Composite Overlays
Overlay generation functions
composite_overlay(segs, colors=None, alpha=0.2, imagery=None, outline=False, merge_outline=True, overlap=True, width=10, side='out', dim=2, palette=DEFAULT_PALETTE, h=DEFAULT_H, l=DEFAULT_L, s=DEFAULT_S)
Make a colored composite overlay for a 3d mask from an iterable of masks.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
segs |
Iterable of masked images of the same size. If a dict, colors must be a dict as well. |
required | |
colors |
list-like, dict, or None
|
Iterable of RGB colors of the same size as masks. If a dict, masks must also be a dict and colors
must have all keys in masks. If None, uses |
None
|
alpha |
float
|
Alpha value for the overlay |
0.2
|
imagery |
Image or None
|
If an Image, applies the overlay to the image, by default None |
None
|
outline |
bool
|
If True, produces an outline instead of a flat overay, by default False |
False
|
merge_outline |
bool
|
If True, the merge outline applies to the segmentation as a whole and thus internal contacts are not outlined. |
True
|
overlap |
bool
|
If False, segmentations later in the list will not overlap segmentations earlier on the list. |
True
|
width |
int
|
If outline=True, sets the width of the outline, by default 10 |
10
|
side |
out or 'in'
|
If outline=True, selects if the outline is inside or outside the original segmentation mask, by default 'out' |
'out'
|
dim |
int
|
Determines axis over which slices are iterated if the data is 3 dimensional. Default is 2 (z-axis). |
2
|
Returns:
| Type | Description |
|---|---|
list or Image
|
Image or list of composite overlay images, optionally overlaid over provided imagery. List or single image is determined based on segmentation arrays being 2 or 3 dimensional. |
discrete_colors(segs, palette=DEFAULT_PALETTE, h=DEFAULT_H, l=DEFAULT_L, s=DEFAULT_S)
Generate discrete colors for segmentations from a palette generator. Defaults to perceptually uniform differences with high saturation.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
segs |
list or dict
|
Dict or list of segmentations to provide colors for. |
required |
palette |
'husl', 'hls', or str
|
Which palette system to use, by default 'husl'. Will accept anything allowed by seaborn color_palette function. |
DEFAULT_PALETTE
|
h |
float
|
Hue value if husl or hls palettes are used, by default 0.01 |
DEFAULT_H
|
l |
float
|
Lightness if husl or hls palettes are used, by default 0.6 |
DEFAULT_L
|
s |
int
|
Saturation if husl or hls palettes are used, by default 1 |
DEFAULT_S
|
Returns:
| Type | Description |
|---|---|
List or dict
|
List or dict with one color per segmentation. |
stack_images(images, direction='horizontal', spacing=10)
Stack an iterable of images either veritcally or horizontally
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
images |
list - like
|
Iterable of Image.Image objects |
required |
spacing |
int
|
Spacing between images in pixels, by default 10 |
10
|
direction |
horizontal or vertical
|
Direction of the grid of images, by default 'horizontal' |
'horizontal'
|
Returns:
| Type | Description |
|---|---|
Image
|
Combined grid of images |