APLOSE detections

docs/source/_static/detections/aplose_results.csv

@@ -0,0 +1,53 @@
+project,filename,annotation_id,is_update_of_id,start_time,end_time,start_frequency,end_frequency,min_frequency,max_frequency,annotation,annotator,annotator_expertise,start_datetime,end_datetime,is_box,type,confidence_indicator_label,confidence_indicator_level,comments,signal_quantity,signal_is_intensity_too_low,signal_does_overlap_other_signals,signal_start_frequency,signal_end_frequency,signal_relative_min_frequency_count,signal_relative_max_frequency_count,signal_steps_count,signal_has_harmonics,signal_trend,signal_sidebands,signal_subharmonics,signal_frequency_jumps,signal_deterministic_chaos,created_at_phase,ben,leslie
+doc_osekit,2022_09_25_22_35_15_000000,593717,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:35:15.000+00:00,2022-09-25T22:35:22.000+00:00,0,WEAK,100% sure!,3/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_15_000000,593718,,4.931,6.703,6665.0,22181.0,6665.0,22181.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:35:19.931+00:00,2022-09-25T22:35:21.703+00:00,1,BOX,100% sure!,3/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_15_000000,593727,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,april,,2022-09-25T22:35:15.000+00:00,2022-09-25T22:35:22.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_15_000000,593728,,4.967,5.631,8025.0,15197.0,8025.0,15197.0,Odontocete whistle,april,,2022-09-25T22:35:19.967+00:00,2022-09-25T22:35:20.631+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_15_000000,593729,,6.16,6.658,7463.0,22135.0,7463.0,22135.0,Odontocete whistle,april,,2022-09-25T22:35:21.160+00:00,2022-09-25T22:35:21.658+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_15_000000,593737,,5.658,6.122,8447.0,20400.0,8447.0,20400.0,Odontocete whistle,april,,2022-09-25T22:35:20.658+00:00,2022-09-25T22:35:21.122+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_15_000000,593772,,5.936,5.936,20399.0,20399.0,20399.0,20399.0,Odontocete whistle,ben,EXPERT,2022-09-25T22:35:20.936+00:00,2022-09-25T22:35:20.936+00:00,1,POINT,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,VERIFICATION,,
+doc_osekit,2022_09_25_22_35_15_000000,593773,,5.659,6.681,7260.0,20448.0,7260.0,20448.0,Odontocete whistle,ben,EXPERT,2022-09-25T22:35:20.659+00:00,2022-09-25T22:35:21.681+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,VERIFICATION,,
+doc_osekit,2022_09_25_22_35_22_000000,593719,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:35:22.000+00:00,2022-09-25T22:35:29.000+00:00,0,WEAK,100% sure!,3/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_22_000000,593720,,4.239,5.39,5728.0,20540.0,5728.0,20540.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:35:26.239+00:00,2022-09-25T22:35:27.390+00:00,1,BOX,Quite sure,2/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_22_000000,593738,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,april,,2022-09-25T22:35:22.000+00:00,2022-09-25T22:35:29.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_22_000000,593739,,4.855,5.299,6525.0,15947.0,6525.0,15947.0,Odontocete whistle,april,,2022-09-25T22:35:26.855+00:00,2022-09-25T22:35:27.299+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_22_000000,593740,,4.164,4.77,9479.0,19182.0,9479.0,19182.0,Odontocete whistle,april,,2022-09-25T22:35:26.164+00:00,2022-09-25T22:35:26.770+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,False,True
