Update Notebooks

[ctuguinay]

• Primary Changes:
  • Placed all functionality for both classes in 1 notebook.
  • Notebook order is as follows: Parse EVL/EVR -> Look at DataFrame / manipulate it -> Load and plot Sv -> Show masking functionality -> Show saving functionality.
  • All data now is being grabbed from the feature branch. I'll change it to the main branch right before I merge this branch.
  • I kept in the old notebooks just as a reference. I will remove them before merging.
• Secondary Changes:
  • Made use of select_region earlier in r2d.mask to simplify both region_id selection and mask_labels creation (when passed in mask_labels is None)
  • Modified EVR trawl region to make it smaller
  • Fix region plot bug where dataframe was being passed into close_region even though close_region doesn't take in dataframes
  • Added kwaargs to to_csv
    • Index value should be something the user wishes to pass in

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 89.56%. Comparing base (8f58a52) to head (c8e7640). Report is 1 commits behind head on main.

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```diff @@ Coverage Diff @@ ## main #184 +/- ## ========================================== - Coverage 90.58% 89.56% -1.02% ========================================== Files 13 13 Lines 616 556 -60 ========================================== - Hits 558 498 -60 Misses 58 58 ```

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[ctuguinay]

@valentina-s Thanks for the review! I added Echoregions to ReviewNB incorporated most of your changes with just a few comments of my own:

Getting Started

manual annotations -> turns out some annotations from Echoview are automatic annotations. Maybe we can say directly "Echoview" annotations (since this is the focus now)

Mention Echoview earlier

In the previous revision of the description, Wu-Jung made changes that were less Echoview-focused so that this package was not locked into Echoview. I think I agree with these changes too since the annotations don't necessarily need to come from EVL EVR, for instance we can create annotations with our model (in this case it would not be manual though 😆).

Regions2d and Lines

bottom_contours: I usually think of contour as something closed (although I know it is is not necessary). I wonder if bottom boundary is better or maybe there is another term?

bottom_contours (often contour is through to be closed)

Perhaps in this PR, we can sort out this naming issue. I think bottom boundary does not reflect what the data we actually get is: points. Perhaps bottom boundary points? Or bottom boundary vertices? I am also thinking of changing the region contour name with something like region boundary points/vertices.

[valentina-s]

@valentina-s Thanks for the review! I added Echoregions to ReviewNB incorporated most of your changes with just a few comments of my own:

Getting Started

manual annotations -> turns out some annotations from Echoview are automatic annotations. Maybe we can say directly "Echoview" annotations (since this is the focus now) Mention Echoview earlier

In the previous revision of the description, Wu-Jung made changes that were less Echoview-focused so that this package was not locked into Echoview. I think I agree with these changes too since the annotations don't necessarily need to come from EVL EVR, for instance we can create annotations with our model (in this case it would not be manual though 😆).

Regions2d and Lines

bottom_contours: I usually think of contour as something closed (although I know it is is not necessary). I wonder if bottom boundary is better or maybe there is another term?

bottom_contours (often contour is through to be closed)

Perhaps in this PR, we can sort out this naming issue. I think bottom boundary does not reflect what the data we actually get is: points. Perhaps bottom boundary points? Or bottom boundary vertices? I am also thinking of changing the region contour name with something like region boundary points/vertices.

Thanks for adding ReviewNB @ctuguinay, it was very nice to use it! I went through the notebooks again and marked some small things which you can see in the viewer.

• regarding the annotations: maybe we just call them annotations (no need to say manual, often that is assumed anyway). And the first time you introduce Echoview software, provide a link to it

• for the bottom: how about just bottom points: Echoview uses this terminology here and there discussing how a point is part of the bottom?

[ctuguinay]

@valentina-s Thanks for the 2nd round of review! I incorporated all your suggestions. An additional thing I added/changed (based on Wu-Jung's suggestion) was the use of the words sonar, backscatter/Sv data, and echogram. I was using them interchangeably prior, but I tried to make a more clear distinction between them. Let me know what you think of these changes.

[valentina-s]

@ctuguinay Could you just change Echoregion's to Echoregions' since the "s" is part of the package name (in both notebooks). Otherwise it all looks good and the notebooks run fine.