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

celldetective/gui/viewers/channel_offset_viewer.py

@@ -0,0 +1,331 @@
+import gc
+
+import numpy as np
+from PyQt5.QtCore import Qt
+from PyQt5.QtGui import QKeySequence
+from PyQt5.QtWidgets import QHBoxLayout, QLabel, QComboBox, QPushButton, QShortcut
+from superqt import QLabeledDoubleSlider, QLabeledDoubleRangeSlider
+
+from celldetective.gui.base.components import QHSeperationLine
+from celldetective.gui.gui_utils import QuickSliderLayout, ThresholdLineEdit
+from celldetective.gui.viewers.base_viewer import StackVisualizer
+from celldetective.utils.image_loaders import load_frames, auto_load_number_of_frames, _get_img_num_per_channel
+from celldetective import get_logger
+
+logger = get_logger(__name__)
+
+class ChannelOffsetViewer(StackVisualizer):
+
+    def __init__(self, parent_window=None, *args, **kwargs):
+
+        self.parent_window = parent_window
+        self.overlay_target_channel = -1
+        self.shift_vertical = 0
+        self.shift_horizontal = 0
+        super().__init__(*args, **kwargs)
+
+        self.load_stack()
+        self.canvas.layout.addWidget(QHSeperationLine())
+
+        self.generate_overlay_channel_cb()
+        self.generate_overlay_imshow()
+
+        self.generate_overlay_alpha_slider()
+        self.generate_overlay_contrast_slider()
+
+        self.generate_overlay_shift()
+        self.generate_add_to_parent_btn()
+
+        if self.overlay_target_channel == -1:
+            index = len(self.channel_names) - 1
+        else:
+            index = self.overlay_target_channel
+        self.channels_overlay_cb.setCurrentIndex(index)
+        self.frame_slider.valueChanged.connect(self.change_overlay_frame)
+
+        self.define_keyboard_shortcuts()
+
+        self.channels_overlay_cb.setCurrentIndex(
+            self.parent_window.channels_cb.currentIndex()
+        )
+        self.set_channel_index(0)
+
+        self.setAttribute(Qt.WA_DeleteOnClose)
+
+    def generate_overlay_imshow(self):
+        self.im_overlay = self.ax.imshow(
+            self.overlay_init_frame,
+            cmap="Blues",
+            interpolation="none",
+            alpha=0.5,
+            **self.imshow_kwargs,
+        )
+
+    def generate_overlay_alpha_slider(self):
+        # Generate the contrast slider if enabled
+
+        self.overlay_alpha_slider = QLabeledDoubleSlider()
+        alpha_layout = QuickSliderLayout(
+            label="Overlay\ntransparency: ",
+            slider=self.overlay_alpha_slider,
+            slider_initial_value=0.5,
+            slider_range=(0, 1.0),
+            decimal_option=True,
+            precision=5,
+        )
+        alpha_layout.setContentsMargins(15, 0, 15, 0)
+        self.overlay_alpha_slider.valueChanged.connect(self.change_alpha_overlay)
+        self.canvas.layout.addLayout(alpha_layout)
+
+    def generate_overlay_contrast_slider(self):
+        # Generate the contrast slider if enabled
+
+        self.overlay_contrast_slider = QLabeledDoubleRangeSlider()
+        contrast_layout = QuickSliderLayout(
+            label="Overlay contrast: ",
+            slider=self.overlay_contrast_slider,
+            slider_initial_value=[
+                np.nanpercentile(self.overlay_init_frame, 0.1),
+                np.nanpercentile(self.overlay_init_frame, 99.99),
+            ],
+            slider_range=(
+                np.nanmin(self.overlay_init_frame),
+                np.nanmax(self.overlay_init_frame),
+            ),
+            decimal_option=True,
+            precision=5,
+        )
+        contrast_layout.setContentsMargins(15, 0, 15, 0)
+        self.im_overlay.set_clim(
+            vmin=np.nanpercentile(self.overlay_init_frame, 0.1),
+            vmax=np.nanpercentile(self.overlay_init_frame, 99.99),
+        )
+        self.overlay_contrast_slider.valueChanged.connect(self.change_contrast_overlay)
+        self.canvas.layout.addLayout(contrast_layout)
+
+    def set_overlay_channel_index(self, value):
+        # Set the channel index based on dropdown value
+
+        self.overlay_target_channel = value
+        self.overlay_init_contrast = True
+        if self.mode == "direct":
