| subcell_pipeline/__init__.py |
(no function) |
0 |
0 |
0 |
100% |
| subcell_pipeline/analysis/__init__.py |
(no function) |
0 |
0 |
0 |
100% |
| subcell_pipeline/analysis/compression_metrics/compression_analysis.py |
get_compression_metric_data |
18 |
18 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_analysis.py |
calculate_compression_metrics |
9 |
9 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_analysis.py |
save_compression_metrics |
1 |
1 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_analysis.py |
plot_metrics_vs_time |
28 |
28 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_analysis.py |
plot_metric_distribution |
19 |
19 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_analysis.py |
(no function) |
15 |
15 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_metric.py |
CompressionMetric.label |
2 |
2 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_metric.py |
CompressionMetric.description |
2 |
2 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_metric.py |
CompressionMetric.bounds |
2 |
2 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_metric.py |
CompressionMetric.calculate_metric |
2 |
2 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/compression_metric.py |
(no function) |
19 |
19 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/constants.py |
(no function) |
8 |
0 |
0 |
100% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_end_to_end_axis_distances_and_projections |
8 |
8 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_average_distance_from_end_to_end_axis |
3 |
3 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_asymmetry_of_peak |
6 |
6 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_pca_polymer_trace_projection |
2 |
2 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_contour_length_from_trace |
1 |
0 |
0 |
100% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_bending_energy_from_trace |
13 |
13 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_2d_polymer_trace |
3 |
3 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_normalized_tangent_vectors |
6 |
6 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_twist_angle |
7 |
7 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_chirality |
10 |
10 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_total_fiber_twist |
16 |
16 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_total_fiber_twist_project |
9 |
9 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_total_fiber_twist_pca |
3 |
3 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_angle_between_vectors |
11 |
11 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_total_fiber_twist_2d |
16 |
16 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
fit_pca_to_polymer_trace |
3 |
3 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_third_component_variance |
2 |
2 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_sum_bending_energy |
1 |
1 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
get_compression_ratio |
2 |
2 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/polymer_trace.py |
(no function) |
24 |
0 |
0 |
100% |
| subcell_pipeline/analysis/compression_metrics/vectors.py |
get_unit_vector |
4 |
4 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/vectors.py |
get_end_to_end_unit_vector |
4 |
4 |
0 |
0% |
| subcell_pipeline/analysis/compression_metrics/vectors.py |
(no function) |
4 |
0 |
0 |
100% |
| subcell_pipeline/analysis/dimensionality_reduction/fiber_data.py |
get_merged_data |
20 |
20 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/fiber_data.py |
align_fibers |
11 |
11 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/fiber_data.py |
align_fiber |
7 |
7 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/fiber_data.py |
reshape_fibers |
7 |
7 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/fiber_data.py |
save_aligned_fibers |
7 |
7 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/fiber_data.py |
plot_fibers_by_key_and_seed |
18 |
18 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/fiber_data.py |
(no function) |
15 |
0 |
0 |
100% |
| subcell_pipeline/analysis/dimensionality_reduction/pacmap_dim_reduction.py |
run_pacmap |
6 |
6 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pacmap_dim_reduction.py |
plot_pacmap_feature_scatter |
14 |
14 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pacmap_dim_reduction.py |
(no function) |
8 |
8 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pca_dim_reduction.py |
run_pca |
6 |
6 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pca_dim_reduction.py |
save_pca_results |
3 |
3 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pca_dim_reduction.py |
save_pca_trajectories |
5 |
5 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pca_dim_reduction.py |
save_pca_transforms |
9 |
9 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pca_dim_reduction.py |
plot_pca_feature_scatter |
14 |
