Imaging tasks

How to use

These tasks come from ewoksndreg. It can be installed with

pip install ewoksndreg

ℹ️ These tasks are used at the following ESRF beamlines: ID16b, ID21

Example2DStack

Generate example images with successive transformations to test registration methods.

Identifier:

ewoksndreg.tasks.example2d_stack.Example2DStack

Task type:

class

Required inputs:

name, transformation_type

Optional inputs:

add_noise_dim, nimages, shape

Outputs:

imagestack, transformations

FluoStack

Fetch a stack of images corresponding to the given counter from the given h5 file

Identifier:

ewoksndreg.tasks.fluo_stack.FluoStack

Task type:

class

Required inputs:

path, stack

Optional inputs:

exclude, normalize

Outputs:

energies, imagestack, stack_name

FluoAllStacks

Fetch all of the different counters from a given h5 file

Identifier:

ewoksndreg.tasks.fluo_stack.FluoAllStacks

Task type:

class

Required inputs:

path

Optional inputs:

exclude, normalize, stack_names

Outputs:

imagestacks, stack_names

ID16BFileRead

Identifier:

ewoksndreg.tasks.id16b_file_read.ID16BFileRead

Task type:

class

Required inputs:

recsuffix, scandir

Optional inputs:

normalize, url

Outputs:

imagestack

Reg2DFeatures

Use an feature-based registration method to calculate transformations to register the images in the stack.

Identifier:

ewoksndreg.tasks.reg2d_features.Reg2DFeatures

Task type:

class

Required inputs:

detector, imagestack, mapper, matcher, transformation_type

Optional inputs:

inputs_are_stacks, reference

Outputs:

features, matches, transformations

Reg2DIntensities

Use an intensity-based registration method to calculate transformations to register the 2D-images in the stack.

Identifier:

ewoksndreg.tasks.reg2d_intensities.Reg2DIntensities

Task type:

class

Required inputs:

imagestack, mapper, transformation_type

Optional inputs:

block_size, inputs_are_stacks, mask, method_options, preprocessing_options, reference

Outputs:

transformations

Reg2DPreEvaluation

Given several different stacks of images requiring the same alignment, create a ranking of which stacks might be the most suitable to get a correct alignment.

Identifier:

ewoksndreg.tasks.reg2d_multistack.Reg2DPreEvaluation

Task type:

class

Required inputs:

imagestacks

Optional inputs:

inputs_are_stacks, preferences, relevant_stacks, stack_names

Outputs:

full_ranking, ranking, stack_names

Reg2DPostEvaluation

Given several stacks of images requiring the same alignment and their calculated transformations, determine the stack and list of transformations that resulted in the best registration.

Identifier:

ewoksndreg.tasks.reg2d_multistack.Reg2DPostEvaluation

Task type:

class

Required inputs:

imagestacks, transformations

Optional inputs:

chosen_stack, inputs_are_stacks, url

Outputs:

imagestack, imagestacks, transformations

Reg2DTransform

Apply transformations calculated from image registration to images.

Identifier:

ewoksndreg.tasks.reg2d_transform.Reg2DTransform

Task type:

class

Required inputs:

imagestack, transformations

Optional inputs:

crop, inputs_are_stacks, interpolation_order, stack_names, url

Outputs:

imagestack

SelectSlice

Slice out a subvolume of the imagestack

Identifier:

ewoksndreg.tasks.select_slice.SelectSlice

Task type:

class

Required inputs:

imagestack

Optional inputs:

inputs_are_stacks, url, x, y, z

Outputs:

imagestack