imars3d.backend package

iMars3D’s backend packages: the core of the application.

The main entry point for the back end software.

This can be invoked using

python -m imars3d.backend <configfile>

The built-in help will give the options when supplied a --help flag.

Subpackages

• imars3d.backend.corrections package
  • Submodules
  • imars3d.backend.corrections.denoise module
    • denoise
    • denoise_by_bilateral()
    • denoise_by_bilateral_2d()
    • denoise_by_median()
    • measure_noiseness()
    • measure_sharpness()
  • imars3d.backend.corrections.gamma_filter module
    • gamma_filter
  • imars3d.backend.corrections.intensity_fluctuation_correction module
    • intensity_fluctuation_correction
    • intensity_fluctuation_correction_skimage()
    • normalize_roi
  • imars3d.backend.corrections.ring_removal module
    • bm3d_ring_removal
    • remove_ring_artifact
    • remove_ring_artifact_Ketcham
• imars3d.backend.diagnostics package
  • Submodules
  • imars3d.backend.diagnostics.rotation module
    • find_rotation_center
      • find_rotation_center.num_pairs
  • imars3d.backend.diagnostics.tilt module
    • apply_tilt_correction
    • calculate_dissimilarity()
    • calculate_shift()
    • calculate_tilt()
    • find_180_deg_pairs_idx()
    • tilt_correction
• imars3d.backend.dataio package
  • Submodules
  • imars3d.backend.dataio.config module
    • save_config()
  • imars3d.backend.dataio.data module
    • Foldernames
    • load_data
    • save_checkpoint
      • save_checkpoint.rot_angles
    • save_data
      • save_data.rot_angles
  • imars3d.backend.dataio.phantom module
• imars3d.backend.morph package
  • Submodules
  • imars3d.backend.morph.crop module
    • crop
    • detect_bounds()
• imars3d.backend.preparation package
  • Submodules
  • imars3d.backend.preparation.normalization module
    • minus_log
    • normalization
• imars3d.backend.workflow package
  • Submodules
  • imars3d.backend.workflow.engine module
    • WorkflowEngine
      • WorkflowEngine.registry
    • WorkflowEngineAuto
      • WorkflowEngineAuto.run()
    • WorkflowEngineError
      • WorkflowEngineError.exit_code
    • WorkflowEngineExitCodes
      • WorkflowEngineExitCodes.ERROR_GENERAL
      • WorkflowEngineExitCodes.ERROR_VALIDATION
      • WorkflowEngineExitCodes.SUCCESS
    • WorkflowValidationError
      • WorkflowValidationError.exit_code
  • imars3d.backend.workflow.validate module
    • JSONValid
      • JSONValid.required()
    • JSONValidationError
    • todict()

Submodules

imars3d.backend.reconstruction module

reconstruction module for imars3d package.

class imars3d.backend.reconstruction.recon(*args, **params)

Bases: ParameterizedFunction

Perform reconstruction on a stack of tomographic data.

Parameters

• arrays (np.ndarray) – Input stack of tomography data

• theta (np.array) – Projection angles (in radians)

• center (float) – Rotation center

• algorithm (str) – Name of reconstruction algorithm

• filter_name (str) – Name of filter used for reconstruction

• is_radians (boolean) – True if input theta is in radians, false if in degrees

• perform_minus_log (boolean) – True if we want to run tomopy.minus_log on the arrays data before reconstruction

Returns

Reconstructed tomographic data

Return type

np.ndarray

max_workers = 0

imars3d.backend.autoredux module

Provides functions that are used in the auto reduction scripts.

imars3d.backend.autoredux.auto_reduction_ready(data_file: Union[str, Path]) → bool

Check if the data file is ready for auto reduction.

Expected directory tree for data_file is /SNS/CG1D/IPTS-XXXXX/raw/_IMAGING_TYPE_/

Parameters

data_file – The data file to check. Assumes the file exists

Returns

True if the data file is ready for auto reduction, False otherwise.

Return type

bool

imars3d.backend.autoredux.extract_info_from_path(data_file: Union[str, Path]) → dict

Extract information from the data file path.

The data file path must conform to the following directory hierarchy .. code-block:: sh

/FACILITY/INSTRUMENT/IPTS/raw/[PREPATH]/ct_scans/[SUBPATH]/IMAGENAME.tiff

PREPATH and SUBPATH are optional and can encompass one or more directories.

Examples

/HFIR/CG1D/IPTS-25777/raw/ct_scans/20191029_ironman_small_0070_000_000_0002.tiff
/HFIR/CG1D/IPTS-25777/raw/2019_Oct/ct_scans/20191029_ironman_small_0070_000_000_0002.tiff
/HFIR/CG1D/IPTS-25777/raw/2019_Oct/29/ct_scans/20191029_ironman_small_0070_000_000_0002.tiff
/HFIR/CG1D/IPTS-25777/raw/2019_Oct/29/ct_scans/iron_man/XYZ/20191029_ironman_small_0070_000_000_0002.tiff

Parameters

data_file – The data file to extract information

Returns

The extracted information with the following keys: facility, instrument, ipts, prepath, subpath

Return type

dict

imars3d.backend.autoredux.load_template_config(config_path: Union[str, Path]) → dict

Load the given path as a template configuration file.

Parameters

config_path (Union[str, pathlib.Path]) – Path of template config to be loaded

Returns

The template configuration file.

Return type

dict

Raises

• FileNotFoundError – If the given path cannot be resolved

• JSONDecodeError – If the resolved file cannot be parsed as JSON

imars3d.backend.autoredux.substitute_template(config: dict, values: dict) → dict

Update the template configuration with actual values.

Parameters

• config – dictionary resulting from loading the template JSON configuration file

• values – dictionary resulting from scanning the path to the input radiograph with function extract_info_from_path

Return type

dictionary with template keywords substituted with actual values