Cross-Dataset Comparison

napari_relax.relax_multipledatasets.manager_widget

Manager Manipulation entry of the Cross Lineagetree comparison widget.

CrossEmbryo

Bases: LayerCorrectorTreeProducer

Create, load, edit and save a LineageTreeManager.

The manager is sent to the other cross-dataset widgets through send_manager_to_classes whenever it changes.

Parameters:

Name	Type	Description	Default
napari_viewer	Viewer	The napari viewer.	required

update_layer_list()

Map the manager names of the viewer layers to the layers.

save_manager()

Save the manager to the selected file.

add_a_new_embryo()

Add the selected .lT files to the manager.

add_a_new_embryo_from_viewer()

Not implemented.

remove_embryo(source, pos)

Remove the dataset under the cursor from the manager.

Parameters:

Name	Type	Description	Default
source	QListWidget	The list of datasets.	required
pos	QPoint	Position of the right click in the list.	required

load_a_manager()

Load a LineageTreeManager from the selected file.

add_new_layer(name=None)

Add datasets of the manager to the viewer.

Parameters:

Name	Type	Description	Default
name	list of QListWidgetItem	Items to add; the items selected in the list are used if None. Datasets already in the viewer are skipped.	None

create_a_manager()

Create a new LineageTreeManager from all LineageTree layers.

update_Qlistwidget()

Refresh the list of datasets from the manager.

eventFilter(source, event)

Show the context menu of the dataset list on right click.

The menu offers "Change Time Resolution" and "Remove Embryo".

Parameters:

Name	Type	Description	Default
source	QObject	The object receiving the event.	required
event	QEvent	The event.	required

Returns:

Type	Description
bool	True if the event was handled.

change_time_resolution(source, pos)

Ask for a new time resolution for the dataset under the cursor.

Parameters:

Name	Type	Description	Default
source	QListWidget	The list of datasets.	required
pos	QPoint	Position of the right click in the list.	required

resizeEvent(event)

Keep the help button in the top right corner.

Parameters:

Name	Type	Description	Default
event	QResizeEvent	The resize event.	required

napari_relax.relax_multipledatasets.cross_comparisons_handler

Cross Distance Calculation entry of the Cross Lineagetree comparison widget.

CrossHandler

Bases: LayerCorrectorTreeProducer

Two dataset viewers plus tabs to configure and inspect comparisons.

Parameters:

Name	Type	Description	Default
napari_viewer	Viewer	The napari viewer.	required

get_lt_manager(signal)

Receive the manager whenever it changes.

Parameters:

Name	Type	Description	Default
signal	LineageTreeManager	The updated manager.	required

kill_thread(dummy_event=None)

Stop the comparison thread and close the progress bar.

Parameters:

Name	Type	Description	Default
dummy_event	object	Event of the signal that triggered the stop, unused.	None

thread_handler()

Start the cross-dataset comparisons in a background thread.

Warns first if a dataset name is longer than 6 characters.

update_comparisons(product)

Send the results yielded by the comparison thread to the plots.

Parameters:

Name	Type	Description	Default
product	tuple	Comparisons, sublineage names and normalizations, one entry per level of comparison computed so far.	required

napari_relax.relax_multipledatasets.cross_config

Configuration tab of the Cross Distance Calculation.

CrossConfig

Bases: LayerCorrectorTreeProducer

Approximation style, dataset selection and one tab per dataset.

Parameters:

Name	Type	Description	Default
napari_viewer	Viewer	The napari viewer.	required

lcm property

Least common multiple of the time resolutions of the datasets.

Returns:

Type	Description
int	The least common multiple, or 1 if no dataset is selected.

get_lt_manager(signal)

Receive the manager whenever it changes and list its datasets.

Parameters:

Name	Type	Description	Default
signal	LineageTreeManager	The updated manager.	required

tab_maker()

Create one configuration tab per selected dataset.

roots_selector()

Compute the pairwise distances of sublineages across datasets.

Yields:

Type	Description
tuple	Comparisons, sublineage names and normalizations, one entry per level of comparison computed so far.

kill_thread()

Stop the comparison thread.

update_comparisons(product)

Store the results yielded by the comparison thread.

Parameters:

Name	Type	Description	Default
product	tuple	Comparisons, sublineage names and normalizations.	required

update_tree_style()

Show the downsampling box only for the downsampled style.

change_downsampling_rates()

Reset the downsampling rates offered.

change_tooltip_for_downsample()

Show the real downsampling rate of each dataset in the tooltip.

resizeEvent(event)

Keep the help button in the top right corner.

Parameters:

Name	Type	Description	Default
event	QResizeEvent	The resize event.	required

napari_relax.relax_multipledatasets.cross_embryo_comparison

Plots tab of the Cross Distance Calculation.

CrossClustermap

Bases: LayerCorrectorTreeProducer

Tree plots, clustermap and save widgets for cross-dataset results.

