spacr 0.2.61__py3-none-any.whl → 0.2.65__py3-none-any.whl

spacr/__init__.py

@@ -17,7 +17,6 @@ from . import gui_utils
 from . import gui_elements
 from . import gui_core
 from . import gui
-from . import gui
 from . import app_make_masks
 from . import app_mask
 from . import app_measure
@@ -35,7 +34,7 @@ __all__ = [
     "plot",
     "measure",
     "sim",
-    "sequencing"
+    "sequencing",
     "timelapse",
     "deep_spacr",
     "app_annotate",
@@ -43,7 +42,6 @@ __all__ = [
     "gui_elements",
     "gui_core",
     "gui",
-    "gui",
     "app_make_masks",
     "app_mask",
     "app_measure",

spacr/gui_core.py

@@ -83,12 +83,22 @@ def toggle_settings(button_scrollable_frame):
 def process_fig_queue():
     global canvas, fig_queue, canvas_widget, parent_frame, uppdate_frequency, figures, figure_index
 
+    from .gui_elements import standardize_figure
     try:
         while not fig_queue.empty():
             fig = fig_queue.get_nowait()
+
+            if fig is None:
+                print("Warning: Retrieved a None figure from fig_queue.")
+                continue  # Skip processing if the figure is None
+
+            # Standardize the figure appearance before adding it to the list
+            standardize_figure(fig)
+
             figures.append(fig)
-            figure_index = len(figures) - 1
-            display_figure(fig)
+            if figure_index == len(figures) - 2:
+                figure_index += 1
+                display_figure(fig)
     except Exception as e:
         traceback.print_exc()
     finally:
@@ -98,8 +108,23 @@ def process_fig_queue():
 def display_figure(fig):
     global canvas, canvas_widget
 
+    from .gui_elements import modify_figure_properties, save_figure_as_format, modify_figure
+
+    # Apply the dark style to the context menu
+    style_out = set_dark_style(ttk.Style())
+    bg_color = style_out['bg_color']
+    fg_color = style_out['fg_color']
+
+    # Initialize the scale factor for zooming
+    scale_factor = 1.0
+
+    # Save the original x and y limits of the first axis (assuming all axes have the same limits)
+    original_xlim = [ax.get_xlim() for ax in fig.get_axes()]
+    original_ylim = [ax.get_ylim() for ax in fig.get_axes()]
+
     # Clear previous canvas content
-    canvas.get_tk_widget().destroy()
+    if canvas:
+        canvas.get_tk_widget().destroy()
 
     # Create a new canvas for the figure
     new_canvas = FigureCanvasTkAgg(fig, master=canvas_widget.master)
@@ -109,154 +134,141 @@ def display_figure(fig):
     # Update the global canvas and canvas_widget references
     canvas = new_canvas
     canvas_widget = new_canvas.get_tk_widget()
-
-    # Apply the dark style to the context menu
-    style_out = set_dark_style(ttk.Style())
-    bg_color = style_out['bg_color']
-    fg_color = style_out['fg_color']
-
-    # Define the save functions for the context menu
-    def save_figure_as_format(format):
-        file_path = filedialog.asksaveasfilename(defaultextension=f".{format}", filetypes=[(f"{format.upper()} files", f"*.{format}"), ("All files", "*.*")])
-        if file_path:
-            fig.savefig(file_path, format=format)
-
-    def modify_figure():
-        def apply_modifications():
-            try:
-                x_width = float(x_width_var.get())
-                y_height = float(y_height_var.get())
-                line_width = float(line_width_var.get())
-                font_size = int(font_size_var.get())
-                modify_figure_properties(fig, x_width=x_width, y_height=y_height, line_width=line_width)
-                for ax in fig.get_axes():
-                    for label in ax.get_xticklabels() + ax.get_yticklabels():
-                        label.set_fontsize(font_size)
-                    ax.title.set_fontsize(font_size)
-                    ax.xaxis.label.set_fontsize(font_size)
-                    ax.yaxis.label.set_fontsize(font_size)
-                canvas.draw_idle()  # Redraw the canvas after modifications
-            except ValueError:
-                print("Invalid input; please enter numeric values.")
-
-        # Create a new window for user input
-        modify_window = tk.Toplevel()
-        modify_window.title("Modify Figure Properties")
-
-        # Apply dark style to the popup window
-        modify_window.configure(bg=bg_color)
-
-        # Create and style the input fields
-        tk.Label(modify_window, text="X Axis Width:", bg=bg_color, fg=fg_color).grid(row=0, column=0, padx=10, pady=5)
-        x_width_var = tk.StringVar()
-        tk.Entry(modify_window, textvariable=x_width_var, bg=bg_color, fg=fg_color).grid(row=0, column=1, padx=10, pady=5)
-
-        tk.Label(modify_window, text="Y Axis Height:", bg=bg_color, fg=fg_color).grid(row=1, column=0, padx=10, pady=5)
-        y_height_var = tk.StringVar()
-        tk.Entry(modify_window, textvariable=y_height_var, bg=bg_color, fg=fg_color).grid(row=1, column=1, padx=10, pady=5)
-
-        tk.Label(modify_window, text="Line Width:", bg=bg_color, fg=fg_color).grid(row=2, column=0, padx=10, pady=5)
-        line_width_var = tk.StringVar()
-        tk.Entry(modify_window, textvariable=line_width_var, bg=bg_color, fg=fg_color).grid(row=2, column=1, padx=10, pady=5)
-
-        tk.Label(modify_window, text="Font Size:", bg=bg_color, fg=fg_color).grid(row=3, column=0, padx=10, pady=5)
-        font_size_var = tk.StringVar()
-        tk.Entry(modify_window, textvariable=font_size_var, bg=bg_color, fg=fg_color).grid(row=3, column=1, padx=10, pady=5)
-
-        # Apply button
-        apply_button = tk.Button(modify_window, text="Apply", command=apply_modifications, bg=bg_color, fg=fg_color)
-        apply_button.grid(row=4, column=0, columnspan=2, pady=10)
+    canvas_widget.configure(bg=bg_color)
 
