spacr.gui_elements

Module Contents

spacr.gui_elements.fig = None

spacr.gui_elements.restart_gui_app(root)

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

spacr.gui_elements.create_menu_bar(root)

spacr.gui_elements.set_element_size()

spacr.gui_elements.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')

class spacr.gui_elements.spacrFont(font_name, font_style, font_size=12)

font_name

font_style

font_size = 12

font_path

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.

load_font()

Loads the font into Tkinter.

get_font(size=None)

Returns the font in the specified size.

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

Returns: - tkFont.Font object.

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

Bases: tkinter.Frame

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

orient = 'vertical'

bg = 'lightgrey'

sash_thickness = 10

panes = []

sashes = []

add(widget, stretch='always')

create_sash()

reposition_panes()

on_configure(event)

on_enter_sash(event)

on_leave_sash(event)

start_resize(event)

perform_resize(event)

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

Bases: tkinter.Frame

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

bg_color = 'dark_gray'

active_color = 'blue'

fg_color = 'white'

outline = False

font_family = 'OpenSans'

font_size = 12

font_loader

canvas_height = 40

canvas

draw_rounded_rectangle(color)

on_focus_in(event)

on_focus_out(event)

class spacr.gui_elements.spacrCheck(parent, text='', variable=None, *args, **kwargs)

Bases: tkinter.Frame

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

bg_color = 'black'

active_color = 'blue'

fg_color = 'white'

inactive_color = 'dark_gray'

variable = None

canvas_width = 20

canvas_height = 20

canvas

draw_rounded_square(color)

update_check(*args)

toggle_variable(event)

class spacr.gui_elements.spacrCombo(parent, textvariable=None, values=None, width=None, *args, **kwargs)

Bases: tkinter.Frame

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

bg_color = 'black'

active_color = 'blue'

fg_color = 'white'

inactive_color = 'dark_gray'

font_family = 'OpenSans'

font_size = 12

font_loader

values = []

canvas_width = None

canvas_height = 40

canvas

var

selected_value

dropdown_menu = None

draw_rounded_rectangle(color)

on_click(event)

open_dropdown()

close_dropdown()

on_select(value)

set(value)

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

Bases: tkinter.Frame

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

variable

options

command = None

text = 'Settings'

size = 50

font_size = 12

font_loader

button_width = 150

canvas_width = 154

canvas_height = 54

canvas

inactive_color = 'dark_gray'

active_color = 'blue'

fg_color = 'white'

bg_color = 'black'

button_bg

button_text

menu

create_rounded_rectangle(x1, y1, x2, y2, radius=20, **kwargs)

on_enter(event=None)

on_leave(event=None)

on_click(event=None)

post_menu()

on_select(option)

update_styles(active_categories=None)

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

Bases: tkinter.ttk.Checkbutton

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

text = ''

variable

command = None

class spacr.gui_elements.spacrProgressBar(parent, label=True, *args, **kwargs)

Bases: 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.

fg_color = 'white'

bg_color = 'black'

active_color = 'blue'

inactive_color = 'dark_gray'

font_size = 12

font_loader

style

label = True

operation_type = None

additional_info = None

set_label_position()

update_label()

class spacr.gui_elements.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: tkinter.Frame

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

specified_length = None

knob_radius = 10

thickness = 2

knob_position = 10

slider_line = None

knob = None

position = ''

offset = 0

from_ = 0

to = 100

value = None

show_index = False

command = None

fg_color = 'white'

bg_color = 'black'

active_color = 'blue'

inactive_color = 'dark_gray'

canvas

length = None

resize_slider(event)

value_to_position(value)

position_to_value(position)

draw_slider(inactive=False)

move_knob(event)

activate_knob(event)

release_knob(event)

set_to(new_to)

get()

set(value)

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

jump_to_click(event)

update_slider_from_entry(event)

Update the slider’s value from the entry.

spacr.gui_elements.spacrScrollbarStyle(style, inactive_color, active_color)