Parameters:

Name	Type	Description	Default
napari_viewer	Viewer	The napari viewer.	required
dataset_viewers	list of napari.components.ViewerModel	The two viewers showing the compared datasets.	required

get_lt_manager(signal)

Receive the manager whenever it changes.

Parameters:

Name	Type	Description	Default
signal	LineageTreeManager	The updated manager.	required

send_data()

Plot the comparisons of the level selected by the slider.

add_spot_on_graph(cell, index, lineagetree_name)

Add a cell to its graph if it is in the middle of a chain.

Parameters:

Name	Type	Description	Default
cell	int	ID of the cell.	required
index	int	Index of the graph in the list of graphs.	required
lineagetree_name	str	Name of the dataset in the layers and the manager.	required

paint_sublineage(cell, index, color, lineagetree_name)

Return the node colors of a graph with a sublineage highlighted.

Parameters:

Name	Type	Description	Default
cell	int	Root of the sublineage.	required
index	int	Index of the graph in the list of graphs.	required
color	int or color	Highlight color; 0 means magenta and 1 cyan.	required
lineagetree_name	str	Name of the dataset in the layers and the manager.	required

Returns:

Type	Description
list	Color of each node of the graph; other nodes are black.

reset_graph(cell, index, lineagetree_name)

Remove a cell added by add_spot_on_graph from its graph.

Parameters:

Name	Type	Description	Default
cell	int	ID of the cell.	required
index	int	Index of the graph in the list of graphs.	required
lineagetree_name	str	Name of the dataset in the layers and the manager.	required

tree_painter(node, lineagetree_name, color, ax)

Draw a lineage with a sublineage highlighted on a tree plot.

Parameters:

Name	Type	Description	Default
node	int	The first node of the sublineage.	required
lineagetree_name	str	Name of the dataset in the manager and the layers.	required
color	color	Color of the sublineage.	required
ax	Axes	Axes of the tree plot.	required

sub_points_painter(node, lineagetree_name, viewer, color)

Show a dataset in a dataset viewer with a sublineage colored.

Parameters:

Name	Type	Description	Default
node	int	The first node of the sublineage.	required
lineagetree_name	str	Name of the dataset in the manager and the layers.	required
viewer	ViewerModel	The dataset viewer to draw in.	required
color	color	Color of the sublineage; other cells are white.	required

save_dictionary()

Save the comparisons and the manager to the selected .pkl file.

time_changer()

Show the clustermap of the level selected by the slider.

resizeEvent(event)

Keep the help button in the top right corner.

Parameters:

Name	Type	Description	Default
event	QResizeEvent	The resize event.	required

napari_relax.relax_multipledatasets.cross_clustermap_canvas

Matplotlib canvas drawing the cross-dataset clustermap.

CrossClusterMapCanvas

Bases: ClusterMapCanvas

Clustermap canvas for sublineages of several datasets.

clear_data()

Clear the plot, the data and the manager.

annotation_maker(x, y, offset_xy, ha, value)

Create the hover box of a clustermap cell.

Parameters:

Name	Type	Description	Default
x	float	Column of the cell.	required
y	float	Row of the cell.	required
offset_xy	tuple of int	Offset of the box from the cell, in points.	required
ha	str	Horizontal alignment of the box.	required
value	float	Score shown in the box.	required

napari_relax.relax_multipledatasets.cell_size

Point size sliders of the two dataset viewers.

MinimalCellSize

Bases: LayerCorrectorTreeProducer

Point size sliders for the two dataset viewers.

Parameters:

Name	Type	Description	Default
napari_viewer	Viewer	The main napari viewer.	required
napari_viewer_1	ViewerModel	The first dataset viewer.	required
napari_viewer_2	ViewerModel	The second dataset viewer.	required

change(viewer, slider, other_viewer, other_slider, event)

Apply a slider value to its viewer, or to both viewers.

Parameters:

Name	Type	Description	Default
viewer	ViewerModel	The viewer of the moved slider.	required
slider	QSlider	The moved slider.	required
other_viewer	ViewerModel	The other viewer.	required
other_slider	QSlider	The slider of the other viewer.	required
event	object	The slider event, unused.	required

napari_relax._util_classes.tab_template

TabTemplate

Bases: QWidget

Per-dataset configuration tab of the cross-dataset comparison.

Parameters:

Name	Type	Description	Default
lineagetree	LineageTree	The dataset configured by this tab.	required
name	str	Name of the dataset in the manager.	required

time_cropping()

Read the crop time typed by the user.

show_roots()

Return the roots selected for the comparison.

Returns:

Type	Description
list	The selected root IDs.

times_selector()

Read the timepoints to compare.

They are either a comma-separated list or a range built from start, stop and step.

ret_times()

Read and return the timepoints to compare.

Returns:

Type	Description
list	The timepoints.