     # Create the context menu
     context_menu = tk.Menu(canvas_widget, tearoff=0, bg=bg_color, fg=fg_color)
-    context_menu.add_command(label="Save Figure as PDF", command=lambda: save_figure_as_format('pdf'))
-    context_menu.add_command(label="Save Figure as PNG", command=lambda: save_figure_as_format('png'))
-    context_menu.add_command(label="Modify Figure", command=modify_figure)
+    context_menu.add_command(label="Save Figure as PDF", command=lambda: save_figure_as_format(fig, 'pdf'))
+    context_menu.add_command(label="Save Figure as PNG", command=lambda: save_figure_as_format(fig, 'png'))
+    context_menu.add_command(label="Modify Figure", command=lambda: modify_figure(fig))
+    context_menu.add_command(label="Reset Zoom", command=lambda: reset_zoom(fig))  # Add Reset Zoom option
+
+    def reset_zoom(fig):
+        global scale_factor
+        scale_factor = 1.0  # Reset the scale factor
+
+        for i, ax in enumerate(fig.get_axes()):
+            ax.set_xlim(original_xlim[i])
+            ax.set_ylim(original_ylim[i])
+        fig.canvas.draw_idle()
 
     def on_right_click(event):
         context_menu.post(event.x_root, event.y_root)
 
-    new_canvas.get_tk_widget().bind("<Button-3>", on_right_click)
+    def on_hover(event):
+        widget_width = event.widget.winfo_width()
+        x_position = event.x
+
+        if x_position < widget_width / 2:
+            canvas_widget.config(cursor="hand2")
+        else:
+            canvas_widget.config(cursor="hand2")
+
+    def on_leave(event):
+        canvas_widget.config(cursor="arrow")
+
+    def flash_feedback(side):
+        flash = tk.Toplevel(canvas_widget.master)
+        flash.overrideredirect(True)
+        flash_width = int(canvas_widget.winfo_width() / 2)
+        flash_height = canvas_widget.winfo_height()
+        flash.configure(bg='white')
+        flash.attributes('-alpha', 0.9)
+
+        if side == "left":
+            flash.geometry(f"{flash_width}x{flash_height}+{canvas_widget.winfo_rootx()}+{canvas_widget.winfo_rooty()}")
+        else:
+            flash.geometry(f"{flash_width}x{flash_height}+{canvas_widget.winfo_rootx() + flash_width}+{canvas_widget.winfo_rooty()}")
+
+        flash.lift()
+
+        # Ensure the flash covers the correct area only
+        flash.update_idletasks()
+        flash.after(100, flash.destroy)
+
+    def on_click(event):
+        widget_width = event.widget.winfo_width()
+        x_position = event.x
+
+        if x_position < widget_width / 2:
+            #flash_feedback("left")
+            show_previous_figure()
+        else:
+            #flash_feedback("right")
+            show_next_figure()
+
+    def zoom(event):
+        nonlocal scale_factor
+
+        zoom_speed = 0.1  # Adjust the zoom speed for smoother experience
+
+        # Adjust zoom factor based on the operating system and mouse event
+        if event.num == 4 or event.delta > 0:  # Scroll up
+            scale_factor *= (1 + zoom_speed)
+        elif event.num == 5 or event.delta < 0:  # Scroll down
+            scale_factor /= (1 + zoom_speed)
+
+        # Get mouse position relative to the figure
+        x_mouse, y_mouse = event.x, event.y
+        x_ratio = x_mouse / canvas_widget.winfo_width()
+        y_ratio = y_mouse / canvas_widget.winfo_height()
+
+        for ax in fig.get_axes():
+            xlim = ax.get_xlim()
+            ylim = ax.get_ylim()
+
+            # Calculate the new limits
+            x_center = xlim[0] + x_ratio * (xlim[1] - xlim[0])
+            y_center = ylim[0] + (1 - y_ratio) * (ylim[1] - ylim[0])
+
+            x_range = (xlim[1] - xlim[0]) * scale_factor
+            y_range = (ylim[1] - ylim[0]) * scale_factor
+
+            ax.set_xlim([x_center - x_range * x_ratio, x_center + x_range * (1 - x_ratio)])
+            ax.set_ylim([y_center - y_range * (1 - y_ratio), y_center + y_range * y_ratio])
+
+        # Redraw the figure
+        fig.canvas.draw_idle()
+
+    # Bind events for hover, click interactions, and zoom
+    canvas_widget.bind("<Motion>", on_hover)
+    canvas_widget.bind("<Leave>", on_leave)
+    canvas_widget.bind("<Button-1>", on_click)
+    canvas_widget.bind("<Button-3>", on_right_click)
+
+    # Bind mouse wheel for zooming (cross-platform)
+    canvas_widget.bind("<MouseWheel>", zoom)  # Windows
+    canvas_widget.bind("<Button-4>", zoom)  # Linux/macOS Scroll Up
+    canvas_widget.bind("<Button-5>", zoom)  # Linux/macOS Scroll Down
 
