searchindex.js

Search.setIndex({"docnames": ["index", "toc/api", "toc/api/algotom.io.converter", "toc/api/algotom.io.loadersaver", "toc/api/algotom.post.postprocessing", "toc/api/algotom.prep.calculation", "toc/api/algotom.prep.conversion", "toc/api/algotom.prep.correction", "toc/api/algotom.prep.filtering", "toc/api/algotom.prep.phase", "toc/api/algotom.prep.removal", "toc/api/algotom.rec.reconstruction", "toc/api/algotom.rec.vertrec", "toc/api/algotom.util.calibration", "toc/api/algotom.util.correlation", "toc/api/algotom.util.simulation", "toc/api/algotom.util.utility", "toc/credits", "toc/highlights", "toc/links", "toc/section1", "toc/section1/section1_1", "toc/section1/section1_2", "toc/section1/section1_3", "toc/section1/section1_4", "toc/section1/section1_5", "toc/section1/section1_6", "toc/section2", "toc/section3", "toc/section4", "toc/section4/section4_1", "toc/section4/section4_2", "toc/section4/section4_3", "toc/section4/section4_4", "toc/section4/section4_5", "toc/section5", "toc/section5/section5_1", "toc/section5/section5_2", "toc/section6"], "filenames": ["index.rst", "toc\\api.rst", "toc\\api\\algotom.io.converter.rst", "toc\\api\\algotom.io.loadersaver.rst", "toc\\api\\algotom.post.postprocessing.rst", "toc\\api\\algotom.prep.calculation.rst", "toc\\api\\algotom.prep.conversion.rst", "toc\\api\\algotom.prep.correction.rst", "toc\\api\\algotom.prep.filtering.rst", "toc\\api\\algotom.prep.phase.rst", "toc\\api\\algotom.prep.removal.rst", "toc\\api\\algotom.rec.reconstruction.rst", "toc\\api\\algotom.rec.vertrec.rst", "toc\\api\\algotom.util.calibration.rst", "toc\\api\\algotom.util.correlation.rst", "toc\\api\\algotom.util.simulation.rst", "toc\\api\\algotom.util.utility.rst", "toc\\credits.rst", "toc\\highlights.rst", "toc\\links.rst", "toc\\section1.rst", "toc\\section1\\section1_1.rst", "toc\\section1\\section1_2.rst", "toc\\section1\\section1_3.rst", "toc\\section1\\section1_4.rst", "toc\\section1\\section1_5.rst", "toc\\section1\\section1_6.rst", "toc\\section2.rst", "toc\\section3.rst", "toc\\section4.rst", "toc\\section4\\section4_1.rst", "toc\\section4\\section4_2.rst", "toc\\section4\\section4_3.rst", "toc\\section4\\section4_4.rst", "toc\\section4\\section4_5.rst", "toc\\section5.rst", "toc\\section5\\section5_1.rst", "toc\\section5\\section5_2.rst", "toc\\section6.rst"], "titles": ["Data processing algorithms for tomography", "<span class=\"section-number\">7. </span>API Reference", "<span class=\"section-number\">7.1.1. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.io.converter</span></code>", "<span class=\"section-number\">7.1.2. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.io.loadersaver</span></code>", "<span class=\"section-number\">7.4.1. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.post.postprocessing</span></code>", "<span class=\"section-number\">7.2.1. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.prep.calculation</span></code>", "<span class=\"section-number\">7.2.2. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.prep.conversion</span></code>", "<span class=\"section-number\">7.2.3. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.prep.correction</span></code>", "<span class=\"section-number\">7.2.4. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.prep.filtering</span></code>", "<span class=\"section-number\">7.2.6. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.prep.phase</span></code>", "<span class=\"section-number\">7.2.5. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.prep.removal</span></code>", "<span class=\"section-number\">7.3.1. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.rec.reconstruction</span></code>", "<span class=\"section-number\">7.3.2. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.rec.vertrec</span></code>", "<span class=\"section-number\">7.5.1. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.util.calibration</span></code>", "<span class=\"section-number\">7.5.4. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.util.correlation</span></code>", "<span class=\"section-number\">7.5.2. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.util.simulation</span></code>", "<span class=\"section-number\">7.5.3. </span><code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">algotom.util.utility</span></code>", "<span class=\"section-number\">8. </span>Credits", "<span class=\"section-number\">9. </span>Highlights", "<span class=\"section-number\">10. </span>Quick links", "<span class=\"section-number\">1. </span>Basic tutorials", "<span class=\"section-number\">1.1. </span>Python for tomography scientists as beginners", "<span class=\"section-number\">1.2. </span>Common data format at synchrotron facilities", "<span class=\"section-number\">1.3. </span>Basic components of an X-ray tomography system", "<span