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

Bases: tkinter.ttk.Frame

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

inactive_color = 'dark_gray'

active_color = 'blue'

fg_color = 'white'

rounded_rectangle(canvas, x1, y1, x2, y2, radius=20, **kwargs)

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

Bases: tkinter.Frame

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

text = ''

align = 'right'

style_out

font_style = 'OpenSans'

font_size = 12

font_family = 'OpenSans'

font_loader

canvas

style = None

set_text(text)

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

Bases: tkinter.Frame

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

text = ''

command = None

icon_name = ''

size = 50

show_text = True

outline = False

animation = True

font_size = 12

font_loader

canvas

inactive_color = 'dark_gray'

bg_color = 'dark_gray'

active_color = 'blue'

fg_color = 'white'

is_zoomed_in = False

load_icon()

get_icon_path(icon_name)

on_enter(event=None)

on_leave(event=None)

on_click(event=None)

create_rounded_rectangle(x1, y1, x2, y2, radius=20, **kwargs)

update_description(event)

clear_description(event)

animate_zoom(target_scale, steps=10, delay=10)

zoom_icon(scale_factor)

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

Bases: tkinter.ttk.Frame

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

text = ''

variable

command = None

canvas

switch_bg

switch

label

toggle(event=None)

update_switch()

animate_switch()

animate_movement(start_x, end_x, final_color)

get()

set(value)

create_rounded_rectangle(x1, y1, x2, y2, radius=9, **kwargs)

class spacr.gui_elements.spacrToolTip(widget, text)

widget

text

tooltip_window = None

show_tooltip(event)

hide_tooltip(event)

class spacr.gui_elements.ModifyMaskApp(root, folder_path, scale_factor)

root

folder_path

scale_factor

image_filenames

masks_folder

current_image_index = 0

canvas_width

canvas_height

update_display()

update_original_mask_from_zoom()

update_original_mask(zoomed_mask, x0, x1, y0, y1)

get_scaling_factors(img_width, img_height, canvas_width, canvas_height)

canvas_to_image(x_canvas, y_canvas)

apply_zoom_on_enter(event)

normalize_image(image, lower_quantile, upper_quantile)

resize_arrays(img, mask)

load_first_image()

setup_canvas()

initialize_flags()

update_mouse_info(event)

setup_navigation_toolbar()

setup_mode_toolbar()

setup_function_toolbar()

setup_zoom_toolbar()

load_image_and_mask(index)

display_image()

display_zoomed_image()

overlay_mask_on_image(image, mask, alpha=0.5)

previous_image()

next_image()

save_mask()

set_zoom_rectangle_start(event)

set_zoom_rectangle_end(event)

update_zoom_box(event)

toggle_zoom_mode()

toggle_brush_mode()

image_to_canvas(x_image, y_image)

toggle_dividing_line_mode()

start_dividing_line(event)

finish_dividing_line(event)

update_dividing_line_preview(event)

apply_dividing_line()

toggle_draw_mode()

toggle_magic_wand_mode()

toggle_erase_mode()

apply_brush_release(event)

erase_brush_release(event)

apply_brush(event)

erase_brush(event)

erase_object(event)

use_magic_wand(event)

apply_magic_wand(image, mask, seed_point, tolerance, maximum, action='add')

magic_wand_normal(seed_point, tolerance, action)

magic_wand_zoomed(seed_point, tolerance, action)

draw(event)

draw_on_zoomed_mask(draw_coordinates)

finish_drawing(event)

finish_drawing_if_active(event)

apply_normalization()

fill_objects()

relabel_objects()

clear_objects()

invert_mask()

remove_small_objects()

class spacr.gui_elements.AnnotateApp(root, db_path, src, image_type=None, channels=None, image_size=200, annotation_column='annotate', percentiles=(1, 99), measurement=None, threshold=None, normalize_channels=None, outline=None, outline_threshold_factor=1, outline_sigma=1, edge_thickness=1, edge_transparency=100, edge_image=False, object_size=(0, 0))

root

db_path

src

index = 0

SENTINEL

orig_annotation_columns = 'annotate'

