Index

_

__augment() (contraction_net.data.DataProcess method) (contraction_net.DataProcess method) __create_loi_data() (sarcasm.Motion method) (sarcasm.motion.Motion method) __curved_line_profile_coordinates() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) __deserialize_field() (sarcasm.IOUtils static method) (sarcasm.ioutils.IOUtils static method) __dir__() (sarcasm.core.SarcAsM method) (sarcasm.SarcAsM method) (sarcasm.training_data_generation.TrainingDataGenerator method) __get_loi_data_file_name() (sarcasm.Motion method) (sarcasm.motion.Motion method) __get_shape_from_file() (sarcasm.meta_data_handler.MetaDataHandler static method) __get_structure_data_file() (sarcasm.Structure method) (sarcasm.structure.Structure method) __getattr__() (sarcasm.core.SarcAsM method) (sarcasm.SarcAsM method) (sarcasm.training_data_generation.TrainingDataGenerator method) __getitem__() (contraction_net.data.DataProcess method), [1] (contraction_net.DataProcess method), [1] __iterate() (contraction_net.Trainer method) (contraction_net.training.Trainer method) __json_serializable_to_sparse() (sarcasm.IOUtils static method) (sarcasm.ioutils.IOUtils static method) __len__() (contraction_net.data.DataProcess method), [1] (contraction_net.DataProcess method), [1] __load_analysed_data_or_create() (sarcasm.Motion method) (sarcasm.motion.Motion method) __load_and_edit() (contraction_net.data.DataProcess method) (contraction_net.DataProcess method) __read_image() (sarcasm.meta_data_handler.MetaDataHandler static method)

__serialize_field() (sarcasm.IOUtils static method) (sarcasm.ioutils.IOUtils static method) __sparse_to_json_serializable() (sarcasm.IOUtils static method) (sarcasm.ioutils.IOUtils static method) __str__() (sarcasm.core.SarcAsM method) (sarcasm.SarcAsM method) __version__ (in module sarcasm) (in module sarcasm._version) _analyze_domains() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) _analyze_z_bands() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) _cluster_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method) _filter_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method) _fit_straight_line() (sarcasm.Structure method) (sarcasm.structure.Structure method) _grow_line() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) _grow_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method) _hausdorff_distance_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method) _load_structure_data() (sarcasm.Structure method) (sarcasm.structure.Structure method) _longest_in_cluster() (sarcasm.Structure method) (sarcasm.structure.Structure method) _random_from_cluster() (sarcasm.Structure method) (sarcasm.structure.Structure method) _random_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method)

A

alpha (contraction_net.losses.SmoothnessLoss attribute) analysis_dir (sarcasm.core.SarcAsM attribute), [1] (sarcasm.SarcAsM attribute), [1] analyze_cell_mask() (sarcasm.Structure method) (sarcasm.structure.Structure method) analyze_correlations() (sarcasm.Motion method) (sarcasm.motion.Motion method) analyze_myofibrils() (sarcasm.Structure method) (sarcasm.structure.Structure method) analyze_orientations() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) analyze_oscillations() (sarcasm.Motion method) (sarcasm.motion.Motion method) analyze_popping() (sarcasm.Motion method) (sarcasm.motion.Motion method) analyze_sarcomere_domains() (sarcasm.Structure method) (sarcasm.structure.Structure method)

analyze_sarcomere_vectors() (sarcasm.Structure method) (sarcasm.structure.Structure method) analyze_trajectories() (sarcasm.Motion method) (sarcasm.motion.Motion method) analyze_z_bands() (sarcasm.Structure method) (sarcasm.structure.Structure method) argmax_wavelets() (sarcasm.training_data_generation.TrainingDataGenerator static method) attention (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) aug_factor (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) aug_p (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) auto_save (sarcasm.core.SarcAsM attribute) (sarcasm.Motion attribute) (sarcasm.motion.Motion attribute) (sarcasm.SarcAsM attribute)

B

base_dir (sarcasm.core.SarcAsM attribute), [1] (sarcasm.SarcAsM attribute), [1] basename (sarcasm.training_data_generation.TrainingDataGenerator attribute) batch_size (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) bce_loss (contraction_net.losses.BCEDiceLoss attribute) BCEDiceLoss (class in contraction_net.losses) best_loss (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute)

binary_kernel() (sarcasm.training_data_generation.TrainingDataGenerator static method) bn2 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) bn3 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) bn4 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) boxplot_with_points() (sarcasm.plot_utils.PlotUtils method) (sarcasm.PlotUtils method)

