Coverage report: 22%

Files Functions Classes

coverage.py v7.5.0, created at 2024-04-29 16:21 +0000

File function statements missing excluded coverage
src/thunderfish/__init__.py (no function) 3 0 0 100%
src/thunderfish/bestwindow.py clip_amplitudes 19 3 0 84%
src/thunderfish/bestwindow.py plot_clipping 10 10 0 0%
src/thunderfish/bestwindow.py add_clip_config 8 0 0 100%
src/thunderfish/bestwindow.py clip_args 3 0 0 100%
src/thunderfish/bestwindow.py best_window_indices 68 10 0 85%
src/thunderfish/bestwindow.py best_window_times 2 0 0 100%
src/thunderfish/bestwindow.py best_window 2 0 0 100%
src/thunderfish/bestwindow.py plot_best_window 29 1 0 97%
src/thunderfish/bestwindow.py plot_data_window 15 2 0 87%
src/thunderfish/bestwindow.py add_best_window_config 11 0 0 100%
src/thunderfish/bestwindow.py best_window_args 1 0 0 100%
src/thunderfish/bestwindow.py analysis_window 61 10 0 84%
src/thunderfish/bestwindow.py main 30 5 0 83%
src/thunderfish/bestwindow.py (no function) 25 5 0 80%
src/thunderfish/checkpulse.py check_pulse 23 23 0 0%
src/thunderfish/checkpulse.py check_pulse.ratio 5 5 0 0%
src/thunderfish/checkpulse.py add_check_pulse_config 5 5 0 0%
src/thunderfish/checkpulse.py check_pulse_args 2 2 0 0%
src/thunderfish/checkpulse.py (no function) 28 28 0 0%
src/thunderfish/chirp.py true_chirp_power_drop 13 13 0 0%
src/thunderfish/chirp.py true_chirp_power_rise_above 10 10 0 0%
src/thunderfish/chirp.py chirp_detection 29 29 0 0%
src/thunderfish/chirp.py chirp_detection_plot 12 12 0 0%
src/thunderfish/chirp.py chirp_analysis 6 6 0 0%
src/thunderfish/chirp.py (no function) 17 17 0 0%
src/thunderfish/collectfish.py collect_fish 288 288 0 0%
src/thunderfish/collectfish.py collect_fish.file_iter 12 12 0 0%
src/thunderfish/collectfish.py collect_fish.find_recording 6 6 0 0%
src/thunderfish/collectfish.py rangestr 10 10 0 0%
src/thunderfish/collectfish.py main 110 110 0 0%
src/thunderfish/collectfish.py (no function) 22 22 0 0%
src/thunderfish/consistentfishes.py find_consistency 8 8 0 0%
src/thunderfish/consistentfishes.py consistent_fishes 12 12 0 0%
src/thunderfish/consistentfishes.py plot_consistent_fishes 12 12 0 0%
src/thunderfish/consistentfishes.py (no function) 27 27 0 0%
src/thunderfish/efield.py efish_monopoles 24 24 0 0%
src/thunderfish/efield.py object_monopoles 11 11 0 0%
src/thunderfish/efield.py epotential 9 9 0 0%
src/thunderfish/efield.py epotential_meshgrid 3 3 0 0%
src/thunderfish/efield.py efield 13 13 0 0%
src/thunderfish/efield.py efield_meshgrid 7 7 0 0%
src/thunderfish/efield.py projection 4 4 0 0%
src/thunderfish/efield.py fieldline 24 24 0 0%
src/thunderfish/efield.py squareroot_transform 10 10 0 0%
src/thunderfish/efield.py plot_fieldlines 32 32 0 0%
src/thunderfish/efield.py main 28 28 0 0%
src/thunderfish/efield.py (no function) 16 16 0 0%
src/thunderfish/eodanalysis.py eod_waveform 31 11 0 65%
src/thunderfish/eodanalysis.py unfilter 11 11 0 0%
