Merge branch 'main' into 53_custom_color_new

cellpose/gui/gui.py

@@ -54,8 +54,6 @@ def __init__(self, parent, name, color):
         """)
         self.show()
 
-
-
     def levelChanged(self, parent):
         parent.level_change(self.name)
 
@@ -147,6 +145,15 @@ def make_cmap(cm=0):
     return cmap
 
 def rgb_to_hex(rgb_tuple):
+    """
+    Converts an RGB tuple to a hex color string.
+
+    Args:
+        rgb_tuple (tuple): The RGB tuple (e.g., (255, 0, 0) for red).
+
+    Returns:
+        str: The hex color string (e.g., '#ff0000' for red).
+    """
     return '#{:02x}{:02x}{:02x}'.format(rgb_tuple[0], rgb_tuple[1], rgb_tuple[2])
 
 
@@ -308,6 +315,9 @@ def __init__(self, image=None, logger=None):
         self.reset()
         self.minimap_window_instance = None
 
+        # if the view of the image is changed, the method onViewChanged is called
+        self.p0.sigRangeChanged.connect(self.onViewChanged)
+
         # Custom multi-page tiff image stack
         self.grayscale_image_stack = []
         self.colors_stack = []
@@ -364,8 +374,6 @@ def minimap_window(self):
                 self.minimap_window_instance.deleteLater()
                 self.minimap_window_instance = None
 
-
-
     def color_initialization(self):
         """
         Initializes the color stack by assigning every layer a standard color by repeating colors in the list.
@@ -514,6 +522,55 @@ def center_view_on_position(self, normalized_x, normalized_y):
         self.p0.setXRange(*new_x_range, padding=0)
         self.p0.setYRange(*new_y_range, padding=0)
 
+    def onViewChanged(self):
+        """
+        This function is called whenever the view of the image in the view box is changed.
+        This includes it being zoomed in or zoomed out, as well as it being moved around.
+        It normalizes coordinates and dimensions of the view box in relation to the current image.
+
+        Returns:
+            Normalized coordinates of the view box (normalized_x, normalized_y)
+            Normalized dimensions of the view box (normalized_width, normalized_height)
+        """
+
+        # Access the positional values of the view box p0 in form of a rectangle using viewRect()
+        view_rect = self.p0.viewRect()
+
+        # Extract the x and y coordinates of the view box
+        x_coordinates = [view_rect.left(), view_rect.right()]
+        y_coordinates = [view_rect.top(), view_rect.bottom()]
+
+        # Extract the dimensions of the view box
+        width = view_rect.width()
+        height = view_rect.height()
+
+        try:
+
+            # Get the size of the image
+            img_height = self.img.image.shape[0]
+            img_width = self.img.image.shape[1]
+
+            # Calculate the normalized coordinates in relation to the image size
+            normalized_x = tuple(
+                coordinate / img_width for coordinate in x_coordinates)
+            normalized_y = tuple(
+                coordinate / img_height for coordinate in y_coordinates)
+
+            # Calculate the normalized dimensions
+            normalized_width = width / img_width
+            normalized_height = height / img_height
+
+            # Set the highlight area in the minimap window
+            self.minimap_window_instance.set_highlight_area(normalized_x[0], normalized_y[0], normalized_width, normalized_height)
+
+            return normalized_x, normalized_y, normalized_width, normalized_height
+
+        except Exception as e:
+
+            # if an exception of any kind occurs, the specific exception is printed to the console
+            print(f"An error occurred while changing the view: {e}")
+
+
 
     def generate_multi_channel_ui(self, n):
         c = 0  # Position der Elemente im Layout
@@ -617,25 +674,32 @@ def make_buttons(self):
         self.autobtn.setChecked(True)
         self.satBoxG.addWidget(self.autobtn, b0, 1, 1, 8)
 
-
+        #--- Initialization of Non-Tiff cases ---#
         c = 0  # position of the elements in the right side menu
 
+        # Define color names and labels for non-TIFF images
+        colornames = ["red", "Chartreuse", "DodgerBlue"]
+        names = ["red", "green", "blue"]
+        colors = ["red", "green", "blue"]
+
+        # Initialize sliders list
         self.sliders = []
         # ---Create a list (extendable) of color/on-off buttons  ---#
-        colors = ["red", "green", "blue"]
         # self.marker_buttons = [self.create_color_button(color, None) for color in colors]
         # self.on_off_buttons = [self.create_on_off_button(i) for i in range self.]
 