C

calculate_surplus_motion_index() (sarcasm.Motion method) (sarcasm.motion.Motion method) cell_mask (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) change_color_spines() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) channel (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) check_meta_data_exists() (sarcasm.meta_data_handler.MetaDataHandler static method) cluster_sarcomeres() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) column_weighted_quantiles() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) commit() (sarcasm.meta_data_handler.MetaDataHandler method) (sarcasm.Motion method) (sarcasm.motion.Motion method) (sarcasm.Structure method) (sarcasm.structure.Structure method) conditions (sarcasm.export.MultiLOIAnalysis attribute), [1] (sarcasm.export.MultiStructureAnalysis attribute), [1] (sarcasm.MultiLOIAnalysis attribute), [1] (sarcasm.MultiStructureAnalysis attribute), [1] contraction_net module contraction_net.annotation module contraction_net.contraction_net module contraction_net.data module contraction_net.losses module contraction_net.prediction module

contraction_net.training module contraction_net.utils module ContractionNet (class in contraction_net) (class in contraction_net.contraction_net) conv1 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) conv2 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) conv3 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) conv4 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) conv_out (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) convert_lists_to_arrays_in_dict() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) convolve_image_with_bank() (sarcasm.training_data_generation.TrainingDataGenerator static method) correct_phase_confocal() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) create_distance_map() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) create_loi_data() (sarcasm.Structure method) (sarcasm.structure.Structure method) create_meta_data() (sarcasm.meta_data_handler.MetaDataHandler method) create_myofibril_length_map() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) create_orientation_map() (sarcasm.training_data_generation.TrainingDataGenerator method) create_sarcomere_mask() (sarcasm.training_data_generation.TrainingDataGenerator method) create_wavelet_bank() (sarcasm.training_data_generation.TrainingDataGenerator static method) current_file_index (contraction_net.annotation.TimeSeriesAnnotator attribute) custom_diff() (sarcasm.Utils static method) (sarcasm.utils.Utils static method)

D

data (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) (sarcasm.export.MultiLOIAnalysis attribute), [1] (sarcasm.export.MultiStructureAnalysis attribute), [1] (sarcasm.MultiLOIAnalysis attribute), [1] (sarcasm.MultiStructureAnalysis attribute), [1] (sarcasm.Structure attribute) (sarcasm.structure.Structure attribute) data_dir (sarcasm.core.SarcAsM attribute), [1] (sarcasm.SarcAsM attribute), [1] data_folder (sarcasm.meta_data_handler.MetaDataHandler attribute) DataProcess (class in contraction_net) (class in contraction_net.data) delete_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method) detect_analyze_contractions() (sarcasm.Motion method) (sarcasm.motion.Motion method) detect_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method)

detect_sarcomeres() (sarcasm.Structure method) (sarcasm.structure.Structure method) detect_z_bands_fast_movie() (sarcasm.Structure method) (sarcasm.structure.Structure method) detekt_peaks() (sarcasm.Motion method) (sarcasm.motion.Motion method) device (in module contraction_net.prediction) (in module contraction_net.training) (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) dice_loss() (contraction_net.losses.BCEDiceLoss method), [1] dim (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) distance_transform() (in module contraction_net.utils) dpi (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute) dropout_attention (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) dropout_pre_output (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute)

E

end_contraction (contraction_net.annotation.TimeSeriesAnnotator attribute) experiment (sarcasm.export.MultiStructureAnalysis attribute), [1] (sarcasm.MultiStructureAnalysis attribute), [1] Export (class in sarcasm.export) export_data() (sarcasm.export.MultiLOIAnalysis method) (sarcasm.export.MultiStructureAnalysis method) (sarcasm.MultiLOIAnalysis method) (sarcasm.MultiStructureAnalysis method)

export_motion_data() (sarcasm.export.Export static method) export_structure_data() (sarcasm.export.Export static method) extract_meta_data() (sarcasm.meta_data_handler.MetaDataHandler static method)

