Added full tests coverage to array functions

docs/data_schemas/index.md

@@ -19,7 +19,7 @@ objects encountered in bioacoustic analysis. These include:
 
 Delving into the core of acoustic analysis, we have schemas for:
 
-- [Recordings](audio_content.md#recordins): Complete audio files.
+- [Recordings](audio_content.md#recordings): Complete audio files.
 - [Dataset](audio_content.md#datasets): A collection of recordings from a common
   source.
 

docs/reference/arrays.md

@@ -0,0 +1,30 @@
+# Arrays Module
+
+???+ info "Additional dependencies"
+
+    To use the `soundevent.arrays` module you need to install some additional
+    dependencies. Make sure you have them installed by running the following
+    command:
+
+    ```bash
+    pip install soundevent[audio]
+    ```
+
+::: soundevent.arrays
+    options:
+        members: false
+
+
+::: soundevent.arrays.dimensions
+    options:
+        show_root_members_full_path: true
+
+
+::: soundevent.arrays.attributes
+    options:
+        show_root_members_full_path: true
+
+
+::: soundevent.arrays.operations
+    options:
+        show_root_members_full_path: true

docs/user_guide/1_saving_and_loading.py

@@ -1,4 +1,4 @@
-"""# Saving and Loading data
+"""# Saving and Loading data.
 
 In `soundevent`, we use the **Acoustic Objects Exchange Format** (**AOEF**) for
 storing and exchanging audio objects. **AOEF** is a JSON-based format
@@ -88,8 +88,8 @@
 # ### Loading Annotation Projects
 # The [`load`][soundevent.io.load]
 # function can be used to load the annotations into Python and obtain an
-# [`AnnotationProject`](../../data_schemas/annotation.md#annotation_projects) object
-# directly.
+# [`AnnotationProject`](../../data_schemas/annotation.md#annotation_project)
+# object directly.
 
 nips4b_sample = io.load(annotation_path, type="annotation_set")
 print(repr(nips4b_sample))
@@ -130,8 +130,8 @@
 # [`save`][soundevent.io.save] and
 # [`load`][soundevent.io.load] functions, respectively. The
 # loading function reads the **AOEF** file and returns a
-# [`ModelRun`](../../data_schemas/prediction.md#model_run) object that can be used
-# for further analysis.
+# [`ModelRun`](../../data_schemas/prediction.md#model_runs) object that can be
+# used for further analysis.
 #
 # By utilizing the saving and loading functions provided by soundevent, you can
 # easily manage and exchange acoustic data objects in AOEF format, promoting