class=\"section-number\">1.4. </span>Basic workflow for processing tomographic data", "<span class=\"section-number\">1.5. </span>Parallel processing in Python", "<span class=\"section-number\">1.6. </span>Alignment for a parallel-beam tomography system", "<span class=\"section-number\">2. </span>Features", "<span class=\"section-number\">3. </span>Installation", "<span class=\"section-number\">4. </span>Demonstrations", "<span class=\"section-number\">4.1. </span>Setting up a Python workspace", "<span class=\"section-number\">4.2. </span>Exploring raw data and making use of the input-output module", "<span class=\"section-number\">4.3. </span>Methods and tools for removing ring artifacts", "<span class=\"section-number\">4.4. </span>Comparison of ring removal methods on challenging sinograms", "<span class=\"section-number\">4.5. </span>Complete workflow for processing tomographic data", "<span class=\"section-number\">5. </span>Technical notes", "<span class=\"section-number\">5.1. </span>Implementations of X-ray speckle-based phase-contrast tomography", "<span class=\"section-number\">5.2. </span>Implementations of direct vertical-slice reconstruction for tomography", "<span class=\"section-number\">6. </span>Update notes"], "terms": {"welcom": 0, "algotom": [0, 1, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38], "": [0, 8, 16, 17, 18, 21, 22, 23, 24, 26, 28, 30, 31, 32, 33, 34, 36, 37], "document": [0, 9, 11, 12, 15, 19, 24, 30, 31, 33], "about": [0, 19, 21, 28, 33, 34, 37], "thi": [0, 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"module-algotom.rec.reconstruction"]], "algotom.rec.vertrec": [[12, "algotom-rec-vertrec"]], "algotom.util.calibration": [[13, "module-algotom.util.calibration"]], "algotom.util.correlation": [[14, "module-algotom.util.correlation"]], "algotom.util.simulation": [[15, "module-algotom.util.simulation"]], "algotom.util.utility": [[16, "module-algotom.util.utility"]], "Credits": [[17, "credits"]], "Citations": [[17, "citations"]], "References": [[17, "references"]], "Highlights": [[18, "highlights"]], "Quick links": [[19, "quick-links"]], "Basic tutorials": [[20, "basic-tutorials"]], "Python for tomography scientists as beginners": [[21, "python-for-tomography-scientists-as-beginners"]], "Installing Python and tools for writing codes": [[21, "installing-python-and-tools-for-writing-codes"]], "Python ecosystem of libraries": [[21, "python-ecosystem-of-libraries"]], "Where/how to start coding": [[21, "where-how-to-start-coding"]], "Common data format at synchrotron facilities": [[22, "common-data-format-at-synchrotron-facilities"]], "Hdf format": [[22, "hdf-format"]], "Tiff format": [[22, "tiff-format"]], "Basic components of an X-ray tomography system": [[23, "basic-components-of-an-x-ray-tomography-system"], [23, "id1"]], "How tomography works": [[23, "how-tomography-works"]], "X-ray source": [[23, "x-ray-source"]], "Stage": [[23, "stage"]], "Sample": [[23, "sample"]], "Detector": [[23, "detector"]], "Computing resources": [[23, "computing-resources"]], "Basic workflow for processing tomographic data": [[24, "basic-workflow-for-processing-tomographic-data"]], "Read/write data": [[24, "read-write-data"]], "Flat-field correction": [[24, "flat-field-correction"]], "Zinger removal": [[24, "zinger-removal"]], "Ring artifact removal": [[24, "ring-artifact-removal"]], "Center-of-rotation determination": [[24, "center-of-rotation-determination"]], "Denoising or contrast enhancement": [[24, "denoising-or-contrast-enhancement"]], "Image reconstruction": [[24, "image-reconstruction"]], "Other data processing steps": [[24, "other-data-processing-steps"]], "Distortion correction": [[24, "distortion-correction"]], "Sinogram stitching for a half-acquisition scan": [[24, "sinogram-stitching-for-a-half-acquisition-scan"]], "Parallel processing in Python": [[25, "parallel-processing-in-python"]], "Alignment for a parallel-beam tomography system": [[26, "alignment-for-a-parallel-beam-tomography-system"]], "Features": [[27, "features"]], "Capabilities": [[27, "capabilities"]], "Development principles": [[27, "development-principles"]], "Installation": [[28, "installation"]], "Using conda": [[28, "using-conda"]], "Using pip": [[28, "using-pip"]], "From source": [[28, "from-source"]], "Notes": [[28, "notes"]], "Demonstrations": [[29, "demonstrations"], [37, "demonstrations"]], "Setting up a Python workspace": [[30, "setting-up-a-python-workspace"]], "Exploring raw data and making use of the input-output module": [[31, "exploring-raw-data-and-making-use-of-the-input-output-module"]], "Nxs/hdf files": [[31, "nxs-hdf-files"]], "Tiff files": [[31, "tiff-files"]], "Mrc files": [[31, "mrc-files"]], "Other file formats": [[31, "other-file-formats"]], "Methods and tools for removing ring artifacts": [[32, "methods-and-tools-for-removing-ring-artifacts"]], "Improvements": [[32, "improvements"]], "Tools