Index

_

__init__() (FrameData method) (ParticleData method) (ReaddyLoader method) (ReaddyPostProcessor method) (TopologyData method)

A

ABSOLUTE_TOLERANCE (in module subcell_pipeline.analysis.compression_metrics.constants) ACTIN_PARTICLE_TYPES (in module subcell_pipeline.simulation.readdy.post_processor) ACTIN_START_PARTICLE_PHRASE (in module subcell_pipeline.simulation.readdy.post_processor) add_fiber_annotation_agents() (in module subcell_pipeline.visualization.spatial_annotator)

add_sphere_annotation_agents() (in module subcell_pipeline.visualization.spatial_annotator) align_fiber() (in module subcell_pipeline.analysis.dimensionality_reduction.fiber_data) align_fibers() (in module subcell_pipeline.analysis.dimensionality_reduction.fiber_data) align_trajectory() (ReaddyPostProcessor method) AVERAGE_PERP_DISTANCE (CompressionMetric attribute)

B

bounds() (CompressionMetric method) BOX_SIZE (in module subcell_pipeline.simulation.readdy.parser) (in module subcell_pipeline.visualization.combined_trajectory) (in module subcell_pipeline.visualization.dimensionality_reduction) (in module subcell_pipeline.visualization.individual_trajectory)

box_size (ReaddyPostProcessor attribute)

C

CALC_BENDING_ENERGY (CompressionMetric attribute) calculate_compression_metrics() (in module subcell_pipeline.analysis.compression_metrics.compression_analysis) calculate_metric() (CompressionMetric method) check_and_save_job_logs() (in module subcell_pipeline.simulation.batch_simulations) COLUMN_DTYPES (in module subcell_pipeline.simulation.cytosim.post_processing) (in module subcell_pipeline.simulation.readdy.parser) COLUMN_NAMES (in module subcell_pipeline.simulation.cytosim.post_processing) (in module subcell_pipeline.simulation.readdy.parser)

COMPRESSION_DISTANCE (in module subcell_pipeline.simulation.readdy.parser) COMPRESSION_RATIO (CompressionMetric attribute) CompressionMetric (class in subcell_pipeline.analysis.compression_metrics.compression_metric) CONTOUR_LENGTH (CompressionMetric attribute) copy_simulation_outputs() (in module subcell_pipeline.simulation.batch_simulations) CYTOSIM_RIGIDITY (in module subcell_pipeline.simulation.cytosim.post_processing) CYTOSIM_SCALE_FACTOR (in module subcell_pipeline.simulation.cytosim.post_processing)

D

DEFAULT_BENDING_CONSTANT (in module subcell_pipeline.analysis.compression_metrics.constants) DEFAULT_COMPRESSION_DISTANCE (in module subcell_pipeline.analysis.compression_metrics.constants)

description() (CompressionMetric method) download_readdy_hdf5() (in module subcell_pipeline.simulation.readdy.parser)

E

edge_ids (FrameData attribute)

edge_positions() (ReaddyPostProcessor method) ENERGY_ASYMMETRY (CompressionMetric attribute)

F

fiber_bond_energies() (ReaddyPostProcessor method)

fit_pca_to_polymer_trace() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) FrameData (class in subcell_pipeline.simulation.readdy.data_structures)

G

generate_configs_from_file() (in module subcell_pipeline.simulation.batch_simulations) generate_configs_from_template() (in module subcell_pipeline.simulation.batch_simulations) generate_trajectory_converter_for_fiber_points() (in module subcell_pipeline.visualization.fiber_points) get_2d_polymer_trace() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_angle_between_vectors() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_asymmetry_of_peak() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_average_distance_from_end_to_end_axis() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_bending_energy_from_trace() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_branched_tomography_data() (in module subcell_pipeline.analysis.tomography_data.tomography_data) get_chirality() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_compression_metric_data() (in module subcell_pipeline.analysis.compression_metrics.compression_analysis) get_compression_ratio() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_contour_length_from_trace() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_end_to_end_axis_distances_and_projections() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_end_to_end_unit_vector() (in module subcell_pipeline.analysis.compression_metrics.vectors)

get_merged_data() (in module subcell_pipeline.analysis.dimensionality_reduction.fiber_data) get_normalized_tangent_vectors() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_pca_polymer_trace_projection() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_readdy_display_data() (in module subcell_pipeline.visualization.display_data) get_sum_bending_energy() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_third_component_variance() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_tomography_data() (in module subcell_pipeline.analysis.tomography_data.tomography_data) get_total_fiber_twist() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_total_fiber_twist_2d() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_total_fiber_twist_pca() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_total_fiber_twist_project() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_twist_angle() (in module subcell_pipeline.analysis.compression_metrics.polymer_trace) get_unbranched_tomography_data() (in module subcell_pipeline.analysis.tomography_data.tomography_data) get_unit_vector() (in module subcell_pipeline.analysis.compression_metrics.vectors) get_wall_clock_time_from_logs() (in module subcell_pipeline.analysis.wall_clock_time.log_data)