+doc_osekit,2022_09_25_22_35_29_000000,593721,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete click,ron,EXPERT,2022-09-25T22:35:29.000+00:00,2022-09-25T22:35:36.000+00:00,0,WEAK,Quite sure,2/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_29_000000,593722,,6.498,7.0,9571.0,23868.0,9571.0,23868.0,Odontocete click,ron,EXPERT,2022-09-25T22:35:35.498+00:00,2022-09-25T22:35:36.000+00:00,1,BOX,Quite sure,2/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_29_000000,593741,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete click,april,,2022-09-25T22:35:29.000+00:00,2022-09-25T22:35:36.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_29_000000,593742,,6.485,6.971,1322.0,24000.0,1322.0,24000.0,Odontocete click,april,,2022-09-25T22:35:35.485+00:00,2022-09-25T22:35:35.971+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_35_29_000000,593743,,0.0,7.0,0.0,24000.0,0.0,24000.0,Boat,april,,2022-09-25T22:35:29.000+00:00,2022-09-25T22:35:36.000+00:00,0,WEAK,Not sure at all,1/3,,,,,,,,,,,,,,,,ANNOTATION,True,False
+doc_osekit,2022_09_25_22_35_29_000000,593744,,3.431,5.786,1979.0,5447.0,1979.0,5447.0,Boat,april,,2022-09-25T22:35:32.431+00:00,2022-09-25T22:35:34.786+00:00,1,BOX,Not sure at all,1/3,,,,,,,,,,,,,,,,ANNOTATION,False,False
+doc_osekit,2022_09_25_22_36_04_000000,593723,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:36:04.000+00:00,2022-09-25T22:36:11.000+00:00,0,WEAK,Quite sure,2/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_04_000000,593724,,5.042,7.0,8493.0,21337.0,8493.0,21337.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:36:09.042+00:00,2022-09-25T22:36:11.000+00:00,1,BOX,Quite sure,2/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,False
+doc_osekit,2022_09_25_22_36_04_000000,593747,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,april,,2022-09-25T22:36:04.000+00:00,2022-09-25T22:36:11.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_04_000000,593748,,5.913,6.589,12104.0,16135.0,12104.0,16135.0,Odontocete whistle,april,,2022-09-25T22:36:09.913+00:00,2022-09-25T22:36:10.589+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_04_000000,593767,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,ann,AVERAGE,2022-09-25T22:36:04.000+00:00,2022-09-25T22:36:11.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_04_000000,593768,,4.975,6.724,11400.0,19041.0,11400.0,19041.0,Odontocete whistle,ann,AVERAGE,2022-09-25T22:36:08.975+00:00,2022-09-25T22:36:10.724+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,False
+doc_osekit,2022_09_25_22_36_04_000000,593805,593724,5.918468342784749,6.571428453600085,13133.0,21336.0,13133.0,21336.0,Odontocete whistle,leslie,EXPERT,2022-09-25T22:36:09.918+00:00,2022-09-25T22:36:10.571+00:00,1,BOX,Quite sure,2/3,,MULTIPLE,,,,,,,,,,,,,,VERIFICATION,,
+doc_osekit,2022_09_25_22_36_04_000000,593806,593768,5.913256081835184,6.596589371964738,12806.0,19040.0,12806.0,19040.0,Odontocete whistle,leslie,EXPERT,2022-09-25T22:36:09.913+00:00,2022-09-25T22:36:10.596+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,VERIFICATION,,
+doc_osekit,2022_09_25_22_36_11_000000,593725,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete click,ron,EXPERT,2022-09-25T22:36:11.000+00:00,2022-09-25T22:36:18.000+00:00,0,WEAK,Quite sure,2/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_11_000000,593726,,5.008,7.0,12337.0,23868.0,12337.0,23868.0,Odontocete click,ron,EXPERT,2022-09-25T22:36:16.008+00:00,2022-09-25T22:36:18.000+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_11_000000,593749,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete click,april,,2022-09-25T22:36:11.000+00:00,2022-09-25T22:36:18.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_11_000000,593750,,5.048,6.971,11729.0,23916.0,11729.0,23916.0,Odontocete click,april,,2022-09-25T22:36:16.048+00:00,2022-09-25T22:36:17.971+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_11_000000,593751,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete buzz,april,,2022-09-25T22:36:11.000+00:00,2022-09-25T22:36:18.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,False
+doc_osekit,2022_09_25_22_36_11_000000,593752,,3.616,3.774,4229.0,23447.0,4229.0,23447.0,Odontocete buzz,april,,2022-09-25T22:36:14.616+00:00,2022-09-25T22:36:14.774+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,False,False
