Ewoks Tasks

Example2DStacks

Generate one or more stacks of transformed images to test registration methods.

Identifier:

ewoksndreg.tasks.example2d_stacks.Example2DStacks

Task type:

class

Required inputs:

name, transformation_type

Optional inputs:

nimages, noise, nstacks, shape

Outputs:

image_stacks, transformations

Reg2DFeatures

Use a feature-based registration method to calculate transformations between the images in one or more stacks.

Identifier:

ewoksndreg.tasks.reg2d_features.Reg2DFeatures

Task type:

class

Required inputs:

detector, image_stacks, mapper, matcher, transformation_type

Optional inputs:

mask, output_configuration, reference_image, reference_stack

Outputs:

features, image_stacks, matches, output_configuration, reference_stack, transformations

Reg2DIntensities

Use an intensity-based registration method to calculate transformations between the images in one or more stacks.

Identifier:

ewoksndreg.tasks.reg2d_intensities.Reg2DIntensities

Task type:

class

Required inputs:

image_stacks, mapper, transformation_type

Optional inputs:

block_size, mapper_options, mask, output_configuration, preprocessing_options, reference_image, reference_stack

Outputs:

image_stacks, output_configuration, reference_stack, transformations

Reg2DPostEvaluation

Given several stacks of images and their image transformations, determine the stack and list of transformations that results in the best registration.

Identifier:

ewoksndreg.tasks.reg2d_posteval.Reg2DPostEvaluation

Task type:

class

Required inputs:

image_stacks, transformations

Optional inputs:

output_configuration, output_root_uri, reference_stack, skip

Outputs:

image_stacks, output_configuration, ranked_stack_names, reference_stack, transformations

Reg2DPreEvaluation

Given several stacks of images requiring the same alignment, determine the stack which is most suitable to get a correct alignment.

Identifier:

ewoksndreg.tasks.reg2d_preeval.Reg2DPreEvaluation

Task type:

class

Required inputs:

image_stacks

Optional inputs:

output_configuration, reference_stack, skip

Outputs:

image_stacks, output_configuration, ranked_stack_names, reference_stack

Reg2DTransform

Apply transformations calculated from image registration to the images of one or more stacks.

Identifier:

ewoksndreg.tasks.reg2d_transform.Reg2DTransform

Task type:

class

Required inputs:

image_stacks, transformations

Optional inputs:

crop, image_stacks_nxmetadata, interpolation_order, output_configuration, output_root_uri

Outputs:

image_stacks, output_configuration

SelectNXdataImageStacks

Find image stacks by searching recursively for 3D NXdata signals under a root HDF5 URL.

Identifier:

ewoksndreg.tasks.select_nxdata.SelectNXdataImageStacks

Task type:

class

Required inputs:

input_root_uri

Optional inputs:

output_root_uri

Outputs:

image_stacks, image_stacks_nxmetadata, output_root_uri