for designing ring removal methods": [[32, "tools-for-designing-ring-removal-methods"]], "Back-and-forth sorting": [[32, "back-and-forth-sorting"]], "Separation of frequency components": [[32, "separation-of-frequency-components"]], "Polynomial fitting along an axis": [[32, "polynomial-fitting-along-an-axis"]], "Wavelet decomposition and reconstruction": [[32, "wavelet-decomposition-and-reconstruction"]], "Stripe interpolation": [[32, "stripe-interpolation"]], "Transformation between Cartesian and polar coordinate system": [[32, "transformation-between-cartesian-and-polar-coordinate-system"]], "Transformation between sinogram space and reconstruction space": [[32, "transformation-between-sinogram-space-and-reconstruction-space"]], "Comparison of ring removal methods on challenging sinograms": [[33, "comparison-of-ring-removal-methods-on-challenging-sinograms"]], "Same sample-type and slice but different in shape": [[33, "same-sample-type-and-slice-but-different-in-shape"]], "Partial ring artifacts": [[33, "partial-ring-artifacts"]], "All types of ring artifacts": [[33, "all-types-of-ring-artifacts"]], "Having valid stripes (not artifacts)": [[33, "having-valid-stripes-not-artifacts"]], "For cone-beam tomography": [[33, "for-cone-beam-tomography"]], "Complete workflow for processing tomographic data": [[34, "complete-workflow-for-processing-tomographic-data"]], "Assessing raw data": [[34, "assessing-raw-data"]], "Reconstructing several slices": [[34, "reconstructing-several-slices"]], "Finding the center of rotation": [[34, "finding-the-center-of-rotation"]], "Tweaking parameters of preprocessing methods": [[34, "tweaking-parameters-of-preprocessing-methods"]], "Choosing a reconstruction method": [[34, "choosing-a-reconstruction-method"]], "Performing full reconstruction": [[34, "performing-full-reconstruction"]], "Automating the workflow": [[34, "automating-the-workflow"]], "Downsampling, rescaling, and reslicing reconstructed volume": [[34, "downsampling-rescaling-and-reslicing-reconstructed-volume"]], "Common mistakes and useful tips": [[34, "common-mistakes-and-useful-tips"]], "Data analysis": [[34, "data-analysis"]], "Technical notes": [[35, "technical-notes"]], "Implementations of X-ray speckle-based phase-contrast tomography": [[36, "implementations-of-x-ray-speckle-based-phase-contrast-tomography"]], "Introduction": [[36, "introduction"], [37, "introduction"]], "Data acquisition": [[36, "data-acquisition"]], "Data processing": [[36, "data-processing"]], "Finding pixel shifts": [[36, "finding-pixel-shifts"]], "Surface reconstruction": [[36, "surface-reconstruction"]], "Extracting transmission and dark-field signals": [[36, "extracting-transmission-and-dark-field-signals"]], "Tomographic reconstruction": [[36, "tomographic-reconstruction"]], "Implementation": [[36, "implementation"], [37, "implementation"]], "Design principles": [[36, "design-principles"]], "Building blocks": [[36, "building-blocks"]], "Demonstration": [[36, "demonstration"]], "Implementations of direct vertical-slice reconstruction for tomography": [[37, "implementations-of-direct-vertical-slice-reconstruction-for-tomography"]], "Requirements": [[37, "requirements"]], "Geometry definition": [[37, "geometry-definition"]], "Back projection, the ramp filter, and reconstruction": [[37, "back-projection-the-ramp-filter-and-reconstruction"]], "Center of rotation determination": [[37, "center-of-rotation-determination"]], "Practical insights": [[37, "practical-insights"]], "Workflows": [[37, "workflows"]], "Update notes": [[38, "update-notes"]]}, "indexentries": 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module algotom.prep.conversion)": [[6, "algotom.prep.conversion.stitch_image"]], "stitch_image_multiple() (in module algotom.prep.conversion)": [[6, "algotom.prep.conversion.stitch_image_multiple"]], "algotom.prep.correction": [[7, "module-algotom.prep.correction"]], "beam_hardening_correction() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.beam_hardening_correction"]], "flat_field_correction() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.flat_field_correction"]], "generate_tilted_profile_chunk() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.generate_tilted_profile_chunk"]], "generate_tilted_profile_line() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.generate_tilted_profile_line"]], "generate_tilted_sinogram() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.generate_tilted_sinogram"]], "generate_tilted_sinogram_chunk() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.generate_tilted_sinogram_chunk"]], "mtf_deconvolution() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.mtf_deconvolution"]], "non_linear_function() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.non_linear_function"]], "unwarp_projection() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.unwarp_projection"]], "unwarp_sinogram() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.unwarp_sinogram"]], "unwarp_sinogram_chunk() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.unwarp_sinogram_chunk"]], "upsample_sinogram() (in