmax=p99,
+            **self.imshow_kwargs,
+        )
+        if self.PxToUm is not None:
+            from matplotlib_scalebar.scalebar import ScaleBar
+
+            scalebar = ScaleBar(
+                self.PxToUm,
+                "um",
+                length_fraction=0.25,
+                location="upper right",
+                border_pad=0.4,
+                box_alpha=0.95,
+                color="white",
+                box_color="black",
+                font_properties={"weight": "bold", "size": 10},
+            )
+            self.ax.add_artist(scalebar)
+        self.ax.axis("off")
+
+    def generate_channel_cb(self):
+
+        self.channel_cb = QComboBox()
+        if self.channel_names is not None and len(self.channel_names) > 0:
+            for name in self.channel_names:
+                self.channel_cb.addItem(name)
+        else:
+            for i in range(self.n_channels):
+                self.channel_cb.addItem(f"Channel {i}")
+        self.channel_cb.currentIndexChanged.connect(self.set_channel_index)
+
+        layout = QHBoxLayout()
+        layout.addWidget(QLabel("Channel: "), 15)
+        layout.addWidget(self.channel_cb, 85)
+        self.canvas.layout.addLayout(layout)
+
+    def set_contrast_decimals(self):
+        from celldetective.utils.types import is_integer_array
+
+        if is_integer_array(self.init_frame):
+            self.contrast_decimals = 0
+        else:
+            self.contrast_decimals = 2
+
+    def generate_contrast_slider(self):
+        # Generate the contrast slider if enabled
+
+        layout = QHBoxLayout()
+        self.set_contrast_decimals()
+        self.contrast_slider = QLabeledDoubleRangeSlider(Qt.Horizontal)
+        if np.all(np.isnan(self.init_frame)):
+            min_val, max_val = 0, 1
+        else:
+            min_val = np.nanmin(self.init_frame)
+            max_val = np.nanmax(self.init_frame)
+
+        if np.isnan(min_val):
+            min_val = 0
+        if np.isnan(max_val):
+            max_val = 1
+
+        self.contrast_slider.setRange(min_val, max_val)
+
+        # Set initial value to percentiles to avoid outliers
+        if np.all(np.isnan(self.init_frame)):
+            p01, p99 = 0, 1
+        else:
+            p01 = np.nanpercentile(self.init_frame, 0.1)
+            p99 = np.nanpercentile(self.init_frame, 99.9)
+
+        if np.isnan(p01):
+            p01 = min_val
+        if np.isnan(p99):
+            p99 = max_val
+
+        if p99 > p01:
+            self.contrast_slider.setValue((p01, p99))
+        else:
+            self.contrast_slider.setValue((min_val, max_val))
+
+        self.contrast_slider.setEdgeLabelMode(
+            QLabeledDoubleRangeSlider.EdgeLabelMode.NoLabel
+        )
+        self.contrast_slider.setDecimals(self.contrast_decimals)
+
+        self.contrast_slider.valueChanged.connect(self.change_contrast)
+        layout.addWidget(QLabel("Contrast: "), 15)
+        layout.addWidget(self.contrast_slider, 85)
+        self.canvas.layout.addLayout(layout)
+
+    def generate_frame_slider(self):
+        # Generate the frame slider if enabled
+
+        layout = QHBoxLayout()
+        self.frame_slider = QLabeledSlider(Qt.Horizontal)
+        self.frame_slider.setRange(0, self.stack_length - 1)
+        self.frame_slider.setValue(self.mid_time)
+        self.frame_slider.valueChanged.connect(self.change_frame)
+        layout.addWidget(QLabel("Time: "), 15)
+        layout.addWidget(self.frame_slider, 85)
+        self.canvas.layout.addLayout(layout)
+
+    def set_target_channel(self, value):
+        self.target_channel = value
+        self.init_frame = self.stack[self.mid_time, :, :, self.target_channel]
+        self.im.set_data(self.init_frame)
+        self.canvas.draw()
+        self.update_profile()
+
+    def change_contrast(self, value):
+        # Change contrast based on slider value
+        if not self.init_contrast:
+            self.im.set_clim(vmin=value[0], vmax=value[1])
+            self.canvas.draw()
+
+    def set_channel_index(self, value):
+        self.target_channel = value
+        self.channel_trigger = True
+        if self.create_frame_slider:
+            self.change_frame_from_channel_switch(self.frame_slider.value())
+        else:
+            if self.stack is not None and self.stack.ndim == 4:
+                self.init_frame = self.stack[self.mid_time, :, :, self.target_channel]
+                self.im.set_data(self.init_frame)
+                self.canvas.draw()
+                self.update_profile()
+
+    def change_frame_from_channel_switch(self, value):
+        self._min = 0
+        self._max = 0
+        self.change_frame(value)
+        if self.channel_trigger:
+            p01 = np.nanpercentile(self.init_frame, 0.1)
+            p99 = np.nanpercentile(self.init_frame, 99.9)
+            self.im.set_clim(vmin=p01, vmax=p99)
+            self.contrast_slider.setValue((p01, p99))
+            self.channel_trigger = False
+            self.canvas.draw()
+
+    def change_frame(self, value):
+
+        self.current_time_index = value
+
+        if self.mode == "direct":
+            self.init_frame = self.stack[value, :, :, self.target_channel]
+
+        elif self.mode == "virtual":
+            # Check cache first
+            cache_key = (self.target_channel, value)
+            if cache_key in self.frame_cache:
+                self.init_frame = self.frame_cache[cache_key]
+                self.frame_cache.move_to_end(cache_key)  # Mark as recently used
+            else:
+                self.init_frame = load_frames(
+                    self.img_num_per_channel[self.target_channel, value],
+                    self.stack_path,
+                    normalize_input=False,
+                )[:, :, 0]
+
+                # Add to cache
+                self.frame_cache[cache_key] = self.init_frame
+                # Enforce size limit
+                if len(self.frame_cache) > self.max_cache_size:
+                    self.frame_cache.popitem(last=False)  # Remove oldest
+
+        self.im.set_data(self.init_frame)
+        rescale_contrast = False
+
+        # Optimization: Check min/max on subsampled array for large images
+        if self.init_frame.size > 1000000:
+            view = self.init_frame[::30, ::30]
+        else:
+            view = self.init_frame
+
+        curr_min = np.nanmin(view)
+        curr_max = np.nanmax(view)
+
+        if curr_min < self._min:
+            self._min = curr_min
+            rescale_constrast = True
+        if curr_max > self._max:
+            self._max = curr_max
+            rescale_contrast = True
+
+        if rescale_contrast:
+            self.contrast_slider.setRange(self._min, self._max)
+        self.canvas.canvas.draw_idle()
+        self.update_profile()
+
+    def closeEvent(self, event):
+        # Event handler for closing the widget
+        if hasattr(self, "frame_cache") and isinstance(self.frame_cache, OrderedDict):
+            self.frame_cache.clear()
+        self.canvas.close()