src/thunderfish/eodanalysis.py fourier_series 5 0 0 100%
src/thunderfish/eodanalysis.py analyze_wave 135 36 0 73%
src/thunderfish/eodanalysis.py exp_decay 1 1 0 0%
src/thunderfish/eodanalysis.py analyze_pulse 215 48 0 78%
src/thunderfish/eodanalysis.py adjust_eodf 1 1 0 0%
src/thunderfish/eodanalysis.py load_species_waveforms 43 43 0 0%
src/thunderfish/eodanalysis.py wave_similarity 48 48 0 0%
src/thunderfish/eodanalysis.py pulse_similarity 30 30 0 0%
src/thunderfish/eodanalysis.py clipped_fraction 7 7 0 0%
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src/thunderfish/eodanalysis.py pulse_quality 19 19 0 0%
src/thunderfish/eodanalysis.py plot_eod_recording 23 23 0 0%
src/thunderfish/eodanalysis.py plot_pulse_eods 41 41 0 0%
src/thunderfish/eodanalysis.py plot_eod_snippets 16 16 0 0%
src/thunderfish/eodanalysis.py plot_eod_waveform 83 48 0 42%
src/thunderfish/eodanalysis.py plot_wave_spectrum 24 24 0 0%
src/thunderfish/eodanalysis.py plot_pulse_spectrum 28 2 0 93%
src/thunderfish/eodanalysis.py save_eod_waveform 7 7 0 0%
src/thunderfish/eodanalysis.py load_eod_waveform 4 4 0 0%
src/thunderfish/eodanalysis.py save_wave_eodfs 8 8 0 0%
src/thunderfish/eodanalysis.py load_wave_eodfs 9 9 0 0%
src/thunderfish/eodanalysis.py save_wave_fish 44 44 0 0%
src/thunderfish/eodanalysis.py load_wave_fish 27 27 0 0%
src/thunderfish/eodanalysis.py save_pulse_fish 43 43 0 0%
src/thunderfish/eodanalysis.py load_pulse_fish 24 24 0 0%
src/thunderfish/eodanalysis.py save_wave_spectrum 7 7 0 0%
src/thunderfish/eodanalysis.py load_wave_spectrum 4 4 0 0%
src/thunderfish/eodanalysis.py save_pulse_spectrum 5 5 0 0%
src/thunderfish/eodanalysis.py load_pulse_spectrum 3 3 0 0%
src/thunderfish/eodanalysis.py save_pulse_peaks 7 7 0 0%
src/thunderfish/eodanalysis.py load_pulse_peaks 6 6 0 0%
src/thunderfish/eodanalysis.py save_pulse_times 12 12 0 0%
src/thunderfish/eodanalysis.py load_pulse_times 3 3 0 0%
src/thunderfish/eodanalysis.py parse_filename 26 26 0 0%
src/thunderfish/eodanalysis.py save_analysis 24 24 0 0%
src/thunderfish/eodanalysis.py save_analysis.write_file_zip 11 11 0 0%
src/thunderfish/eodanalysis.py load_analysis 69 69 0 0%
src/thunderfish/eodanalysis.py load_recording 21 21 0 0%
src/thunderfish/eodanalysis.py add_eod_analysis_config 16 16 0 0%
src/thunderfish/eodanalysis.py eod_waveform_args 2 2 0 0%
src/thunderfish/eodanalysis.py analyze_wave_args 2 2 0 0%
src/thunderfish/eodanalysis.py analyze_pulse_args 2 2 0 0%
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src/thunderfish/eodanalysis.py wave_quality_args 2 2 0 0%
src/thunderfish/eodanalysis.py pulse_quality_args 2 2 0 0%
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src/thunderfish/eodanalysis.py (no function) 66 1 0 98%
src/thunderfish/eodexplorer.py EODExplorer.__init__ 54 54 0 0%
src/thunderfish/eodexplorer.py EODExplorer.__init__.get_spectra 4 4 0 0%
