spacr.gui_elements
==================

.. py:module:: spacr.gui_elements








Module Contents
---------------

.. py:data:: fig
   :value: None


.. py:function:: restart_gui_app(root)

   Restarts the GUI application by destroying the current instance
   and launching a fresh one.


.. py:function:: create_menu_bar(root)

.. py:function:: set_element_size()

.. py:function:: set_dark_style(style, parent_frame=None, containers=None, widgets=None, font_family='OpenSans', font_size=12, bg_color='black', fg_color='white', active_color='blue', inactive_color='dark_gray')

.. py:class:: spacrFont(font_name, font_style, font_size=12)

   .. py:attribute:: font_name


   .. py:attribute:: font_style


   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: font_path


   .. py:method:: get_font_path(font_name, font_style)

      Returns the font path based on the font name and style.

      Parameters:
      - font_name: str, the name of the font.
      - font_style: str, the style of the font.

      Returns:
      - str, the path to the font file.



   .. py:method:: load_font()

      Loads the font into Tkinter.



   .. py:method:: get_font(size=None)

      Returns the font in the specified size.

      Parameters:
      - size: int, the size of the font (optional).

      Returns:
      - tkFont.Font object.



.. py:class:: spacrContainer(parent, orient=tk.VERTICAL, bg=None, *args, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: orient
      :value: 'vertical'



   .. py:attribute:: bg
      :value: 'lightgrey'



   .. py:attribute:: sash_thickness
      :value: 10



   .. py:attribute:: panes
      :value: []



   .. py:attribute:: sashes
      :value: []



   .. py:method:: add(widget, stretch='always')


   .. py:method:: create_sash()


   .. py:method:: reposition_panes()


   .. py:method:: on_configure(event)


   .. py:method:: on_enter_sash(event)


   .. py:method:: on_leave_sash(event)


   .. py:method:: start_resize(event)


   .. py:method:: perform_resize(event)


.. py:class:: spacrEntry(parent, textvariable=None, outline=False, width=None, *args, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: bg_color
      :value: 'dark_gray'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: outline
      :value: False



   .. py:attribute:: font_family
      :value: 'OpenSans'



   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: font_loader


   .. py:attribute:: canvas_height
      :value: 40



   .. py:attribute:: canvas


   .. py:method:: draw_rounded_rectangle(color)


   .. py:method:: on_focus_in(event)


   .. py:method:: on_focus_out(event)


.. py:class:: spacrCheck(parent, text='', variable=None, *args, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: bg_color
      :value: 'black'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: variable
      :value: None



   .. py:attribute:: canvas_width
      :value: 20



   .. py:attribute:: canvas_height
      :value: 20



   .. py:attribute:: canvas


   .. py:method:: draw_rounded_square(color)


   .. py:method:: update_check(*args)


   .. py:method:: toggle_variable(event)


.. py:class:: spacrCombo(parent, textvariable=None, values=None, width=None, *args, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: bg_color
      :value: 'black'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: font_family
      :value: 'OpenSans'



   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: font_loader


   .. py:attribute:: values
      :value: []



   .. py:attribute:: canvas_width
      :value: None



   .. py:attribute:: canvas_height
      :value: 40



   .. py:attribute:: canvas


   .. py:attribute:: var


   .. py:attribute:: selected_value


   .. py:attribute:: dropdown_menu
      :value: None



   .. py:method:: draw_rounded_rectangle(color)


   .. py:method:: on_click(event)


   .. py:method:: open_dropdown()


   .. py:method:: close_dropdown()


   .. py:method:: on_select(value)


   .. py:method:: set(value)


.. py:class:: spacrDropdownMenu(parent, variable, options, command=None, font=None, size=50, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: variable


   .. py:attribute:: options


   .. py:attribute:: command
      :value: None



   .. py:attribute:: text
      :value: 'Settings'



   .. py:attribute:: size
      :value: 50



   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: font_loader


   .. py:attribute:: button_width
      :value: 150



   .. py:attribute:: canvas_width
      :value: 154



   .. py:attribute:: canvas_height
      :value: 54



   .. py:attribute:: canvas


   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: bg_color
      :value: 'black'



   .. py:attribute:: button_bg


   .. py:attribute:: button_text


   .. py:attribute:: menu


   .. py:method:: create_rounded_rectangle(x1, y1, x2, y2, radius=20, **kwargs)


   .. py:method:: on_enter(event=None)


   .. py:method:: on_leave(event=None)


   .. py:method:: on_click(event=None)


   .. py:method:: post_menu()


   .. py:method:: on_select(option)


   .. py:method:: update_styles(active_categories=None)


.. py:class:: spacrCheckbutton(parent, text='', variable=None, command=None, *args, **kwargs)

   Bases: :py:obj:`tkinter.ttk.Checkbutton`


   Ttk Checkbutton widget which is either in on- or off-state.


