Index

A

add_edge() (pyfibre.model.core.base_graph.BaseGraph method) add_node() (pyfibre.model.core.base_graph.BaseGraph method) alpha (pyfibre.pyfibre_runner.PyFibreRunner attribute) analyse() (pyfibre.addons.shg_pl_trans.metric_analysers.PLMetricAnalyser method) (pyfibre.addons.shg_pl_trans.metric_analysers.SHGMetricAnalyser method) (pyfibre.model.analysers.metric_analyser.MetricAnalyser method)

analysis_path() (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser property) angle() (pyfibre.model.objects.fibre.Fibre property) angle_analysis() (in module pyfibre.model.tools.analysis) append() (pyfibre.core.base_multi_image.BaseMultiImage method) (pyfibre.core.i_multi_image.IMultiImage method) assign_fibres() (pyfibre.model.tools.fibre_assigner.FibreAssigner method)

B

BaseFileParser (class in pyfibre.core.base_file_parser) BaseGraph (class in pyfibre.model.core.base_graph) BaseGraphSegment (class in pyfibre.model.core.base_graph_segment) BaseKmeansFilter (class in pyfibre.model.tools.base_kmeans_filter) BaseMultiImage (class in pyfibre.core.base_multi_image) BaseMultiImageAnalyser (class in pyfibre.core.base_multi_image_analyser) BaseMultiImageReader (class in pyfibre.core.base_multi_image_reader) BasePyFibreObject (class in pyfibre.model.core.base_pyfibre_object) BasePyFibrePlugin (class in pyfibre.core.base_pyfibre_plugin)

BaseSegment (class in pyfibre.model.core.base_segment) bbox_indices() (in module pyfibre.model.tools.utilities) bbox_sample() (in module pyfibre.model.tools.utilities) binary_classifier_spherical() (in module pyfibre.addons.shg_pl_trans.tools.shg_pl_trans_kmeans_filter) binary_to_regions() (in module pyfibre.model.tools.convertors) binary_to_segments() (in module pyfibre.model.tools.convertors) binary_to_stack() (in module pyfibre.model.tools.convertors) branch_angles() (in module pyfibre.model.tools.fibre_utilities) build_network() (in module pyfibre.model.tools.network_extraction)

C

calculate_metric() (in module pyfibre.model.tools.feature) can_load() (pyfibre.addons.shg_pl_trans.shg_reader.SHGReader method) (pyfibre.core.base_multi_image_reader.BaseMultiImageReader method) (pyfibre.core.i_multi_image_reader.IMultiImageReader method) CellSegment (class in pyfibre.model.objects.segments) cellular_classifier() (pyfibre.addons.shg_pl_trans.tools.shg_pl_trans_kmeans_filter.SHGPLTransKmeansFilter method) (pyfibre.model.tools.base_kmeans_filter.BaseKmeansFilter method) check_2D_arrays() (in module pyfibre.model.tools.fibre_utilities) check_file_name() (in module pyfibre.io.utilities) check_string() (in module pyfibre.io.utilities) clean_network() (in module pyfibre.model.tools.network_extraction) clear_border() (in module pyfibre.utilities) clip_intensities() (in module pyfibre.model.tools.preprocessing) cos_sin_theta_2D() (in module pyfibre.model.tools.fibre_utilities) create_angle_reference() (in module pyfibre.model.tools.figures) create_fibre_filter() (in module pyfibre.model.tools.segmentation) create_figure() (in module pyfibre.model.tools.figures)

create_figures() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser method) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser method) create_file_name() (in module pyfibre.io.object_io) create_hsb_image() (in module pyfibre.model.tools.figures) create_image_stack() (pyfibre.addons.shg_pl_trans.shg_pl_trans_reader.SHGPLTransReader method) (pyfibre.core.base_multi_image_reader.BaseMultiImageReader method) (pyfibre.core.i_multi_image_reader.IMultiImageReader method) create_metrics() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) (pyfibre.addons.shg_pl_trans.shg_pl_trans_analyser.SHGPLTransAnalyser method) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser method) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser method) create_network() (pyfibre.model.tools.fire_algorithm.FIREAlgorithm method) create_network_image() (in module pyfibre.model.tools.figures) create_region_image() (in module pyfibre.model.tools.figures) create_shg_figures() (in module pyfibre.addons.shg_pl_trans.tools.figures) create_shg_pl_trans_figures() (in module pyfibre.addons.shg_pl_trans.tools.figures) create_tensor_image() (in module pyfibre.model.tools.figures)

