ibl_alignment_gui.app.shank_view

Classes

ShankView

View for displaying plots for a shank on a probe for a given recording configuration.

class ibl_alignment_gui.app.shank_view.ShankView(name, index, config)

Bases: object

View for displaying plots for a shank on a probe for a given recording configuration.

Parameters:

• name (str) – The name of the shank

• index (int) – The index of the shank

• config (str) – The config of the shank

COLOURS = ['#cc0000', '#6aa84f', '#1155cc', '#a64d79']

HEADER_STYLE = {'deselected': '\n                QLabel {\n                    background-color: rgb(240, 240, 240);\n                    border: 1px solid lightgrey;\n                    color: black;\n                    padding: 6px;\n                    font-weight: bold;\n                }\n                ', 'selected': 'QLabel {\n                    background-color: #c92d0e;\n                    border: 1px solid lightgrey;\n                    color: white;\n                    padding: 6px;\n                    font-weight: bold;\n                }\n                '}

add_reference_lines_to_display()

Add all reference lines to the respective plots.

Return type:

None

align_reference_lines_and_points()

Align the position of the track reference lines and scatter points.

The position is updated based on the new positions of their corresponding feature reference lines.

Return type:

None

clear_channels(fig_slice)

Clear channels and reference lines from the slice plot.

Parameters:

fig_slice (pg.ViewBox) – The fig slice to remove the channels and reference lines from

Return type:

None

clear_feature()

Clear items from the probe plot.

Return type:

None

clear_fit()

Clear the data from fit lines.

Return type:

None

clear_histology(fig)

Clear items from the histology plot.

clear_line()

Clear items from the scatter plot.

Return type:

None

clear_probe()

Clear items from the probe plot.

Return type:

None

clear_scale_factor()

Clear items from the scale factor plot.

clear_scatter()

Clear items from the scatter/ image plot.

Return type:

None

clear_slice()

Clear items from the slice plot.

create_ephys_plots()

Create plots for the electrophysiology panels.

Return type:

None

create_fit_items()

Create plot items to put on the fit figure.

The actual fit PlotItem is stored in the app_view as it is shared across the different shanks.

Return type:

None

create_histology_plots()

Create the plots the histology panels.

Return type:

None

static create_line_style(colour=None)

Generate a random line style (color and dash style) for reference lines.

If the colour is given this is used.

Parameters:

colour (QtGui.QColor, optional) – The colour to use for the line. If None, a random colour is chosen.

Return type:

tuple[QPen, QBrush]

Returns:

• pen (QtGui.QPen) – A pen object defining the line color, dash style, and width.

• brush (QtGui.QBrush) – A brush object with the same color as the pen for use with filled items.

create_reference_line_and_point(pos, fix_colour=False)

Create a new reference line.

Creates a feature reference line on the line, image and probe figures, a track reference line on the histology figure and a scatter point to be added to the fit figure

Parameters:

• pos (float) – Y-axis position at which to draw the horizontal line.

• fix_colour (bool) – Whether to use a fixed colour for the reference line or choose a random color

Return type:

tuple[InfiniteLine, list[InfiniteLine], PlotDataItem]

Returns:

• line_track (pg.InfiniteLine) – The track reference line

• line_feature (list[pg.InfiniteLine]) – The feature reference lines

• point (pg.PlotDataItem) – The scatter point

create_slice_items()

Create the slice figure area to show the coronal slices and channels.

Return type:

None

delete_reference_line_and_point(line_idx)

Delete a reference line (track, feature and point) from the tracking arrays.

Parameters:

line_idx (int) – The index of the reference line to remove.

Return type:

None

get_feature_and_track_coords()

Return the values of the track and feature reference lines.

Return type:

tuple[ndarray, ndarray]

Returns:

• line_track (np.ndarray) – An array containing the positions of the track reference lines

• line_feature (np.ndarray) – An array containing the positions of the track reference lines

init_plot_items()

Initialise all plot items and attributes used to keep track of plots.

Return type:

None

init_reference_line_arrays()

Initialise arrays used to keep track of reference lines and points.

Return type:

None

static make_transform(scale, offset)

Create a Qt transform matrix based on scaling and offset values.