+        # Add labels and sliders for non-TIFF images
         for r in range(3):
             c += 1
 
-            label = QLabel(f'Marker {r + 1}')  # create a label for each marker
-            # color_button = self.marker_buttons[r]  # get the corresponding color button
-            self.marker_buttons = [self.create_color_button(color, None) for color in colors]
-            # on_off_button = self.on_off_buttons[r]  # get the corresponding on-off button
-            label.setStyleSheet("color: white")
-            label.setFont(self.boldmedfont)
+            # Create a label for each color channel
+            if r == 0:
+                label = QLabel('<font color="gray">gray/</font><br>red')
+            else:
+                label = QLabel(names[r] + ":")
+            label.setStyleSheet(f"color: {colornames[r]}")
             self.rightBoxLayout.addWidget(label, c, 0, 1, 1)
+
             # self.rightBoxLayout.addWidget(color_button, c, 9, 1, 1)  # add the color button to the layout
             # self.rightBoxLayout.addWidget(on_off_button, c, 10, 1, 1)  # add the on-off button to the layout
             self.sliders.append(Slider(self, colors[r], None))
@@ -1230,7 +1294,7 @@ def get_color_button_style(self, color_name):
                 height: 12px;
                 width: 12px;
                 }}
-                """
+            """
 
 
     def set_image_opacity(self, image, opacity):
@@ -1298,12 +1362,12 @@ def adjust_channel_bounds(self, channel, bounds):
 
 
     def level_change(self, r):
-        if self.tiff_loaded:
-            if int(r) < len(self.sliders):
+        if self.tiff_loaded:                  # if tiff is loaded, sliders adjust contrast of each layer
+            if int(r) < len(self.sliders):    # make sure the list of sliders already filled
                 r_index = r
                 if self.on_off_buttons[r].isChecked():
-                    self.adjust_channel_bounds(r_index, self.sliders[r_index].value())
-                    self.update_plot()
+                    self.adjust_channel_bounds(r_index, self.sliders[r_index].value())  # adjust contrast of layer
+                    self.update_plot()  # update plot
 
         else:
             r = ["red", "green", "blue"].index(r)
@@ -1504,6 +1568,7 @@ def disable_buttons_removeROIs(self):
         self.saveSet.setEnabled(False)
         self.savePNG.setEnabled(False)
         self.saveFlows.setEnabled(False)
+        self.saveFeaturesCsv.setEnabled(False)
         self.saveOutlines.setEnabled(False)
         self.saveROIs.setEnabled(False)
         self.minimapWindow.setEnabled(False)
@@ -1532,6 +1597,26 @@ def toggle_saving(self):
             self.saveOutlines.setEnabled(False)
             self.saveROIs.setEnabled(False)
 
+    def toggle_save_features_csv(self):
+        """
+        Toggles the save features csv button based on the image file type.
+        If the image is a tiff or tif file, the button is enabled. Otherwise, it is disabled.
+        This method is called after a segmentation has taken place.
+
+        Args:
+            None
+
+        Returns:
+            None
+        """
+
+        filetype = imghdr.what(self.filename)
+
+        if filetype in ['tiff', 'tif']:
+            self.saveFeaturesCsv.setEnabled(True)
+        else:
+            self.saveFeaturesCsv.setEnabled(False)
+
     def toggle_removals(self):
         if self.ncells > 0:
             self.ClearButton.setEnabled(True)

cellpose/gui/guiparts.py

@@ -451,6 +451,20 @@ def __init__(self, parent=None):
         # This marks the menu button as checked
         parent.minimapWindow.setChecked(True)
 
+        # Create and add a highlight rectangle to the minimap with initial position [0, 0] and size [100, 100], outlined
+        # in white with a 3-pixel width.
+        self.highlight_area = pg.RectROI([0, 0], [100, 100], pen=pg.mkPen('w', width=3), resizable=False, movable=False)
+        self.highlight_area.hoverEvent = lambda event: None
+        # Remove all resize handles after initialization
+        QtCore.QTimer.singleShot(0, lambda: [self.highlight_area.removeHandle(handle) for handle in
+                                             self.highlight_area.getHandles()])
+
+
+        # Set the highlight area to cover the entire image by default
+        self.set_highlight_area(0, 0, 1, 1)
+        # Add the highlight area to the viewbox
+        self.viewbox.addItem(self.highlight_area)
+
     def closeEvent(self, event: QEvent):
         """
         Method to uncheck the button in the menu if the window is closed.
@@ -501,6 +515,45 @@ def update_minimap(self, parent):
         else:
             self.setFixedSize(self.minimapSize, self.minimapSize)
 
