`CHAP.tomo.processor`¶

File : processor.py Author : Rolf Verberg Description: Module for Processors used only by tomography experiments

Module Contents¶

Classes¶

`TomoCHESSMapConverter`	A processor to convert a CHESS style tomography map with dark and bright field configurations to an nexusformat.nexus.NXtomo style input format.
`TomoDataProcessor`	A processor to reconstruct a set of tomographic images returning either a dictionary or a nexusformat.nexus.NXroot object containing the (meta) data after processing each individual step.
`SetNumexprThreads`	Class that sets and keeps track of the number of processors used by the code in general and by the num_expr package specifically.
`Tomo`	Reconstruct a set of tomographic images.
`TomoSimFieldProcessor`	A processor to create a simulated tomography data set returning a `nexusformat.nexus.NXroot` object containing the simulated tomography detector images.
`TomoDarkFieldProcessor`	A processor to create the dark field associated with a simulated tomography data set created by TomoSimProcessor.
`TomoBrightFieldProcessor`	A processor to create the bright field associated with a simulated tomography data set created by TomoSimProcessor.
`TomoSpecProcessor`	A processor to create a tomography SPEC file associated with a simulated tomography data set created by TomoSimProcessor.

Functions¶

get_nxroot

Look through data for an item whose value for the 'schema' key matches schema (if supplied) and whose value for the 'data' key matches a nexusformat.nexus.NXobject object and return this object.

Data¶

NUM_CORE_TOMOPY_LIMIT

API¶

CHAP.tomo.processor.NUM_CORE_TOMOPY_LIMIT¶: 24

CHAP.tomo.processor.get_nxroot(data, schema=None, remove=True)¶

Look through data for an item whose value for the 'schema' key matches schema (if supplied) and whose value for the 'data' key matches a nexusformat.nexus.NXobject object and return this object.

Parameters:

data (list[PipelineData]) – Input list of PipelineData objects.
schema (str, optional) – Name associated with the nexusformat.nexus.NXobject object to match in data.
remove (bool, optional) – Removes the matching entry in data when found, defaults to True.

Raises:

ValueError – Found an invalid matching object or multiple matching objects.

Returns:

Object matching with schema or None when not found.

Return type:

None, nexusformat.nexus.NXroot

class CHAP.tomo.processor.TomoCHESSMapConverter¶

Bases: CHAP.processor.Processor

A processor to convert a CHESS style tomography map with dark and bright field configurations to an nexusformat.nexus.NXtomo style input format.

Initialization

Constructor of PipelineItem class

process(data)¶

Process the input map and configuration and return a nexusformat.nexus.NXroot object based on the nexusformat.nexus.NXtomo style format.

Parameters:: data (list[PipelineData]) – Input map and configuration for tomographic image reduction/reconstruction.
Raises:: ValueError – Invalid input or configuration parameter.
Returns:: nexusformat.nexus.NXtomo style tomography input configuration.
Return type:: nexusformat.nexus.NXroot

class CHAP.tomo.processor.TomoDataProcessor¶

Bases: CHAP.processor.Processor

A processor to reconstruct a set of tomographic images returning either a dictionary or a nexusformat.nexus.NXroot object containing the (meta) data after processing each individual step.

Initialization

Constructor of PipelineItem class

process(data, outputdir='.', interactive=False, reduce_data=False, find_center=False, calibrate_center=False, reconstruct_data=False, combine_data=False, save_figs='no')¶

Process the input map or configuration with the step specific instructions and return either a dictionary or a nexusformat.nexus.NXroot object with the processed result.

Parameters:

data (list[PipelineData]) – Input configuration and specific step instructions for tomographic image reduction.
outputdir (str, optional) – Output folder name, defaults to ‘.’.
interactive (bool, optional) – Allows for user interactions, defaults to False.
reduce_data (bool, optional) – Generate reduced tomography images, defaults to False.
find_center (bool, optional) – Generate calibrated center axis info, defaults to False.
calibrate_center (bool, optional) – Calibrate the rotation axis, defaults to False.
reconstruct_data (bool, optional) – Reconstruct the tomography data, defaults to False.
combine_data (bool, optional) – Combine the reconstructed tomography stacks, defaults to False.
save_figs (Literal['yes', 'no', 'only'], optional) – Safe figures to file (‘yes’ or ‘only’) and/or display figures (‘yes’ or ‘no’), defaults to ‘no’.