docs/user_guide/example_dataset.json

@@ -1 +1 @@
-{"version":"1.1.0","created_on":"2023-11-27T19:53:00.688910","data":{"uuid":"b1096756-eea2-4489-9e6a-b98b559647bb","collection_type":"dataset","created_on":"2023-11-21T13:43:14.742002","recordings":[{"uuid":"89957d47-f67d-4bfe-8352-bf0fe5a8ce3e","path":"recording1.wav","duration":10.0,"channels":1,"samplerate":44100,"time_expansion":10.0,"hash":"1234567890abcdef","date":"2021-01-01","time":"21:34:56","latitude":12.345,"longitude":34.567,"tags":[0,1,2],"features":{"SNR":10.0,"ACI":0.5},"notes":[{"uuid":"2931b864-43e4-4fb1-aae1-a214dccca6e3","message":"This is a note.","created_by":"04ef3927-3a3d-40df-9d6e-2cc5e21482a0","is_issue":false,"created_on":"2023-11-21T13:43:14.742073"}],"owners":["d6eb0862-a619-4919-992c-eb3625692c13"]},{"uuid":"bd30f886-3abb-475b-aacb-c7148a4d4420","path":"recording2.wav","duration":8.0,"channels":1,"samplerate":441000,"time_expansion":10.0,"hash":"234567890abcdef1","date":"2021-01-02","time":"19:34:56","latitude":13.345,"longitude":32.567,"tags":[3,4,5],"features":{"SNR":7.0,"ACI":0.3},"notes":[{"uuid":"713b6c15-0e3d-4cc5-acc6-3f1093209a40","message":"Unsure about the species.","created_by":"04ef3927-3a3d-40df-9d6e-2cc5e21482a0","is_issue":false,"created_on":"2023-11-21T13:43:14.742147"}],"owners":["d6eb0862-a619-4919-992c-eb3625692c13"]}],"tags":[{"id":0,"key":"species","value":"Myotis myotis"},{"id":1,"key":"sex","value":"female"},{"id":2,"key":"behaviour","value":"foraging"},{"id":3,"key":"species","value":"Eptesicus serotinus"},{"id":4,"key":"sex","value":"male"},{"id":5,"key":"behaviour","value":"social calls"}],"users":[{"uuid":"04ef3927-3a3d-40df-9d6e-2cc5e21482a0","name":"John Doe"},{"uuid":"d6eb0862-a619-4919-992c-eb3625692c13","email":"[email protected]","name":"Data Collector"}],"name":"test_dataset","description":"A test dataset"}}
+{"version":"1.1.0","created_on":"2024-05-05T17:07:27.856998","data":{"uuid":"b1096756-eea2-4489-9e6a-b98b559647bb","collection_type":"dataset","created_on":"2023-11-21T13:43:14.742002","recordings":[{"uuid":"89957d47-f67d-4bfe-8352-bf0fe5a8ce3e","path":"recording1.wav","duration":10.0,"channels":1,"samplerate":44100,"time_expansion":10.0,"hash":"1234567890abcdef","date":"2021-01-01","time":"21:34:56","latitude":12.345,"longitude":34.567,"tags":[0,1,2],"features":{"SNR":10.0,"ACI":0.5},"notes":[{"uuid":"2931b864-43e4-4fb1-aae1-a214dccca6e3","message":"This is a note.","created_by":"04ef3927-3a3d-40df-9d6e-2cc5e21482a0","is_issue":false,"created_on":"2023-11-21T13:43:14.742073"}],"owners":["d6eb0862-a619-4919-992c-eb3625692c13"]},{"uuid":"bd30f886-3abb-475b-aacb-c7148a4d4420","path":"recording2.wav","duration":8.0,"channels":1,"samplerate":441000,"time_expansion":10.0,"hash":"234567890abcdef1","date":"2021-01-02","time":"19:34:56","latitude":13.345,"longitude":32.567,"tags":[3,4,5],"features":{"SNR":7.0,"ACI":0.3},"notes":[{"uuid":"713b6c15-0e3d-4cc5-acc6-3f1093209a40","message":"Unsure about the species.","created_by":"04ef3927-3a3d-40df-9d6e-2cc5e21482a0","is_issue":false,"created_on":"2023-11-21T13:43:14.742147"}],"owners":["d6eb0862-a619-4919-992c-eb3625692c13"]}],"tags":[{"id":0,"key":"species","value":"Myotis myotis"},{"id":1,"key":"sex","value":"female"},{"id":2,"key":"behaviour","value":"foraging"},{"id":3,"key":"species","value":"Eptesicus serotinus"},{"id":4,"key":"sex","value":"male"},{"id":5,"key":"behaviour","value":"social calls"}],"users":[{"uuid":"04ef3927-3a3d-40df-9d6e-2cc5e21482a0","name":"John Doe"},{"uuid":"d6eb0862-a619-4919-992c-eb3625692c13","email":"[email protected]","name":"Data Collector"}],"name":"test_dataset","description":"A test dataset"}}