D

data_path() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser property) database_names (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser attribute) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser attribute) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser attribute) derivatives() (in module pyfibre.model.tools.filters)

deserialize_networkx_graph() (in module pyfibre.io.utilities) direction() (pyfibre.model.objects.fibre.Fibre property) distance_matrix() (in module pyfibre.model.tools.fibre_utilities) distance_sum() (in module pyfibre.addons.shg_pl_trans.tools.shg_pl_trans_kmeans_filter) draw_network() (in module pyfibre.model.tools.figures)

E

edge_count() (pyfibre.model.tools.fibre_assigner.FibreAssigner property)

euclid_l() (pyfibre.model.objects.fibre.Fibre property) extract_prefix() (in module pyfibre.addons.shg_pl_trans.utils)

F

Fibre (class in pyfibre.model.objects.fibre) fibre_assigner() (pyfibre.model.objects.fibre_network.FibreNetwork property) fibre_cell_region_swap() (in module pyfibre.addons.shg_pl_trans.tools.segmentation) fibre_l() (pyfibre.model.objects.fibre.Fibre property) fibre_metrics() (in module pyfibre.model.tools.metrics) fibre_network_assignment() (in module pyfibre.model.tools.network_extraction) fibre_network_metrics() (in module pyfibre.model.tools.metrics) FibreAssigner (class in pyfibre.model.tools.fibre_assigner) FibreNetwork (class in pyfibre.model.objects.fibre_network) FibreSegment (class in pyfibre.model.objects.segments) fig_path() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser property) FileSet (class in pyfibre.core.base_file_parser) filter_image() (pyfibre.model.tools.base_kmeans_filter.BaseKmeansFilter method) filter_input_files() (in module pyfibre.addons.shg_pl_trans.utils)

fire_parameters (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser attribute) FIREAlgorithm (class in pyfibre.model.tools.fire_algorithm) FixedStackImage (class in pyfibre.model.multi_image.fixed_stack_image) flatten_list() (in module pyfibre.utilities) form_nematic_tensor() (in module pyfibre.model.tools.filters) form_structure_tensor() (in module pyfibre.model.tools.filters) fourier_transform_analysis() (in module pyfibre.model.tools.analysis) from_array() (pyfibre.core.base_multi_image.BaseMultiImage class method) (pyfibre.model.core.base_graph.BaseGraph class method) (pyfibre.model.core.base_pyfibre_object.BasePyFibreObject class method) (pyfibre.model.core.base_segment.BaseSegment class method) from_json() (pyfibre.model.core.base_graph.BaseGraph class method) (pyfibre.model.core.base_pyfibre_object.BasePyFibreObject class method) (pyfibre.model.core.base_segment.BaseSegment class method) (pyfibre.model.objects.fibre_network.FibreNetwork class method)

G

gaussian() (in module pyfibre.model.tools.filters) generate_database() (pyfibre.model.core.base_pyfibre_object.BasePyFibreObject method) (pyfibre.model.core.base_segment.BaseSegment method) (pyfibre.model.objects.fibre.Fibre method) (pyfibre.model.objects.fibre_network.FibreNetwork method) generate_fibres() (pyfibre.model.objects.fibre_network.FibreNetwork method) generate_red_graph() (pyfibre.model.objects.fibre_network.FibreNetwork method) get_accumulation_number() (in module pyfibre.addons.shg_pl_trans.shg_reader) get_analysis_options() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) get_edge_list() (in module pyfibre.model.tools.fibre_utilities) get_file_names() (in module pyfibre.io.utilities) get_file_sets() (pyfibre.addons.shg_pl_trans.shg_pl_trans_parser.SHGPLTransParser method) (pyfibre.core.base_file_parser.BaseFileParser method) (pyfibre.core.i_file_parser.IFileParser method) get_filenames() (pyfibre.addons.shg_pl_trans.shg_pl_trans_reader.SHGPLTransReader method) (pyfibre.addons.shg_pl_trans.shg_reader.SHGReader method) (pyfibre.core.base_multi_image_reader.BaseMultiImageReader method) (pyfibre.core.i_multi_image_reader.IMultiImageReader method) get_files_prefixes() (in module pyfibre.addons.shg_pl_trans.utils) get_fluoview_param() (in module pyfibre.addons.shg_pl_trans.shg_reader) get_image_type() (in module pyfibre.addons.shg_pl_trans.utils) get_imagej_param() (in module pyfibre.addons.shg_pl_trans.shg_reader)

