Data processing algorithms for tomography

Welcome to Algotom’s documentation about data processing algorithms for tomography. This documentation is not only to explain functions available in the Algotom package but also to present tomography-related tutorials, technical notes, and applications.

Source code: https://github.com/algotom/algotom

Table of Contents

• 1. Basic tutorials
  • 1.1. Python for tomography scientists as beginners
    • 1.1.1. Installing Python and tools for writing codes
    • 1.1.2. Python ecosystem of libraries
    • 1.1.3. Where/how to start coding
  • 1.2. Common data format at synchrotron facilities
    • 1.2.1. Hdf format
    • 1.2.2. Tiff format
  • 1.3. Basic components of an X-ray tomography system
    • 1.3.1. How tomography works
    • 1.3.2. Basic components of an X-ray tomography system
      • 1.3.2.1. X-ray source
      • 1.3.2.2. Stage
      • 1.3.2.3. Sample
      • 1.3.2.4. Detector
      • 1.3.2.5. Computing resources
  • 1.4. Basic workflow for processing tomographic data
    • 1.4.1. Read/write data
    • 1.4.2. Flat-field correction
    • 1.4.3. Zinger removal
    • 1.4.4. Ring artifact removal
    • 1.4.5. Center-of-rotation determination
    • 1.4.6. Denoising or contrast enhancement
    • 1.4.7. Image reconstruction
    • 1.4.8. Other data processing steps
      • 1.4.8.1. Distortion correction
      • 1.4.8.2. Sinogram stitching for a half-acquisition scan
  • 1.5. Parallel processing in Python
  • 1.6. Alignment for a parallel-beam tomography system
• 2. Features
  • 2.1. Capabilities
  • 2.2. Development principles
• 3. Installation
  • 3.1. Using conda
  • 3.2. Using pip
  • 3.3. From source
  • 3.4. Notes
• 4. Demonstrations
  • 4.1. Setting up a Python workspace
  • 4.2. Exploring raw data and making use of the input-output module
    • 4.2.1. Nxs/hdf files
    • 4.2.2. Tiff files
    • 4.2.3. Mrc files
    • 4.2.4. Other file formats
  • 4.3. Methods and tools for removing ring artifacts
    • 4.3.1. Improvements
    • 4.3.2. Tools for designing ring removal methods
      • 4.3.2.1. Back-and-forth sorting
      • 4.3.2.2. Separation of frequency components
      • 4.3.2.3. Polynomial fitting along an axis
      • 4.3.2.4. Wavelet decomposition and reconstruction
      • 4.3.2.5. Stripe interpolation
      • 4.3.2.6. Transformation between Cartesian and polar coordinate system
      • 4.3.2.7. Transformation between sinogram space and reconstruction space
  • 4.4. Comparison of ring removal methods on challenging sinograms
    • 4.4.1. Same sample-type and slice but different in shape
    • 4.4.2. Partial ring artifacts
    • 4.4.3. All types of ring artifacts
    • 4.4.4. Having valid stripes (not artifacts)
    • 4.4.5. For cone-beam tomography
  • 4.5. Complete workflow for processing tomographic data
    • 4.5.1. Assessing raw data
    • 4.5.2. Reconstructing several slices
    • 4.5.3. Finding the center of rotation
    • 4.5.4. Tweaking parameters of preprocessing methods
    • 4.5.5. Choosing a reconstruction method
    • 4.5.6. Performing full reconstruction
    • 4.5.7. Automating the workflow
    • 4.5.8. Downsampling, rescaling, and reslicing reconstructed volume
    • 4.5.9. Common mistakes and useful tips
    • 4.5.10. Data analysis
• 5. Technical notes
  • 5.1. Implementations of X-ray speckle-based phase-contrast tomography
    • 5.1.1. Introduction
    • 5.1.2. Data acquisition
    • 5.1.3. Data processing
      • 5.1.3.1. Finding pixel shifts
      • 5.1.3.2. Surface reconstruction
      • 5.1.3.3. Extracting transmission and dark-field signals
      • 5.1.3.4. Tomographic reconstruction
    • 5.1.4. Implementation
      • 5.1.4.1. Design principles
      • 5.1.4.2. Building blocks
    • 5.1.5. Demonstration