 def clear_unused_figures():
     global figures, figure_index
 
     lower_bound = max(0, figure_index - 20)
     upper_bound = min(len(figures), figure_index + 20)
-
     # Clear figures outside of the +/- 20 range
     figures = deque([fig for i, fig in enumerate(figures) if lower_bound <= i <= upper_bound])
-
     # Update the figure index after clearing
     figure_index = min(max(figure_index, 0), len(figures) - 1)
 
 def show_previous_figure():
-    global figure_index, figures
+    global figure_index, figures, fig_queue
     if figure_index is not None and figure_index > 0:
         figure_index -= 1
         display_figure(figures[figure_index])
         clear_unused_figures()
 
 def show_next_figure():
-    global figure_index, figures
+    global figure_index, figures, fig_queue
     if figure_index is not None and figure_index < len(figures) - 1:
         figure_index += 1
         display_figure(figures[figure_index])
         clear_unused_figures()
-
-def save_figure_as_format(fig, file_format):
-    file_path = filedialog.asksaveasfilename(defaultextension=f".{file_format}", filetypes=[(f"{file_format.upper()} files", f"*.{file_format}"), ("All files", "*.*")])
-    if file_path:
-        try:
-            fig.savefig(file_path, format=file_format)
-            print(f"Figure saved as {file_format.upper()} at {file_path}")
-        except Exception as e:
-            print(f"Error saving figure: {e}")
-
-def modify_figure_properties(fig, x_width=None, y_height=None, line_width=None):
-    """
-    Modifies the properties of the figure, including axis dimensions and line widths.
-    
-    Parameters:
-    - fig: The matplotlib figure object to modify.
-    - x_width: Desired width for the x-axis (optional).
-    - y_height: Desired height for the y-axis (optional).
-    - line_width: Desired line width for all lines (optional).
-    """
-    for ax in fig.get_axes():
-        # Scaling the figure
-        if x_width is not None or y_height is not None:
-            # Get the current axis limits
-            current_xlim = ax.get_xlim()
-            current_ylim = ax.get_ylim()
-
-            # Set new limits
-            if x_width is not None:
-                scale_factor_x = x_width / (current_xlim[1] - current_xlim[0])
-            else:
-                scale_factor_x = 1
-
-            if y_height is not None:
-                scale_factor_y = y_height / (current_ylim[1] - current_ylim[0])
-            else:
-                scale_factor_y = 1
-
-            # Adjust the figure size and elements proportionally
-            fig.set_size_inches(fig.get_size_inches() * scale_factor_x * scale_factor_y, forward=True)
-            ax.set_xlim(left=current_xlim[0] * scale_factor_x, right=current_xlim[1] * scale_factor_x)
-            ax.set_ylim(bottom=current_ylim[0] * scale_factor_y, top=current_ylim[1] * scale_factor_y)
-
-        # Adjust line width and other elements if specified
-        if line_width is not None:
-            for line in ax.get_lines():
-                line.set_linewidth(line_width)
-            for spine in ax.spines.values():  # Modify width of spines (e.g., scale bars)
-                spine.set_linewidth(line_width)
-            ax.tick_params(width=line_width)  # Modify width of ticks
-            for text in ax.get_xticklabels() + ax.get_yticklabels():
-                text.set_fontsize(ax.get_xticklabels()[0].get_fontsize())
-
-    fig.canvas.draw_idle()
+    elif figure_index == len(figures) - 1 and not fig_queue.empty():
+        fig = fig_queue.get_nowait()
+        figures.append(fig)
+        figure_index += 1
+        display_figure(fig)
 
 def set_globals(thread_control_var, q_var, console_output_var, parent_frame_var, vars_dict_var, canvas_var, canvas_widget_var, scrollable_frame_var, fig_queue_var, figures_var, figure_index_var, progress_bar_var, usage_bars_var, fig_memory_limit_var, figure_current_memory_usage_var):
     global thread_control, q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, fig_queue, figures, figure_index, progress_bar, usage_bars, fig_memory_limit, figure_current_memory_usage
@@ -416,7 +428,7 @@ def setup_plot_section(vertical_container):
     plot_frame.grid_columnconfigure(0, weight=1)
 
     canvas.draw()
-    canvas.figure = figure
+    canvas.figure = figure  # Ensure that the figure is linked to the canvas
     style_out = set_dark_style(ttk.Style())
 
