ibl_alignment_gui.plugins.ephys_features

Functions

`callback`	Open the ephys features viewer.
`setup`	Set up the ephys features plugin in the controller.

Classes

`EphysFeatureView`	A view for displaying ephys features within regions.
`EphysFeatures`	A plugin for visualising ephys features within brain regions.

class ibl_alignment_gui.plugins.ephys_features.EphysFeatureView(title, controller, step=10)[source] 

Bases: PopupWindow

A view for displaying ephys features within regions.

Parameters:

title (str) – The title of the popup window
controller (AlignmentGUIController) – The main application controller.
step (int) – The number of probes to show per page.

Variables:

plots_hist (list) – A list of plot items for the histology regions.
plots_feat (list) – A list of plot items for the ephys features.
plots_cbar (list) – A list of plot items for the colorbars.
fig_areas (list) – A list of graphics layout widgets for each probe.
step (int) – The number of probes to show per page.
controller (AlignmentGUIController) – The main application controller.

property aligned: bool : Whether the plots are aligned.

clear_plots()[source] 

Clear all plots.

Return type:: None

static create_figures()[source] 

Create the plot items for each probe.

Return type:: tuple[GraphicsLayoutWidget, PlotItem, PlotItem, PlotItem]

property normalised: bool : Whether the plots are normalised.

plot_probe(idx, data, offset, levels=None, label=None)[source] 

Plot the feature data for a single probe.

Parameters:

idx (int) – The index of the probe to plot.
data (dict) – The feature data for the probe.
offset (float) – The offset to apply to the y-axis.
levels (list, optional) – The color levels to use for the plot.
label (str, optional) – A label to display above the colorbar (used to mark the reference column).

Return type:

None

plot_region(idx, data, offset, selected_region)[source] 

Plot the histology regions for a single probe.

Parameters:

idx (int) – The index of the probe to plot.
data (dict) – The region data for the probe.
offset (float) – The offset to apply to the y-axis.
selected_region (int) – The id of the currently selected region.

Return type:

None

setup()[source] 

Add widgets to the main layout.

Return type:: None

class ibl_alignment_gui.plugins.ephys_features.EphysFeatures(title, controller)[source] 

Bases: object

A plugin for visualising ephys features within brain regions.

Parameters:

title (str) – The title of the popup window.
controller (AlignmentGUIController) – The main application controller.

Variables:

page_num (int) – The total number of pages.
page_idx (int) – The current page index.
step (int) – The number of probes to show per page.
max_idx (int) – The maximum index of probes.
levels (list) – The current color levels.
max_levels (list) – The maximum color levels across all probes within the region.
plot_name (str) – The name of the feature to plot.
plot_idx (int) – The index of the feature to plot.
cmap (str) – The name of the colormap to use.
chosen_region (int) – The id of the currently selected region.
pids (list) – The list of probe ids that pass through the chosen region.
current_pids (list) – The list of probe ids for the current page.
selected_pid (str) – The currently selected probe id.
selected_idx (int) – The index of the currently selected probe within the current page.
reference_pid (str or None) – The GUI’s currently selected insertion, pinned as a fixed reference in column 0 on every page. None if the insertion is unavailable or absent from the features table.
feature_data (Bunch) – A bunch containing the feature data for each pid.
region_data (Bunch) – A bunch containing the region data for each pid.
offset_data (Bunch) – A bunch containing the offset data for each pid.

property aligned: bool : Whether the plots are aligned.

get_features()[source] 

Load the full ephys atlas features table.

Reuses the same table downloaded by FeatureLoaderOne while loading the insertion, reading every insertion’s rows rather than only the selected pid’s.

Returns:: The ephys atlas features table for all insertions.
Return type:: pd.DataFrame

get_pids()[source] 

Get the list of probe ids for the current page.

When a reference insertion is set it is prepended so that it always occupies the first column, with the remaining columns holding the paginated probes.

Returns:: An array of probe ids for the current page.
Return type:: np.ndarray

get_regions(controller)[source] 

Get all unique Allen region ids for the shanks in the controller.