src/thunderfish/eodexplorer.py EODExplorer.__init__.get_spectra 3 3 0 0%
src/thunderfish/eodexplorer.py EODExplorer.fix_scatter_plot 40 40 0 0%
src/thunderfish/eodexplorer.py EODExplorer.fix_waveform_plot 55 55 0 0%
src/thunderfish/eodexplorer.py EODExplorer.list_selection 24 24 0 0%
src/thunderfish/eodexplorer.py EODExplorer.analyze_selection 32 32 0 0%
src/thunderfish/eodexplorer.py EODExplorer.select_EOD_properties 94 94 0 0%
src/thunderfish/eodexplorer.py load_waveform 23 23 0 0%
src/thunderfish/eodexplorer.py main 108 108 0 0%
src/thunderfish/eodexplorer.py (no function) 44 44 0 0%
src/thunderfish/fakefish.py abbrv_genus 2 0 0 100%
src/thunderfish/fakefish.py wavefish_spectrum 18 0 0 100%
src/thunderfish/fakefish.py wavefish_eods 11 0 0 100%
src/thunderfish/fakefish.py normalize_wavefish 18 0 0 100%
src/thunderfish/fakefish.py export_wavefish 29 0 0 100%
src/thunderfish/fakefish.py chirps 23 4 0 83%
src/thunderfish/fakefish.py rises 14 0 0 100%
src/thunderfish/fakefish.py pulsefish_peaks 16 0 0 100%
src/thunderfish/fakefish.py pulsefish_eods 22 0 0 100%
src/thunderfish/fakefish.py normalize_pulsefish 12 0 0 100%
src/thunderfish/fakefish.py export_pulsefish 42 0 0 100%
src/thunderfish/fakefish.py generate_waveform 64 1 0 98%
src/thunderfish/fakefish.py demo 62 0 0 100%
src/thunderfish/fakefish.py main 12 1 0 92%
src/thunderfish/fakefish.py (no function) 34 2 0 94%
src/thunderfish/fishfinder.py SignalPlot.__init__ 101 101 0 0%
src/thunderfish/fishfinder.py SignalPlot.__del__ 1 1 0 0%
src/thunderfish/fishfinder.py SignalPlot.remove_peak_annotation 6 6 0 0%
src/thunderfish/fishfinder.py SignalPlot.annotate_peak 11 11 0 0%
src/thunderfish/fishfinder.py SignalPlot.annotate_fish 6 6 0 0%
src/thunderfish/fishfinder.py SignalPlot.update_plots 124 124 0 0%
src/thunderfish/fishfinder.py SignalPlot.keypress 221 221 0 0%
src/thunderfish/fishfinder.py SignalPlot.buttonpress 34 34 0 0%
src/thunderfish/fishfinder.py SignalPlot.onpick 3 3 0 0%
src/thunderfish/fishfinder.py SignalPlot.resize 14 14 0 0%
src/thunderfish/fishfinder.py SignalPlot.plot_waveform 26 26 0 0%
src/thunderfish/fishfinder.py SignalPlot.play_segment 5 5 0 0%
src/thunderfish/fishfinder.py SignalPlot.save_segment 9 9 0 0%
src/thunderfish/fishfinder.py SignalPlot.play_all 1 1 0 0%
src/thunderfish/fishfinder.py SignalPlot.play_tone 1 1 0 0%
src/thunderfish/fishfinder.py short_user_warning 6 6 0 0%
src/thunderfish/fishfinder.py main 28 28 0 0%
src/thunderfish/fishfinder.py (no function) 38 38 0 0%
src/thunderfish/fishshapes.py fish_shape 7 0 0 100%
src/thunderfish/fishshapes.py plot_fish 33 0 0 100%
src/thunderfish/fishshapes.py plot_object 1 0 0 100%
src/thunderfish/fishshapes.py plot_fishfinder 25 0 0 100%
src/thunderfish/fishshapes.py plot_pathes 14 0 0 100%
src/thunderfish/fishshapes.py fish_surface 38 1 0 97%
src/thunderfish/fishshapes.py surface_normals 9 0 0 100%
src/thunderfish/fishshapes.py extract_path 21 3 0 86%