     figure.patch.set_facecolor(style_out['bg_color'])
@@ -425,19 +437,6 @@ def setup_plot_section(vertical_container):
     widgets = [canvas_widget]
     style = ttk.Style(vertical_container)
     _ = set_dark_style(style, containers=containers, widgets=widgets)
-
-    # Add navigation buttons using spacrButton
-    button_frame = tk.Frame(plot_frame, bg=style_out['bg_color'])
-    button_frame.grid(row=1, column=0, sticky='ew', pady=5)
-
-    size_dict = set_element_size()
-
-    btn_size = int(size_dict['btn_size']*0.75)
-    prev_button = spacrButton(button_frame, text="Previous", command=show_previous_figure, bg=style_out['bg_color'], show_text=False, size=btn_size, animation=False)
-    prev_button.pack(side='left', padx=5)
-
-    next_button = spacrButton(button_frame, text="Next", command=show_next_figure, bg=style_out['bg_color'], show_text=False, size=btn_size, animation=False)
-    next_button.pack(side='right', padx=5)
     
     return canvas, canvas_widget
 
@@ -842,7 +841,7 @@ def initiate_root(parent, settings_type='mask'):
     from .gui_utils import setup_frame
     from .settings import descriptions
 
-    uppdate_frequency = 1000
+    uppdate_frequency = 100
 
     # Start tracemalloc and initialize global variables
     tracemalloc.start()

spacr/gui_elements.py

@@ -2,6 +2,7 @@ import os, threading, time, sqlite3, webbrowser, pyautogui
 import tkinter as tk
 from tkinter import ttk
 import tkinter.font as tkFont
+from tkinter import filedialog
 from tkinter import font
 from queue import Queue
 from tkinter import Label, Frame, Button
@@ -16,6 +17,7 @@ from skimage.draw import polygon, line
 from skimage.transform import resize
 from scipy.ndimage import binary_fill_holes, label
 from tkinter import ttk, scrolledtext
+fig = None
 
 def set_element_size():
 
@@ -2081,6 +2083,7 @@ class AnnotateApp:
                                 print(f"median threshold measurement: {np.median(df[self.measurement])}")
                                 df = df[df[f'threshold_measurement_{idx}'] > thd]
                         after = len(df)
+            
             elif isinstance(self.measurement, list):
                 df['threshold_measurement'] = df[self.measurement[0]]/df[self.measurement[1]]
                 print(f"mean threshold measurement: {np.mean(df['threshold_measurement'])}")
@@ -2089,6 +2092,7 @@ class AnnotateApp:
                 after = len(df)
                 self.measurement = 'threshold_measurement'
                 print(f'Removed: {before-after} rows, retained {after}')
+            
             else:
                 print(f"mean threshold measurement: {np.mean(df[self.measurement])}")
                 print(f"median threshold measurement: {np.median(df[self.measurement])}")
@@ -2370,4 +2374,300 @@ def create_menu_bar(root):
     app_menu.add_command(label="Exit", command=root.quit)
 