   .. py:attribute:: text
      :value: ''



   .. py:attribute:: variable


   .. py:attribute:: command
      :value: None



.. py:class:: spacrProgressBar(parent, label=True, *args, **kwargs)

   Bases: :py:obj:`tkinter.ttk.Progressbar`


   Ttk Progressbar widget shows the status of a long-running
   operation. They can operate in two modes: determinate mode shows the
   amount completed relative to the total amount of work to be done, and
   indeterminate mode provides an animated display to let the user know
   that something is happening.


   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: bg_color
      :value: 'black'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: font_loader


   .. py:attribute:: style


   .. py:attribute:: label
      :value: True



   .. py:attribute:: operation_type
      :value: None



   .. py:attribute:: additional_info
      :value: None



   .. py:method:: set_label_position()


   .. py:method:: update_label()


.. py:class:: spacrSlider(master=None, length=None, thickness=2, knob_radius=10, position='center', from_=0, to=100, value=None, show_index=False, command=None, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: specified_length
      :value: None



   .. py:attribute:: knob_radius
      :value: 10



   .. py:attribute:: thickness
      :value: 2



   .. py:attribute:: knob_position
      :value: 10



   .. py:attribute:: slider_line
      :value: None



   .. py:attribute:: knob
      :value: None



   .. py:attribute:: position
      :value: ''



   .. py:attribute:: offset
      :value: 0



   .. py:attribute:: from_
      :value: 0



   .. py:attribute:: to
      :value: 100



   .. py:attribute:: value
      :value: None



   .. py:attribute:: show_index
      :value: False



   .. py:attribute:: command
      :value: None



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: bg_color
      :value: 'black'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: canvas


   .. py:attribute:: length
      :value: None



   .. py:method:: resize_slider(event)


   .. py:method:: value_to_position(value)


   .. py:method:: position_to_value(position)


   .. py:method:: draw_slider(inactive=False)


   .. py:method:: move_knob(event)


   .. py:method:: activate_knob(event)


   .. py:method:: release_knob(event)


   .. py:method:: set_to(new_to)


   .. py:method:: get()


   .. py:method:: set(value)

      Set the slider's value and update the knob position.



   .. py:method:: jump_to_click(event)


   .. py:method:: update_slider_from_entry(event)

      Update the slider's value from the entry.



.. py:function:: spacrScrollbarStyle(style, inactive_color, active_color)

.. py:class:: spacrFrame(container, width=None, *args, bg='black', radius=20, scrollbar=True, textbox=False, **kwargs)

   Bases: :py:obj:`tkinter.ttk.Frame`


   Ttk Frame widget is a container, used to group other widgets
   together.


   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:method:: rounded_rectangle(canvas, x1, y1, x2, y2, radius=20, **kwargs)


.. py:class:: spacrLabel(parent, text='', font=None, style=None, align='right', height=None, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: text
      :value: ''



   .. py:attribute:: align
      :value: 'right'



   .. py:attribute:: style_out


   .. py:attribute:: font_style
      :value: 'OpenSans'



   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: font_family
      :value: 'OpenSans'



   .. py:attribute:: font_loader


   .. py:attribute:: canvas


   .. py:attribute:: style
      :value: None



   .. py:method:: set_text(text)


.. py:class:: spacrButton(parent, text='', command=None, font=None, icon_name=None, size=50, show_text=True, outline=False, animation=True, *args, **kwargs)

   Bases: :py:obj:`tkinter.Frame`


   Frame widget which may contain other widgets and can have a 3D border.


   .. py:attribute:: text
      :value: ''



   .. py:attribute:: command
      :value: None



   .. py:attribute:: icon_name
      :value: ''



   .. py:attribute:: size
      :value: 50



   .. py:attribute:: show_text
      :value: True



   .. py:attribute:: outline
      :value: False



   .. py:attribute:: animation
      :value: True



   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: font_loader


   .. py:attribute:: canvas


   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: bg_color
      :value: 'dark_gray'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: is_zoomed_in
      :value: False



   .. py:method:: load_icon()


   .. py:method:: get_icon_path(icon_name)


   .. py:method:: on_enter(event=None)


   .. py:method:: on_leave(event=None)


   .. py:method:: on_click(event=None)


   .. py:method:: create_rounded_rectangle(x1, y1, x2, y2, radius=20, **kwargs)


   .. py:method:: update_description(event)


   .. py:method:: clear_description(event)


   .. py:method:: animate_zoom(target_scale, steps=10, delay=10)


   .. py:method:: zoom_icon(scale_factor)


.. py:class:: spacrSwitch(parent, text='', variable=None, command=None, *args, **kwargs)

   Bases: :py:obj:`tkinter.ttk.Frame`


   Ttk Frame widget is a container, used to group other widgets
   together.