src/thunderfish/fishshapes.py bbox_pathes 14 0 0 100%
src/thunderfish/fishshapes.py translate_pathes 3 0 0 100%
src/thunderfish/fishshapes.py center_pathes 4 0 0 100%
src/thunderfish/fishshapes.py rotate_pathes 6 0 0 100%
src/thunderfish/fishshapes.py flipx_pathes 2 0 0 100%
src/thunderfish/fishshapes.py flipy_pathes 2 0 0 100%
src/thunderfish/fishshapes.py mirror_path 4 0 0 100%
src/thunderfish/fishshapes.py normalize_path 6 0 0 100%
src/thunderfish/fishshapes.py bend_path 12 0 0 100%
src/thunderfish/fishshapes.py export_path 7 0 0 100%
src/thunderfish/fishshapes.py export_fish 10 0 0 100%
src/thunderfish/fishshapes.py export_fish_demo 19 0 0 100%
src/thunderfish/fishshapes.py main 37 0 0 100%
src/thunderfish/fishshapes.py (no function) 43 1 0 98%
src/thunderfish/harmonics.py group_candidate 97 16 0 84%
src/thunderfish/harmonics.py update_group 26 1 0 96%
src/thunderfish/harmonics.py build_harmonic_group 46 1 0 98%
src/thunderfish/harmonics.py retrieve_harmonic_group 14 7 0 50%
src/thunderfish/harmonics.py expand_group 28 4 0 86%
src/thunderfish/harmonics.py extract_fundamentals 83 21 0 75%
src/thunderfish/harmonics.py threshold_estimate 8 0 0 100%
src/thunderfish/harmonics.py harmonic_groups 35 3 0 91%
src/thunderfish/harmonics.py fundamental_freqs 14 1 0 93%
src/thunderfish/harmonics.py fundamental_freqs_and_power 16 1 0 94%
src/thunderfish/harmonics.py add_relative_power 1 0 0 100%
src/thunderfish/harmonics.py add_power_ranks 7 0 0 100%
src/thunderfish/harmonics.py similar_indices 31 8 0 74%
src/thunderfish/harmonics.py unique_mask 27 4 0 85%
src/thunderfish/harmonics.py unique 24 7 0 71%
src/thunderfish/harmonics.py colors_markers 24 0 0 100%
src/thunderfish/harmonics.py plot_harmonic_groups 44 13 0 70%
src/thunderfish/harmonics.py plot_psd_harmonic_groups 13 0 0 100%
src/thunderfish/harmonics.py add_psd_peak_detection_config 7 0 0 100%
src/thunderfish/harmonics.py psd_peak_detection_args 1 0 0 100%
src/thunderfish/harmonics.py add_harmonic_groups_config 14 0 0 100%
src/thunderfish/harmonics.py harmonic_groups_args 1 0 0 100%
src/thunderfish/harmonics.py main 58 5 0 91%
src/thunderfish/harmonics.py (no function) 37 5 0 86%
src/thunderfish/hopkinsloader.py load_hopkins 41 41 0 0%
src/thunderfish/hopkinsloader.py analyse_hopkins 27 27 0 0%
src/thunderfish/hopkinsloader.py (no function) 20 20 0 0%
src/thunderfish/pulseplots.py warn 1 1 0 0%
src/thunderfish/pulseplots.py darker 23 23 0 0%
src/thunderfish/pulseplots.py lighter 23 23 0 0%
src/thunderfish/pulseplots.py xscalebar 53 53 0 0%
src/thunderfish/pulseplots.py yscalebar 53 53 0 0%
src/thunderfish/pulseplots.py arrowed_spines 5 5 0 0%
src/thunderfish/pulseplots.py loghist 1 1 0 0%
src/thunderfish/pulseplots.py plot_all 18 18 0 0%
src/thunderfish/pulseplots.py plot_clustering 118 118 0 0%
src/thunderfish/pulseplots.py plot_bgm 59 59 0 0%
src/thunderfish/pulseplots.py plot_feature_extraction 54 54 0 0%