     # Configure the menu for the root window
-    root.config(menu=menu_bar)
+    root.config(menu=menu_bar)
+
+def standardize_figure(fig):
+    from .gui_elements import set_dark_style
+    from matplotlib.font_manager import FontProperties
+
+    style_out = set_dark_style(ttk.Style())
+    bg_color = style_out['bg_color']
+    fg_color = style_out['fg_color']
+    font_size = style_out['font_size']
+    font_loader = style_out['font_loader']
+
+    # Get the custom font path from the font loader
+    font_path = font_loader.font_path
+    font_prop = FontProperties(fname=font_path, size=font_size)
+
+    """
+    Standardizes the appearance of the figure:
+    - Font size: from style
+    - Font color: from style
+    - Font family: custom OpenSans from font_loader
+    - Removes top and right spines
+    - Figure and subplot background: from style
+    - Line width: 1
+    - Line color: from style
+    """
+
+    for ax in fig.get_axes():
+        # Set font properties for title and labels
+        ax.title.set_fontsize(font_size)
+        ax.title.set_color(fg_color)
+        ax.title.set_fontproperties(font_prop)
+
+        ax.xaxis.label.set_fontsize(font_size)
+        ax.xaxis.label.set_color(fg_color)
+        ax.xaxis.label.set_fontproperties(font_prop)
+
+        ax.yaxis.label.set_fontsize(font_size)
+        ax.yaxis.label.set_color(fg_color)
+        ax.yaxis.label.set_fontproperties(font_prop)
+
+        # Set font properties for tick labels
+        for label in ax.get_xticklabels() + ax.get_yticklabels():
+            label.set_fontsize(font_size)
+            label.set_color(fg_color)
+            label.set_fontproperties(font_prop)
+
+        # Remove top and right spines
+        ax.spines['top'].set_visible(False)
+        ax.spines['right'].set_visible(False)
+        ax.spines['left'].set_visible(True)
+        ax.spines['bottom'].set_visible(True)
+
+        # Set spine line width and color
+        for spine in ax.spines.values():
+            spine.set_linewidth(1)
+            spine.set_edgecolor(fg_color)
+
+        # Set line width and color
+        for line in ax.get_lines():
+            line.set_linewidth(1)
+            line.set_color(fg_color)
+
+        # Set subplot background color
+        ax.set_facecolor(bg_color)
+
+        # Adjust the grid if needed
+        ax.grid(True, color='gray', linestyle='--', linewidth=0.5)
+
+    # Set figure background color
+    fig.patch.set_facecolor(bg_color)
+
+    fig.canvas.draw_idle()
+
+def modify_figure_properties(fig, scale_x=None, scale_y=None, line_width=None, font_size=None, x_lim=None, y_lim=None, grid=False, legend=None, title=None, x_label_rotation=None, remove_axes=False, bg_color=None, text_color=None, line_color=None):
+    """
+    Modifies the properties of the figure, including scaling, line widths, font sizes, axis limits, x-axis label rotation, background color, text color, line color, and other common options.
+
+    Parameters:
+    - fig: The Matplotlib figure object to modify.
+    - scale_x: Scaling factor for the width of subplots (optional).
+    - scale_y: Scaling factor for the height of subplots (optional).
+    - line_width: Desired line width for all lines (optional).
+    - font_size: Desired font size for all text (optional).
+    - x_lim: Tuple specifying the x-axis limits (min, max) (optional).
+    - y_lim: Tuple specifying the y-axis limits (min, max) (optional).
+    - grid: Boolean to add grid lines to the plot (optional).
+    - legend: Boolean to show/hide the legend (optional).
+    - title: String to set as the title of the plot (optional).
+    - x_label_rotation: Angle to rotate the x-axis labels (optional).
+    - remove_axes: Boolean to remove or show the axes labels (optional).
+    - bg_color: Color for the figure and subplot background (optional).
+    - text_color: Color for all text in the figure (optional).
+    - line_color: Color for all lines in the figure (optional).
+    """
+    if fig is None:
+        print("Error: The figure provided is None.")
+        return
+
+    for ax in fig.get_axes():
+        # Rescale subplots if scaling factors are provided
+        if scale_x is not None or scale_y is not None:
+            bbox = ax.get_position()
+            width = bbox.width * (scale_x if scale_x else 1)
+            height = bbox.height * (scale_y if scale_y else 1)
+            new_bbox = [bbox.x0, bbox.y0, width, height]
+            ax.set_position(new_bbox)
+
+        # Set axis limits if provided
+        if x_lim is not None:
+            ax.set_xlim(x_lim)
+        if y_lim is not None:
+            ax.set_ylim(y_lim)
+
+        # Set grid visibility only
+        ax.grid(grid)
+
+        # Adjust line width and color if specified
+        if line_width is not None or line_color is not None:
+            for line in ax.get_lines():
+                if line_width is not None:
+                    line.set_linewidth(line_width)
+                if line_color is not None:
+                    line.set_color(line_color)
+            for spine in ax.spines.values():  # Modify width and color of spines (e.g., scale bars)
+                if line_width is not None:
+                    spine.set_linewidth(line_width)
+                if line_color is not None:
+                    spine.set_edgecolor(line_color)
+            ax.tick_params(width=line_width, colors=text_color if text_color else 'black')
+
+        # Adjust font size if specified
+        if font_size is not None:
+            for label in ax.get_xticklabels() + ax.get_yticklabels():
+                label.set_fontsize(font_size)
+            ax.title.set_fontsize(font_size)
+            ax.xaxis.label.set_fontsize(font_size)
+            ax.yaxis.label.set_fontsize(font_size)
+            if ax.legend_:
+                for text in ax.legend_.get_texts():
+                    text.set_fontsize(font_size)
+
+        # Rotate x-axis labels if rotation is specified
+        if x_label_rotation is not None:
+            for label in ax.get_xticklabels():
+                label.set_rotation(x_label_rotation)
+                if 0 <= x_label_rotation <= 90:
+                    label.set_ha('center')
+
+        # Toggle axes labels visibility without affecting the grid or spines
+        if remove_axes:
+            ax.xaxis.set_visible(False)
+            ax.yaxis.set_visible(False)
+        else:
+            ax.xaxis.set_visible(True)
+            ax.yaxis.set_visible(True)
+
+        # Set text color if specified
+        if text_color:
+            ax.title.set_color(text_color)
+            ax.xaxis.label.set_color(text_color)
+            ax.yaxis.label.set_color(text_color)
+            ax.tick_params(colors=text_color)
+            for label in ax.get_xticklabels() + ax.get_yticklabels():
+                label.set_color(text_color)
+
+        # Set background color for subplots if specified
+        if bg_color:
+            ax.set_facecolor(bg_color)
+
+    # Set figure background color if specified
+    if bg_color:
+        fig.patch.set_facecolor(bg_color)
+
+    fig.canvas.draw_idle()
+
+def save_figure_as_format(fig, file_format):
+    file_path = filedialog.asksaveasfilename(defaultextension=f".{file_format}", filetypes=[(f"{file_format.upper()} files", f"*.{file_format}"), ("All files", "*.*")])
+    if file_path:
+        try:
+            fig.savefig(file_path, format=file_format)
+            print(f"Figure saved as {file_format.upper()} at {file_path}")
+        except Exception as e:
+            print(f"Error saving figure: {e}")
+
+def modify_figure(fig):
+    from .gui_core import display_figure
+    def apply_modifications():
+        try:
+            # Only apply changes if the fields are filled
+            scale_x = float(scale_x_var.get()) if scale_x_var.get() else None
+            scale_y = float(scale_y_var.get()) if scale_y_var.get() else None
+            line_width = float(line_width_var.get()) if line_width_var.get() else None
+            font_size = int(font_size_var.get()) if font_size_var.get() else None
+            x_lim = eval(x_lim_var.get()) if x_lim_var.get() else None
+            y_lim = eval(y_lim_var.get()) if y_lim_var.get() else None
+            title = title_var.get() if title_var.get() else None
+            bg_color = bg_color_var.get() if bg_color_var.get() else None
+            text_color = text_color_var.get() if text_color_var.get() else None
+            line_color = line_color_var.get() if line_color_var.get() else None
+            x_label_rotation = int(x_label_rotation_var.get()) if x_label_rotation_var.get() else None
+
+            modify_figure_properties(
+                fig,
+                scale_x=scale_x,
+                scale_y=scale_y,
+                line_width=line_width,
+                font_size=font_size,
+                x_lim=x_lim,
+                y_lim=y_lim,
+                grid=grid_var.get(),
+                legend=legend_var.get(),
+                title=title,
+                x_label_rotation=x_label_rotation,
+                remove_axes=remove_axes_var.get(),
+                bg_color=bg_color,
+                text_color=text_color,
+                line_color=line_color
+            )
+            display_figure(fig)
+        except ValueError:
+            print("Invalid input; please enter numeric values.")
+
+    def toggle_spleens():
+        for ax in fig.get_axes():
+            if spleens_var.get():
+                ax.spines['top'].set_visible(False)
+                ax.spines['right'].set_visible(False)
+                ax.spines['left'].set_visible(True)
+                ax.spines['bottom'].set_visible(True)
+                ax.spines['top'].set_linewidth(2)
+                ax.spines['right'].set_linewidth(2)
+            else:
+                ax.spines['top'].set_visible(True)
+                ax.spines['right'].set_visible(True)
+            display_figure(fig)
+
+    # Create a new window for user input
+    modify_window = tk.Toplevel()
+    modify_window.title("Modify Figure Properties")
+
+    # Apply dark style to the popup window
+    style = ttk.Style()
+    style.configure("TCheckbutton", background="#2E2E2E", foreground="white", selectcolor="blue")
+
+    modify_window.configure(bg="#2E2E2E")
+
+    # Create and style the input fields
+    scale_x_var = tk.StringVar()
+    scale_y_var = tk.StringVar()
+    line_width_var = tk.StringVar()
+    font_size_var = tk.StringVar()
+    x_lim_var = tk.StringVar()
+    y_lim_var = tk.StringVar()
+    title_var = tk.StringVar()
+    bg_color_var = tk.StringVar()
+    text_color_var = tk.StringVar()
+    line_color_var = tk.StringVar()
+    x_label_rotation_var = tk.StringVar()
+    remove_axes_var = tk.BooleanVar()
+    grid_var = tk.BooleanVar()
+    legend_var = tk.BooleanVar()
+    spleens_var = tk.BooleanVar()
+
+    options = [
+        ("Rescale X:", scale_x_var),
+        ("Rescale Y:", scale_y_var),
+        ("Line Width:", line_width_var),
+        ("Font Size:", font_size_var),
+        ("X Axis Limits (tuple):", x_lim_var),
+        ("Y Axis Limits (tuple):", y_lim_var),
+        ("Title:", title_var),
+        ("X Label Rotation (degrees):", x_label_rotation_var),
+        ("Background Color:", bg_color_var),
+        ("Text Color:", text_color_var),
+        ("Line Color:", line_color_var)
+    ]
+
+    for i, (label_text, var) in enumerate(options):
+        tk.Label(modify_window, text=label_text, bg="#2E2E2E", fg="white").grid(row=i, column=0, padx=10, pady=5)
+        tk.Entry(modify_window, textvariable=var, bg="#2E2E2E", fg="white").grid(row=i, column=1, padx=10, pady=5)
+
+    checkboxes = [
+        ("Grid", grid_var),
+        ("Legend", legend_var),
+        ("Spleens", spleens_var),
+        ("Remove Axes", remove_axes_var)
+    ]
+
+    for i, (label_text, var) in enumerate(checkboxes, start=len(options)):
+        ttk.Checkbutton(modify_window, text=label_text, variable=var, style="TCheckbutton").grid(row=i, column=0, padx=10, pady=5, columnspan=2, sticky='w')
+
+    spleens_var.trace_add("write", lambda *args: toggle_spleens())
+
+    # Apply button
+    apply_button = tk.Button(modify_window, text="Apply", command=apply_modifications, bg="#2E2E2E", fg="white")
+    apply_button.grid(row=len(options) + len(checkboxes), column=0, columnspan=2, pady=10)