+            self.overlay_last_frame = self.stack[-1, :, :, self.overlay_target_channel]
+        elif self.mode == "virtual":
+            self.overlay_last_frame = load_frames(
+                self.img_num_per_channel[
+                    self.overlay_target_channel, self.stack_length - 1
+                ],
+                self.stack_path,
+                normalize_input=False,
+            ).astype(float)[:, :, 0]
+        self.change_overlay_frame(self.frame_slider.value())
+        self.overlay_init_contrast = False
+
+    def generate_overlay_channel_cb(self):
+
+        assert self.channel_names is not None
+        assert len(self.channel_names) == self.n_channels
+
+        channel_layout = QHBoxLayout()
+        channel_layout.setContentsMargins(15, 0, 15, 0)
+        channel_layout.addWidget(QLabel("Overlay channel: "), 25)
+
+        self.channels_overlay_cb = QComboBox()
+        self.channels_overlay_cb.addItems(self.channel_names)
+        self.channels_overlay_cb.currentIndexChanged.connect(
+            self.set_overlay_channel_index
+        )
+        channel_layout.addWidget(self.channels_overlay_cb, 75)
+        self.canvas.layout.addLayout(channel_layout)
+
+    def generate_overlay_shift(self):
+
+        shift_layout = QHBoxLayout()
+        shift_layout.setContentsMargins(15, 0, 15, 0)
+        shift_layout.addWidget(QLabel("shift (h): "), 20, alignment=Qt.AlignRight)
+
+        self.apply_shift_btn = QPushButton("Apply")
+        self.apply_shift_btn.setStyleSheet(self.button_style_sheet_2)
+        self.apply_shift_btn.setToolTip("Apply the shift to the overlay channel.")
+        self.apply_shift_btn.clicked.connect(self.shift_generic)
+
+        self.set_shift_btn = QPushButton("Set")
+
+        self.horizontal_shift_le = ThresholdLineEdit(
+            init_value=self.shift_horizontal,
+            connected_buttons=[self.apply_shift_btn, self.set_shift_btn],
+            placeholder="horizontal shift [pixels]",
+            value_type="float",
+        )
+        shift_layout.addWidget(self.horizontal_shift_le, 20)
+
+        shift_layout.addWidget(QLabel("shift (v): "), 20, alignment=Qt.AlignRight)
+
+        self.vertical_shift_le = ThresholdLineEdit(
+            init_value=self.shift_vertical,
+            connected_buttons=[self.apply_shift_btn, self.set_shift_btn],
+            placeholder="vertical shift [pixels]",
+            value_type="float",
+        )
+        shift_layout.addWidget(self.vertical_shift_le, 20)
+
+        shift_layout.addWidget(self.apply_shift_btn, 20)
+
+        self.canvas.layout.addLayout(shift_layout)
+
+    def change_overlay_frame(self, value):
+        # Change the displayed frame based on slider value
+
+        if self.mode == "virtual":
+
+            self.overlay_init_frame = load_frames(
+                self.img_num_per_channel[self.overlay_target_channel, value],
+                self.stack_path,
+                normalize_input=False,
+            ).astype(float)[:, :, 0]
+        elif self.mode == "direct":
+            self.overlay_init_frame = self.stack[
+                value, :, :, self.overlay_target_channel
+            ].copy()
+
+        self.im_overlay.set_data(self.overlay_init_frame)
+
+        if self.overlay_init_contrast:
+            self.im_overlay.autoscale()
+            I_min, I_max = self.im_overlay.get_clim()
+            self.overlay_contrast_slider.setRange(
+                np.nanmin([self.overlay_init_frame, self.overlay_last_frame]),
+                np.nanmax([self.overlay_init_frame, self.overlay_last_frame]),
+            )
+            self.overlay_contrast_slider.setValue((I_min, I_max))
+
+        if self.create_contrast_slider:
+            self.change_contrast_overlay(self.overlay_contrast_slider.value())
+
+    def locate_image_virtual(self):
+        from tifffile import imread
+
+        # Locate the stack of images if provided as a file
+        self.stack_length = auto_load_number_of_frames(self.stack_path)
+        if self.stack_length is None:
+            stack = imread(self.stack_path)
+            self.stack_length = len(stack)
+            del stack
+            gc.collect()
