Refactor echogram and associated components using accessor #93

ldr426 · 2023-06-12T20:45:19Z

This PR aims to refactor echoshader project in a dataset-centric and user-based way with xarray accessor.
Related issue(s): #82

Features have been built:

Use xarray accessor.
Generate general echogram visualizations without specified channel and control widgets
- Single frequency mode: Come with a tab for the channels
- Multiple frequency mode: Images vertically displayed in sequence
- Composite mode: Refactor Echogram(s); Tricolor Echogram for Distinguishing Fish Species #82. Include caculating RGB value for grams in get_rgb.py.
Generate an echogram visualization for a specific channel and settings, which can be controlled by widgets.
- channel select: Selet widget to input specific channel
- Sv range slider: Slider to narrow or edit range of Sv presenting.
- color map: Text input widget to input colormap.
For color map, we can customize using list input. Input list like ['#0000ff', ...] into color map widget or as parameter. Converting from str to list is done in get_string_list.py.

test.py is a testing and displaying file using in dev period, and concatenated_MVBS.nc is testing dataset.
EC2 example: http://34.209.26.1:5008/test

for more information, see https://pre-commit.ci

ldr426 · 2023-06-14T18:42:28Z

@ldr426 : I took a look at the the pre-commit failing. Could you correct these? The one with the undefined names, I think you could use Literal -- google a bit to see what is the most appropriate.

@leewujung: Thanks for reviewing and instruction! Has solved the issue

ldr426 · 2023-06-14T18:43:46Z

@ldr426 : Could you change the file names of echoshader/Test.ipynb and echoshader/new_version/test.ipynb?

The first one seems to be used as a demo? If that's the case, could you put that into the documentation? Give the notebook a name that is specific to the echogram module.

The second one seems to be your prototyping notebook? If that's the case, I suggest that you make a new folder notebooks_prototype for that usage and give the notebook a name specific to the module you are prototyping.

@leewujung: The jupyter files are for testing, as their names imply. I just delete them.

leewujung · 2023-06-14T19:18:31Z

Hey @ldr426 : one suggestion: could you restrict the panning motion to only move horizontally (so it is a left-right scrolling motion), so that the echogram does not get out of view vertically? Thanks!

ldr426 · 2023-06-14T19:26:31Z

Hey @ldr426 : one suggestion: could you restrict the panning motion to only move horizontally (so it is a left-right scrolling motion), so that the echogram does not get out of view vertically? Thanks!

Hey @leewujung : Actually, you could switch pan tool to moving vertically and horizontally. (Click and hold the button for about one sec, the tool options will show)

leewujung · 2023-06-14T22:42:26Z

Ah I see -- great, I didn't know that! And you are right that if we restrict the pan to be horizontal, it'll have problems once people zoom in.

valentina-s

I added a few comments. I played a bit with the demo: my main challenge is that after I changed the values several times for the Sv_range the demo stopped making any changes: most probably it queued all the options I gave it while I wanted it to register only the last one. That made click even more which most probably made it worse. If there is a way to cancel or time out a sequence of requests it will make it better.

valentina-s · 2023-06-15T03:33:10Z

echoshader/new_version/echogram.py

+        )
+
+        self.color_map = panel.widgets.TextInput(
+            name="Color Map", value="jet", placeholder="jet"


Colormap is one word

Hard to know if one needs to type in, and what colormap options are. I wonder if there is an option to have a drop down menu with a few popular colormaps and then Other option in which to type an extra colormap. Add a link to colormaps.

valentina-s · 2023-06-15T16:03:16Z

echoshader/new_version/echogram.py

+
+        self.Sv_range_slider = panel.widgets.EditableRangeSlider(
+            name="Sv Range Slider",
+            start=self.MVBS_ds.Sv.actual_range[0],


I forgot if we decided this variable is always called MVBS_ds, or we can make it more general. For now I guess it is fine but in future maybe somebody will try to plot an echogram before MVBS.

I think we can do the overall change from MVBS_ds to just ds.

To ensure people put in the right type of dataset, I think we should add a input checking method that is called in Echogram.__init__ to check for the following:

existence of the Sv data variable

Sv data variable should have dimensions ("channel", "ping_time", "echo_range")

We should also allow depth in the last dimension, but we can do that later -- I'll create an issue so that we do not forget.