H

h5_file_path (ReaddyLoader attribute)

I

IDEAL_ACTIN_POSITIONS (in module subcell_pipeline.simulation.readdy.post_processor)

IDEAL_ACTIN_VECTOR_TO_AXIS (in module subcell_pipeline.simulation.readdy.post_processor)

L

label() (CompressionMetric method) linear_fiber_axis_positions() (ReaddyPostProcessor method)

linear_fiber_chain_ids() (ReaddyPostProcessor method) linear_fiber_control_points() (ReaddyPostProcessor static method) linear_fiber_normals() (ReaddyPostProcessor method)

M

make_empty_histogram_plots() (in module subcell_pipeline.visualization.histogram_plots) make_empty_scatter_plots() (in module subcell_pipeline.visualization.scatter_plots) max_time_ix (ReaddyLoader attribute) min_time_ix (ReaddyLoader attribute) module subcell_pipeline.analysis subcell_pipeline.analysis.compression_metrics subcell_pipeline.analysis.compression_metrics.compression_analysis subcell_pipeline.analysis.compression_metrics.compression_metric subcell_pipeline.analysis.compression_metrics.constants subcell_pipeline.analysis.compression_metrics.polymer_trace subcell_pipeline.analysis.compression_metrics.vectors subcell_pipeline.analysis.dimensionality_reduction subcell_pipeline.analysis.dimensionality_reduction.fiber_data subcell_pipeline.analysis.dimensionality_reduction.pacmap_dim_reduction subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction subcell_pipeline.analysis.tomography_data subcell_pipeline.analysis.tomography_data.tomography_data subcell_pipeline.analysis.wall_clock_time subcell_pipeline.analysis.wall_clock_time.log_data subcell_pipeline.simulation subcell_pipeline.simulation.batch_simulations subcell_pipeline.simulation.cytosim subcell_pipeline.simulation.cytosim.post_processing subcell_pipeline.simulation.post_processing subcell_pipeline.simulation.readdy subcell_pipeline.simulation.readdy.data_structures subcell_pipeline.simulation.readdy.loader subcell_pipeline.simulation.readdy.parser subcell_pipeline.simulation.readdy.post_processor subcell_pipeline.visualization subcell_pipeline.visualization.combined_trajectory subcell_pipeline.visualization.dimensionality_reduction subcell_pipeline.visualization.display_data subcell_pipeline.visualization.fiber_points subcell_pipeline.visualization.histogram_plots subcell_pipeline.visualization.individual_trajectory subcell_pipeline.visualization.scatter_plots subcell_pipeline.visualization.spatial_annotator subcell_pipeline.visualization.tomography

N

neighbor_ids (ParticleData attribute)

NON_COPLANARITY (CompressionMetric attribute)

P

parse_cytosim_simulation_curvature_data() (in module subcell_pipeline.simulation.cytosim.post_processing) parse_cytosim_simulation_data() (in module subcell_pipeline.simulation.cytosim.post_processing) parse_readdy_simulation_data() (in module subcell_pipeline.simulation.readdy.parser) parse_readdy_simulation_single_fiber_trajectory() (in module subcell_pipeline.simulation.readdy.parser) particle_ids (TopologyData attribute) ParticleData (class in subcell_pipeline.simulation.readdy.data_structures) particles (FrameData attribute) PEAK_ASYMMETRY (CompressionMetric attribute) periodic_boundary (ReaddyPostProcessor attribute)

pickle_key (ReaddyLoader attribute) pickle_location (ReaddyLoader attribute) plot_fibers_by_key_and_seed() (in module subcell_pipeline.analysis.dimensionality_reduction.fiber_data) plot_metric_distribution() (in module subcell_pipeline.analysis.compression_metrics.compression_analysis) plot_metrics_vs_time() (in module subcell_pipeline.analysis.compression_metrics.compression_analysis) plot_pacmap_feature_scatter() (in module subcell_pipeline.analysis.dimensionality_reduction.pacmap_dim_reduction) plot_pca_feature_scatter() (in module subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction) plot_pca_inverse_transform() (in module subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction) plot_tomography_data_by_dataset() (in module subcell_pipeline.analysis.tomography_data.tomography_data) position (ParticleData attribute)