F

f1_score() (in module contraction_net.losses) fast_profile_lines() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) file_cell_mask (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) file_list (contraction_net.annotation.TimeSeriesAnnotator attribute) file_mbands (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) file_orientation (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) file_sarcomere_mask (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) file_zbands (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) file_zbands_fast_movie (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) filepath (sarcasm.core.SarcAsM attribute), [1] (sarcasm.SarcAsM attribute), [1]

files (sarcasm.export.MultiStructureAnalysis attribute), [1] (sarcasm.MultiStructureAnalysis attribute), [1] find_closest() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) find_txt_files() (in module contraction_net.utils) folder (sarcasm.export.MultiLOIAnalysis attribute), [1] (sarcasm.export.MultiStructureAnalysis attribute), [1] (sarcasm.MultiLOIAnalysis attribute), [1] (sarcasm.MultiStructureAnalysis attribute), [1] fontsize (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute) forward() (contraction_net.contraction_net.ContractionNet method), [1] (contraction_net.ContractionNet method), [1] (contraction_net.losses.BCEDiceLoss method), [1] (contraction_net.losses.SmoothnessLoss method), [1] full_analysis_loi() (sarcasm.Motion method) (sarcasm.motion.Motion method) full_analysis_structure() (sarcasm.Structure method) (sarcasm.structure.Structure method)

G

gaussian_kernel() (sarcasm.training_data_generation.TrainingDataGenerator static method) get_data() (sarcasm.export.MultiLOIAnalysis method) (sarcasm.export.MultiStructureAnalysis method) (sarcasm.MultiLOIAnalysis method) (sarcasm.MultiStructureAnalysis method) get_device() (in module contraction_net.utils) (sarcasm.Utils static method) (sarcasm.utils.Utils static method) get_list_lois() (sarcasm.Structure method) (sarcasm.structure.Structure method) get_loi_name_from_file_name() (sarcasm.Motion static method) (sarcasm.motion.Motion static method) get_lois_of_file() (sarcasm.Utils static method) (sarcasm.utils.Utils static method)

get_meta_data_file() (sarcasm.meta_data_handler.MetaDataHandler method) get_motion_dict() (sarcasm.export.Export static method) get_orientation_angle_map() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) get_pixel_size() (sarcasm.training_data_generation.TrainingDataGenerator static method) get_sarcomere_vectors() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) get_sarcomere_vectors_wavelet() (sarcasm.training_data_generation.TrainingDataGenerator static method) get_structure_dict() (sarcasm.export.Export static method) get_tif_files_in_folder() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) get_trajectories() (sarcasm.Motion method) (sarcasm.motion.Motion method)

H

half_gaussian_kernel() (sarcasm.training_data_generation.TrainingDataGenerator static method)

I

image (sarcasm.training_data_generation.TrainingDataGenerator attribute) image_path (sarcasm.training_data_generation.TrainingDataGenerator attribute) in1 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) in_channels (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) info (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute)

input_len (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) interpolate_distance_map() (sarcasm.training_data_generation.TrainingDataGenerator static method) (sarcasm.Utils static method) (sarcasm.utils.Utils static method) IOUtils (class in sarcasm) (class in sarcasm.ioutils) is_real (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute)

J

jitter() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) json_deserialize() (sarcasm.IOUtils static method) (sarcasm.ioutils.IOUtils static method)

json_serialize() (sarcasm.IOUtils static method) (sarcasm.ioutils.IOUtils static method)

K

kymograph_movie() (sarcasm.Structure static method) (sarcasm.structure.Structure static method)

L

label_all_panels() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) label_panel() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) labelpad (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute) line_growth() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) load_data() (sarcasm.export.MultiLOIAnalysis method) (sarcasm.export.MultiStructureAnalysis method) (sarcasm.MultiLOIAnalysis method) (sarcasm.MultiStructureAnalysis method) load_loi_data() (sarcasm.Motion method) (sarcasm.motion.Motion method) load_meta_data() (sarcasm.meta_data_handler.MetaDataHandler method) load_next_file() (contraction_net.annotation.TimeSeriesAnnotator method), [1]

loi_data (sarcasm.Motion attribute) (sarcasm.motion.Motion attribute) loi_file (sarcasm.Motion attribute) (sarcasm.motion.Motion attribute) loi_folder (sarcasm.Motion attribute) (sarcasm.motion.Motion attribute) loi_name (sarcasm.Motion attribute) (sarcasm.motion.Motion attribute) lois (sarcasm.export.MultiLOIAnalysis attribute), [1] (sarcasm.MultiLOIAnalysis attribute), [1] loss_function (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) loss_params (contraction_net.losses.BCEDiceLoss attribute) (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) lr (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute)