+    def set_highlight_area(self, normalized_x, normalized_y, normalized_width, normalized_height):
+        """
+        Method to set the highlight area on the minimap.
+        The position and size of the rectangle are set based on the calculated normalized coordinates from the
+        onViewChanged method.
+
+        Parameters:
+        normalized_x (float): Normalized x-coordinate for the position.
+        normalized_y (float): Normalized y-coordinate for the position.
+        normalized_width (float): Normalized width for the size.
+        normalized_height (float): Normalized height for the size.
+
+        Returns:
+        tuple: The calculated (x, y, width, height) coordinates.
+        """
+
+        if self.parent().img.image is not None:
+            # Retrieve the height and width of the image
+            img_height = self.parent().img.image.shape[0]
+            img_width = self.parent().img.image.shape[1]
+
+            # Calculate the position and size of the highlight area based on the normalized coordinates
+            x = normalized_x * img_width
+            y = normalized_y * img_height
+            width = normalized_width * img_width
+            height = normalized_height * img_height
+
+            # Set the position of the rectangle  area on the minimap
+            # Move the rectangle to the calculated position
+            self.highlight_area.setPos(x, y)
+
+            # Set the size of the rectangle on the minimap
+            # Adjust the rectangle's size to the calculated width and height
+            self.highlight_area.setSize([width, height])
+
+        else:
+            print("Error: No image loaded in parent.")
+
+
     def sliderValueChanged(self, value):
         """
         Method to change the size of the minimap based on the slider value.

cellpose/gui/io.py

@@ -175,6 +175,8 @@ def _load_image(parent, filename=None, load_seg=True, load_3D=False):
             parent.minimap_window_instance = guiparts.MinimapWindow(parent)
             parent.minimap_window_instance.show()
 
+        parent.saveFeaturesCsv.setEnabled(False)
+
 
 def _initialize_images(parent, image, load_3D=False):
     """ format image for GUI """
@@ -503,6 +505,8 @@ def _load_masks(parent, filename=None):
     if parent.ncells > 0:
         parent.draw_layer()
         parent.toggle_mask_ops()
+        # features can only be saved if masks are loaded
+        parent.toggle_save_features_csv()
     del masks
     gc.collect()
     parent.update_layer()
@@ -582,6 +586,8 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
     if parent.ncells > 0:
         parent.draw_layer()
         parent.toggle_mask_ops()
+        # features can only be saved if masks are loaded
+        parent.toggle_save_features_csv()
     parent.ismanual = np.zeros(parent.ncells, bool)
     parent.zdraw = list(-1 * np.ones(parent.ncells, np.int16))
 
@@ -591,6 +597,7 @@ def _masks_to_gui(parent, masks, outlines=None, colors=None):
     else:
         parent.ViewDropDown.setCurrentIndex(0)
 
+
 def _save_features_csv(parent):
     """
     Saves features to CSV if dataset is 2D.
@@ -605,11 +612,18 @@ def _save_features_csv(parent):
         return
 
     filename = parent.filename
+
     base = os.path.splitext(filename)[0] + "_features.csv"
+
     # check if the dataset is 2D (NZ == 1 implies a single z-layer)
     if parent.NZ == 1:
         print("GUI_INFO: saving features to CSV file")
-        save_features_csv(parent.filename)
+        # this gives us the channels that are currently loaded by converting the images to an array
+        stacked_images = parent.convert_images_to_array(parent.grayscale_image_stack)
+        # reduction to only the relevant light intensity channel
+        channels = stacked_images[:, :, :, 1]
+        # save the features to a CSV file using method in cellpose.io
+        save_features_csv(parent.filename, parent.cellpix, channels)
     else:
         print("ERROR: cannot save features")
 

cellpose/gui/menus.py

@@ -81,12 +81,13 @@ def mainmenu(parent):
     This adds a new menu item for saving features as a .csv file. 
     The user can activate this function to export specific data directly from the GUI.
     The function `_save_features_as_csv` from the `io` module is called when the user clicks on the menu item.
+    It is disabled by default and only activated if an image is segmented and of the type tif/tiff.
     """
     parent.saveFeaturesCsv = QAction("Save Features as .&csv", parent)
     parent.saveFeaturesCsv.setShortcut("Ctrl+Shift+C")
     parent.saveFeaturesCsv.triggered.connect(lambda: io._save_features_csv(parent))
     file_menu.addAction(parent.saveFeaturesCsv)
-    parent.saveFeaturesCsv.setEnabled(True)
+    parent.saveFeaturesCsv.setEnabled(False)
 
     """
     This creates a new menu item for the minimap that the user can activate.