Parameters:: controller (AlignmentGUIController) – The main application controller.
Returns:: An array of unique Allen region ids.
Return type:: np.ndarray

load_data(pids)[source] 

Prepare feature, region and offset data for a list of probe ids.

Will only prepare data for pids that are not already in the respective data dictionaries.

Parameters:: pids (list) – The list of pids to prepare data for.
Return type:: None

property normalised: bool : Whether the plots are normalised.

on_align_plots()[source] 

Align plots based on chosen region.

If align is True then plots are centered on the chosen region.

on_area_clicked(_, idx)[source] 

Highlight selected probe and update slider and pid label.

Only works in non-normalised mode.

Parameters:: idx (int) – The index of the clicked area.
Return type:: None

on_close()[source] 

Triggered when the plugin window is closed.

Deactivate the plugin and callbacks.

Return type:: None

on_cmap_chosen(idx)[source] 

Select colormap to use.

Set new default colormap and re-plot all features.

Parameters:: idx (int) – The index of the chosen colormap.
Return type:: None

on_next_page_pressed()[source] 

Go to the next page of probes.

If data needs to be loaded for the new page, it will first be loaded before plotting.

Return type:: None

on_normalise_plots()[source] 

Normalise all plots to the same color scale.

Return type:: None

on_plot_chosen(idx)[source] 

Select feature to plot.

Set new plot name and prepare data for current pids and plot.

Parameters:: idx (int)
Return type:: None

on_prev_page_pressed()[source] 

Go to the previous page of probes.

If data needs to be loaded for the new page, it will first be loaded before plotting.

Return type:: None

on_region_chosen(idx)[source] 

Select region to display.

Set new chosen region and get the probes that pass through this region.

Parameters:: idx (int) – The index of the chosen region.
Return type:: None

on_reset_levels()[source] 

Reset colour levels to default for the selected probe.

Return type:: None

on_slider_released()[source] 

Update colorbar levels based on slider values.

Return type:: None

property page_step: int : Number of paginated probes per page, reserving column 0 for the reference.

plot_all(pids)[source] 

Update all plots for a list of probe ids.

Parameters:: pids (list or np.ndarray) – The list of probe ids to plot.
Return type:: None

plot_features(pids)[source] 

Plot the feature data for a list of probe ids.

Parameters:: pids (list or np.ndarray) – The list of probe ids to plot.
Return type:: None

plot_regions(pids)[source] 

Plot the region data for a list of probe ids.

Parameters:: pids (list or np.ndarray) – The list of probe ids to plot.
Return type:: None

plot_single_feature()[source] 

Plot the feature data for the currently selected probe.

Return type:: None

prepare_feature_data(pids)[source] 

Prepare feature data for a list of probe ids.

Parameters:: pids (list) – The list of pids to prepare data for.
Returns:: feature_data – A bunch containing the feature data for each pid.
Return type:: Bunch

prepare_offset_data(pids)[source] 

Prepare offset data for a list of probe ids.

Parameters:: pids (list) – The list of pids to prepare data for.
Returns:: offset_data – A bunch containing the offset data for each pid.
Return type:: Bunch

prepare_region_data(pids)[source] 

Prepare region data for a list of probe ids.

Parameters:: pids (list) – The list of pids to prepare data for.
Returns:: region_data – A bunch containing the region data for each pid.
Return type:: Bunch

setup()[source] 

Set up the ephys features viewer and connect signals.

Return type:: None

update_page_label()[source] 

Update the label showing the current page index.

Return type:: None

ibl_alignment_gui.plugins.ephys_features.callback(controller)[source] 

Open the ephys features viewer.

Parameters:: controller (AlignmentGUIController) – The main application controller.
Return type:: None

ibl_alignment_gui.plugins.ephys_features.setup(controller)[source] 

Set up the ephys features plugin in the controller.

Parameters:: controller (AlignmentGUIController) – The main application controller.
Return type:: None