Raises:

ValueError – Invalid input or configuration parameter.
RuntimeError – Missing map configuration to generate reduced tomography images.

Returns:

Processed (meta)data of the last step.

Return type:

Union[dict, nexusformat.nexus.NXroot]

class CHAP.tomo.processor.SetNumexprThreads(num_core)¶

Class that sets and keeps track of the number of processors used by the code in general and by the num_expr package specifically.

Initialization

Initialize SetNumexprThreads.

Parameters:: num_core (int) – Number of processors used by the num_expr package.

__enter__()¶

__exit__(exc_type, exc_value, traceback)¶

class CHAP.tomo.processor.Tomo(logger=None, outputdir='.', interactive=False, num_core=-1, save_figs='no')¶

Reconstruct a set of tomographic images.

Initialization

Initialize Tomo.

Parameters:

interactive (bool, optional) – Allows for user interactions, defaults to False.
num_core (int) – Number of processors.
outputdir (str, optional) – Output folder name, defaults to ‘.’.
save_figs (Literal['yes', 'no', 'only'], optional) – Safe figures to file (‘yes’ or ‘only’) and/or display figures (‘yes’ or ‘no’), defaults to ‘no’.

Raises:

ValueError – Invalid input parameter.

reduce_data(nxroot, tool_config=None, calibrate_center_rows=False)¶

Reduced the tomography images.

Parameters:

nxroot (nexusformat.nexus.NXroot) – Data object containing the raw data info and metadata required for a tomography data reduction.
tool_config (CHAP.tomo.models.TomoReduceConfig, optional) – Tool configuration.

Raises:

ValueError – Invalid input or configuration parameter.

Returns:

Reduced tomography data.

Return type:

nexusformat.nexus.NXroot

find_centers(nxroot, tool_config, calibrate_center_rows=False)¶

Find the calibrated center axis info

Parameters:

nxroot – Data object containing the reduced data and metadata required to find the calibrated center axis info.
tool_config (CHAP.tomo.models.TomoFindCenterConfig) – Tool configuration.

Raises:

ValueError – Invalid or missing input or configuration parameter.

Returns:

Calibrated center axis info.

Return type:

dict

reconstruct_data(nxroot, center_info, tool_config)¶

Reconstruct the tomography data.

Parameters:

nxroot – Data object containing the reduced data and metadata required for a tomography data reconstruction.
center_info (dict) – Calibrated center axis info.
tool_config (CHAP.tomo.models.TomoReconstructConfig) – Tool configuration.

Raises:

ValueError – Invalid or missing input or configuration parameter.

Returns:

Reconstructed tomography data.

Return type:

nexusformat.nexus.NXroot

combine_data(nxroot, tool_config)¶

Combine the reconstructed tomography stacks.

Parameters:

nxroot – Data object containing the reconstructed data and metadata required to combine the tomography stacks.
tool_config (CHAP.tomo.models.TomoCombineConfig) – Tool configuration.

Raises:

ValueError – Invalid or missing input or configuration parameter.

Returns:

Combined reconstructed tomography data.

Return type:

nexusformat.nexus.NXroot

_gen_dark(nxentry, reduced_data, image_key)¶: Generate dark field.

_gen_bright(nxentry, reduced_data, image_key)¶: Generate bright field.

_set_detector_bounds(nxentry, reduced_data, image_key, theta, img_row_bounds, calibrate_center_rows)¶: Set vertical detector bounds for each image stack.Right now the range is the same for each set in the image stack.

_gen_thetas(nxentry, image_key)¶: Get the rotation angles for the image stacks.

_set_zoom_or_delta_theta(thetas, delta_theta=None)¶: Set zoom and/or delta theta to reduce memory the requirement for the analysis.

_gen_tomo(nxentry, reduced_data, image_key, calibrate_center_rows)¶: Generate tomography fields.