M

map_array() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) markersize (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute) max_orientation_change() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) mbands (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) median_filter_numba() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) meta_data_handler (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) meta_keys_default (sarcasm.export.Export attribute), [1] metadata (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) MetaDataError MetaDataHandler (class in sarcasm.meta_data_handler) mode (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) model (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) model_dir (sarcasm.core.SarcAsM property) (sarcasm.SarcAsM property) module contraction_net contraction_net.annotation contraction_net.contraction_net contraction_net.data contraction_net.losses contraction_net.prediction contraction_net.training contraction_net.utils sarcasm sarcasm._version sarcasm.core sarcasm.exceptions sarcasm.export sarcasm.feature_dict sarcasm.ioutils sarcasm.meta_data_handler sarcasm.motion sarcasm.plot_utils sarcasm.plots sarcasm.structure sarcasm.training_data_generation sarcasm.utils

most_freq_val() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) Motion (class in sarcasm) (class in sarcasm.motion) motion_feature_dict (in module sarcasm.feature_dict) motion_keys_default (sarcasm.export.Export attribute), [1] MultiLOIAnalysis (class in sarcasm) (class in sarcasm.export) MultiStructureAnalysis (class in sarcasm) (class in sarcasm.export)

N

n_filter (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) nan_low_pass() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) nan_sav_golay() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) nanmedian_filter_numba() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) network (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute)

noise_amp (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) norm1 (contraction_net.contraction_net.ContractionNet attribute) (contraction_net.ContractionNet attribute) normalize (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) num_epochs (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute)

O

open_base_dir() (sarcasm.core.SarcAsM method) (sarcasm.SarcAsM method) open_folder() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) optimizer (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute)

orientation (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) out_channels (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) output_dir (contraction_net.annotation.TimeSeriesAnnotator attribute) output_dirs (sarcasm.training_data_generation.TrainingDataGenerator attribute)

P

peak_by_first_moment() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) peakdetekt() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) plot_box() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) plot_cell_mask() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_delta_slen() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_func_to_img() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) plot_histogram_structure() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_image() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_loi_detection() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_loi_summary_motion() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_lois() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_myofibril_length_map() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_myofibril_lines() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_overlay_delta_slen() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_overlay_velocity() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_phase_space() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_popping_events() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_results() (sarcasm.training_data_generation.TrainingDataGenerator method) plot_sarcomere_domains() (sarcasm.Plots static method) (sarcasm.plots.Plots static method)

plot_sarcomere_mask() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_sarcomere_orientation_field() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_sarcomere_vectors() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_selection_training_data() (in module contraction_net.utils) plot_stack_overlay() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_z_bands() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_z_bands_midlines() (sarcasm.Plots method) (sarcasm.plots.Plots method) plot_z_lateral_connections() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_z_pos() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) plot_z_segmentation() (sarcasm.Plots static method) (sarcasm.plots.Plots static method) Plots (class in sarcasm) (class in sarcasm.plots) PlotUtils (class in sarcasm) (class in sarcasm.plot_utils) polish_xticks() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) polish_yticks() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) predict_contractions() (in module contraction_net) (in module contraction_net.prediction) (sarcasm.Motion static method) (sarcasm.motion.Motion static method) predict_zbands() (sarcasm.training_data_generation.TrainingDataGenerator method) press_callback() (contraction_net.annotation.TimeSeriesAnnotator method), [1] process_contractions() (in module contraction_net.utils) process_frame() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) process_profile() (sarcasm.Utils static method) (sarcasm.utils.Utils static method)

