Basic visualization tools in bmiptools

bmiptools has also basic visualization tools based on matplotlib, which can be used for a rapid inspection of the slices of a stack. In particular, there are:

• the Basic2D class, for some basic 2d visualization tools;

• the Basic3D class, for some basic 3d visualization tools.

About that, the most useful visualisation tools are the 2d ones, whose usage is showed below.

Basic slice visualization

The code below shows how to use some of them to visualize the slice of the stack stack.

from bmiptools.visualization.graphic_tools.basic_graphic_tools import Basic2D as b2d

# plot the slice 0
b2d.show_image(stack[0])

Compare two slices

Another useful operation can be the comparison of two slices of a stack. This can be done easily with the code below.

# compare slice 0 and slice 1
b2d.compare_images(stack[0],stack[1])

Visualizing image grey-levels as surface

For segmentation purposes, it can be useful to visualize the gray level of a slice as a 3d surface. In bmiptools this can be done as follow.

# plot the 2d image of slice 0 as 3d surface
b2d.plot_image_as_surface(stack[0])

Plot masks on slices

Given a mask, it is also possible to visualize it superimposed over the slice of a stack.

# plot a mask on the slice 0
mask = ....                                     # numpy array containig the mask
b2d.show_threshold_on_image(stack[0],mark)