get_multi_image_class() (pyfibre.addons.shg_pl_trans.shg_pl_trans_reader.SHGPLTransReader method) (pyfibre.addons.shg_pl_trans.shg_reader.SHGReader method) (pyfibre.core.base_multi_image_reader.BaseMultiImageReader method) get_multi_image_factories() (pyfibre.core.base_pyfibre_plugin.BasePyFibrePlugin method) get_name() (pyfibre.core.base_pyfibre_plugin.BasePyFibrePlugin method) get_node_coord_array() (in module pyfibre.model.tools.fibre_utilities) get_node_degree_array() (in module pyfibre.model.tools.fibre_utilities) get_supported_file_sets() (pyfibre.addons.shg_pl_trans.shg_reader.SHGReader method) (pyfibre.core.base_multi_image_reader.BaseMultiImageReader method) (pyfibre.core.i_multi_image_reader.IMultiImageReader method) get_tag() (pyfibre.model.core.base_segment.BaseSegment method) (pyfibre.model.objects.segments.CellSegment method) (pyfibre.model.objects.segments.FibreSegment method) get_test_files() (pyfibre.core.base_pyfibre_plugin.BasePyFibrePlugin method) get_tiff_param() (in module pyfibre.addons.shg_pl_trans.shg_reader) get_version() (pyfibre.core.base_pyfibre_plugin.BasePyFibrePlugin method) glcm_difference_props() (in module pyfibre.model.tools.feature) glcm_log_props() (in module pyfibre.model.tools.feature) glcm_product_props() (in module pyfibre.model.tools.feature) glcm_props() (in module pyfibre.model.tools.feature) greycoprops_edit() (in module pyfibre.model.tools.feature) grow_lmp() (pyfibre.model.tools.fire_algorithm.FIREAlgorithm method)

H

hysteresis() (in module pyfibre.model.tools.filters)

I

IFileParser (class in pyfibre.core.i_file_parser) IFileSet (class in pyfibre.core.i_file_parser) image_analysis() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser method) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser method) image_dict (pyfibre.core.base_multi_image.BaseMultiImage attribute) (pyfibre.core.i_multi_image.IMultiImage attribute) (pyfibre.model.multi_image.fixed_stack_image.FixedStackImage attribute)

image_stack (pyfibre.core.base_multi_image.BaseMultiImage attribute) (pyfibre.core.i_multi_image.IMultiImage attribute) IMultiImage (class in pyfibre.core.i_multi_image) IMultiImageAnalyser (class in pyfibre.core.i_multi_image_analyser) IMultiImageReader (class in pyfibre.core.i_multi_image_reader)

L

label_set() (in module pyfibre.utilities) load_cell_segments() (in module pyfibre.addons.shg_pl_trans.shg_analyser) (in module pyfibre.addons.shg_pl_trans.shg_pl_trans_analyser) (in module pyfibre.io.object_io) load_database() (in module pyfibre.io.database_io) load_databases() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser method) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser method) load_fibre_networks() (in module pyfibre.addons.shg_pl_trans.shg_analyser) (in module pyfibre.io.object_io) load_fibre_segments() (in module pyfibre.addons.shg_pl_trans.shg_analyser) (in module pyfibre.addons.shg_pl_trans.shg_pl_trans_analyser) (in module pyfibre.io.object_io) load_fibres() (in module pyfibre.io.object_io)

load_image() (pyfibre.addons.shg_pl_trans.shg_reader.SHGReader method) (pyfibre.core.base_multi_image_reader.BaseMultiImageReader method) (pyfibre.core.i_multi_image_reader.IMultiImageReader method) load_json() (in module pyfibre.io.utilities) load_multi_image() (pyfibre.core.base_multi_image_reader.BaseMultiImageReader method) (pyfibre.core.i_multi_image_reader.IMultiImageReader method) load_network() (in module pyfibre.io.network_io) load_numpy() (in module pyfibre.io.utilities) load_plugins() (in module pyfibre.utilities) load_pyfibre_object() (in module pyfibre.io.object_io) load_pyfibre_objects() (in module pyfibre.io.object_io) load_regions() (in module pyfibre.io.region_io) log_time() (in module pyfibre.utilities) logo() (in module pyfibre.utilities) lookup_page() (in module pyfibre.addons.shg_pl_trans.shg_reader)