+
+        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,
+        ).astype(float)[:, :, 0]
+        self.last_frame = load_frames(
+            self.img_num_per_channel[self.target_channel, self.stack_length - 1],
+            self.stack_path,
+            normalize_input=False,
+        ).astype(float)[:, :, 0]
+        self.overlay_init_frame = load_frames(
+            self.img_num_per_channel[self.overlay_target_channel, self.mid_time],
+            self.stack_path,
+            normalize_input=False,
+        ).astype(float)[:, :, 0]
+        self.overlay_last_frame = load_frames(
+            self.img_num_per_channel[
+                self.overlay_target_channel, self.stack_length - 1
+            ],
+            self.stack_path,
+            normalize_input=False,
+        ).astype(float)[:, :, 0]
+
+    def change_contrast_overlay(self, value):
+        # Change contrast based on slider value
+
+        vmin = value[0]
+        vmax = value[1]
+        self.im_overlay.set_clim(vmin=vmin, vmax=vmax)
+        self.fig.canvas.draw_idle()
+
+    def change_alpha_overlay(self, value):
+        # Change contrast based on slider value
+
+        alpha = value
+        self.im_overlay.set_alpha(alpha)
+        self.fig.canvas.draw_idle()
+
+    def define_keyboard_shortcuts(self):
+
+        self.shift_up_shortcut = QShortcut(QKeySequence(Qt.Key_Up), self.canvas)
+        self.shift_up_shortcut.activated.connect(self.shift_overlay_up)
+
+        self.shift_down_shortcut = QShortcut(QKeySequence(Qt.Key_Down), self.canvas)
+        self.shift_down_shortcut.activated.connect(self.shift_overlay_down)
+
+        self.shift_left_shortcut = QShortcut(QKeySequence(Qt.Key_Left), self.canvas)
+        self.shift_left_shortcut.activated.connect(self.shift_overlay_left)
+
+        self.shift_right_shortcut = QShortcut(QKeySequence(Qt.Key_Right), self.canvas)
+        self.shift_right_shortcut.activated.connect(self.shift_overlay_right)
+
+    def shift_overlay_up(self):
+        self.shift_vertical -= 2
+        self.vertical_shift_le.set_threshold(self.shift_vertical)
+        # self.shift_generic()
+        self.apply_shift_btn.click()
+
+    def shift_overlay_down(self):
+        self.shift_vertical += 2
+        self.vertical_shift_le.set_threshold(self.shift_vertical)
+        # self.shift_generic()
+        self.apply_shift_btn.click()
+
+    def shift_overlay_left(self):
+        self.shift_horizontal -= 2
+        self.horizontal_shift_le.set_threshold(self.shift_horizontal)
+        # self.shift_generic()
+        self.apply_shift_btn.click()
+
+    def shift_overlay_right(self):
+        self.shift_horizontal += 2
+        self.horizontal_shift_le.set_threshold(self.shift_horizontal)
+        # self.shift_generic()
+        self.apply_shift_btn.click()
+
+    def shift_generic(self):
+        from scipy.ndimage import shift
+
+        self.shift_vertical = self.vertical_shift_le.get_threshold()
+        self.shift_horizontal = self.horizontal_shift_le.get_threshold()
+        self.shifted_frame = shift(
+            self.overlay_init_frame,
+            [self.shift_vertical, self.shift_horizontal],
+            prefilter=False,
+        )
+        self.im_overlay.set_data(self.shifted_frame)
+        self.fig.canvas.draw_idle()
+
+    def generate_add_to_parent_btn(self):
+
+        add_hbox = QHBoxLayout()
+        add_hbox.setContentsMargins(0, 5, 0, 5)
+        self.set_shift_btn.clicked.connect(self.set_parent_attributes)
+        self.set_shift_btn.setStyleSheet(self.button_style_sheet)
+        add_hbox.addWidget(QLabel(""), 33)
+        add_hbox.addWidget(self.set_shift_btn, 33)
+        add_hbox.addWidget(QLabel(""), 33)
+        self.canvas.layout.addLayout(add_hbox)
+
+    def set_parent_attributes(self):
+
+        idx = self.channels_overlay_cb.currentIndex()
+        self.parent_window.channels_cb.setCurrentIndex(idx)
+        self.parent_window.vertical_shift_le.set_threshold(
+            self.vertical_shift_le.get_threshold()
+        )
+        self.parent_window.horizontal_shift_le.set_threshold(
+            self.horizontal_shift_le.get_threshold()
+        )
+        self.close()