   .. py:attribute:: text
      :value: ''



   .. py:attribute:: variable


   .. py:attribute:: command
      :value: None



   .. py:attribute:: canvas


   .. py:attribute:: switch_bg


   .. py:attribute:: switch


   .. py:attribute:: label


   .. py:method:: toggle(event=None)


   .. py:method:: update_switch()


   .. py:method:: animate_switch()


   .. py:method:: animate_movement(start_x, end_x, final_color)


   .. py:method:: get()


   .. py:method:: set(value)


   .. py:method:: create_rounded_rectangle(x1, y1, x2, y2, radius=9, **kwargs)


.. py:class:: spacrToolTip(widget, text)

   .. py:attribute:: widget


   .. py:attribute:: text


   .. py:attribute:: tooltip_window
      :value: None



   .. py:method:: show_tooltip(event)


   .. py:method:: hide_tooltip(event)


.. py:class:: ModifyMaskApp(root, folder_path, scale_factor)

   .. py:attribute:: root


   .. py:attribute:: folder_path


   .. py:attribute:: scale_factor


   .. py:attribute:: image_filenames


   .. py:attribute:: masks_folder


   .. py:attribute:: current_image_index
      :value: 0



   .. py:attribute:: canvas_width


   .. py:attribute:: canvas_height


   .. py:method:: update_display()


   .. py:method:: update_original_mask_from_zoom()


   .. py:method:: update_original_mask(zoomed_mask, x0, x1, y0, y1)


   .. py:method:: get_scaling_factors(img_width, img_height, canvas_width, canvas_height)


   .. py:method:: canvas_to_image(x_canvas, y_canvas)


   .. py:method:: apply_zoom_on_enter(event)


   .. py:method:: normalize_image(image, lower_quantile, upper_quantile)


   .. py:method:: resize_arrays(img, mask)


   .. py:method:: load_first_image()


   .. py:method:: setup_canvas()


   .. py:method:: initialize_flags()


   .. py:method:: update_mouse_info(event)


   .. py:method:: setup_navigation_toolbar()


   .. py:method:: setup_mode_toolbar()


   .. py:method:: setup_function_toolbar()


   .. py:method:: setup_zoom_toolbar()


   .. py:method:: load_image_and_mask(index)


   .. py:method:: display_image()


   .. py:method:: display_zoomed_image()


   .. py:method:: overlay_mask_on_image(image, mask, alpha=0.5)


   .. py:method:: previous_image()


   .. py:method:: next_image()


   .. py:method:: save_mask()


   .. py:method:: set_zoom_rectangle_start(event)


   .. py:method:: set_zoom_rectangle_end(event)


   .. py:method:: update_zoom_box(event)


   .. py:method:: toggle_zoom_mode()


   .. py:method:: toggle_brush_mode()


   .. py:method:: image_to_canvas(x_image, y_image)


   .. py:method:: toggle_dividing_line_mode()


   .. py:method:: start_dividing_line(event)


   .. py:method:: finish_dividing_line(event)


   .. py:method:: update_dividing_line_preview(event)


   .. py:method:: apply_dividing_line()


   .. py:method:: toggle_draw_mode()


   .. py:method:: toggle_magic_wand_mode()


   .. py:method:: toggle_erase_mode()


   .. py:method:: apply_brush_release(event)


   .. py:method:: erase_brush_release(event)


   .. py:method:: apply_brush(event)


   .. py:method:: erase_brush(event)


   .. py:method:: erase_object(event)


   .. py:method:: use_magic_wand(event)


   .. py:method:: apply_magic_wand(image, mask, seed_point, tolerance, maximum, action='add')


   .. py:method:: magic_wand_normal(seed_point, tolerance, action)


   .. py:method:: magic_wand_zoomed(seed_point, tolerance, action)


   .. py:method:: draw(event)


   .. py:method:: draw_on_zoomed_mask(draw_coordinates)


   .. py:method:: finish_drawing(event)


   .. py:method:: finish_drawing_if_active(event)


   .. py:method:: apply_normalization()


   .. py:method:: fill_objects()


   .. py:method:: relabel_objects()


   .. py:method:: clear_objects()


   .. py:method:: invert_mask()