_find_center_one_plane(tomo_stacks, stack_index, row, offset_row, thetas, eff_pixel_size, cross_sectional_dim, path=None, num_core=1, center_offset_min=-50, center_offset_max=50, center_search_range=None, gaussian_sigma=None, ring_width=None, prev_center_offset=None)¶

Find center for a single tomography plane.

tomo_stacks data axes order: stack,theta,row,column thetas in radians

_reconstruct_planes(tomo_planes, center_offset, thetas, num_core=1, gaussian_sigma=None, ring_width=None)¶: Invert the sinogram for a single or multiple tomography planes using tomopy’s recon routine.

_select_center_offset(recon_planes, row, preselected_offsets, default_offset_index=0, fig_titles=None, search_button=True, include_all_bad=False)¶: Select a center offset value from reconstructed images for a single reconstructed tomography data plane.

_reconstruct_one_tomo_stack(tomo_stack, thetas, center_offsets=None, num_core=1, algorithm='gridrec', secondary_iters=0, gaussian_sigma=None, remove_stripe_sigma=None, ring_width=None)¶: Reconstruct a single tomography stack.

_resize_reconstructed_data(data, x_bounds=None, y_bounds=None, z_bounds=None, combine_data=False)¶: Resize the reconstructed tomography data.

class CHAP.tomo.processor.TomoSimFieldProcessor¶

Bases: CHAP.processor.Processor

A processor to create a simulated tomography data set returning a nexusformat.nexus.NXroot object containing the simulated tomography detector images.

Initialization

Constructor of PipelineItem class

process(data)¶

Process the input configuration and return a nexusformat.nexus.NXroot object with the simulated tomography detector images.

Parameters:: data (list[PipelineData]) – Input configuration for the simulation.
Raises:: ValueError – Invalid input or configuration parameter.
Returns:: Simulated tomographic images.
Return type:: nexusformat.nexus.NXroot

_create_pathlength_solid_square(dim, thetas, pixel_size, detector_size)¶: Create the x-ray path length through a solid square crosssection for a set of rotation angles.

class CHAP.tomo.processor.TomoDarkFieldProcessor¶

Bases: CHAP.processor.Processor

A processor to create the dark field associated with a simulated tomography data set created by TomoSimProcessor.

Initialization

Constructor of PipelineItem class

process(data, num_image=5)¶

Process the input configuration and return a nexusformat.nexus.NXroot object with the simulated dark field detector images.

Parameters:

data (list[PipelineData]) – Input configuration for the simulation.
num_image (int, optional.) – Number of dark field images, defaults to 5.

Raises:

ValueError – Missing or invalid input or configuration parameter.

Returns:

Simulated dark field images.

Return type:

nexusformat.nexus.NXroot

class CHAP.tomo.processor.TomoBrightFieldProcessor¶

Bases: CHAP.processor.Processor

A processor to create the bright field associated with a simulated tomography data set created by TomoSimProcessor.

Initialization

Constructor of PipelineItem class

process(data, num_image=5)¶

Process the input configuration and return a nexusformat.nexus.NXroot object with the simulated bright field detector images.

Parameters:

data (list[PipelineData]) – Input configuration for the simulation.
num_image (int, optional.) – Number of bright field images, defaults to 5.

Raises:

ValueError – Missing or invalid input or configuration parameter.

Returns:

Simulated bright field images.

Return type:

nexusformat.nexus.NXroot

class CHAP.tomo.processor.TomoSpecProcessor¶

Bases: CHAP.processor.Processor

A processor to create a tomography SPEC file associated with a simulated tomography data set created by TomoSimProcessor.

Initialization

Constructor of PipelineItem class

process(data, scan_numbers=[1])¶

Process the input configuration and return a list of strings representing a plain text SPEC file.

Parameters:

data (list[PipelineData]) – Input configuration for the simulation.
scan_numbers (list[int]) – List of SPEC scan numbers, defaults to [1].

Raises:

ValueError – Invalid input or configuration parameter.

Returns:

Simulated SPEC file.

Return type:

list[str]

`CHAP.tomo.processor`¶

Module Contents¶

Classes¶

Functions¶

Data¶

API¶

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`CHAP.tomo.processor`¶