+doc_osekit,2022_09_25_22_36_11_000000,593769,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete click,ann,AVERAGE,2022-09-25T22:36:11.000+00:00,2022-09-25T22:36:18.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_11_000000,593770,,0.0,1.245,13041.0,24000.0,13041.0,24000.0,Odontocete click,ann,AVERAGE,2022-09-25T22:36:11.000+00:00,2022-09-25T22:36:12.245+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_11_000000,593771,,5.18,6.986,10040.0,24000.0,10040.0,24000.0,Odontocete click,ann,AVERAGE,2022-09-25T22:36:16.180+00:00,2022-09-25T22:36:17.986+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_11_000000,593807,,3.857,3.857,6337.0,6337.0,6337.0,6337.0,Odontocete buzz,leslie,EXPERT,2022-09-25T22:36:14.857+00:00,2022-09-25T22:36:14.857+00:00,1,POINT,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,VERIFICATION,,
+doc_osekit,2022_09_25_22_36_18_000000,593730,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:25.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593731,,1.977,3.533,5071.0,20399.0,5071.0,20399.0,Odontocete whistle,ron,EXPERT,2022-09-25T22:36:19.977+00:00,2022-09-25T22:36:21.533+00:00,1,BOX,100% sure!,3/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,False,True
+doc_osekit,2022_09_25_22_36_18_000000,593732,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete click,ron,EXPERT,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:25.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593733,,0.0,0.9,12665.0,24000.0,12665.0,24000.0,Odontocete click,ron,EXPERT,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:18.900+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593734,,0.0,7.0,0.0,24000.0,0.0,24000.0,Boat,ron,EXPERT,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:25.000+00:00,0,WEAK,Not sure at all,1/3,,,,,,,,,,,,,,,,ANNOTATION,True,False
+doc_osekit,2022_09_25_22_36_18_000000,593735,,6.178,6.405,3524.0,24000.0,3524.0,24000.0,Boat,ron,EXPERT,2022-09-25T22:36:24.178+00:00,2022-09-25T22:36:24.405+00:00,1,BOX,Quite sure,2/3,,,,,,,,,,,,,,,,ANNOTATION,False,False
+doc_osekit,2022_09_25_22_36_18_000000,593736,,1.737,3.722,4086.0,11539.0,4086.0,11539.0,Boat,ron,EXPERT,2022-09-25T22:36:19.737+00:00,2022-09-25T22:36:21.722+00:00,1,BOX,100% sure!,3/3,,,,,,,,,,,,,,,,ANNOTATION,False,False
+doc_osekit,2022_09_25_22_36_18_000000,593753,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,april,,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:25.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593754,,1.689,4.095,2869.0,22744.0,2869.0,22744.0,Odontocete whistle,april,,2022-09-25T22:36:19.689+00:00,2022-09-25T22:36:22.095+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,False,False
+doc_osekit,2022_09_25_22_36_18_000000,593774,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete click,ann,AVERAGE,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:25.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593775,,4.234,6.423,2822.0,24000.0,2822.0,24000.0,Odontocete click,ann,AVERAGE,2022-09-25T22:36:22.234+00:00,2022-09-25T22:36:24.423+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593776,,0.0,0.797,9244.0,24000.0,9244.0,24000.0,Odontocete click,ann,AVERAGE,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:18.797+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593777,,0.0,7.0,0.0,24000.0,0.0,24000.0,Odontocete whistle,ann,AVERAGE,2022-09-25T22:36:18.000+00:00,2022-09-25T22:36:25.000+00:00,0,WEAK,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,ANNOTATION,True,True
+doc_osekit,2022_09_25_22_36_18_000000,593778,,2.079,3.384,6104.0,20213.0,6104.0,20213.0,Odontocete whistle,ann,AVERAGE,2022-09-25T22:36:20.079+00:00,2022-09-25T22:36:21.384+00:00,1,BOX,Not sure at all,1/3,,SINGLE,,,11494.0,6666.0,1,1,,,MOD,,,,,ANNOTATION,False,True
+doc_osekit,2022_09_25_22_36_18_000000,593808,593754,2.1098456069769544,3.164478905872949,6290.0,20493.0,6290.0,20493.0,Odontocete whistle,leslie,EXPERT,2022-09-25T22:36:20.109+00:00,2022-09-25T22:36:21.164+00:00,1,BOX,Not sure at all,1/3,,MULTIPLE,,,,,,,,,,,,,,VERIFICATION,,