14 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pca_dim_reduction.py |
plot_pca_inverse_transform |
28 |
28 |
0 |
0% |
| subcell_pipeline/analysis/dimensionality_reduction/pca_dim_reduction.py |
(no function) |
16 |
16 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
test_consecutive_segment_angles |
4 |
4 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
read_tomography_data |
7 |
7 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
rescale_tomography_data |
3 |
3 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
get_branched_tomography_data |
1 |
1 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
get_unbranched_tomography_data |
1 |
1 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
get_tomography_data |
17 |
17 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
sample_tomography_data |
19 |
19 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
plot_tomography_data_by_dataset |
16 |
16 |
0 |
0% |
| subcell_pipeline/analysis/tomography_data/tomography_data.py |
(no function) |
18 |
18 |
0 |
0% |
| subcell_pipeline/analysis/wall_clock_time/log_data.py |
get_wall_clock_time_from_logs |
11 |
11 |
0 |
0% |
| subcell_pipeline/analysis/wall_clock_time/log_data.py |
(no function) |
4 |
4 |
0 |
0% |
| subcell_pipeline/simulation/__init__.py |
(no function) |
0 |
0 |
0 |
100% |
| subcell_pipeline/simulation/batch_simulations.py |
generate_configs_from_file |
7 |
7 |
0 |
0% |
| subcell_pipeline/simulation/batch_simulations.py |
generate_configs_from_template |
14 |
14 |
0 |
0% |
| subcell_pipeline/simulation/batch_simulations.py |
register_and_run_simulations |
13 |
13 |
0 |
0% |
| subcell_pipeline/simulation/batch_simulations.py |
check_and_save_job_logs |
11 |
11 |
0 |
0% |
| subcell_pipeline/simulation/batch_simulations.py |
copy_simulation_outputs |
11 |
11 |
0 |
0% |
| subcell_pipeline/simulation/batch_simulations.py |
(no function) |
14 |
14 |
0 |
0% |
| subcell_pipeline/simulation/cytosim/post_processing.py |
parse_cytosim_simulation_data |
12 |
12 |
0 |
0% |
| subcell_pipeline/simulation/cytosim/post_processing.py |
parse_cytosim_simulation_curvature_data |
26 |
26 |
0 |
0% |
| subcell_pipeline/simulation/cytosim/post_processing.py |
(no function) |
16 |
16 |
0 |
0% |
| subcell_pipeline/simulation/post_processing.py |
sample_simulation_data |
12 |
12 |
0 |
0% |
| subcell_pipeline/simulation/post_processing.py |
sample_simulation_data_points |
13 |
13 |
0 |
0% |
| subcell_pipeline/simulation/post_processing.py |
(no function) |
9 |
9 |
0 |
0% |
| subcell_pipeline/simulation/readdy/data_structures.py |
TopologyData.__init__ |
3 |
3 |
0 |
0% |
| subcell_pipeline/simulation/readdy/data_structures.py |
TopologyData.__str__ |
1 |
1 |
0 |
0% |
| subcell_pipeline/simulation/readdy/data_structures.py |
ParticleData.__init__ |
4 |
4 |
0 |
0% |
| subcell_pipeline/simulation/readdy/data_structures.py |
ParticleData.__str__ |
1 |
1 |
0 |
0% |
| subcell_pipeline/simulation/readdy/data_structures.py |
FrameData.__init__ |
4 |
4 |
0 |
0% |
| subcell_pipeline/simulation/readdy/data_structures.py |
FrameData.__str__ |
7 |
7 |
0 |
0% |
| subcell_pipeline/simulation/readdy/data_structures.py |
(no function) |
33 |
0 |
0 |
100% |
| subcell_pipeline/simulation/readdy/loader.py |
ReaddyLoader.__init__ |
9 |
9 |
0 |
0% |
| subcell_pipeline/simulation/readdy/loader.py |
ReaddyLoader.readdy_trajectory |
3 |
3 |
0 |
0% |
| subcell_pipeline/simulation/readdy/loader.py |
ReaddyLoader._frame_edges |
8 |
8 |
0 |
0% |
| subcell_pipeline/simulation/readdy/loader.py |
ReaddyLoader._shape_trajectory_data |
22 |
22 |
0 |
0% |
| subcell_pipeline/simulation/readdy/loader.py |
ReaddyLoader.trajectory |
13 |
13 |
0 |
0% |
| subcell_pipeline/simulation/readdy/loader.py |
(no function) |
33 |
33 |
0 |
0% |
| subcell_pipeline/simulation/readdy/parser.py |
_download_s3_file |
10 |
10 |
0 |
0% |
| subcell_pipeline/simulation/readdy/parser.py |
download_readdy_hdf5 |
5 |
5 |
0 |
0% |
| subcell_pipeline/simulation/readdy/parser.py |
parse_readdy_simulation_single_fiber_trajectory |
20 |
20 |
0 |
0% |
| subcell_pipeline/simulation/readdy/parser.py |
_round_2_sig_figs |
1 |
1 |
0 |
0% |
| subcell_pipeline/simulation/readdy/parser.py |
_velocity_for_cond |
1 |
1 |
0 |
0% |
| subcell_pipeline/simulation/readdy/parser.py |
parse_readdy_simulation_data |
15 |
15 |
0 |
0% |
| subcell_pipeline/simulation/readdy/parser.py |
(no function) |
27 |
27 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.__init__ |
3 |
3 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.times |
2 |
2 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor._id_for_neighbor_of_types |
8 |
8 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor._ids_for_chain_of_types |
9 |
9 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor._non_periodic_position |
7 |
7 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor._vector_is_invalid |
1 |
1 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor._normalize |
3 |
1 |
0 |
67% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor._orientation_from_positions |
5 |
5 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor._rotation |
3 |
3 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.rotate_positions |
5 |
5 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.align_trajectory |
9 |
9 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.linear_fiber_chain_ids |
20 |
20 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.linear_fiber_axis_positions |
33 |
33 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.linear_fiber_normals |
14 |
14 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.linear_fiber_control_points |
27 |
0 |
0 |
100% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.fiber_bond_energies |
28 |
28 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
ReaddyPostProcessor.edge_positions |
6 |
6 |
0 |
0% |
| subcell_pipeline/simulation/readdy/post_processor.py |
(no function) |
43 |
0 |
0 |
100% |
| subcell_pipeline/visualization/combined_trajectory.py |
_load_fiber_points_from_dataframe |
9 |
9 |
0 |
0% |
| subcell_pipeline/visualization/combined_trajectory.py |
_get_combined_trajectory_converter |
5 |
5 |
0 |
0% |
| subcell_pipeline/visualization/combined_trajectory.py |
_add_combined_plots |
8 |
8 |
0 |
0% |
| subcell_pipeline/visualization/combined_trajectory.py |
visualize_combined_trajectories |
34 |
34 |
0 |
0% |
| subcell_pipeline/visualization/combined_trajectory.py |
(no function) |
19 |
19 |
0 |
0% |
| subcell_pipeline/visualization/dimensionality_reduction.py |
_rgb_to_hex_color |
2 |
2 |
0 |
0% |
| subcell_pipeline/visualization/dimensionality_reduction.py |
_pca_fiber_points_over_time |
15 |
15 |
0 |
0% |
| subcell_pipeline/visualization/dimensionality_reduction.py |
_pca_fiber_points_one_timestep |
19 |
19 |
0 |
0% |
| subcell_pipeline/visualization/dimensionality_reduction.py |
_generate_simularium_and_save |
12 |
12 |
0 |
0% |
| subcell_pipeline/visualization/dimensionality_reduction.py |
visualize_dimensionality_reduction |
30 |
30 |
0 |
0% |
| subcell_pipeline/visualization/dimensionality_reduction.py |
(no function) |
18 |
18 |
0 |
0% |
| subcell_pipeline/visualization/display_data.py |
get_readdy_display_data |
7 |
7 |
0 |
0% |
| subcell_pipeline/visualization/display_data.py |
(no function) |
2 |
2 |
0 |
0% |
| subcell_pipeline/visualization/fiber_points.py |
generate_trajectory_converter_for_fiber_points |
10 |
10 |
0 |
0% |
| subcell_pipeline/visualization/fiber_points.py |
(no function) |
3 |
3 |
0 |
0% |
| subcell_pipeline/visualization/histogram_plots.py |
make_empty_histogram_plots |
4 |
4 |
0 |
0% |
| subcell_pipeline/visualization/histogram_plots.py |
(no function) |
3 |
3 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
_add_individual_plots |
4 |
4 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
_add_readdy_spatial_annotations |
13 |
13 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
_get_readdy_simularium_converter |
2 |
2 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
visualize_individual_readdy_trajectory |
15 |
15 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
visualize_individual_readdy_trajectories |
19 |
19 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
_find_time_units |
3 |
3 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
_filter_time |
5 |
5 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
_align_cytosim_fiber |
8 |
8 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
_get_cytosim_simularium_converter |
11 |
11 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
visualize_individual_cytosim_trajectory |
9 |
9 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
visualize_individual_cytosim_trajectories |
18 |
18 |
0 |
0% |
| subcell_pipeline/visualization/individual_trajectory.py |
(no function) |
38 |
38 |
0 |
0% |
| subcell_pipeline/visualization/scatter_plots.py |
make_empty_scatter_plots |
13 |
13 |
0 |
0% |
| subcell_pipeline/visualization/scatter_plots.py |
(no function) |
5 |
5 |
0 |
0% |
| subcell_pipeline/visualization/spatial_annotator.py |
_added_dimensions_for_fibers |
13 |
13 |
0 |
0% |
| subcell_pipeline/visualization/spatial_annotator.py |
add_fiber_annotation_agents |
19 |
19 |
0 |
0% |
| subcell_pipeline/visualization/spatial_annotator.py |
_added_dimensions_for_spheres |
7 |
7 |
0 |
0% |
| subcell_pipeline/visualization/spatial_annotator.py |
add_sphere_annotation_agents |
22 |
22 |
0 |
0% |
| subcell_pipeline/visualization/spatial_annotator.py |
(no function) |
7 |
7 |
0 |
0% |
| subcell_pipeline/visualization/tomography.py |
_add_tomography_plots |
7 |
7 |
0 |
0% |
| subcell_pipeline/visualization/tomography.py |
_get_tomography_spatial_center_and_size |
8 |
8 |
0 |
0% |
| subcell_pipeline/visualization/tomography.py |
visualize_tomography |
21 |
21 |
0 |
0% |
| subcell_pipeline/visualization/tomography.py |
(no function) |
17 |
17 |
0 |
0% |