src/thunderfish/pulseplots.py plot_moving_fish 45 45 0 0%
src/thunderfish/pulseplots.py (no function) 34 34 0 0%
src/thunderfish/pulses.py warn 1 1 0 0%
src/thunderfish/pulses.py jit 2 2 0 0%
src/thunderfish/pulses.py jit.decorator_jit 1 1 0 0%
src/thunderfish/pulses.py unique_counts 10 10 0 0%
src/thunderfish/pulses.py extract_pulsefish 51 51 0 0%
src/thunderfish/pulses.py detect_pulses 56 56 0 0%
src/thunderfish/pulses.py assign_side_peaks 23 23 0 0%
src/thunderfish/pulses.py cluster 133 133 0 0%
src/thunderfish/pulses.py BGM 36 36 0 0%
src/thunderfish/pulses.py merge_gaussians 11 11 0 0%
src/thunderfish/pulses.py extract_snippet_features 6 6 0 0%
src/thunderfish/pulses.py cluster_on_shape 7 7 0 0%
src/thunderfish/pulses.py subtract_slope 8 8 0 0%
src/thunderfish/pulses.py remove_artefacts 17 17 0 0%
src/thunderfish/pulses.py delete_unreliable_fish 14 14 0 0%
src/thunderfish/pulses.py delete_wavefish_and_sidepeaks 34 34 0 0%
src/thunderfish/pulses.py merge_clusters 33 33 0 0%
src/thunderfish/pulses.py extract_means 17 17 0 0%
src/thunderfish/pulses.py find_clipped_clusters 12 12 0 0%
src/thunderfish/pulses.py delete_moving_fish 78 78 0 0%
src/thunderfish/pulses.py remove_sparse_detections 9 9 0 0%
src/thunderfish/pulses.py (no function) 39 39 0 0%
src/thunderfish/pulsetracker.py makeeventlist 38 38 0 0%
src/thunderfish/pulsetracker.py discardnearbyevents 21 21 0 0%
src/thunderfish/pulsetracker.py crosscorrelation 1 1 0 0%
src/thunderfish/pulsetracker.py interpol 3 3 0 0%
src/thunderfish/pulsetracker.py interpolated_array 1 1 0 0%
src/thunderfish/pulsetracker.py cut_snippets 33 33 0 0%
src/thunderfish/pulsetracker.py pc 3 3 0 0%
src/thunderfish/pulsetracker.py chebyshev 7 7 0 0%
src/thunderfish/pulsetracker.py dbscan 8 8 0 0%
src/thunderfish/pulsetracker.py cluster_events 5 5 0 0%
src/thunderfish/pulsetracker.py Peaklist.__init__ 9 9 0 0%
src/thunderfish/pulsetracker.py connect_blocks 9 9 0 0%
src/thunderfish/pulsetracker.py alignclusterlabels 18 18 0 0%
src/thunderfish/pulsetracker.py ampwalkclassify3_refactor 127 127 0 0%
src/thunderfish/pulsetracker.py discard_wave_pulses 21 21 0 0%
src/thunderfish/pulsetracker.py plot_events_on_data 16 16 0 0%
src/thunderfish/pulsetracker.py discard_short_classes 8 8 0 0%
src/thunderfish/pulsetracker.py path_leaf 3 3 0 0%
src/thunderfish/pulsetracker.py save_EOD_events_to_npmmp 7 7 0 0%
src/thunderfish/pulsetracker.py create_threshold_array 5 5 0 0%
src/thunderfish/pulsetracker.py alignlabels 10 10 0 0%
src/thunderfish/pulsetracker.py analyze_pulse_data 136 136 0 0%
src/thunderfish/pulsetracker.py main 2 2 0 0%
