Update Notebooks (#184)

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* Merge Main to Feature (#188)

* docs: README and docs/index revision (#185)

* separate out the goal and specific current dev for Echoview

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* Import Transect Checking from Hake-Labels (#162)

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* Disentangle Nested If Else in Select Region and Add Region Class Selections (#160)

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* Update echoregions/regions2d/regions2d.py

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* revise trawl for transect evr

* use mask label region ids to separate the region ids passed in to the mask labels used in masking

* add notebook update docs so far

* add line for testing close regions

* allow kwaargs in to_csv

* add notebooks

* fix _toc yaml

* Merge Main to Feature (#189)

* docs: README and docs/index revision (#185)

* separate out the goal and specific current dev for Echoview

* small wording changes

* Import Transect Checking from Hake-Labels (#162)

* import transect checking from hake-labels, reduce strictness

* add small bbox distance threshold test

* simplify logic and fix bt et test

* Update echoregions/regions2d/regions2d.py

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* Disentangle Nested If Else in Select Region and Add Region Class Selections (#160)

* Disentangle nested if-else under Regions2D.select_region

* update regions2d functions for region_id docstring and typehints

* add region class

* Update echoregions/regions2d/regions2d.py

Co-authored-by: Wu-Jung Lee <[email protected]>

* Update echoregions/regions2d/regions2d.py

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* add wu jung's suggestions

* add test for both non NaN region id and region class

* small tweak of select_region docstring

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* Merge Main to Feature retry 1 (#190)

* docs: README and docs/index revision (#185)

* separate out the goal and specific current dev for Echoview

* small wording changes

* Import Transect Checking from Hake-Labels (#162)

* import transect checking from hake-labels, reduce strictness

* add small bbox distance threshold test

* simplify logic and fix bt et test

* Update echoregions/regions2d/regions2d.py

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* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Bump actions/download-artifact from 3 to 4 (#164)

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* Disentangle Nested If Else in Select Region and Add Region Class Selections (#160)

* Disentangle nested if-else under Regions2D.select_region

* update regions2d functions for region_id docstring and typehints

* add region class

* Update echoregions/regions2d/regions2d.py

Co-authored-by: Wu-Jung Lee <[email protected]>

* Update echoregions/regions2d/regions2d.py

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* add wu jung's suggestions

* add test for both non NaN region id and region class

* small tweak of select_region docstring

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* refactor region id selection and mask label construction in r2d.mask

* add test for checking when mask labels keys and region ids are not matching

* incorporate valentinas suggestions

* revise 3d and 2d wording

* incorporate valentinas 2nd round review comments

* revise echogram data reading and plotting

* Echoregion's to Echoregions'

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README.md

@@ -5,13 +5,13 @@
 
 ![example workflow](https://github.com/OSOceanAcoustics/echoregions/actions/workflows/pytest.yml/badge.svg)
 
-Echoregions is a tool that interfaces annotations of water column sonar data with Machine Learning (ML) models.
+Echoregions is a Python Package that interfaces with annotations of water column sonar data for training machine learning models or doing other downstream processing such as biomass estimation.
 
 The annotations are typically regions indicating the presence of specific animal species or lines delineating ocean boundaries, such as the seafloor or sea surface, in the "echogram" (sonar images formed by echo returns). The interfacing functionalities operate in two directions:
-- Annotation to ML: Parsing and organizing manual annotations for preparing training and test datasets for ML developments
+- Annotation to ML: Parsing and organizing annotations for preparing training and test datasets for ML developments
 - ML to annotation: Generating annotations from ML predictions that can be used for further downstream processing
 
-At present, functionalities in the Annotation to ML direction have been built for interfacing the Echoview software that is widely used in the fisheries acoustics community. We plan to add functionalities in the ML to Annotation direction in the near future.
+At present, functionalities in the Annotation to ML direction have been built for interfacing the [Echoview](https://echoview.com/products-and-services/echoview/) software that is widely used in the fisheries acoustics community. We plan to add functionalities in the ML to Annotation direction in the near future.
 
 ## Functionalities
 

docs/source/.gitignore

@@ -0,0 +1,2 @@
+transect.*
+.*csv