module algotom.prep.correction)": [[7, "algotom.prep.correction.upsample_sinogram"]], "algotom.prep.filtering": [[8, "module-algotom.prep.filtering"]], "double_wedge_filter() (in module algotom.prep.filtering)": [[8, "algotom.prep.filtering.double_wedge_filter"]], "fresnel_filter() (in module algotom.prep.filtering)": [[8, "algotom.prep.filtering.fresnel_filter"]], "make_double_wedge_mask() (in module algotom.prep.filtering)": [[8, "algotom.prep.filtering.make_double_wedge_mask"]], "make_fresnel_window() (in module algotom.prep.filtering)": [[8, "algotom.prep.filtering.make_fresnel_window"]], "algotom.prep.phase": [[9, "module-algotom.prep.phase"]], "align_image_stacks() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.align_image_stacks"]], "find_shift_between_image_stacks() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.find_shift_between_image_stacks"]], "find_shift_between_sample_images() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.find_shift_between_sample_images"]], "get_quality_map() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.get_quality_map"]], "get_transmission_dark_field_signal() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.get_transmission_dark_field_signal"]], "get_weight_mask() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.get_weight_mask"]], "reconstruct_surface_from_gradient_fc_method() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.reconstruct_surface_from_gradient_FC_method"]], "reconstruct_surface_from_gradient_scs_method() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.reconstruct_surface_from_gradient_SCS_method"]], "retrieve_phase_based_speckle_tracking() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.retrieve_phase_based_speckle_tracking"]], "unwrap_phase_based_cosine_transform() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.unwrap_phase_based_cosine_transform"]], "unwrap_phase_based_fft() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.unwrap_phase_based_fft"]], "unwrap_phase_iterative_fft() (in module algotom.prep.phase)": [[9, "algotom.prep.phase.unwrap_phase_iterative_fft"]], "algotom.prep.removal": [[10, "module-algotom.prep.removal"]], "check_zinger_size() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.check_zinger_size"]], "generate_blob_mask() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.generate_blob_mask"]], "remove_all_stripe() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_all_stripe"]], "remove_blob() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_blob"]], "remove_blob_1d() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_blob_1d"]], "remove_dead_stripe() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_dead_stripe"]], "remove_large_stripe() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_large_stripe"]], "remove_stripe_based_2d_filtering_sorting() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_2d_filtering_sorting"]], "remove_stripe_based_fft() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_fft"]], "remove_stripe_based_filtering() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_filtering"]], "remove_stripe_based_fitting() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_fitting"]], "remove_stripe_based_interpolation() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_interpolation"]], "remove_stripe_based_normalization() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_normalization"]], "remove_stripe_based_regularization() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_regularization"]], "remove_stripe_based_sorting() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_sorting"]], "remove_stripe_based_wavelet_fft() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_stripe_based_wavelet_fft"]], "remove_zinger() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.remove_zinger"]], "select_zinger() (in module