docs/user_guide/nips4b_plus_sample.json

@@ -1 +1 @@
-{"version":"1.1.0","created_on":"2023-11-27T19:53:01.364978","data":{"uuid":"c18624a1-8145-4657-a3f1-b3512134ecf6","collection_type":"annotation_set","recordings":[{"uuid":"8392b0ff-293f-4d5b-bc1b-d40d2a0eb0dc","path":"train/nips4b_birds_trainfile079.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"35e120d0-1633-4864-88c9-063aca992747","path":"train/nips4b_birds_trainfile237.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"7ee23c44-1bc6-4833-8d66-14aa4a8e8634","path":"train/nips4b_birds_trainfile587.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"24eceb91-535e-42f0-80e4-8c670465bac8","path":"train/nips4b_birds_trainfile106.wav","duration":4.069297052154195,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"24dd23da-ca07-40eb-80e6-af8b6b2a75ee","path":"train/nips4b_birds_trainfile430.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"8954beed-21d0-4f20-98bd-58c14264d853","path":"train/nips4b_birds_trainfile661.wav","duration":1.3873922902494331,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"69f7bf42-087a-4d88-b312-f26688597974","path":"train/nips4b_birds_trainfile429.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"b98b5a59-3518-45e5-9306-67c522540ae1","path":"train/nips4b_birds_trainfile633.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"52e329a3-afbb-475e-938c-f70c88580723","path":"train/nips4b_birds_trainfile200.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"6eeca672-f3ec-41ca-a551-54ddec0dd1a7","path":"train/nips4b_birds_trainfile545.wav","duration":2.7921995464852607,"channels":1,"samplerate":44100,"owners":[]}],"clips":[{"uuid":"b283a71f-4aa8-4ee2-ac83-7c7d5d0af2bc","recording":"8392b0ff-293f-4d5b-bc1b-d40d2a0eb0dc","start_time":0.0,"end_time":5.00390022675737},{"uuid":"e2ec7571-bfe1-4682-8d4d-15e3e34edfc9","recording":"35e120d0-1633-4864-88c9-063aca992747","start_time":0.0,"end_time":5.00390022675737},{"uuid":"ab5bcc8f-078e-4194-97a4-763998d289fa","recording":"7ee23c44-1bc6-4833-8d66-14aa4a8e8634","start_time":0.0,"end_time":5.00390022675737},{"uuid":"dd9ad126-8b15-4121-84f5-f59dc3f85802","recording":"24eceb91-535e-42f0-80e4-8c670465bac8","start_time":0.0,"end_time":4.069297052154195},{"uuid":"0a53e14f-f51c-4ade-9567-87c2b02bd197","recording":"24dd23da-ca07-40eb-80e6-af8b6b2a75ee","start_time":0.0,"end_time":5.00390022675737},{"uuid":"ae455d97-d1fa-43a1-b179-907bee8471e6","recording":"8954beed-21d0-4f20-98bd-58c14264d853","start_time":0.0,"end_time":1.3873922902494331},{"uuid":"0b42c9e1-0289-4f03-b3cb-10859a80103e","recording":"69f7bf42-087a-4d88-b312-f26688597974","start_time":0.0,"end_time":5.00390022675737},{"uuid":"56329c3c-5beb-48ed-8a79-be4e9bd2d9ed","recording":"b98b5a59-3518-45e5-9306-67c522540ae1","start_time":0.0,"end_time":5.00390022675737},{"uuid":"57e0b23a-8663-49f3-8455-997e0f4d2b49","recording":"52e329a3-afbb-475e-938c-f70c88580723","start_time":0.0,"end_time":5.00390022675737},{"uuid":"c7b6f927-fd3b-40ac-9b25-d682eec2d3ac","recording":"6eeca672-f3ec-41ca-a551-54ddec0dd1a7","start_time":0.0,"end_time":2.7921995464852607}],"clip_annotations":[{"uuid":"0e7a786e-48e4-4424-a8da-bf080bdefd9e","clip":"b283a71f-4aa8-4ee2-ac83-7c7d5d0af2bc","created_on":"2023-11-23T20:44:32.913233"},{"uuid":"af9713a7-2bf4-45df-bdff-63d47de34d71","clip":"e2ec7571-bfe1-4682-8d4d-15e3e34edfc9","created_on":"2023-11-23T20:44:32.913255"},{"uuid":"70738dff-3c98-4838-979c-0ed073edd0ea","clip":"ab5bcc8f-078e-4194-97a4-763998d289fa","created_on":"2023-11-23T20:44:32.913264"},{"uuid":"fa0fc36e-0c1a-450f-900b-5a32df17a159","clip":"dd9ad126-8b15-4121-84f5-f59dc3f85802","created_on":"2023-11-23T20:44:32.913377"},{"uuid":"178bf156-2bab-4970-8a76-4abfdc4b31b7","clip":"0a53e14f-f51c-4ade-9567-87c2b02bd197","created_on":"2023-11-23T20:44:32.913386"},{"uuid":"dc71d06a-54d6-4fad-ac6a-205bbee7ec96","clip":"ae455d97-d1fa-43a1-b179-907bee8471e6","created_on":"2023-11-23T20:44:32.913392"},{"uuid":"b418abd6-52cc-4ef4-9725-33d3d38b7878","clip":"0b42c9e1-0289-4f03-b3cb-10859a80103e","created_on":"2023-11-23T20:44:32.913400"},{"uuid":"d18ca56f-2f13-44dd-be43-f995e4d2edb6","clip":"56329c3c-5beb-48ed-8a79-be4e9bd2d9ed","created_on":"2023-11-23T20:44:32.913415"},{"uuid":"8dfa7d26-5f8b-4f37-bf0a-c031373b22f7","clip":"57e0b23a-8663-49f3-8455-997e0f4d2b49","created_on":"2023-11-23T20:44:32.913430"},{"uuid":"ebc5e8d0-bd3e-4d01-95e0-d9a0ce337ac9","clip":"c7b6f927-fd3b-40ac-9b25-d682eec2d3ac","created_on":"2023-11-23T20:44:32.913437"}],"created_on":"2023-11-23T20:44:32.913488"}}
