ibl_alignment_gui.app.shank_controller

Classes

ShankController

Controller for handling data and plots on a shank of a probe for a given configuration.

class ibl_alignment_gui.app.shank_controller.ShankController(model, name, index, config)[source] 

Bases: object

Controller for handling data and plots on a shank of a probe for a given configuration.

Parameters:

model (ShankHandler) – The model containing all the data for the shank and config combination
name (str) – The name of shank
index (int) – The index of the shank
config (str) – The config of the shank

name

The name of shank

Type:: str

index

The index of the shank

Type:: int

config: The config of the shank

model

The model containing all the data for the shank and config combination

Type:: ShankHandler

view

The view containing all the plots for the shank and config combination

Type:: ShankView

cluster

Whether the chosen scatter plot contains cluster data

Type:: bool

cluster_data

The cluster data for the chosen scatter plot if it exists

Type:: np.ndarray | None

add_reference_lines_to_display()[source] 

See ShankView.add_reference_lines_to_display() for details.

Return type:: None

align_reference_lines_and_points()[source] 

See ShankView.align_reference_lines() for details.

Return type:: None

create_reference_line_and_point(*args, **kwargs)[source] 

See ShankView.create_reference_line_and_point() for details.

Return type:: tuple

delete_reference_line_and_point(*args)[source] 

See ShankView.delete_reference_line_and_point() for details.

Return type:: None

filter_units(filter_type)[source] 

See ShankHandler.filter_units() for details.

Return type:: None

get_scaled_histology()[source] 

See ShankHandler.get_scaled_histology() for details.

Return type:: None

get_yaxis_lims()[source] 

Get the y-axis limits from the model.

Returns:: The ymin and ymax values from the model
Return type:: list[float, float]

init_plot_items()[source] : See ShankView.init_plot_items() for details.

init_reference_line_arrays()[source] : See ShankView.init_reference_line_arrays() for details.

match_feature_line(*args)[source] 

See ShankView.match_feature_line() for details.

Return type:: tuple[int | None, list | ndarray | None]

match_track_line(*args)[source] 

See ShankView.match_track_line() for details.

Return type:: int | None

offset_hist_data(*args)[source] 

See ShankHandler.offset_hist_data() for details.

Return type:: None

plot_channels(fig_slice, colour=None)[source] 

Plot channels on a slice plot.

Parameters:

fig_slice (pg.ViewBox) – The slice fig to add the channel items to
colour (str) – The colour of the scatter points used to plot the channels

Return type:

None

Notes

fig_slice is passed in as a parameter as for the dual config display the channels

plotted on a different slice figure than the one stored in the view.

plot_feature(plot_key)[source] 

Plot a feature plot.

Parameters:: plot_key (str) – The key of the plot to display
Return type:: None

plot_fit()[source] 

Plot fit lines on the fit figure.

Return type:: None

plot_histology()[source] 

Plot the histology plot.

Returns:: A pg.LinearRegionItem corresponding to the second last brain region added to the histology plot
Return type:: pg.LinearRegionItem

plot_histology_ref()[source] 

Plot the histology reference plot.

Return type:: None

plot_image(plot_key, levels=None)[source] 

Plot an image plot.

Parameters:

plot_key (str) – The key of the plot to display
levels (list | None) – The levels used to scale the colorbar on the plot

Returns:

cbar – The colobar abject that was added to the plot

Return type:

ColorBar

plot_line(plot_key)[source] 

Plot a line plot.

Parameters:: plot_key (str) – The key of the plot to display
Return type:: None

plot_probe(plot_key, levels=None)[source] 

Plot a probe plot.

Parameters:

plot_key (str) – The key of the plot to display
levels (list | None) – The levels used to scale the colorbar on the plot

Returns:

cbar – The colobar abject that was added to the plot

Return type:

ColorBar

plot_scale_factor()[source] 

Plot the scale factor along the probe.

Returns:: cbar – The ColorBar object added to the plot
Return type:: ColorBar

plot_scatter(plot_key, levels=None)[source] 

Plot a scatter plot.

Parameters:

plot_key (str) – The key of the plot to display
levels (list | None) – The levels used to scale the colorbar on the plot

Returns:

cbar – The colobar abject that was added to the plot

Return type:

ColorBar

plot_slice(plot_key)[source] 

Plot a slice plot showing a coronal slice through the brain.

Parameters:

plot_key (str) – The key of the plot to display

Return type:

tuple[ViewBox, ImageItem, ColorBar]

Returns:

fig (pg.ViewBox) – The viewbox that contains the image
img (pg.ImageItem) – The image item that was added to the plot
cbar (ColorBar) – The colobar object that was added to the plot

property points: list[ScatterPlotItem] : Return the points stored in the view.

remove_reference_line(*args)[source] 

See ShankView.remove_reference_line() for details.

Return type:: None

remove_reference_lines_from_display()[source] 

See ShankView.remove_reference_lines_to_display() for details.

Return type:: None

reset_levels()[source] 

See ShankHandler.reset_levels() for details.

Return type:: None

reset_slice_axis()[source] 

See ShankView.reset_slice_axis() for details.

Return type:: None

scale_hist_data(extend_feature, lin_fit)[source] 

Scale brain regions along the probe track based on reference lines.

Parameters:

extend_feature (float) – Amount to extend for linear fit
lin_fit (bool) – Whether to use a linear fit or not

Return type:

None

set_feature_title(feature_title)[source] 

See ShankView.set_feature_title() for details.

Return type:: None

set_header_style(*args)[source] 

See ShankView.set_header_style() for details.

Return type:: None

set_probe_lims()[source] 

Set the limits for the probe tip and probe top based on values stored in model.

Return type:: None

set_scale_title(hover_item)[source] 

Update the title of the scale plot color bar based on the hovered region.

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

set_xaxis_range(fig)[source] 

Set the x-axis range of the specified figure.

Parameters:: fig (str) – The attribute name of the figure to set the x-axis for
Return type:: None

set_yaxis_lims(*args)[source] 

See ShankView.set_yaxis_lims() for details.

Return type:: None

set_yaxis_range(fig)[source] 

Set the y-axis range of the specified figure.

Parameters:: fig (str) – The attribute name of the figure to set the y-axis for
Return type:: None

toggle_channels(*args)[source] 

See ShankView.toggle_channels() for details.

Return type:: None

toggle_labels(*args)[source] 

See ShankView.toggle_labels() for details.

Return type:: None

update_feature_reference_line_and_point(*args)[source] 

See ShankView.update_feature_reference_line_and_point() for details.

Return type:: None

update_track_reference_line_and_point(*args)[source] 

See ShankView.update_track_reference_line_and_point() for details.

Return type:: None