R

random_drift (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) random_offset (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) random_outlier (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) random_subsampling (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) random_swap (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) read_imgs() (sarcasm.core.SarcAsM method) (sarcasm.SarcAsM method) read_profile_data() (sarcasm.Motion method) (sarcasm.motion.Motion method)

release_callback() (contraction_net.annotation.TimeSeriesAnnotator method), [1] remove_all_spines() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) remove_arrays_dataframe() (sarcasm.export.Export static method) remove_intermediate_tiffs() (sarcasm.core.SarcAsM method) (sarcasm.SarcAsM method) remove_spines() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) remove_ticks() (sarcasm.plot_utils.PlotUtils static method) (sarcasm.PlotUtils static method) reset_annotations() (contraction_net.annotation.TimeSeriesAnnotator method), [1] reset_button (contraction_net.annotation.TimeSeriesAnnotator attribute) restart (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) round_up_to_odd() (sarcasm.training_data_generation.TrainingDataGenerator static method)

S

sarc_obj (sarcasm.meta_data_handler.MetaDataHandler attribute) sarcasm module SarcAsM (class in sarcasm) (class in sarcasm.core) sarcasm._version module sarcasm.core module sarcasm.exceptions module sarcasm.export module sarcasm.feature_dict module sarcasm.ioutils module sarcasm.meta_data_handler module sarcasm.motion module sarcasm.plot_utils module sarcasm.plots module sarcasm.structure module sarcasm.training_data_generation module sarcasm.utils module sarcomere_mask (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute) sarcomere_mask() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) save_and_load_next() (contraction_net.annotation.TimeSeriesAnnotator method), [1] save_button (contraction_net.annotation.TimeSeriesAnnotator attribute) save_data() (sarcasm.export.MultiLOIAnalysis method) (sarcasm.export.MultiStructureAnalysis method) (sarcasm.MultiLOIAnalysis method) (sarcasm.MultiStructureAnalysis method)

save_dir (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) save_format (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute) save_iter (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) save_name (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) scheduler (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) segment_z_bands() (sarcasm.Structure static method) (sarcasm.structure.Structure static method) shape (sarcasm.training_data_generation.TrainingDataGenerator attribute) shuffle_labels() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) simulate_training_data() (in module contraction_net.utils) smooth_loss (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) smooth_orientation_map() (sarcasm.training_data_generation.TrainingDataGenerator method) SmoothnessLoss (class in contraction_net.losses) source_dir (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute) split_trace() (in module contraction_net.annotation) start() (contraction_net.Trainer method) (contraction_net.training.Trainer method) start_contraction (contraction_net.annotation.TimeSeriesAnnotator attribute) store_loi_data() (sarcasm.Motion method) (sarcasm.motion.Motion method) store_meta_data() (sarcasm.meta_data_handler.MetaDataHandler method) store_structure_data() (sarcasm.Structure method) (sarcasm.structure.Structure method) Structure (class in sarcasm) (class in sarcasm.structure) structure_feature_dict (in module sarcasm.feature_dict) structure_keys_default (sarcasm.export.Export attribute), [1]

T

test_file (in module sarcasm.structure) TimeSeriesAnnotator (class in contraction_net.annotation) today_date() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) track_z_bands() (sarcasm.Motion method) (sarcasm.motion.Motion method)

train_loader (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute) Trainer (class in contraction_net) (class in contraction_net.training) TrainingDataGenerator (class in sarcasm.training_data_generation) two_sample_t_test() (sarcasm.Utils static method) (sarcasm.utils.Utils static method)

U

use_gui (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute)

Utils (class in sarcasm) (class in sarcasm.utils)

V

val_loader (contraction_net.Trainer attribute) (contraction_net.training.Trainer attribute)

val_split (contraction_net.data.DataProcess attribute) (contraction_net.DataProcess attribute)

W

wavelet_analysis() (sarcasm.training_data_generation.TrainingDataGenerator method) wavelet_analysis_oscillations() (sarcasm.Motion static method) (sarcasm.motion.Motion static method) wavelet_dict (sarcasm.training_data_generation.TrainingDataGenerator attribute) weighted_avg_and_std() (sarcasm.Utils static method) (sarcasm.utils.Utils static method) weighted_quantile() (sarcasm.Utils static method) (sarcasm.utils.Utils static method)

width_1cols (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute) width_1p5cols (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute) width_2cols (sarcasm.plot_utils.PlotUtils attribute) (sarcasm.PlotUtils attribute)

Z

zbands (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute)

zbands_fast_movie (sarcasm.core.SarcAsM attribute) (sarcasm.SarcAsM attribute)