M

make_directories() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser method) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser method) matrix_split() (in module pyfibre.utilities) mean_binary() (in module pyfibre.model.tools.utilities) message (pyfibre.utilities.NotSupportedError attribute)

metric_averaging() (in module pyfibre.model.analysers.metric_analyser) MetricAnalyser (class in pyfibre.model.analysers.metric_analyser) multi_image (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser attribute) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser attribute) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser attribute) multi_image_factories (pyfibre.core.base_pyfibre_plugin.BasePyFibrePlugin attribute)

N

n_dim (pyfibre.core.i_multi_image.IMultiImage attribute) name (pyfibre.core.base_multi_image.BaseMultiImage attribute) (pyfibre.core.base_pyfibre_plugin.BasePyFibrePlugin attribute) (pyfibre.core.i_multi_image.IMultiImage attribute) nanmean() (in module pyfibre.utilities) ndim() (pyfibre.core.base_multi_image.BaseMultiImage property) network_analysis() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) network_metrics() (in module pyfibre.model.tools.metrics) networks_to_binary() (in module pyfibre.model.tools.convertors) networks_to_regions() (in module pyfibre.model.tools.convertors) new_branches() (in module pyfibre.model.tools.fibre_utilities)

nl_means() (in module pyfibre.model.tools.preprocessing) node_coord() (pyfibre.model.core.base_graph.BaseGraph property) (pyfibre.model.tools.fibre_assigner.FibreAssigner property) node_list() (pyfibre.model.core.base_graph.BaseGraph property) NoiseError nonzero_mean() (in module pyfibre.addons.shg_pl_trans.tools.shg_pl_trans_kmeans_filter) normalise_stack() (in module pyfibre.model.tools.segmentation) NotSupportedError number_of_edges() (pyfibre.model.core.base_graph.BaseGraph property) number_of_nodes() (pyfibre.model.core.base_graph.BaseGraph property) numpy_remove() (in module pyfibre.utilities) numpy_to_python_recursive() (in module pyfibre.io.utilities)

O

ow_metric (pyfibre.pyfibre_runner.PyFibreRunner attribute)

ow_network (pyfibre.pyfibre_runner.PyFibreRunner attribute) ow_segment (pyfibre.pyfibre_runner.PyFibreRunner attribute)

P

p_denoise (pyfibre.pyfibre_runner.PyFibreRunner attribute) p_intensity (pyfibre.model.multi_image.fixed_stack_image.FixedStackImage attribute) pad() (in module pyfibre.model.tools.base_kmeans_filter) parse_file_path() (in module pyfibre.io.utilities) path (pyfibre.core.base_multi_image.BaseMultiImage attribute) pl_image (pyfibre.addons.shg_pl_trans.shg_pl_trans_image.SHGPLTransImage attribute) PLMetricAnalyser (class in pyfibre.addons.shg_pl_trans.metric_analysers) plugin_id() (in module pyfibre.ids) pop_dunder_recursive() (in module pyfibre.io.utilities) pop_recursive() (in module pyfibre.io.utilities) pop_under_recursive() (in module pyfibre.io.utilities) preprocess_images() (pyfibre.core.base_multi_image.BaseMultiImage method) (pyfibre.core.i_multi_image.IMultiImage method) (pyfibre.model.multi_image.fixed_stack_image.FixedStackImage method) pyfibre (module) pyfibre.addons (module) pyfibre.addons.shg_pl_trans (module) pyfibre.addons.shg_pl_trans.metric_analysers (module) pyfibre.addons.shg_pl_trans.shg_analyser (module) pyfibre.addons.shg_pl_trans.shg_image (module) pyfibre.addons.shg_pl_trans.shg_pl_trans_analyser (module) pyfibre.addons.shg_pl_trans.shg_pl_trans_image (module) pyfibre.addons.shg_pl_trans.shg_pl_trans_parser (module) pyfibre.addons.shg_pl_trans.shg_pl_trans_reader (module) pyfibre.addons.shg_pl_trans.shg_reader (module) pyfibre.addons.shg_pl_trans.tools (module) pyfibre.addons.shg_pl_trans.tools.figures (module) pyfibre.addons.shg_pl_trans.tools.segmentation (module) pyfibre.addons.shg_pl_trans.tools.shg_pl_trans_kmeans_filter (module) pyfibre.addons.shg_pl_trans.utils (module) pyfibre.core (module) pyfibre.core.base_file_parser (module) pyfibre.core.base_multi_image (module) pyfibre.core.base_multi_image_analyser (module) pyfibre.core.base_multi_image_reader (module) pyfibre.core.base_pyfibre_plugin (module) pyfibre.core.i_file_parser (module) pyfibre.core.i_multi_image (module) pyfibre.core.i_multi_image_analyser (module) pyfibre.core.i_multi_image_reader (module)

