stitching_plots#

Plot functions and Layout/Alignment plot mixins for rigid and wobbly stitching.

Mixins are injected at runtime via @lazy_mixin, so matplotlib is never imported on a headless cluster unless a plot method is actually called.

Standalone functions duck-type on layout / source / alignment objects and only import from stitching_rigid / stitching_wobbly locally when they need to construct helper objects.

class AlignmentBasePlotMixin[source]#

Bases: object

Plot methods for AlignmentBase, injected via @lazy_mixin.

overlay(**kwargs)[source]#: Return a colour-overlay array of the two sources.

overlay_mip(*args, **kwargs)[source]#: Overlay using max intensity projection.

overlay_overlap(max_shifts=0)[source]#: Return the overlapping sub-arrays of pre and post.

plot(*args, **kwargs)[source]#: Plot the two sources overlayed.

plot_mip(*args, **kwargs)[source]#: Plot using max intensity projection.

plot_overlap(**kwargs)[source]#: Display the overlap region with the 3D viewer.

plot_overlay(**kwargs)[source]#: Overlay and display with 3D viewer.

class AlignmentPlotMixin[source]#

Bases: AlignmentBasePlotMixin

Plot methods for Alignment.

Overrides plot to shift post by the computed displacement before overlaying.

plot(*args, **kwargs)[source]#: Plot the two sources overlayed.

class LayoutPlotMixin[source]#

Bases: object

Plot methods for Layout, injected via @lazy_mixin.

overlay(colors=None, percentile=98, normalize=True, coordinate=None, axis=2)[source]#

plot(colors=None, percentile=98, normalize=True, color_ids=None, coordinate=None, axis=2)[source]#

Plots overlayed sources to check their placement.

Arguments

colorslist of tuple of floats or color names: The optional RGB colors to use.
percentileint: Use this percentile as upper cutoff in the resulting image to enhance contrast.
normalizebool: If True normalize image to floats between 0 and 1.
color_idslist of ints: Use specific color ids for the sources contributing to the layout.
coordinateint or None: Optional coordinate at which to take a slice.
axisint: Optional axis to take the slice in.

Returns

imagearray: A color image.

plot_alignments(cmap=None, annotate=True, axes=None)[source]#

Overlays and plots regions to check the alignment of this layout.

Arguments

cmapcolormap: The color map to use to color the regions.
annotatebool: Use annotation or not.
axestuple of ints: Axes to use if sources are larger than 2d.

plot_regions(cmap=None, annotate=True, axes=None)[source]#

Overlays and plots regions to check the alignment of this layout.

Arguments

cmapcolormap: The color map to use to color the regions.
annotatebool: Use annotation or not.
axestuple of ints: Axes to use if sources are larger than 2d.

class WobblyAlignmentPlotMixin[source]#

Bases: object

Plot methods for WobblyAlignment, injected via @lazy_mixin.

overlay_mip_wobbly(overlap=True, mip_axis=None, percentile=98, normalize=True)[source]#: Colour MIP overlay of the wobbly alignment.

plot_mip_wobbly(overlap=True, mip_axis=None, percentile=98)[source]#: Display wobbly MIP overlay with matplotlib.

plot_overlay_wobbly()[source]#: Display wobbly overlay with 3D viewer.

class WobblyLayoutPlotMixin[source]#

Bases: object

Plot methods for WobblyLayout, injected via @lazy_mixin.

alignment_info(tile_position, coordinate, plot=True, use_displacements=True, **kwargs)[source]#: Diagnostic: gather alignment info and optionally overlay a slice.

plot_wobble()[source]#: Plot per-alignment displacement curves.

layout_along_axis_mip(src1, src2, axis=2, depth=10, max_shifts=10, ranges=None, verbose=False)[source]#: Build a Layout from MIP-projected sources.

layout_coloring(layout, colors=None, color_ids=None)[source]#: Assign colours to sources based on adjacency colouring.

overlay_along_axis_mip(src1, src2, axis=2, depth=10, max_shifts=10, ranges=None, verbose=False, **kwargs)[source]#: Build a colour overlay of a MIP-projected alignment.

overlay_layout(layout, colors=None, percentile=98, normalize=True, color_ids=None)[source]#

Build a colour-overlay array of all sources in a layout.

Arguments

layoutLayout: The layout with the sources to overlay.
colorslist of colours, 'ids', or None: RGB colours, or 'ids' to return per-channel arrays.
percentileint: Upper cutoff percentile for contrast enhancement.
normalizebool: Normalize to [0, 1] floats.
color_idslist of int or None: Explicit colour index per source.

Returns

imagearray: A colour image (or list of single-channel images when colors='ids').

overlay_sources(sources, colors=None, percentile=98, normalize=True)[source]#

Overlays the sources to check their placement.

Arguments

sourceslist of Source: The sources to overlay.
colorslist of tuple of floats or color names: The optional RGB colors to use.
percentileint: Use this percentile as upper cutoff in the resulting image to enhance contrast.
normalizebool: If True normalize image to floats between 0 and 1.

Returns

imagearray: A color image.

plot_alignments(alignments, sources=None, axes=None, annotate=True, min_quality=-inf, cmap=None)[source]#: Plot alignment edges coloured by quality.

plot_along_axis_mip(src1, src2, axis=2, depth=10, max_shifts=10, ranges=None, verbose=False, **kwargs)[source]#: Plot a MIP-projected alignment.

plot_layout(layout, colors=None, percentile=98, normalize=True, color_ids=None)[source]#

Overlays and plots sources in a layout to check alignment.

..Note::: For 2-D layouts uses matplotlib; for 3-D uses Plot3d.

Arguments

layoutLayout class: The layout to use for plotting.
colorslist of colors or None: The optional RGB colors to use.
percentileint: Use this percentile as upper cutoff in the resulting image to enhance contrast.
normalizebool: If True normalize image to floats between 0 and 1.

Returns

imagearray: A color image of the overlayed sources.

plot_regions(regions, sources=None, cmap=None, annotate=True, axes=None)[source]#

Overlays and plots regions to check the alignment.

Arguments

regionslist of Region classes: The regions to plot.
sourceslist of Source or None: Sources used for annotation ids.
cmapcolormap: The color map to use to color the regions.
annotatebool: Use annotation or not.

plot_sources(sources, colors=None, percentile=98, normalize=True)[source]#

Overlays and plots sources in a layout to check alignment.

Arguments

sourceslist of Source: The sources to overlay.
colorslist of colors or None: The optional RGB colors to use.
percentileint: Use this percentile as upper cutoff in the resulting image to enhance contrast.
normalizebool: If True normalize image to floats between 0 and 1.

Returns

imagearray: A color image of the overlayed sources.