algotom.prep.removal)": [[10, "algotom.prep.removal.select_zinger"]], "algotom.rec.reconstruction": [[11, "module-algotom.rec.reconstruction"]], "apply_circular_ramp_filter() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.apply_circular_ramp_filter"]], "apply_ramp_filter() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.apply_ramp_filter"]], "astra_reconstruction() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.astra_reconstruction"]], "back_projection_cpu() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.back_projection_cpu"]], "back_projection_gpu() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.back_projection_gpu"]], "back_projection_gpu_chunk() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.back_projection_gpu_chunk"]], "bpf_reconstruction() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.bpf_reconstruction"]], "dfi_reconstruction() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.dfi_reconstruction"]], "fbp_reconstruction() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.fbp_reconstruction"]], "find_center_based_slice_metric() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.find_center_based_slice_metric"]], "find_center_visual_slices() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.find_center_visual_slices"]], "generate_mapping_coordinate() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.generate_mapping_coordinate"]], "gridrec_reconstruction() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.gridrec_reconstruction"]], "make_2d_ramp_window() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.make_2d_ramp_window"]], "make_circular_ramp_window() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.make_circular_ramp_window"]], "make_smoothing_window() (in module algotom.rec.reconstruction)": [[11, "algotom.rec.reconstruction.make_smoothing_window"]], "algotom.rec.vertrec": [[12, "module-algotom.rec.vertrec"]], "find_center_vertical_slice() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.find_center_vertical_slice"]], "find_center_visual_vertical_slices() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.find_center_visual_vertical_slices"]], "vertical_back_projection_cpu() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.vertical_back_projection_cpu"]], "vertical_back_projection_cpu_chunk() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.vertical_back_projection_cpu_chunk"]], "vertical_back_projection_gpu() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.vertical_back_projection_gpu"]], "vertical_back_projection_gpu_chunk() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.vertical_back_projection_gpu_chunk"]], "vertical_reconstruction() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.vertical_reconstruction"]], "vertical_reconstruction_different_angles() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.vertical_reconstruction_different_angles"]], "vertical_reconstruction_multiple() (in module algotom.rec.vertrec)": [[12, "algotom.rec.vertrec.vertical_reconstruction_multiple"]], "algotom.util.calibration": [[13, "module-algotom.util.calibration"]], "binarize_image() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.binarize_image"]], "calculate_distance() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.calculate_distance"]], "calculate_threshold() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.calculate_threshold"]], "check_dot_size() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.check_dot_size"]], "find_tilt_roll() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.find_tilt_roll"]], "find_tilt_roll_based_ellipse_fit() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.find_tilt_roll_based_ellipse_fit"]], "find_tilt_roll_based_linear_fit() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.find_tilt_roll_based_linear_fit"]], "fit_points_to_ellipse() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.fit_points_to_ellipse"]], "get_dot_size() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.get_dot_size"]], "invert_dot_contrast() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.invert_dot_contrast"]], "normalize_background() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.normalize_background"]], "normalize_background_based_fft() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.normalize_background_based_fft"]], "select_dot_based_size() (in module algotom.util.calibration)": [[13, "algotom.util.calibration.select_dot_based_size"]], "algotom.util.correlation": [[14, "module-algotom.util.correlation"]], "find_global_shift_based_local_shifts() (in module algotom.util.correlation)": [[14, "algotom.util.correlation.find_global_shift_based_local_shifts"]], "find_local_shifts() (in module algotom.util.correlation)": [[14, "algotom.util.correlation.find_local_shifts"]], "find_local_shifts_umpa() (in module algotom.util.correlation)": [[14, "algotom.util.correlation.find_local_shifts_umpa"]], "find_shift_based_correlation_map() (in module algotom.util.correlation)": [[14, "algotom.util.correlation.find_shift_based_correlation_map"]], "generate_correlation_map() (in module algotom.util.correlation)": [[14, "algotom.util.correlation.generate_correlation_map"]], "locate_peak() (in module algotom.util.correlation)": [[14, "algotom.util.correlation.locate_peak"]], "normalize_image() (in module