Parameters:

• scale (list or np.ndarray) – The x-scale and y-scale factors to apply.

• offset (list or np.ndarray) – The x-offset and y-offset translations to apply.

Returns:

The constructed transformation matrix.

Return type:

QtGui.QTransform

match_feature_line(feature_line)

Find the index of the feature reference line matching the given line.

Also find the indices of the feature plots that this line does not belong to.

Parameters:

feature_line (pg.InfiniteLine) – The feature line to match

Return type:

tuple[int | None, list | ndarray | None]

Returns:

• line_idx (int or None) – The index of the matching feature line or None if not found

• fig_idx (np.ndarray or None) – An array containing the indices of the other plots, or None if not found.

match_linear_region(hover_item)

Find the index of a hovered linear region within the list of scale regions.

Parameters:

hover_item (pg.LinearRegionItem) – The region item currently hovered over.

Returns:

region_idx – The index of the hovered region in the scale regions list.

Return type:

int

match_track_line(track_line)

Find the index of the track reference line matching the given line.

Parameters:

track_line (pg.InfiniteLine) – The track line to match

Returns:

line_idx – The index of the matching track line or None if not found

Return type:

int or None

plot_channels(fig_slice, data, colour='r')

Plot the locations of electrode channels and track reference lines on the histology slice.

Note special case as the fig_slice may not come from the current item so it is passed in.

Parameters:

• fig_slice (pg.ViewBox) – The fig slice to plot the channels and reference lines on

• data (Bunch) – A Bunch object containing the channels data

• colour (str) – The colour to use to plot the channels

Return type:

None

plot_empty(fig, fig_cb=None, img=False)

Create an empty placeholder plot when no data is available.

Parameters:

• fig (pg.PlotItem) – The figure to display empty data

• fig_cb (pg.PlotItem) – An optional colourbar to reset

• img (bool) – Whether the figure is an image plot or not

Return type:

None

plot_feature(data)

Plot a 2D feature plot of electrophysiology data.

This is made up of many individual probe plots stacked horizontally.

Parameters:

data (Bunch[str, ProbeData]) – A Bunch object containing data to plot

Return type:

None

plot_fit(data)

Plot data onto fit lines.

Parameters:

data (Bunch) – A Bunch object containing the fit data

Return type:

None

plot_histology(fig, data, ax='left')

Plot histology regions on the given figure.

Shows brain regions intersecting with the probe track.

Parameters:

• fig (pg.PlotItem) – The figure on which to plot the histology regions.

• data (Bunch) – A Bunch object containing the histology data.

• ax (str, default='left') – Orientation of the axis on which to add labels. ‘left’ for the main histology figure (fig_hist), and ‘right’ for the reference figure (fig_hist_ref).

Return type:

None

plot_histology_cumulative(fig, data, ax='right')

Plot cumulative histology probabilities on the given figure.

Parameters:

• fig (pg.PlotItem) – The figure on which to plot the histology regions.

• data (Bunch) – A Bunch object containing the histology data.

• ax (str, default='left') – Orientation of the axis on which to add labels. ‘left’ for the main histology figure (fig_hist), and ‘right’ for the reference figure (fig_hist_ref).

Return type:

None

plot_image(data, levels=None)

Plot a 2D image plot of electrophysiology data.

Parameters:

• data (ImageData) – An ImageData object containing data to plot

• levels (list or np.ndarray, optional) – A list or array containing the levels to set for the colorbar. Defaults to data.levels

Returns:

The created colorbar

Return type:

ColorBar

plot_line(data)

Plot a 1D line plot of electrophysiology data.

Parameters:

data (LineData) – A LineData object containing data to plot

Return type:

None

plot_probe(data, levels=None)

Plot a 2D probe plot of electrophysiology data.

Parameters:

• data (ProbeData) – A ProbeData object containing data to plot

• levels (list or np.ndarray, optional) – A list or array containing the levels to set for the colorbar. Defaults to data.levels

Returns:

The created colorbar

Return type:

ColorBar

plot_scale_factor(data)

Plot the scale factor applied to brain regions alongside the histology figure.