src/thunderfish/pulsetracker.py (no function) 46 46 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.__init__ 193 193 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.__del__ 1 1 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.plot_pulses 23 23 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.plot_pulses.plot_pulse_traces 13 13 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.update_plots 18 18 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.on_pick 60 60 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.resize 9 9 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.keypress 144 144 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.play_segment 6 6 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.play_all 1 1 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.save_segment 11 11 0 0%
src/thunderfish/thunderbrowse.py SignalPlot.plot_traces 39 39 0 0%
src/thunderfish/thunderbrowse.py short_user_warning 6 6 0 0%
src/thunderfish/thunderbrowse.py main 25 25 0 0%
src/thunderfish/thunderbrowse.py (no function) 28 28 0 0%
src/thunderfish/thunderfish.py configuration 18 18 0 0%
src/thunderfish/thunderfish.py save_configuration 10 10 0 0%
src/thunderfish/thunderfish.py detect_eods 141 141 0 0%
src/thunderfish/thunderfish.py remove_eod_files 8 8 0 0%
src/thunderfish/thunderfish.py plot_style 4 4 0 0%
src/thunderfish/thunderfish.py axes_style 4 4 0 0%
src/thunderfish/thunderfish.py plot_eods 202 202 0 0%
src/thunderfish/thunderfish.py plot_eods.keypress 9 9 0 0%
src/thunderfish/thunderfish.py plot_eods.recording_format_coord 1 1 0 0%
src/thunderfish/thunderfish.py plot_eods.recordingzoom_format_coord 1 1 0 0%
src/thunderfish/thunderfish.py plot_eods.psd_format_coord 1 1 0 0%
src/thunderfish/thunderfish.py plot_eods.meaneod_format_coord 1 1 0 0%
src/thunderfish/thunderfish.py plot_eods.ampl_format_coord 1 1 0 0%
src/thunderfish/thunderfish.py plot_eods.phase_format_coord 1 1 0 0%
src/thunderfish/thunderfish.py plot_eods.pulsepsd_format_coord 1 1 0 0%
src/thunderfish/thunderfish.py plot_eod_subplots 146 146 0 0%
src/thunderfish/thunderfish.py thunderfish_plot 63 63 0 0%
src/thunderfish/thunderfish.py thunderfish 80 80 0 0%
src/thunderfish/thunderfish.py run_thunderfish 17 17 0 0%
src/thunderfish/thunderfish.py main 133 133 0 0%
src/thunderfish/thunderfish.py (no function) 63 63 0 0%
src/thunderfish/thunderlogger.py add_thunderlogger_config 6 6 0 0%
src/thunderfish/thunderlogger.py extract_eods 104 104 0 0%
src/thunderfish/thunderlogger.py save_times 14 14 0 0%
src/thunderfish/thunderlogger.py load_times 9 9 0 0%
src/thunderfish/thunderlogger.py save_power 8 8 0 0%
src/thunderfish/thunderlogger.py load_power 17 17 0 0%
src/thunderfish/thunderlogger.py save_data 29 29 0 0%
src/thunderfish/thunderlogger.py load_data 61 61 0 0%
src/thunderfish/thunderlogger.py plot_signal_power 28 28 0 0%
src/thunderfish/thunderlogger.py merge_fish 32 32 0 0%
src/thunderfish/thunderlogger.py plot_eod_occurances 64 64 0 0%
src/thunderfish/thunderlogger.py main 119 119 0 0%
src/thunderfish/thunderlogger.py (no function) 38 38 0 0%
src/thunderfish/version.py (no function) 7 0 0 100%
Total   8631 6724 0 22%

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