iblatlas.gui.atlasview

TopView is the main Widget with the related ControllerTopView Class There are several SliceView windows (sagittal, coronal, possibly tilted etc…) that each have a SliceController object The underlying data model object is an iblatlas.atlas.AllenAtlas object

TopView(QMainWindow) ControllerTopView(PgImageController)

SliceView(QWidget) SliceController(PgImageController)

Functions

main
view	application entry point

Classes

ControllerTopView	TopView ControllerTopView
ImageLayer	Class for keeping track of image layers.
PgImageController	Abstract class that implements mapping fr`om axes to voxels for any window.
SliceController
SliceView	Window containing a volume slice
TopView	Main Window of the application.

class TopView(**kwargs)

Bases: QMainWindow

Main Window of the application. This is a top view of the brain with 2 movable lines allowing to select sagittal and coronal slices.

focusInEvent(self, a0: QFocusEvent | None)

closeEvent(self, a0: QCloseEvent | None)

add_scatter_feature(data)

add_image_layer(**kwargs)

Parameters:

pg_kwargs – pyqtgraph setImage arguments: {‘levels’: None, ‘lut’: None,

‘opacity’: 1.0} :param slice_kwargs: iblatlas.atlas.slice arguments: {‘volume’: ‘image’, ‘mode’: ‘clip’} :return:

add_regions_feature(values, cmap, opacity=1.0)

slider_alpha_move()

mouseMoveEvent(self, a0: QMouseEvent | None)

on_brain_tree_selection(rid)

set_volume(volume: ndarray, colormap: str = 'magma', levels=None)

class SliceView(topview: TopView, waxis, haxis, daxis, **kwargs)

Bases: QWidget

Window containing a volume slice

add_scatter()

add_image_layer(name=None, **kwargs)

Parameters:

pg_kwargs – pyqtgraph setImage arguments: {‘levels’: None, ‘lut’: None,

‘opacity’: 1.0} :param slice_kwargs: iblatlas.atlas.slice arguments: {‘volume’: ‘image’, ‘mode’: ‘clip’} :return:

closeEvent(self, a0: QCloseEvent | None)

keyPressEvent(self, a0: QKeyEvent | None)

mouseClick(event)

mouseMoveEvent(self, a0: QMouseEvent | None)

replace_image_layer(index, **kwargs)

class PgImageController(win, res=25)

Bases: object

Abstract class that implements mapping fr`om axes to voxels for any window. Not instantiated directly.

cursor2xyamp(qpoint)

Used for the mouse hover function over image display

cursor2ind(qpoint)

image coordinates over the image display

property imageItem

returns the first image item

set_image(pg_image_item, im, dw, dh, w0, h0, **pg_kwargs)

Parameters:

• im

• dw

• dh

• w0

• h0

• pgkwargs – og.ImageItem.setImage() parameters: level=None, lut=None, opacity=1

Returns:

set_points(x=None, y=None)

class ControllerTopView(qmain: TopView, res: int = 25, volume='image', atlas=None, **kwargs)

Bases: PgImageController

TopView ControllerTopView

property lines_sagittal

property lines_coronal

property lines_horizontal

property slices: dict

property figures: dict

set_slice(fig, coord=0, mapping='Allen')

set_top()

set_scatter(fig, coord=0)

class SliceController(fig, waxis=None, haxis=None, daxis=None, wdir=1, hdir=1)

Bases: PgImageController

cursor2xyamp(qpoint)

Extends the superclass method to also get the brain region from the model

Parameters:

qpoint

Returns:

class ImageLayer(image_item: ~pyqtgraph.graphicsItems.ImageItem.ImageItem = <factory>, pg_kwargs: dict = <factory>, slice_kwargs: dict = <factory>)

Bases: object

Class for keeping track of image layers.

:param image_item :param pg_kwargs: pyqtgraph setImage arguments: {‘levels’: None, ‘lut’: None, ‘opacity’: 1.0} :param slice_kwargs: iblatlas.atlas.slice arguments: {‘volume’: ‘image’, ‘mode’: ‘clip’} :param

image_item: ImageItem

pg_kwargs: dict

slice_kwargs: dict

view(res=25, title=None, atlas=None)

application entry point

main()