Parameters:

data (Bunch) – A Bunch object containing the scaling data

Returns:

cbar – The created colorbar

Return type:

ColorBar

plot_scatter(data, levels=None)

Plot a 2D scatter plot of electrophysiology data.

Parameters:

• data (ScatterData) – A ScatterData object containing the data to plot

• levels (list or np.ndarray, optional) – A list or array containing the levels to set for the colorbar. Defaults to data.levels

Returns:

The created colorbar

Return type:

ColorBar

plot_slice(data, data_traj)

Plot a slice image showing a coronal histology slice.

Add a trajectory line showing the probe location through the slice.

Parameters:

• data (Bunch) – A Bunch object containing the slice data

• data_traj (Bunch) – A Bunch object containing the trajectory data

Return type:

tuple[ImageItem, ColorBar | None]

Returns:

• pg.ImageItem – The created image item.

• ColorBar – The created colorbar.

static remove_items(fig, item, delete=True)

Remove all items from a plot item and optionally delete them.

Parameters:

• fig (pg.PlotItem) – The plot item from which to remove items

• item (list[pg.GraphicsItem] or pg.GraphicsItem) – A list of items or a single item to remove

• delete (bool, default=True) – Whether the item should be deleted

remove_reference_line(line_idx)

Remove a reference line (track and feature) from the displays.

Parameters:

line_idx (int) – The index of the reference line to remove

Return type:

None

remove_reference_lines_from_display()

Remove all reference lines from the respective plots.

Return type:

None

reset_slice_axis()

Reset the axis range of the slice image.

Return type:

None

set_feature_title(feature)

Update the axis of the feature label to display the current hovered feature.

Parameters:

feature (str) – The feature name to display in the axis label.

Return type:

None

set_fig_scale_title(value)

Update the label of the scale plot axis to display the current scale value.

Parameters:

value (float) – The scale factor to display in the axis label. The value is rounded to two decimal places before updating the label.

Return type:

None

set_header_style(selected)

Set the stylesheet of the header item.

Update style based on whether the current shank is selected or not.

Parameters:

selected (bool) – Whether the current shank is selected or not

Return type:

None

set_probe_lims(min_val, max_val)

Set the values of the probe tip and probe top.

Update all the associated lines showing the new probe extent.

Parameters:

• min_val (float) – The value for probe tip

• max_val (float) – The value for the probe top

Return type:

None

set_xaxis_range(fig, xrange=None)

Set the x-axis range of a given figure.

Parameters:

• fig (pg.PlotItem) – The figure whose x-axis range will be updated

• xrange (list, optional) – The xrange values to use. If None, the default values are used.

Return type:

None

set_yaxis_lims(min_val, max_val)

Set the yrange values that are used to set the y-axis limits used to display plots.

Parameters:

• min_val (float) – The minimum y-axis value

• max_val (float) – The maximum y-axis value

Return type:

None

set_yaxis_range(fig)

Set the y-axis range of a given figure.

Parameters:

fig (pg.PlotItem) – The figure whose y-axis range will be updated

Return type:

None

toggle_channels(fig_slice, show)

Show/hide the channels and traj line on the slice plot.

Parameters:

• fig_slice (pg.ViewBox) – The fig slice to add or remove the items

• show (bool) – Whether to show the channels and traj line or not

Return type:

None

toggle_labels(show)

Show/hide the brain region axis labels on the histology plot.

Parameters:

show (bool) – Whether to show the labels or not.

Return type:

None

update_feature_reference_line_and_point(feature_line, line_idx, fig_idx)

Update the feature lines to match the coordinate of the moved feature line.

Also update the scatter point location.

Parameters:

• feature_line (pyqtgraph.InfiniteLine) – The feature line instance that was moved by the user.

• line_idx (int) – The index of the reference line in the tracking arrays.

• fig_idx (list) – The index of the figures where the feature line position needs to be updated.

Return type:

None

update_track_reference_line_and_point(track_line, line_idx)

Update the scatter point location to match the coordinate of the moved track line.

Parameters:

• track_line (pg.InfiniteLine) – The track line instance that was moved by the user.

• line_idx (int) – The index of the reference line in the tracking arrays.

Return type:

None