ClearMap.Visualization package

This sub-package provides tools for the visualization of the alignment and analysis results

ClearMap.Visualization.Plot module

Plotting routines for overlaying labels, tilings, and sectioning of 3d data sets

Supported functionality:

• plot volumetric data as a sequence of tiles via plotTiling()
• overlay points on images via overlayPoints() and plotOverlayPoints()
• overlay labeled images on gray scale images via overlayLabel() and plotOverlayLabel()

plotTiling(dataSource, tiling='automatic', maxtiles=20, x=<built-in function all>, y=<built-in function all>, z=<built-in function all>, inverse=False)

Plot 3d image as 2d tiles

Parameters:

• dataSouce (str or array) – volumetric image data
• tiling (str or tuple) – tiling specification
• maxtiles – maximalnumber of tiles
• x, y, z (all or tuple) – sub-range specification
• inverse (bool) – invert image

Returns:

(object) – figure handle

overlayLabel(dataSource, labelSource, sink=None, alpha=False, labelColorMap='jet', x=<built-in function all>, y=<built-in function all>, z=<built-in function all>)

Overlay a gray scale image with colored labeled image

Parameters:

• dataSouce (str or array) – volumetric image data
• labelSource (str or array) – labeled image to be overlayed on the image data
• sink (str or None) – destination for the overlayed image
• alpha (float or False) – transparency
• labelColorMap (str or object) – color map for the labels
• x, y, z (all or tuple) – sub-range specification

Returns:

(array or str) – figure handle

See also

overlayPoints()

plotOverlayLabel(dataSource, labelSource, alpha=False, labelColorMap='jet', x=<built-in function all>, y=<built-in function all>, z=<built-in function all>, tiling='automatic', maxtiles=20)

Plot gray scale image overlayed with labeled image

Parameters:

• dataSouce (str or array) – volumetric image data
• labelSource (str or array) – labeled image to be overlayed on the image data
• alpha (float or False) – transparency
• labelColorMap (str or object) – color map for the labels
• x, y, z (all or tuple) – sub-range specification
• tiling (str or tuple) – tiling specification
• maxtiles – maximalnumber of tiles

Returns:

(object) – figure handle

See also

overlayLabel()

overlayPoints(dataSource, pointSource, sink=None, pointColor=[1, 0, 0], x=<built-in function all>, y=<built-in function all>, z=<built-in function all>)

Overlay points on 3D data and return as color image

Parameters:

• dataSouce (str or array) – volumetric image data
• pointSource (str or array) – point data to be overlayed on the image data
• pointColor (array) – RGB color for the overlayed points
• x, y, z (all or tuple) – sub-range specification

Returns:

(str or array) – image overlayed with points

See also

overlayLabel()

plotOverlayPoints(dataSource, pointSource, pointColor=[1, 0, 0], x=<built-in function all>, y=<built-in function all>, z=<built-in function all>)

Plot points overlayed on gray scale 3d image as tiles.

Parameters:

• dataSouce (str or array) – volumetric image data
• pointSource (str or array) – point data to be overlayed on the image data
• pointColor (array) – RGB color for the overlayed points
• x, y, z (all or tuple) – sub-range specification

Returns:

(object) – figure handle

See also

plotTiling()

test()

Test Plot module