+{"version":"1.1.0","created_on":"2024-05-05T17:07:28.277844","data":{"uuid":"c18624a1-8145-4657-a3f1-b3512134ecf6","collection_type":"annotation_set","recordings":[{"uuid":"8392b0ff-293f-4d5b-bc1b-d40d2a0eb0dc","path":"train/nips4b_birds_trainfile079.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"35e120d0-1633-4864-88c9-063aca992747","path":"train/nips4b_birds_trainfile237.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"7ee23c44-1bc6-4833-8d66-14aa4a8e8634","path":"train/nips4b_birds_trainfile587.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"24eceb91-535e-42f0-80e4-8c670465bac8","path":"train/nips4b_birds_trainfile106.wav","duration":4.069297052154195,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"24dd23da-ca07-40eb-80e6-af8b6b2a75ee","path":"train/nips4b_birds_trainfile430.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"8954beed-21d0-4f20-98bd-58c14264d853","path":"train/nips4b_birds_trainfile661.wav","duration":1.3873922902494331,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"69f7bf42-087a-4d88-b312-f26688597974","path":"train/nips4b_birds_trainfile429.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"b98b5a59-3518-45e5-9306-67c522540ae1","path":"train/nips4b_birds_trainfile633.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"52e329a3-afbb-475e-938c-f70c88580723","path":"train/nips4b_birds_trainfile200.wav","duration":5.00390022675737,"channels":1,"samplerate":44100,"owners":[]},{"uuid":"6eeca672-f3ec-41ca-a551-54ddec0dd1a7","path":"train/nips4b_birds_trainfile545.wav","duration":2.7921995464852607,"channels":1,"samplerate":44100,"owners":[]}],"clips":[{"uuid":"b283a71f-4aa8-4ee2-ac83-7c7d5d0af2bc","recording":"8392b0ff-293f-4d5b-bc1b-d40d2a0eb0dc","start_time":0.0,"end_time":5.00390022675737},{"uuid":"e2ec7571-bfe1-4682-8d4d-15e3e34edfc9","recording":"35e120d0-1633-4864-88c9-063aca992747","start_time":0.0,"end_time":5.00390022675737},{"uuid":"ab5bcc8f-078e-4194-97a4-763998d289fa","recording":"7ee23c44-1bc6-4833-8d66-14aa4a8e8634","start_time":0.0,"end_time":5.00390022675737},{"uuid":"dd9ad126-8b15-4121-84f5-f59dc3f85802","recording":"24eceb91-535e-42f0-80e4-8c670465bac8","start_time":0.0,"end_time":4.069297052154195},{"uuid":"0a53e14f-f51c-4ade-9567-87c2b02bd197","recording":"24dd23da-ca07-40eb-80e6-af8b6b2a75ee","start_time":0.0,"end_time":5.00390022675737},{"uuid":"ae455d97-d1fa-43a1-b179-907bee8471e6","recording":"8954beed-21d0-4f20-98bd-58c14264d853","start_time":0.0,"end_time":1.3873922902494331},{"uuid":"0b42c9e1-0289-4f03-b3cb-10859a80103e","recording":"69f7bf42-087a-4d88-b312-f26688597974","start_time":0.0,"end_time":5.00390022675737},{"uuid":"56329c3c-5beb-48ed-8a79-be4e9bd2d9ed","recording":"b98b5a59-3518-45e5-9306-67c522540ae1","start_time":0.0,"end_time":5.00390022675737},{"uuid":"57e0b23a-8663-49f3-8455-997e0f4d2b49","recording":"52e329a3-afbb-475e-938c-f70c88580723","start_time":0.0,"end_time":5.00390022675737},{"uuid":"c7b6f927-fd3b-40ac-9b25-d682eec2d3ac","recording":"6eeca672-f3ec-41ca-a551-54ddec0dd1a7","start_time":0.0,"end_time":2.7921995464852607}],"clip_annotations":[{"uuid":"0e7a786e-48e4-4424-a8da-bf080bdefd9e","clip":"b283a71f-4aa8-4ee2-ac83-7c7d5d0af2bc","created_on":"2023-11-23T20:44:32.913233"},{"uuid":"af9713a7-2bf4-45df-bdff-63d47de34d71","clip":"e2ec7571-bfe1-4682-8d4d-15e3e34edfc9","created_on":"2023-11-23T20:44:32.913255"},{"uuid":"70738dff-3c98-4838-979c-0ed073edd0ea","clip":"ab5bcc8f-078e-4194-97a4-763998d289fa","created_on":"2023-11-23T20:44:32.913264"},{"uuid":"fa0fc36e-0c1a-450f-900b-5a32df17a159","clip":"dd9ad126-8b15-4121-84f5-f59dc3f85802","created_on":"2023-11-23T20:44:32.913377"},{"uuid":"178bf156-2bab-4970-8a76-4abfdc4b31b7","clip":"0a53e14f-f51c-4ade-9567-87c2b02bd197","created_on":"2023-11-23T20:44:32.913386"},{"uuid":"dc71d06a-54d6-4fad-ac6a-205bbee7ec96","clip":"ae455d97-d1fa-43a1-b179-907bee8471e6","created_on":"2023-11-23T20:44:32.913392"},{"uuid":"b418abd6-52cc-4ef4-9725-33d3d38b7878","clip":"0b42c9e1-0289-4f03-b3cb-10859a80103e","created_on":"2023-11-23T20:44:32.913400"},{"uuid":"d18ca56f-2f13-44dd-be43-f995e4d2edb6","clip":"56329c3c-5beb-48ed-8a79-be4e9bd2d9ed","created_on":"2023-11-23T20:44:32.913415"},{"uuid":"8dfa7d26-5f8b-4f37-bf0a-c031373b22f7","clip":"57e0b23a-8663-49f3-8455-997e0f4d2b49","created_on":"2023-11-23T20:44:32.913430"},{"uuid":"ebc5e8d0-bd3e-4d01-95e0-d9a0ce337ac9","clip":"c7b6f927-fd3b-40ac-9b25-d682eec2d3ac","created_on":"2023-11-23T20:44:32.913437"}],"created_on":"2023-11-23T20:44:32.913488"}}