algotom.util.correlation)": [[14, "algotom.util.correlation.normalize_image"]], "add_background_fluctuation() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.add_background_fluctuation"]], "add_noise() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.add_noise"]], "add_stripe_artifact() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.add_stripe_artifact"]], "algotom.util.simulation": [[15, "module-algotom.util.simulation"]], "convert_to_xray_image() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.convert_to_Xray_image"]], "make_elliptic_mask() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.make_elliptic_mask"]], "make_face_phantom() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.make_face_phantom"]], "make_line_target() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.make_line_target"]], "make_rectangular_mask() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.make_rectangular_mask"]], "make_sinogram() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.make_sinogram"]], "make_triangular_mask() (in module algotom.util.simulation)": [[15, "algotom.util.simulation.make_triangular_mask"]], "algotom.util.utility": [[16, "module-algotom.util.utility"]], "apply_1d_regularizer() (in module algotom.util.utility)": [[16, "algotom.util.utility.apply_1d_regularizer"]], "apply_filter_to_wavelet_component() (in module algotom.util.utility)": [[16, "algotom.util.utility.apply_filter_to_wavelet_component"]], "apply_gaussian_filter() (in module algotom.util.utility)": [[16, "algotom.util.utility.apply_gaussian_filter"]], "apply_method_to_multiple_sinograms() (in module algotom.util.utility)": [[16, "algotom.util.utility.apply_method_to_multiple_sinograms"]], "apply_regularization_filter() (in module algotom.util.utility)": [[16, "algotom.util.utility.apply_regularization_filter"]], "apply_wavelet_decomposition() (in module algotom.util.utility)": [[16, "algotom.util.utility.apply_wavelet_decomposition"]], "apply_wavelet_reconstruction() (in module algotom.util.utility)": [[16, "algotom.util.utility.apply_wavelet_reconstruction"]], "calculate_regularization_coefficient() (in module algotom.util.utility)": [[16, "algotom.util.utility.calculate_regularization_coefficient"]], "check_level() (in module algotom.util.utility)": [[16, "algotom.util.utility.check_level"]], "detect_sample() (in module algotom.util.utility)": [[16, "algotom.util.utility.detect_sample"]], "detect_stripe() (in module algotom.util.utility)": [[16, "algotom.util.utility.detect_stripe"]], "find_center_visual_sinograms() (in module algotom.util.utility)": [[16, "algotom.util.utility.find_center_visual_sinograms"]], "find_center_visual_slices() (in module algotom.util.utility)": [[16, "algotom.util.utility.find_center_visual_slices"]], "fix_non_sample_areas() (in module algotom.util.utility)": [[16, "algotom.util.utility.fix_non_sample_areas"]], "generate_fitted_image() (in module algotom.util.utility)": [[16, "algotom.util.utility.generate_fitted_image"]], "generate_spiral_positions() (in module algotom.util.utility)": [[16, "algotom.util.utility.generate_spiral_positions"]], "interpolate_inside_stripe() (in module algotom.util.utility)": [[16, "algotom.util.utility.interpolate_inside_stripe"]], "locate_slice() (in module algotom.util.utility)": [[16, "algotom.util.utility.locate_slice"]], "locate_slice_chunk() (in module algotom.util.utility)": [[16, "algotom.util.utility.locate_slice_chunk"]], "make_2d_butterworth_window() (in module algotom.util.utility)": [[16, "algotom.util.utility.make_2d_butterworth_window"]], "make_2d_damping_window() (in module algotom.util.utility)": [[16, "algotom.util.utility.make_2d_damping_window"]], "make_2d_gaussian_window() (in module algotom.util.utility)": [[16, "algotom.util.utility.make_2d_gaussian_window"]], "make_circle_mask() (in module algotom.util.utility)": [[16, "algotom.util.utility.make_circle_mask"]], "mapping() (in module algotom.util.utility)": [[16, "algotom.util.utility.mapping"]], "parallel_process_slices() (in module algotom.util.utility)": [[16, "algotom.util.utility.parallel_process_slices"]], "polar_from_rectangular() (in module algotom.util.utility)": [[16, "algotom.util.utility.polar_from_rectangular"]], "rectangular_from_polar() (in module algotom.util.utility)": [[16, "algotom.util.utility.rectangular_from_polar"]], "separate_frequency_component() (in module algotom.util.utility)": [[16, "algotom.util.utility.separate_frequency_component"]], "sort_backward() (in module algotom.util.utility)": [[16, "algotom.util.utility.sort_backward"]], "sort_forward() (in module algotom.util.utility)": [[16, "algotom.util.utility.sort_forward"]], "transform_1d_window_to_2d() (in module algotom.util.utility)": [[16, "algotom.util.utility.transform_1d_window_to_2d"]], "transform_slice_backward() (in module algotom.util.utility)": [[16, "algotom.util.utility.transform_slice_backward"]], "transform_slice_forward() (in module algotom.util.utility)": [[16, "algotom.util.utility.transform_slice_forward"]]}})