annotation_column = 'annotate'

image_type = None

channels = None

percentiles = (1, 99)

images

pending_updates

labels = []

adjusted_to_original_paths

terminate = False

update_queue

measurement = None

threshold = None

normalize_channels = None

outline = None

outline_threshold_factor = 1

outline_sigma = 1

edge_thickness = 1

edge_transparency = 100

edge_image = False

object_size = (0, 0)

font_loader

font_size = 12

bg_color = 'black'

fg_color = 'white'

active_color = 'blue'

inactive_color = 'dark_gray'

worker_busy = False

filtered_paths_annotations = []

db_update_thread

grid_frame

status_label

button_frame

next_button

previous_button

exit_button

settings_button

clear_button

count_button

dl_train_button

open_umap_window()

open_settings_window()

update_settings(**kwargs)

recreate_image_grid()

update_display()

swich_back_annotation_column()

calculate_grid_dimensions()

prefilter_paths_annotations()

load_images()

show_class_counts()

load_single_image(path_annotation_tuple)

static fill_holes(mask, min_size=0)

Fill holes inside True regions of a binary mask.

Parameters:

• mask (ndarray[bool]) – Binary mask where True denotes foreground.

• min_size (int) – Minimum hole area to fill (in pixels). - <= 0 : fill ALL internal holes. - > 0 : fill only holes smaller than min_size; reopen larger ones.

Returns:

Hole-filled mask.

Return type:

ndarray[bool]

outline_image(base_img, full_img, edge_sigma=1, edge_thickness=1, fill_holes=True, object_size=(0, 0))

Anti-aliased outlines with sub-pixel thickness that never get dimmer as they get thinner. Uses peak normalization so outline brightness is thickness-invariant (then scaled only by edge_transparency).

Parameters:

• base_img (PIL.Image) – already filtered (visible base)

• full_img (PIL.Image) – normalized RGB before filtering (edge detection / underlay)

• edge_sigma (float) – Gaussian smoothing before thresholding

• edge_thickness (float) – outline thickness in output pixels (supports < 1, e.g. 0.01)

• fill_holes (bool) – fill internal holes in foreground masks before boundary extraction

• object_size (tuple[int,int]) – (min_px, max_px) connected-component area filter. 0 disables that bound.

static normalize_image(img, percentiles=(1, 99), normalize_channels=None)

If normalize_channels is None or [], do nothing. Otherwise normalize only those channels (r/g/b).

add_colored_border(img, border_width, border_color)

filter_channels(img)

get_on_image_click(path, label, img)

static update_html(text)

clear_current_annotation()

update_database_worker()

shutdown()

next_page()

previous_page()

update_gui_text(text)

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. 7) Refresh the UI.

static convert_settings_dict_for_gui(settings)

Decide widget type per setting: - ‘check’ => Checkbutton (bools) - ‘combo’ => readonly Combobox (predefined choices) - ‘entry’ => Entry (free text / numbers / lists) Returns: {key: (kind, options, initial)}

build_multi_annotation(source_columns, target_column='multi_annot')

Consolidate multiple {1,2,NULL} columns into a single integer code column. Unique per combination. If all inputs NULL -> store NULL. Sets self.annotation_column to target_column and refreshes UI.

Encoding: per col: NULL->0, 1->1, 2->2 code = 1 + sum( digit_i * (3^i) ), i = 0..N-1 (all digits 0) => store NULL instead of 1

ensure_multi_annot_from_selection(source_columns, target_column='class_column', force_rebuild=True)

If one column selected -> use it directly (no consolidation). If >=2 selected -> build a consolidated column. If target_column already exists, auto-bump to target_column_1, target_column_2, … and use that actual name everywhere.

Returns the effective annotation column name.

open_deep_spacr_window()

spacr.gui_elements.standardize_figure(fig)

spacr.gui_elements.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).

spacr.gui_elements.save_figure_as_format(fig, file_format)

spacr.gui_elements.modify_figure(fig)

spacr.gui_elements.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.