spacr/gui_utils.py

@@ -76,6 +76,18 @@ def load_app(root, app_name, app_func):
         proceed_with_app(root, app_name, app_func)
     
 def parse_list(value):
+    """
+    Parses a string representation of a list and returns the parsed list.
+
+    Args:
+        value (str): The string representation of the list.
+
+    Returns:
+        list: The parsed list.
+
+    Raises:
+        ValueError: If the input value is not a valid list format or contains mixed types or unsupported types.
+    """
     try:
         parsed_value = ast.literal_eval(value)
         if isinstance(parsed_value, list):
@@ -93,7 +105,26 @@ def parse_list(value):
 
 # Usage example in your create_input_field function
 def create_input_field(frame, label_text, row, var_type='entry', options=None, default_value=None):
+    """
+    Create an input field in the specified frame.
+
+    Args:
+        frame (tk.Frame): The frame in which the input field will be created.
+        label_text (str): The text to be displayed as the label for the input field.
+        row (int): The row in which the input field will be placed.
+        var_type (str, optional): The type of input field to create. Defaults to 'entry'.
+        options (list, optional): The list of options for a combo box input field. Defaults to None.
+        default_value (str, optional): The default value for the input field. Defaults to None.
+
+    Returns:
+        tuple: A tuple containing the label, input widget, variable, and custom frame.
+
+    Raises:
+        Exception: If an error occurs while creating the input field.
+
+    """
     from .gui_elements import set_dark_style, set_element_size
+    
     label_column = 0
     widget_column = 0  # Both label and widget will be in the same column
 
@@ -205,6 +236,12 @@ def annotate(settings):
 
 def generate_annotate_fields(frame):
     from .settings import set_annotate_default_settings
+    from .gui_elements import set_dark_style
+
+    style_out = set_dark_style(ttk.Style())
+    font_loader = style_out['font_loader']
+    font_size = style_out['font_size'] - 2
+
     vars_dict = {}
     settings = set_annotate_default_settings(settings={})
     
@@ -216,8 +253,8 @@ def generate_annotate_fields(frame):
 
     # Arrange input fields and labels
     for row, (name, data) in enumerate(vars_dict.items()):
-        ttk.Label(frame, text=f"{name.replace('_', ' ').capitalize()}:",
-                  background="black", foreground="white").grid(row=row, column=0)
+        tk.Label(frame, text=f"{name.replace('_', ' ').capitalize()}:", bg=style_out['bg_color'], fg=style_out['fg_color'], font=font_loader.get_font(size=font_size)).grid(row=row, column=0)
+        #ttk.Label(frame, text=f"{name.replace('_', ' ').capitalize()}:", background="black", foreground="white").grid(row=row, column=0)
         if isinstance(data['value'], list):
             # Convert lists to comma-separated strings
             data['entry'].insert(0, ','.join(map(str, data['value'])))

spacr/plot.py

@@ -125,7 +125,7 @@ def plot_image_mask_overlay(file, channels, cell_channel, nucleus_channel, patho
 
     return
 
-def plot_masks(batch, masks, flows, cmap='inferno', figuresize=20, nr=1, file_type='.npz', print_object_number=True):
+def plot_masks(batch, masks, flows, cmap='inferno', figuresize=10, nr=1, file_type='.npz', print_object_number=True):
     """
     Plot the masks and flows for a given batch of images.
 
@@ -476,7 +476,7 @@ def _filter_objects_in_plot(stack, cell_mask_dim, nucleus_mask_dim, pathogen_mas
 
     return stack
 
-def plot_arrays(src, figuresize=50, cmap='inferno', nr=1, normalize=True, q1=1, q2=99):
+def plot_arrays(src, figuresize=10, cmap='inferno', nr=1, normalize=True, q1=1, q2=99):
     """
     Plot randomly selected arrays from a given directory.
 
@@ -870,7 +870,7 @@ def _save_scimg_plot(src, nr_imgs=16, channel_indices=[0,1,2], um_per_pixel=0.1,
 
     return
 
-def _plot_cropped_arrays(stack, filename, figuresize=20, cmap='inferno', threshold=500):
+def _plot_cropped_arrays(stack, filename, figuresize=10, cmap='inferno', threshold=500):
     """
     Plot cropped arrays.
 
@@ -997,7 +997,7 @@ def _display_gif(path):
     with open(path, 'rb') as file:
         display(ipyimage(file.read()))
         
-def _plot_recruitment(df, df_type, channel_of_interest, target, columns=[], figuresize=50):
+def _plot_recruitment(df, df_type, channel_of_interest, target, columns=[], figuresize=10):
     """
     Plot recruitment data for different conditions and pathogens.
 

spacr/sequencing.py

@@ -223,14 +223,10 @@ def save_to_hdf(queue, output_file, complevel=9, compression='zlib'):
     Save data from a queue to an HDF file.
 
     Parameters:
-    - queue: Queue object
-        The queue containing the data to be saved.
-    - output_file: strs
-        The path to the output HDF file.
-    - complevel: int, optional
-        The compression level to use (default is 9).
-    - compression: str, optional
-        The compression algorithm to use (default is 'zlib').
+    - queue: Queue object containing chunks of data to be saved
+    - output_file: Path to the output HDF file
+    - complevel: Compression level (default: 9)
+    - compression: Compression algorithm (default: 'zlib')
 
     Returns:
     None

spacr/utils.py

@@ -3451,7 +3451,7 @@ def setup_plot(figuresize, black_background):
     fig, ax = plt.subplots(1, 1, figsize=(figuresize, figuresize))
     return fig, ax
 
-def plot_clusters(ax, embedding, labels, colors, cluster_centers, plot_outlines, plot_points, smooth_lines, figuresize=50, dot_size=50, verbose=False):
+def plot_clusters(ax, embedding, labels, colors, cluster_centers, plot_outlines, plot_points, smooth_lines, figuresize=10, dot_size=50, verbose=False):
     unique_labels = np.unique(labels)
     for cluster_label, color, center in zip(unique_labels, colors, cluster_centers):
         cluster_data = embedding[labels == cluster_label]

{spacr-0.2.61.dist-info → spacr-0.2.65.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.61
+Version: 0.2.65
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.2.61.dist-info → spacr-0.2.65.dist-info}/RECORD

@@ -1,4 +1,4 @@
-spacr/__init__.py,sha256=pJ7Mm7Kb1DhHIdLmNgMILFVWJ9QAG47pT0M6wtiXl8E,1465
+spacr/__init__.py,sha256=2MqbX2rPedvIqUyAvI5vJ_YGiDeFDF3VU7xSj7TgF5w,1435
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/app_annotate.py,sha256=nEIL7Fle9CDKGo3sucG_03DgjUQt5W1M1IHBIpVBr08,2171
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
@@ -12,19 +12,19 @@ spacr/core.py,sha256=IDme9j7eeC_49KGaNk_xPOKtpxdcXKMhYtoo3xhjQMM,146502
 spacr/deep_spacr.py,sha256=a2YewgkQvLV-95NYJAutnojvJmX4S8z_wv6Tb-XIgUI,34484
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
 spacr/gui.py,sha256=dSEQhzZgIOT7SOonbIp07-zXcLaEt6M7sRiIREpDv64,7226
-spacr/gui_core.py,sha256=8aoxVLwt8evl_mZG6xHxhRgf5nq35bfay12OOSJos5Q,40148
-spacr/gui_elements.py,sha256=z00Xk16TxqMUXKat0rGmw2DHDFzuXoY0C1Tlg6LZpEI,110662
-spacr/gui_utils.py,sha256=h84IcxKqcUZfatLybIMszc_xVVsBrdGKWzPdfV1oM3w,28474
+spacr/gui_core.py,sha256=HXeMfvthY_G371o84Dcr59VLT6AOKQF8r_V9kVzg7h0,38745
+spacr/gui_elements.py,sha256=7YLyIeK5JFqzevzEruvfQOrfDGOS9ZgD8ZE-dxywp3g,122706
+spacr/gui_utils.py,sha256=1pZ9QAh6BCVb6BSXciU0V9qFWOSsTtCiC72iGXUdV0c,29941
 spacr/io.py,sha256=ZtVNbEom8X8p_KfsuWw0glGwLg6S0CfwwevDPGdfiSc,117342
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/measure.py,sha256=4rmzH_a5Y0s1qALVi6YRut3xpnkJXs5vzeTPCEf3QS8,54871
-spacr/plot.py,sha256=CICY2h6sNiY6bGKkw6ZYmro_FixXkKxZpIIOoSuMw94,73963
-spacr/sequencing.py,sha256=dt4urG5tL85qh2sGEi2F9rtOqBQR-eCfcqOvcAtQIzg,75849
+spacr/plot.py,sha256=xVnbML7WpAEzdJdrLeYRk6aPinZSiV2dLAeu4mh7n0k,73963
+spacr/sequencing.py,sha256=y7EB8226B0b0gnGXt6jqBaFVATrM1Y89v3rtHb8XR_k,75746
 spacr/settings.py,sha256=tDvTBWANeuI6YC_fH5vK2HOOuRgQXIkzyNKDmt1vL4c,67745
 spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
 spacr/sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 spacr/timelapse.py,sha256=KMYCgHzf9LTZe-lWl5mvH2EjbKRE6OhpwdY13wEumGc,39504
-spacr/utils.py,sha256=M0lbpquOIxJi4iMH2_GAu0iB7jysifPNW3wzNuH1V4I,188733
+spacr/utils.py,sha256=5Njrrdhd37Tq09W1cm32941AHmlKrAZiODJGUfOwdCQ,188733
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/font/open_sans/OFL.txt,sha256=bGMoWBRrE2RcdzDiuYiB8A9OVFlJ0sA2imWwce2DAdo,4484
 "spacr/resources/font/open_sans/OpenSans-Italic-VariableFont_wdth,wght.ttf",sha256=QSoWv9h46CRX_fdlqFM3O2d3-PF3R1srnb4zUezcLm0,580280
@@ -92,9 +92,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/resources/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.2.61.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.2.61.dist-info/METADATA,sha256=Bh2O70K6G8eMEuz-OQSr66GSsluRZG1mIqMVO6ycLAU,5259
-spacr-0.2.61.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.2.61.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.2.61.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.2.61.dist-info/RECORD,,
+spacr-0.2.65.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.2.65.dist-info/METADATA,sha256=M3kT-VwVosUDjXQ9wd6Pux639rG28yhsjVF9eOdx4OI,5259
+spacr-0.2.65.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.2.65.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.2.65.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.2.65.dist-info/RECORD,,