Adding TS(f) example notebook

.gitignore

@@ -6,6 +6,9 @@ __pycache__/
 # C extensions
 *.so
 
+# Example datasetss
+notebooks/example_data/ts_spectrum_example_data/
+
 # Distribution / packaging
 .Python
 build/

conda/environment-ep-main.yml

@@ -12,6 +12,7 @@ dependencies:
   - numba # Helps ensure a recent version is installed
   - numpy<2
   - pip
+  - pooch
   # -- holoviz --
   - jupyter_bokeh
   - datashader

conda/environment.yml

@@ -10,6 +10,7 @@ dependencies:
   - cartopy
   - scipy
   - numba # Helps ensure a recent version is installed
+  - pooch
   # -- holoviz --
   - jupyter_bokeh
   - datashader

notebooks/_templates/gallery-cards.jinja

@@ -1,7 +1,12 @@
+{% for section in data %}
+
+## {{ section["section"] }}
+
 ::::{grid} 1 2 2 3
 :gutter: 2
+:class-container: gallery-grid
 
-{% for item in data %}
+{% for item in section["items"] %}
 :::{card}
 :link: {{ item.website or item.notebook }}
 {% if item.image %}:img-top: {{ item.image }}{% endif %}
@@ -13,4 +18,6 @@
 :::
 {% endfor %}
 
-:::: 
+::::
+
+{% endfor %}

notebooks/_toc.yml

@@ -1,17 +1,28 @@
-# Table of contents
-# Learn more at https://jupyterbook.org/customize/toc.html
-
 format: jb-book
 root: index
 parts:
-  - caption: Demonstrations
-    numbered: True
+  - caption: Getting started
+    numbered: False
+    chapters:
+      - file: getting_started
+      - file: getting_started_FM_TS
+
+  - caption: Data processing
+    numbered: False
+    chapters:
+      - file: OOI_eclipse
+      - file: seafloor_detection
+      - file: transient_noise
+
+  - caption: Analysis workflows
+    numbered: False
+    chapters:
+      - file: ship_tracks
+      - file: krill_freq_diff
+      - file: hake_mask
+      - file: glider_AZFP
+
+  - caption: Community showcase
+    numbered: False
     chapters:
-    - file: getting_started
-    - file: OOI_eclipse
-    - file: ship_tracks
-    - file: krill_freq_diff
-    - file: hake_mask
-    - file: glider_AZFP
-    - file: seafloor_detection
-    - file: transient_noise
+      - file: community_showcase

notebooks/community_showcase.md

@@ -0,0 +1,6 @@
+# Community showcase
+
+Examples from the echopype community will be highlighted here.
+If you are using echopype in your own workflows, feel free to open an issue or pull request to suggest an example notebook!
+
+(Temporary file to remove)

