widgets#

A set of custom widgets

class DataFrameWidget(df, n_digits=2, parent=None)[source]#

Bases: QWidget

set_content()[source]#

class LandmarksSelectorDialog(src_folder, params=None, app=None)[source]#

Bases: WizardDialog

add_marker()[source]#

connect_buttons()[source]#

fixed_coords()[source]#

get_new_color()[source]#

moving_coords()[source]#

remove_marker()[source]#

set_fixed_coords(x, y, z)[source]#

set_moving_coords(x, y, z)[source]#

setup()[source]#

property colors#

property current_color#

property current_marker#

property style_sheets#

class OrthoViewer(img=None, parent=None)[source]#

Bases: object

Orthogonal viewer for 3D images

This is a class that allows to visualize 3D images in 3 orthogonal views.

add_regions()[source]#: Add the regions to the viewer .. rubric:: Returns

plot_orthogonal_views(img=None, parent=None)[source]#

Plot the orthogonal views of the image

Parameters:

img (np.ndarray) – The image to plot. If None, the image set at initialization will be used
parent (QWidget) – The parent widget to plot into. If None, the parent set at initialization will be used

Returns

setup(img, params, parent=None)[source]#

Initialize the viewer after the object has been created

Parameters:

img (np.ndarray) – The 3D image to visualize
params (UiParameter) – The parameters object
parent (QWidget) – The parent widget

Returns

update_ranges(ranges)[source]#

Update the ranges (min, max) for each axis of the viewer

Parameters:: ranges (list(tuple(float, float)))

Returns

property depth#: Get the depth of the image .. rubric:: Returns

property height#: Get the height of the image .. rubric:: Returns

property shape#: Get the shape of the image .. rubric:: Returns

property width#: Get the width of the image .. rubric:: Returns

class PatternDialog(src_folder, params=None, app=None, min_file_number=10, tile_extension='.ome.tif')[source]#

Bases: WizardDialog

add_group()[source]#

connect_buttons()[source]#

get_patterns()[source]#

get_widgets(image_group_id, axis)[source]#

save_results()[source]#

setup()[source]#

validate_pattern()[source]#

class PerfMonitor(parent, fast_period, slow_period, *args, **kwargs)[source]#

Bases: QWidget

get_cpu_percent()[source]#

get_ram_percent()[source]#

get_thread_percent()[source]#

handle_gpu_vals_updated()[source]#

handle_proc_changed(file_path)[source]#

start()[source]#

stop()[source]#

update_cpu_values()[source]#

update_gpu_values()[source]#

cpu_vals_changed#

gpu_vals_changed#

percent_thread#: The percentage of the CPU used by the most active process of ClearMap

class ProgressWatcher(max_progress=100, main_max_progress=1, parent=None)[source]#

Bases: QWidget

A QWidget that watches the progress of a process. It uses signals to update the progress bar and the text The main setup methods are setup and prepare_for_substep It is meant to be used in conjunction with a ProgressWatcherDialog to which it is connected through its signals

count_dones()[source]#

finish()[source]#

get_progress()[source]#

increment(increment)[source]#

increment_main_progress(increment=1)[source]#

prepare_for_substep(step_length, pattern, step_name)[source]#

Parameters:

step_name – str
step_length – int The number of steps in the operation
pattern – str or re.Pattern or (str, re.Pattern) the text to look for in the logs to check for progress

Returns

reset()[source]#

Reset all the values to their initial state

Returns

reset_log_length()[source]#

set_main_progress(value)[source]#

set_progress(value)[source]#

setup(main_step_name, main_step_length, sub_step_length=0, pattern=None)[source]#

Post initialisation of the

Parameters:

main_step_name
main_step_length
sub_step_length
pattern

Returns

aborted#

finished#

main_max_changed#

property main_max_progress#

main_progress_changed#

property main_step_name#

main_step_name_changed#

max_changed#

property max_progress#

progress_changed#

property sub_step_name#

sub_step_name_changed#

class SamplePickerDialog(src_folder, params=None, app=None)[source]#

Bases: WizardDialog

apply_changes()[source]#

connect_buttons()[source]#

handle_add_group(add_to_params=True)[source]#

handle_group_changed()[source]#

parse_sample_folders()[source]#

setup()[source]#

update_current_group_paths()[source]#

class StructurePickerWidget(parent=None)[source]#

Bases: QTreeWidget

static build_tree(tree=None, parent=None)[source]#

static parse_json()[source]#

print_id(itm, col)[source]#

DARK_COLOR = '#2E3436'#

LIGHT_COLOR = 'white'#

class StructureSelector(src_folder, params=None, app=None)[source]#

Bases: WizardDialog

close()[source]#

connect_buttons()[source]#

setup()[source]#

show()[source]#

class TwoListSelection(parent=None)[source]#

Bases: QWidget

addAvailableItems(items)[source]#

connections()[source]#

get_left_elements()[source]#

get_right_elements()[source]#

layout_buttons()[source]#

on_mBtnDown_clicked()[source]#

on_mBtnMoveToAvailable_clicked()[source]#

on_mBtnMoveToSelected_clicked()[source]#

on_mBtnUp_clicked()[source]#

on_mButtonToAvailable_clicked()[source]#

on_mButtonToSelected_clicked()[source]#

setSelectedItems(items)[source]#

setup_layout()[source]#

update_buttons_status()[source]#

class WizardDialog(src_folder, ui_name, ui_title, size, params=None, app=None)[source]#

Bases: object

connect_buttons()[source]#

static enable_widgets(widgets)[source]#

exec()[source]#

fix_btn_boxes_text()[source]#

static hide_widgets(widgets)[source]#

setup()[source]#

setup_mini_brain(mini_brain_scaling=(5, 5, 5))[source]#

Create a downsampled version of the Allen Brain Atlas for the mini brain widget

Parameters:: mini_brain_scaling (tuple(int, int, int)) – The scaling factors for the mini brain. Default is (5, 5, 5)

Returns

tuple(scale, downsampled_array)