docs/source/aplose.rst

@@ -0,0 +1,64 @@
+.. _aplose:
+
+Working with APLOSE results
+---------------------------
+
+`APLOSE <https://osmose.ifremer.fr/app//>`_ is **OSmOSE**'s web-based annotation platform.
+
+**APLOSE** campaigns `results <https://project-osmose.github.io/APLOSE/user/annotation-campaign/phase-progress-result/>`_ are provided as csv files
+that can be parsed in **OSEkit** as :class:`osekit.core.detection.Detection` instances.
+
+Loading an APLOSE results file
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``Detections`` can be extracted from **APLOSE** results files thanks to the :meth:`osekit.core.detection.Detection.from_csv` method:
+
+.. code-block:: python
+
+    from pathlib import Path
+    from osekit.core.detection import Detection
+
+    detections = Detection.from_csv(csv=Path(r"_static/detections/aplose_results.csv"))
+
+Detection / Audio interaction
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The :class:`osekit.core.detection.Detection` class inherits from the :class:`osekit.core.event.Event` class: detections can easily be used to filter audio and spectro data:
+
+.. code-block:: python
+
+    from osekit.core.spectro_dataset import SpectroDataset
+
+    detection = Detection(...) # Generally Detection.from_csv(...)[i]
+    spectro_dataset = SpectroDataset(...)
+
+    # Find all SpectroData in which detection appear:
+    positive_spectrograms = SpectroDataset([sd for sd in spectro_dataset.data if sd.overlaps(detection)])
+
+Plotting a detection
+^^^^^^^^^^^^^^^^^^^^
+
+Detection boxes can be plotted on spectrograms thanks to the :method:`osekit.core.detection.Detection.to_rectangle` method:
+
+.. code-block:: python
+
+    import matplotlib.pyplot as plt
+    from osekit.core.spectro_data import SpectroData
+    from osekit.core.detection import Detection
+
+    sd = SpectroData(...)
+    detection = Detection(...)
+
+    fig, axs = plt.subplots()
+
+    # Plot the spectrogram
+    sd.plot(ax=ax)
+
+    # Get a rectangle from the detection
+    rectangle = detection.to_rectangle(fill = False)
+
+    # Draw the detection
+    ax.add_patch(rectangle)
+
+    # Show the spectrogram
+    plt.show()

docs/source/coreapi.rst

@@ -23,3 +23,4 @@ Core
    ltasdata
    audiofilemanager
    frequencyscale
+   detection

docs/source/detection.rst

@@ -0,0 +1,25 @@
+.. _detection:
+
+Detection
+----------
+
+.. autoclass:: osekit.core.detection.Detection
+   :members:
+
+.. autoclass:: osekit.core.detection.FrequencyBounds
+   :members:
+
+.. autoclass:: osekit.core.detection.DetectorInfo
+   :members:
+
+.. autoclass:: osekit.core.detection.SignalParameters
+   :members:
+
+.. autoclass:: osekit.core.detection.ConfidenceIndicator
+   :members:
+
+.. autoclass:: osekit.core.detection.DetectionMetaData
+   :members:
+
+.. autoclass:: osekit.core.detection.Verification
+   :members: