API References

The full bmitools repository is available at

• https://gitlab.mpikg.mpg.de/curcuraci/bmiptools

Here below, most of the bmiptools objects are listed.

bmiptools.stack	I/O methods of bmiptools.
bmiptools.pipeline	A pipeline object manage the creation/initialization/application on a stack of sequence of transformation tools (i.e.
bmiptools.setting.installed_plugins	List of the available installed plugins organized in two dictionaries:
bmiptools.setting.configure	Collect functions for the bmiptools configuration.
bmiptools.core.base	Basic class containing general function which can be useful in any object of the library and possibly depending on the global setting of the library..
bmiptools.core.gpu_utils	Work in progress...
bmiptools.core.ip_utils	Utility functions related to image processing.
bmiptools.core.math_utils	Mathematics related utility functions.
bmiptools.core.utils	Generic utility functions
bmiptools.gui.bmiptools_gui	Main objectus used to render the bmiptools gui
bmiptools.gui.gui_basic	Collection the basic elements which can be useful for the gui creation in bmiptools.
bmiptools.transformation.base	Base class for all the transfomation plugins.
bmiptools.transformation.alignment.registrator	Plugin used to apply registration algorithms to a given stack object.
bmiptools.transformation.basic.filters	Basic filters used in bmiptools.
bmiptools.transformation.dynamics.standardizer	Plugin performing the standardization of a stack.
bmiptools.transformation.dynamics.histogram_matcher	Plugin performing the histogram matching of a stack.
bmiptools.transformation.dynamics.equalizer	Plugin performing the equalization of the slices of a stack.
bmiptools.transformation.geometric.cropper	Plugin performing the cropping of a stack.
bmiptools.transformation.geometric.geometric_tools	Collection of a series of tools useful for geometric transformations.
bmiptools.transformation.geometric.affine	Plugin used to apply affine transformations on a stack object.
bmiptools.transformation.restoration._restoration_shared	Collection of core functions/ variables shared among the restoration plugins.
bmiptools.transformation.restoration.decharger	Plugin to remove/reduce the charging artifact typical of FIB-SEM images.
bmiptools.transformation.restoration.denoiser	Plugins performing denoising on a stack.
bmiptools.transformation.restoration.destriper	Plugin for the removal of the stripe artifacts, typical of FIB-SEM images.
bmiptools.transformation.restoration.flatter	Plugin applying the flatter transformation on a stack.
bmiptools.visualization.geometric.change_coordinate_system	Plugin used to visualize a stack in a different reference frame.
bmiptools.visualization.graphic_tools.basic_graphic_tools	Basic visualization tools for a stack object or slices of it.