   .. py:method:: remove_small_objects()


.. py:class:: AnnotateApp(root, db_path, src, image_type=None, channels=None, image_size=200, annotation_column='annotate', normalize=False, percentiles=(1, 99), measurement=None, threshold=None, normalize_channels=None)

   .. py:attribute:: root


   .. py:attribute:: db_path


   .. py:attribute:: src


   .. py:attribute:: index
      :value: 0



   .. py:attribute:: orig_annotation_columns
      :value: 'annotate'



   .. py:attribute:: annotation_column
      :value: 'annotate'



   .. py:attribute:: image_type
      :value: None



   .. py:attribute:: channels
      :value: None



   .. py:attribute:: normalize
      :value: False



   .. py:attribute:: percentiles
      :value: (1, 99)



   .. py:attribute:: images


   .. py:attribute:: pending_updates


   .. py:attribute:: labels
      :value: []



   .. py:attribute:: adjusted_to_original_paths


   .. py:attribute:: terminate
      :value: False



   .. py:attribute:: update_queue


   .. py:attribute:: measurement
      :value: None



   .. py:attribute:: threshold
      :value: None



   .. py:attribute:: normalize_channels
      :value: None



   .. py:attribute:: font_loader


   .. py:attribute:: font_size
      :value: 12



   .. py:attribute:: bg_color
      :value: 'black'



   .. py:attribute:: fg_color
      :value: 'white'



   .. py:attribute:: active_color
      :value: 'blue'



   .. py:attribute:: inactive_color
      :value: 'dark_gray'



   .. py:attribute:: filtered_paths_annotations
      :value: []



   .. py:attribute:: db_update_thread


   .. py:attribute:: status_label


   .. py:attribute:: button_frame


   .. py:attribute:: next_button


   .. py:attribute:: previous_button


   .. py:attribute:: exit_button


   .. py:attribute:: train_button


   .. py:attribute:: settings_button


   .. py:attribute:: grid_frame


   .. py:method:: open_settings_window()


   .. py:method:: update_settings(**kwargs)


   .. py:method:: recreate_image_grid()


   .. py:method:: swich_back_annotation_column()


   .. py:method:: calculate_grid_dimensions()


   .. py:method:: prefilter_paths_annotations()


   .. py:method:: load_images()


   .. py:method:: load_single_image(path_annotation_tuple)


   .. py:method:: normalize_image(img, normalize=False, percentiles=(1, 99), normalize_channels=None)
      :staticmethod:


      Normalize an image based on specific channels (R, G, B).

      :param img: Input image.
      :type img: PIL.Image or np.array
      :param normalize: Whether to normalize the image or not.
      :type normalize: bool
      :param percentiles: Percentiles to use for intensity rescaling.
      :type percentiles: tuple
      :param normalize_channels: List of channels to normalize. E.g., ['r', 'g', 'b'], ['r'], ['g'], etc.
      :type normalize_channels: list

      :returns: Normalized image.
      :rtype: PIL.Image



   .. py:method:: add_colored_border(img, border_width, border_color)


   .. py:method:: filter_channels(img)


   .. py:method:: get_on_image_click(path, label, img)


   .. py:method:: update_html(text)
      :staticmethod:



   .. py:method:: update_database_worker()


   .. py:method:: update_gui_text(text)


   .. py:method:: next_page()


   .. py:method:: previous_page()


   .. py:method:: shutdown()


   .. py:method:: train_and_classify()

      1) Merge data from the relevant DB tables (including png_list).
      2) Collect manual annotations from png_list.<annotation_column> => 'manual_annotation'.
         - 1 => class=1, 2 => class=0 (for training).
      3) If only one class is present, randomly sample unannotated images as the other class.
      4) Train an XGBoost model.
      5) Classify *all* rows -> fill XGboost_score (prob of class=1) & XGboost_annotation (1 or 2 if high confidence).
      6) Write those columns back to sqlite, so every row in png_list has a score (and possibly an annotation).
      7) Refresh the UI (prefilter_paths_annotations + load_images).



.. py:function:: standardize_figure(fig)

.. py:function:: 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).


.. py:function:: save_figure_as_format(fig, file_format)

.. py:function:: modify_figure(fig)

.. py:function:: generate_dna_matrix(output_path='dna_matrix.gif', canvas_width=1500, canvas_height=1000, duration=30, fps=20, base_size=20, transition_frames=30, font_type='arial.ttf', enhance=[1.1, 1.5, 1.2, 1.5], lowercase_prob=0.3)

   Generate a DNA matrix animation and save it as GIF, MP4, or AVI using OpenCV for videos.