R

read_tomography_data() (in module subcell_pipeline.analysis.tomography_data.tomography_data) READDY_SAVED_FRAMES (in module subcell_pipeline.visualization.individual_trajectory) READDY_TIMESTEP (in module subcell_pipeline.simulation.readdy.parser) readdy_trajectory() (ReaddyLoader method) ReaddyLoader (class in subcell_pipeline.simulation.readdy.loader) ReaddyPostProcessor (class in subcell_pipeline.simulation.readdy.post_processor)

register_and_run_simulations() (in module subcell_pipeline.simulation.batch_simulations) rescale_tomography_data() (in module subcell_pipeline.analysis.tomography_data.tomography_data) reshape_fibers() (in module subcell_pipeline.analysis.dimensionality_reduction.fiber_data) rotate_positions() (ReaddyPostProcessor method) run_pacmap() (in module subcell_pipeline.analysis.dimensionality_reduction.pacmap_dim_reduction) run_pca() (in module subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction)

S

SAMPLE_COLUMNS (in module subcell_pipeline.simulation.post_processing) sample_simulation_data() (in module subcell_pipeline.simulation.post_processing) sample_simulation_data_points() (in module subcell_pipeline.simulation.post_processing) sample_tomography_data() (in module subcell_pipeline.analysis.tomography_data.tomography_data) save_aligned_fibers() (in module subcell_pipeline.analysis.dimensionality_reduction.fiber_data) save_compression_metrics() (in module subcell_pipeline.analysis.compression_metrics.compression_analysis) save_pca_results() (in module subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction) save_pca_trajectories() (in module subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction) save_pca_transforms() (in module subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction) SIMULATOR_COLOR_MAP (in module subcell_pipeline.analysis.compression_metrics.constants) subcell_pipeline.analysis module subcell_pipeline.analysis.compression_metrics module subcell_pipeline.analysis.compression_metrics.compression_analysis module subcell_pipeline.analysis.compression_metrics.compression_metric module subcell_pipeline.analysis.compression_metrics.constants module subcell_pipeline.analysis.compression_metrics.polymer_trace module subcell_pipeline.analysis.compression_metrics.vectors module subcell_pipeline.analysis.dimensionality_reduction module subcell_pipeline.analysis.dimensionality_reduction.fiber_data module subcell_pipeline.analysis.dimensionality_reduction.pacmap_dim_reduction module subcell_pipeline.analysis.dimensionality_reduction.pca_dim_reduction module subcell_pipeline.analysis.tomography_data module subcell_pipeline.analysis.tomography_data.tomography_data module subcell_pipeline.analysis.wall_clock_time module subcell_pipeline.analysis.wall_clock_time.log_data module

subcell_pipeline.simulation module subcell_pipeline.simulation.batch_simulations module subcell_pipeline.simulation.cytosim module subcell_pipeline.simulation.cytosim.post_processing module subcell_pipeline.simulation.post_processing module subcell_pipeline.simulation.readdy module subcell_pipeline.simulation.readdy.data_structures module subcell_pipeline.simulation.readdy.loader module subcell_pipeline.simulation.readdy.parser module subcell_pipeline.simulation.readdy.post_processor module subcell_pipeline.visualization module subcell_pipeline.visualization.combined_trajectory module subcell_pipeline.visualization.dimensionality_reduction module subcell_pipeline.visualization.display_data module subcell_pipeline.visualization.fiber_points module subcell_pipeline.visualization.histogram_plots module subcell_pipeline.visualization.individual_trajectory module subcell_pipeline.visualization.scatter_plots module subcell_pipeline.visualization.spatial_annotator module subcell_pipeline.visualization.tomography module SUM_BENDING_ENERGY (CompressionMetric attribute)

T

test_consecutive_segment_angles() (in module subcell_pipeline.analysis.tomography_data.tomography_data) time (FrameData attribute) time_inc (ReaddyLoader attribute) times() (ReaddyPostProcessor method) timestep (ReaddyLoader attribute) TOMOGRAPHY_SAMPLE_COLUMNS (in module subcell_pipeline.analysis.tomography_data.tomography_data) TOMOGRAPHY_VIZ_SCALE (in module subcell_pipeline.visualization.tomography)

topologies (FrameData attribute) TopologyData (class in subcell_pipeline.simulation.readdy.data_structures) TOTAL_FIBER_TWIST (CompressionMetric attribute) trajectory (ReaddyPostProcessor attribute) trajectory() (ReaddyLoader method) TWIST_ANGLE (CompressionMetric attribute) type_name (ParticleData attribute) (TopologyData attribute)

U

uid (ParticleData attribute) (TopologyData attribute)

V

visualize_combined_trajectories() (in module subcell_pipeline.visualization.combined_trajectory) visualize_dimensionality_reduction() (in module subcell_pipeline.visualization.dimensionality_reduction) visualize_individual_cytosim_trajectories() (in module subcell_pipeline.visualization.individual_trajectory)

visualize_individual_cytosim_trajectory() (in module subcell_pipeline.visualization.individual_trajectory) visualize_individual_readdy_trajectories() (in module subcell_pipeline.visualization.individual_trajectory) visualize_individual_readdy_trajectory() (in module subcell_pipeline.visualization.individual_trajectory) visualize_tomography() (in module subcell_pipeline.visualization.tomography)