mkdocs.yml

@@ -15,6 +15,7 @@ nav:
   - Reference:
       - data: reference/data.md
       - io: reference/io.md
+      - arrays: reference/arrays.md
       - audio: reference/audio.md
       - geometry: reference/geometry.md
       - evaluation: reference/evaluation.md
@@ -100,6 +101,9 @@ markdown_extensions:
   - pymdownx.critic
   - pymdownx.keys
   - pymdownx.details
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
   - pymdownx.superfences:
       preserve_tabs: true
       custom_fences:

src/soundevent/arrays/__init__.py

@@ -0,0 +1,50 @@
+"""Module for manipulation of xarray.DataArray objects.
+
+This module provides functions for manipulating xarray.DataArray objects,
+including creating range dimensions, setting dimension attributes, cropping and
+extending axes, getting dimension ranges and widths, and setting values at
+specific positions.
+"""
+
+from soundevent.arrays.attributes import ArrayAttrs, DimAttrs
+from soundevent.arrays.dimensions import (
+    Dimensions,
+    create_frequency_dim_from_array,
+    create_frequency_range,
+    create_range_dim,
+    create_time_dim_from_array,
+    create_time_range,
+    estimate_dim_step,
+    get_dim_range,
+    get_dim_step,
+    get_dim_width,
+    set_dim_attrs,
+)
+from soundevent.arrays.operations import (
+    crop_dim,
+    extend_dim,
+    normalize,
+    set_value_at_pos,
+    to_db,
+)
+
+__all__ = [
+    "ArrayAttrs",
+    "DimAttrs",
+    "Dimensions",
+    "create_frequency_dim_from_array",
+    "create_frequency_range",
+    "create_range_dim",
+    "create_time_dim_from_array",
+    "create_time_range",
+    "crop_dim",
+    "estimate_dim_step",
+    "extend_dim",
+    "get_dim_range",
+    "get_dim_step",
+    "get_dim_width",
+    "set_dim_attrs",
+    "set_value_at_pos",
+    "normalize",
+    "to_db",
+]