spacr 0.2.56__py3-none-any.whl → 0.2.65__py3-none-any.whl

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():
 
@@ -516,6 +518,7 @@ class spacrDropdownMenu(tk.Frame):
         self.inactive_color = color_settings['inactive_color']
         self.active_color = color_settings['active_color']
         self.fg_color = color_settings['fg_color']
+        self.bg_color = style_out['bg_color']
 
         # Create the button with rounded edges
         self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=self.inactive_color, outline=self.inactive_color)
@@ -536,8 +539,8 @@ class spacrDropdownMenu(tk.Frame):
         self.canvas.bind("<Leave>", self.on_leave)
         self.canvas.bind("<Button-1>", self.on_click)
 
-        # Create a popup menu
-        self.menu = tk.Menu(self, tearoff=0)
+        # Create a popup menu with the desired background color
+        self.menu = tk.Menu(self, tearoff=0, bg=self.bg_color, fg=self.fg_color)
         for option in self.options:
             self.menu.add_command(label=option, command=lambda opt=option: self.on_select(opt))
 
@@ -591,7 +594,6 @@ class spacrDropdownMenu(tk.Frame):
                 else:
                     self.menu.entryconfig(idx, background=style_out['bg_color'], foreground=style_out['fg_color'])
 
-
 class spacrCheckbutton(ttk.Checkbutton):
     def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs):
         super().__init__(parent, *args, **kwargs)
@@ -613,17 +615,26 @@ class spacrProgressBar(ttk.Progressbar):
         self.bg_color = style_out['bg_color']
         self.active_color = style_out['active_color']
         self.inactive_color = style_out['inactive_color']
+        self.font_size = style_out['font_size']
+        self.font_loader = style_out['font_loader']
 
         # Configure the style for the progress bar
         self.style = ttk.Style()
+        
+        # Remove any borders and ensure the active color fills the entire space
         self.style.configure(
             "spacr.Horizontal.TProgressbar",
-            troughcolor=self.bg_color,
-            background=self.active_color,
-            thickness=20,
-            troughrelief='flat',
-            borderwidth=0
+            troughcolor=self.inactive_color,       # Set the trough to bg color
+            background=self.active_color,    # Active part is the active color
+            borderwidth=0,                   # Remove border width
+            pbarrelief="flat",               # Flat relief for the progress bar
+            troughrelief="flat",             # Flat relief for the trough
+            thickness=20,                    # Set the thickness of the progress bar
+            darkcolor=self.active_color,     # Ensure darkcolor matches the active color
+            lightcolor=self.active_color,    # Ensure lightcolor matches the active color
+            bordercolor=self.bg_color        # Set the border color to the background color to hide it
         )
+
         self.configure(style="spacr.Horizontal.TProgressbar")
 
         # Set initial value to 0
@@ -641,15 +652,14 @@ class spacrProgressBar(ttk.Progressbar):
                 justify='left',
                 bg=self.inactive_color,
                 fg=self.fg_color,
-                wraplength=300  # Adjust the wraplength as needed
+                wraplength=300,
+                font=self.font_loader.get_font(size=self.font_size)
             )
-            self.progress_label.grid_forget()  # Temporarily hide it
+            self.progress_label.grid_forget()
 
         # Initialize attributes for time and operation
         self.operation_type = None
-        self.time_image = None
-        self.time_batch = None
-        self.time_left = None
+        self.additional_info = None
 
     def set_label_position(self):
         if self.label and self.progress_label:
@@ -664,74 +674,19 @@ class spacrProgressBar(ttk.Progressbar):
             label_text = f"Processing: {self['value']}/{self['maximum']}"
             if self.operation_type:
                 label_text += f", {self.operation_type}"
-            if self.time_image:
-                label_text += f", Time/image: {self.time_image:.3f} sec"
-            if self.time_batch:
-                label_text += f", Time/batch: {self.time_batch:.3f} sec"
-            if self.time_left:
-                label_text += f", Time_left: {self.time_left:.3f} min"
-            self.progress_label.config(text=label_text)
-
-class spacrProgressBar_v1(ttk.Progressbar):
-    def __init__(self, parent, label=True, *args, **kwargs):
-        super().__init__(parent, *args, **kwargs)
-
-        # Get the style colors
-        style_out = set_dark_style(ttk.Style())
-
-        self.fg_color = style_out['fg_color']
-        self.bg_color = style_out['bg_color']
-        self.active_color = style_out['active_color']
-        self.inactive_color = style_out['inactive_color']
-
-        # Configure the style for the progress bar
-        self.style = ttk.Style()
-        self.style.configure(
-            "spacr.Horizontal.TProgressbar",
-            troughcolor=self.bg_color,
-            background=self.active_color,
-            thickness=20,
-            troughrelief='flat',
-            borderwidth=0
-        )
-        self.configure(style="spacr.Horizontal.TProgressbar")
-
-        # Set initial value to 0
-        self['value'] = 0
-
-        # Track whether to show the progress label
-        self.label = label
-
-        # Create the progress label (defer placement)
-        if self.label:
-            self.progress_label = tk.Label(parent, text="Processing: 0/0", anchor='w', justify='left', bg=self.inactive_color, fg=self.fg_color)
-            self.progress_label.grid_forget()  # Temporarily hide it
-
-        # Initialize attributes for time and operation
-        self.operation_type = None
-        self.time_image = None
-        self.time_batch = None
-        self.time_left = None
-
-    def set_label_position(self):
-        if self.label and self.progress_label:
-            row_info = self.grid_info().get('row', 0)
-            col_info = self.grid_info().get('column', 0)
-            col_span = self.grid_info().get('columnspan', 1)
-            self.progress_label.grid(row=row_info + 1, column=col_info, columnspan=col_span, pady=5, padx=5, sticky='ew')
-
-    def update_label(self):
-        if self.label and self.progress_label:
-            # Update the progress label with current progress and additional info
-            label_text = f"Processing: {self['value']}/{self['maximum']}"
-            if self.operation_type:
-                label_text += f", {self.operation_type}"
-            if self.time_image:
-                label_text += f", Time/image: {self.time_image:.3f} sec"
-            if self.time_batch:
-                label_text += f", Time/batch: {self.time_batch:.3f} sec"
-            if self.time_left:
-                label_text += f", Time_left: {self.time_left:.3f} min"
+            if hasattr(self, 'additional_info') and self.additional_info:
+                # Add a space between progress information and additional information
+                label_text += "\n\n"
+                # Split the additional_info into a list of items
+                items = self.additional_info.split(", ")
+                formatted_additional_info = ""
+                # Group the items in pairs, adding them to formatted_additional_info
+                for i in range(0, len(items), 2):
+                    if i + 1 < len(items):
+                        formatted_additional_info += f"{items[i]}, {items[i + 1]}\n\n"
+                    else:
+                        formatted_additional_info += f"{items[i]}\n\n"  # If there's an odd item out, add it alone
+                label_text += formatted_additional_info.strip()
             self.progress_label.config(text=label_text)
 
 def spacrScrollbarStyle(style, inactive_color, active_color):
@@ -2128,6 +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'])}")
@@ -2136,6 +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])}")
@@ -2417,4 +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)