notebooks/gallery.yml

@@ -1,55 +1,71 @@
-- name: Getting Started with Echopype
-  website: https://echopype-examples.readthedocs.io/en/latest/getting_started.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/getting_started.ipynb
-  notebook: getting_started.ipynb
-  summary: A minimum example to get started on Echopype functions.
-  image: images/gallery/01_getting_started.png
-
-- name: Watching Eclipse from a Moored Echosounder
-  website: https://echopype-examples.readthedocs.io/en/latest/OOI_eclipse.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/OOI_eclipse.ipynb
-  notebook: OOI_eclipse.ipynb
-  summary: Pairing acoustic data from an upward-looking echosounder and shortwave irradiance measured by a pyrometer on a surface mooring to observe the movement response of zooplankton to a solar eclipse. (Not binder friendly.)
-  image: images/gallery/02_OOI_eclipse.png
-
-- name: Ship Tracks Visualisation
-  website: https://echopype-examples.readthedocs.io/en/latest/ship_tracks.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/ship_tracks.ipynb
-  notebook: ship_tracks.ipynb
-  summary: Subselect sections of echo data based on ship GPS data embedded in the echosounder raw files to demonstrate the power of label-aware data processing based on standardized netCDF data model. (Not binder friendly.)
-  image: images/gallery/03_subselection.png
-
-- name: Krill Frequency Differencing
-  website: https://echopype-examples.readthedocs.io/en/latest/krill_freq_diff.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/krill_freq_diff.ipynb
-  notebook: krill_freq_diff.ipynb
-  summary: Perform frequency-differencing analysis to identify fluid-like zooplankton scatterers (likely krill) in ship echosounder data, and compute nautical acoustic scattering coefficient (NASC) based on the classification. (Not binder friendly.)
-  image: images/gallery/04_krill.png
-
-- name: Masking Echogram and Computing NASC
-  website: https://echopype-examples.readthedocs.io/en/latest/hake_mask.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/hake_mask.ipynb
-  notebook: hake_mask.ipynb
-  summary: Incorporate an externally generated mask that identify the occurrence of Pacific hake in ship echosounder data, and compute NASC based on the masked outputs.
-  image: images/gallery/05_NASC.png
-
-- name: Glider AZFP Processing
-  website: https://echopype-examples.readthedocs.io/en/latest/glider_AZFP.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/glider_AZFP.ipynb
-  notebook: glider_AZFP.ipynb
-  summary: Process acoustic data from a Slocum glider by incorporating external position, motion, and environmental data and identify zooplankton shoals.
-  image: images/gallery/06_glider.png
-
-- name: Seafloor Detection
-  website: https://echopype-examples.readthedocs.io/en/latest/seafloor_detection.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/seafloor_detection.ipynb
-  notebook: seafloor_detection.ipynb
-  summary: Seafloor detection with echopype (two algorithms) and use of echoregions; compute a bottom line and mask below-bottom data.
-  image: images/gallery/07_seafloor.png
-
-- name: Transient Noise Removal
-  website: https://echopype-examples.readthedocs.io/en/latest/transient_noise.html
-  repository: https://github.com/OSOceanAcoustics/echopype-examples/blob/main/notebooks/transient_noise.ipynb
-  notebook: transient_noise.ipynb
-  summary: Transient noise removal with echopype (two algorithms) and exploring the effects on Sv profiles.
-  image: images/gallery/08_transient_noise.png
+- section: Getting started
+  items:
+    - name: Getting Started with Echopype
+      website: https://echopype-examples.readthedocs.io/en/latest/getting_started.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/getting_started.ipynb
+      notebook: getting_started.ipynb
+      summary: A minimum example to get started on Echopype functions.
+      image: images/gallery/01_getting_started.png
+
+    - name: Getting Started with Echopype for broadband TS
+      website: https://echopype-examples.readthedocs.io/en/latest/getting_started_FM_TS.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/getting_started_FM_TS.ipynb
+      notebook: getting_started_FM_TS.ipynb
+      summary: A minimum example to get started on Echopype functions for broadband target strength (TS) estimation.
+      image: images/gallery/11_getting_started_FM_TS.png
+
+- section: Data processing
+  items:
+    - name: Watching Eclipse from a Moored Echosounder
+      website: https://echopype-examples.readthedocs.io/en/latest/OOI_eclipse.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/OOI_eclipse.ipynb
+      notebook: OOI_eclipse.ipynb
+      summary: Pairing acoustic data from an upward-looking echosounder and shortwave irradiance measured by a pyrometer on a surface mooring to observe the movement response of zooplankton to a solar eclipse. (Not binder friendly.)
+      image: images/gallery/02_OOI_eclipse.png
+
+    - name: Seafloor Detection
+      website: https://echopype-examples.readthedocs.io/en/latest/seafloor_detection.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/seafloor_detection.ipynb
+      notebook: seafloor_detection.ipynb
+      summary: Seafloor detection with echopype (two algorithms) and use of echoregions; compute a bottom line and mask below-bottom data.
+      image: images/gallery/07_seafloor.png
+
+    - name: Transient Noise Removal
+      website: https://echopype-examples.readthedocs.io/en/latest/transient_noise.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/transient_noise.ipynb
+      notebook: transient_noise.ipynb
+      summary: Transient noise removal with echopype (two algorithms) and exploring the effects on Sv profiles.
+      image: images/gallery/08_transient_noise.png
+
+- section: Analysis workflows
+  items:
+    - name: Ship Tracks Visualisation
+      website: https://echopype-examples.readthedocs.io/en/latest/ship_tracks.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/ship_tracks.ipynb
+      notebook: ship_tracks.ipynb
+      summary: Subselect sections of echo data based on ship GPS data embedded in the echosounder raw files to demonstrate the power of label-aware data processing based on standardized netCDF data model. (Not binder friendly.)
+      image: images/gallery/03_subselection.png
+
+    - name: Krill Frequency Differencing
+      website: https://echopype-examples.readthedocs.io/en/latest/krill_freq_diff.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/krill_freq_diff.ipynb
+      notebook: krill_freq_diff.ipynb
+      summary: Perform frequency-differencing analysis to identify fluid-like zooplankton scatterers (likely krill) in ship echosounder data, and compute nautical acoustic scattering coefficient (NASC) based on the classification. (Not binder friendly.)
+      image: images/gallery/04_krill.png
+
+    - name: Masking Echogram and Computing NASC
+      website: https://echopype-examples.readthedocs.io/en/latest/hake_mask.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/hake_mask.ipynb
+      notebook: hake_mask.ipynb
+      summary: Incorporate an externally generated mask that identify the occurrence of Pacific hake in ship echosounder data, and compute NASC based on the masked outputs.
+      image: images/gallery/05_NASC.png
+
+    - name: Glider AZFP Processing
+      website: https://echopype-examples.readthedocs.io/en/latest/glider_AZFP.html
+      repository: https://github.com/echostack-org/echopype-examples/blob/main/notebooks/glider_AZFP.ipynb
+      notebook: glider_AZFP.ipynb
+      summary: Process acoustic data from a Slocum glider by incorporating external position, motion, and environmental data and identify zooplankton shoals.
+      image: images/gallery/06_glider.png
+
+- section: Community showcase
+  items: []