pyfibre.ids (module) pyfibre.io (module) pyfibre.io.database_io (module) pyfibre.io.network_io (module) pyfibre.io.object_io (module) pyfibre.io.region_io (module) pyfibre.io.utilities (module) pyfibre.model (module) pyfibre.model.analysers (module) pyfibre.model.analysers.metric_analyser (module) pyfibre.model.core (module) pyfibre.model.core.base_graph (module) pyfibre.model.core.base_graph_segment (module) pyfibre.model.core.base_pyfibre_object (module) pyfibre.model.core.base_segment (module) pyfibre.model.multi_image (module) pyfibre.model.multi_image.fixed_stack_image (module) pyfibre.model.objects (module) pyfibre.model.objects.fibre (module) pyfibre.model.objects.fibre_network (module) pyfibre.model.objects.segments (module) pyfibre.model.tools (module) pyfibre.model.tools.analysis (module) pyfibre.model.tools.base_kmeans_filter (module) pyfibre.model.tools.convertors (module) pyfibre.model.tools.feature (module) pyfibre.model.tools.fibre_assigner (module) pyfibre.model.tools.fibre_utilities (module) pyfibre.model.tools.figures (module) pyfibre.model.tools.filters (module) pyfibre.model.tools.fire_algorithm (module) pyfibre.model.tools.metrics (module) pyfibre.model.tools.network_extraction (module) pyfibre.model.tools.preprocessing (module) pyfibre.model.tools.segmentation (module) pyfibre.model.tools.utilities (module) pyfibre.pyfibre_runner (module) pyfibre.utilities (module) pyfibre.version (module) PyFibreRunner (class in pyfibre.pyfibre_runner) python_to_numpy_recursive() (in module pyfibre.io.utilities)

R

reduce_coord() (in module pyfibre.model.tools.fibre_utilities) region() (pyfibre.model.core.base_graph_segment.BaseGraphSegment property) region_check() (in module pyfibre.model.tools.utilities) region_shape_metrics() (in module pyfibre.model.tools.metrics) region_swap() (in module pyfibre.model.tools.utilities) region_texture_metrics() (in module pyfibre.model.tools.metrics) regions_to_binary() (in module pyfibre.model.tools.convertors) regions_to_stack() (in module pyfibre.model.tools.convertors) registry (pyfibre.addons.shg_pl_trans.shg_pl_trans_parser.SHGPLTransFileSet attribute)

remove() (pyfibre.core.base_multi_image.BaseMultiImage method) (pyfibre.core.i_multi_image.IMultiImage method) remove_contraction() (in module pyfibre.io.utilities) remove_dunder() (in module pyfibre.io.utilities) remove_redundant_nodes() (in module pyfibre.model.tools.fibre_utilities) remove_under() (in module pyfibre.io.utilities) replace_ext() (in module pyfibre.io.utilities) rgb_segmentation() (in module pyfibre.model.tools.segmentation) ring() (in module pyfibre.utilities) run() (pyfibre.pyfibre_runner.PyFibreRunner method)

S

save_cell_segments() (in module pyfibre.addons.shg_pl_trans.shg_analyser) (in module pyfibre.io.object_io) save_database() (in module pyfibre.io.database_io) save_databases() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) (pyfibre.core.base_multi_image_analyser.BaseMultiImageAnalyser method) (pyfibre.core.i_multi_image_analyser.IMultiImageAnalyser method) save_fibre_networks() (in module pyfibre.addons.shg_pl_trans.shg_analyser) (in module pyfibre.io.object_io) save_fibre_segments() (in module pyfibre.addons.shg_pl_trans.shg_analyser) (in module pyfibre.io.object_io) save_fibres() (in module pyfibre.io.object_io) save_figures (pyfibre.pyfibre_runner.PyFibreRunner attribute) save_json() (in module pyfibre.io.utilities) save_network() (in module pyfibre.io.network_io) save_numpy() (in module pyfibre.io.utilities) save_pyfibre_object() (in module pyfibre.io.object_io) save_pyfibre_objects() (in module pyfibre.io.object_io) save_regions() (in module pyfibre.io.region_io) scale (pyfibre.pyfibre_runner.PyFibreRunner attribute) segment_metrics() (in module pyfibre.model.tools.metrics) segment_parameters (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser attribute) segmentation_algorithm() (pyfibre.addons.shg_pl_trans.shg_image.SHGImage method) (pyfibre.addons.shg_pl_trans.shg_pl_trans_image.SHGPLTransImage method) segmentation_analysis() (pyfibre.addons.shg_pl_trans.shg_analyser.SHGAnalyser method) segments_to_binary() (in module pyfibre.model.tools.convertors) serialize_networkx_graph() (in module pyfibre.io.utilities)