  • 5.2. Implementations of direct vertical-slice reconstruction for tomography
    • 5.2.1. Introduction
    • 5.2.2. Implementation
      • 5.2.2.1. Requirements
      • 5.2.2.2. Geometry definition
      • 5.2.2.3. Back projection, the ramp filter, and reconstruction
      • 5.2.2.4. Center of rotation determination
    • 5.2.3. Demonstrations
      • 5.2.3.1. Practical insights
      • 5.2.3.2. Workflows
• 6. Update notes
• 7. API Reference
  • 7.1. Input-output
    • 7.1.1. algotom.io.converter
      • convert_tif_to_hdf()
      • extract_tif_from_hdf()
      • HdfEmulatorFromTif
    • 7.1.2. algotom.io.loadersaver
      • load_image()
      • get_hdf_information()
      • find_hdf_key()
      • load_hdf()
      • make_folder()
      • make_file_name()
      • make_folder_name()
      • find_file()
      • save_image()
      • open_hdf_stream()
      • load_distortion_coefficient()
      • save_distortion_coefficient()
      • get_hdf_tree()
      • get_reference_sample_stacks_dls()
      • get_reference_sample_stacks()
      • get_tif_stack()
      • get_image_stack()
      • load_image_multiple()
      • save_image_multiple()
  • 7.2. Pre-processing
    • 7.2.1. algotom.prep.calculation
      • make_inverse_double_wedge_mask()
      • calculate_center_metric()
      • coarse_search_cor()
      • fine_search_cor()
      • downsample_cor()
      • find_center_vo()
      • calculate_curvature()
      • correlation_metric()
      • search_overlap()
      • find_overlap()
      • find_overlap_multiple()
      • find_center_360()
      • complex_gradient()
      • find_shift_based_phase_correlation()
      • find_center_based_phase_correlation()
      • find_center_projection()
      • calculate_reconstructable_height()
      • calculate_maximum_index()
    • 7.2.2. algotom.prep.conversion
      • make_weight_matrix()
      • stitch_image()
      • join_image()
      • stitch_image_multiple()
      • join_image_multiple()
      • convert_sinogram_360_to_180()
      • convert_sinogram_180_to_360()
      • extend_sinogram()
      • generate_sinogram_helical_scan()
      • generate_full_sinogram_helical_scan()
    • 7.2.3. algotom.prep.correction
      • flat_field_correction()
      • unwarp_projection()
      • unwarp_sinogram()
      • unwarp_sinogram_chunk()
      • mtf_deconvolution()
      • generate_tilted_sinogram()
      • generate_tilted_sinogram_chunk()
      • generate_tilted_profile_line()
      • generate_tilted_profile_chunk()
      • non_linear_function()
      • beam_hardening_correction()
      • upsample_sinogram()
    • 7.2.4. algotom.prep.filtering
      • make_fresnel_window()
      • fresnel_filter()
      • make_double_wedge_mask()
      • double_wedge_filter()
    • 7.2.5. algotom.prep.removal
      • remove_stripe_based_sorting()
      • remove_stripe_based_filtering()
      • remove_stripe_based_fitting()
      • remove_large_stripe()
      • remove_dead_stripe()
      • remove_all_stripe()
      • remove_stripe_based_2d_filtering_sorting()
      • remove_stripe_based_normalization()
      • remove_stripe_based_regularization()
      • remove_stripe_based_fft()
      • remove_stripe_based_wavelet_fft()
      • remove_stripe_based_interpolation()
      • check_zinger_size()
      • select_zinger()
      • remove_zinger()
      • generate_blob_mask()
      • remove_blob_1d()
      • remove_blob()
    • 7.2.6. algotom.prep.phase
      • get_quality_map()
      • get_weight_mask()
      • unwrap_phase_based_cosine_transform()
      • unwrap_phase_based_fft()
      • unwrap_phase_iterative_fft()
      • reconstruct_surface_from_gradient_FC_method()
      • reconstruct_surface_from_gradient_SCS_method()
      • find_shift_between_image_stacks()
      • find_shift_between_sample_images()
      • align_image_stacks()
      • get_transmission_dark_field_signal()
      • retrieve_phase_based_speckle_tracking()
  • 7.3. Reconstruction
    • 7.3.1. algotom.rec.reconstruction
      • make_smoothing_window()
      • make_2d_ramp_window()
      • apply_ramp_filter()
      • back_projection_gpu()
      • back_projection_gpu_chunk()
      • back_projection_cpu()
      • fbp_reconstruction()
      • make_circular_ramp_window()
      • apply_circular_ramp_filter()
      • bpf_reconstruction()
      • generate_mapping_coordinate()
      • dfi_reconstruction()
      • gridrec_reconstruction()
      • astra_reconstruction()
      • find_center_based_slice_metric()
      • find_center_visual_slices()
    • 7.3.2. algotom.rec.vertrec
      • vertical_back_projection_cpu()
      • vertical_back_projection_cpu_chunk()
      • vertical_back_projection_gpu()
      • vertical_back_projection_gpu_chunk()
      • vertical_reconstruction()
      • vertical_reconstruction_multiple()
      • vertical_reconstruction_different_angles()
      • find_center_vertical_slice()
      • find_center_visual_vertical_slices()
  • 7.4. Post-processing
    • 7.4.1. algotom.post.postprocessing
      • get_statistical_information()
      • get_statistical_information_dataset()
      • downsample()
      • rescale()
      • downsample_dataset()
      • rescale_dataset()
      • reslice_dataset()
      • remove_ring_based_fft()
      • remove_ring_based_wavelet_fft()
  • 7.5. Utilities
    • 7.5.1. algotom.util.calibration
      • normalize_background()
      • normalize_background_based_fft()
      • invert_dot_contrast()
      • calculate_threshold()
      • binarize_image()
      • get_dot_size()
      • check_dot_size()
      • select_dot_based_size()
      • calculate_distance()
      • fit_points_to_ellipse()
      • find_tilt_roll_based_linear_fit()
      • find_tilt_roll_based_ellipse_fit()
      • find_tilt_roll()
    • 7.5.2. algotom.util.simulation
      • make_elliptic_mask()
      • make_rectangular_mask()
      • make_triangular_mask()
      • make_line_target()
      • make_face_phantom()
      • make_sinogram()
      • add_noise()
      • add_stripe_artifact()
      • convert_to_Xray_image()
      • add_background_fluctuation()
    • 7.5.3. algotom.util.utility
      • parallel_process_slices()
      • apply_method_to_multiple_sinograms()
      • mapping()
      • make_circle_mask()
      • sort_forward()
      • sort_backward()
      • separate_frequency_component()
      • generate_fitted_image()
      • detect_stripe()
      • calculate_regularization_coefficient()
      • make_2d_butterworth_window()
      • make_2d_damping_window()
      • apply_wavelet_decomposition()
      • apply_wavelet_reconstruction()
      • check_level()
      • apply_filter_to_wavelet_component()
      • interpolate_inside_stripe()
      • rectangular_from_polar()
      • polar_from_rectangular()
      • transform_slice_forward()
      • transform_slice_backward()
      • make_2d_gaussian_window()
      • apply_gaussian_filter()
      • apply_1d_regularizer()
      • apply_regularization_filter()
      • transform_1d_window_to_2d()
      • detect_sample()
      • fix_non_sample_areas()
      • locate_slice()
      • locate_slice_chunk()
      • generate_spiral_positions()
      • find_center_visual_sinograms()
      • find_center_visual_slices()
    • 7.5.4. algotom.util.correlation
      • normalize_image()
      • generate_correlation_map()
      • locate_peak()
      • find_shift_based_correlation_map()
      • find_local_shifts()
      • find_global_shift_based_local_shifts()
      • find_local_shifts_umpa()
• 8. Credits
  • 8.1. Citations
  • 8.2. References
• 9. Highlights
• 10. Quick links