shape (pyfibre.core.i_multi_image.IMultiImage attribute) shape() (pyfibre.core.base_multi_image.BaseMultiImage property) (pyfibre.model.core.base_graph_segment.BaseGraphSegment property) shg_image (pyfibre.addons.shg_pl_trans.shg_image.SHGImage attribute) shg_pl_trans_segmentation() (in module pyfibre.addons.shg_pl_trans.tools.segmentation) shg_segmentation() (in module pyfibre.addons.shg_pl_trans.tools.segmentation) SHGAnalyser (class in pyfibre.addons.shg_pl_trans.shg_analyser) SHGImage (class in pyfibre.addons.shg_pl_trans.shg_image) SHGMetricAnalyser (class in pyfibre.addons.shg_pl_trans.metric_analysers) SHGPLTransAnalyser (class in pyfibre.addons.shg_pl_trans.shg_pl_trans_analyser) SHGPLTransFileSet (class in pyfibre.addons.shg_pl_trans.shg_pl_trans_parser) SHGPLTransImage (class in pyfibre.addons.shg_pl_trans.shg_pl_trans_image) SHGPLTransKmeansFilter (class in pyfibre.addons.shg_pl_trans.tools.shg_pl_trans_kmeans_filter) SHGPLTransParser (class in pyfibre.addons.shg_pl_trans.shg_pl_trans_parser) SHGPLTransReader (class in pyfibre.addons.shg_pl_trans.shg_pl_trans_reader) SHGReader (class in pyfibre.addons.shg_pl_trans.shg_reader) sigma (pyfibre.pyfibre_runner.PyFibreRunner attribute) simplify_network() (in module pyfibre.model.tools.fibre_utilities) size (pyfibre.core.i_multi_image.IMultiImage attribute) size() (pyfibre.core.base_multi_image.BaseMultiImage property) smooth_binary() (in module pyfibre.model.tools.utilities) sort_by_area() (in module pyfibre.model.tools.convertors) spherical_coords() (in module pyfibre.addons.shg_pl_trans.tools.shg_pl_trans_kmeans_filter) stack_to_binary() (in module pyfibre.model.tools.convertors) stack_to_regions() (in module pyfibre.model.tools.convertors) structure_tensor_metrics() (in module pyfibre.model.tools.metrics)

T

tag() (pyfibre.model.core.base_segment.BaseSegment property) tensor_analysis() (in module pyfibre.model.tools.analysis) theta_thresh() (pyfibre.model.tools.fibre_assigner.FibreAssigner property) (pyfibre.model.tools.fire_algorithm.FIREAlgorithm property) to_array() (pyfibre.core.base_multi_image.BaseMultiImage method) (pyfibre.model.core.base_graph.BaseGraph method) (pyfibre.model.core.base_pyfibre_object.BasePyFibreObject method) (pyfibre.model.core.base_segment.BaseSegment method)

to_json() (pyfibre.model.core.base_graph.BaseGraph method) (pyfibre.model.core.base_graph_segment.BaseGraphSegment method) (pyfibre.model.core.base_pyfibre_object.BasePyFibreObject method) (pyfibre.model.core.base_segment.BaseSegment method) (pyfibre.model.objects.fibre_network.FibreNetwork method) trans_image (pyfibre.addons.shg_pl_trans.shg_pl_trans_image.SHGPLTransImage attribute) transfer_edges() (in module pyfibre.model.tools.fibre_utilities) tubeness() (in module pyfibre.model.tools.filters)

U

unit_vector() (in module pyfibre.utilities)

V

verify_stack() (pyfibre.core.base_multi_image.BaseMultiImage class method) (pyfibre.core.i_multi_image.IMultiImage class method) (pyfibre.model.multi_image.fixed_stack_image.FixedStackImage class method)

version (pyfibre.core.base_pyfibre_plugin.BasePyFibrePlugin attribute)

W

waviness() (pyfibre.model.objects.fibre.Fibre property)

WrongFileSetError WrongFileTypeError