Hey @leewujung, issue for this has been created: #98
please add more details if you want.

valentina-s · 2023-06-15T16:05:13Z

echoshader/echogram.py

@@ -146,7 +148,7 @@ def __init__(self, MVBS_ds):

        # http://holoviews.org/user_guide/Applying_Customizations.html
        self.gram_opts = holoviews.opts(
-            invert_yaxis=False, tools=["hover", "box_select"]
+            invert_yaxis=False, tools=["hover", "box_select", "lasso_select"]


I tried the lasso but I could not understand how to use it.

Nevermind, I tried lasso today and now it is working: yesterday I could make only a box with it?!

Hi @valentina-s, now lasso option is just a option. We need to add corresponding function (plotting and data extracting) later.

valentina-s · 2023-06-15T16:09:01Z

echoshader/new_version/echogram.py

+            rgb_ch = {"R": None, "G": None, "B": None}
+
+            for ch, color in rgb_map.items():
+                rgb_ch[color] = convert_to_color(


one the actual RGB plot when you hover you see value for RGB some big number, what is it? I expected to see 3 values between 0-255.

Hi @valentina-s: Mentioned in #82 (comment). Maybe the number is some encoding of numpy time. Not sure the reason yet.

valentina-s · 2023-06-15T16:31:41Z

echoshader/new_version/get_rgb.py

+import numpy
+
+
+def convert_to_color(ds_Sv, channel_sel, th_bottom, th_top):


Functions like this can have tests associated with them

valentina-s · 2023-06-15T17:13:03Z

Hey @ldr426 : one suggestion: could you restrict the panning motion to only move horizontally (so it is a left-right scrolling motion), so that the echogram does not get out of view vertically? Thanks!

Hey @leewujung : Actually, you could switch pan tool to moving vertically and horizontally. (Click and hold the button for about one sec, the tool options will show)

These are nice features but not so obvious: at some point @ldr426 could record a video of a demo to show off these options :)

valentina-s · 2023-06-15T17:24:21Z

In the demo: single frequency and multiple frequency plots are linked, but tricolor is not: maybe best not to link them since they are three different examples, not one widget.

* Bugs fix (#88) * Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Refactor echogram and associated components using accessor (#93) * Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <[email protected]> * Add feature of select box (#103) * Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset * Add selected box plotting and extracting feature * Add python doc for extracting box function * Delete testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve line too long issue * Change name from ambiguous `gram` to echogram --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <[email protected]> * Feature echomap (#122) * Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset * Add selected box plotting and extracting feature * Add python doc for extracting box function * Delete testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add map plotting * Add features of curtain and some comments * Draft PR for map part * Update track, curtain and linked connection logic * Add colormap type (list) for curtain * Add testing file for demo * Delete .DS_Store * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Store link state of curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete .DS_Store * Add .DS_Store to .gitignore * change name of varaiable "gram_plot" to "echogram" * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Update variable name "old_vmin" to "data_min" --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <[email protected]> * Feature stats (#130) * Change importing format to comply with develop mode * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve that curtain could not dynamically render * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Select box correctly when not inverting y-axis * local testing * y-axis testing * Y-axis testing * add options for echogram * del testing files * add options * set y-axis inversion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing files * rename testing file * a * a * lasso testing * add for testing * 06/06/2023 - testing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete echoshader/new_version directory * Add testing files * rename testing file * a * a * lasso testing * add for testing * Add trigram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ADD testing file * del old one * add test.ipynb * change "= None" to "is None" * little fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Sync * Add docstring and customizing colormap * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Delete .DS_Store * Delete .DS_Store * Solve Undefined Name * Use Literal to solve undefined issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issues * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve 'line too long' issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve "compare False should using is not" * Delete testing files * delete testing toy dataset * Add selected box plotting and extracting feature * Add python doc for extracting box function * Delete testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add map plotting * Add features of curtain and some comments * [pre-commit.ci] pre-commit autoupdate (#105) updates: - [github.com/igorshubovych/markdownlint-cli: v0.34.0 → v0.35.0](igorshubovych/markdownlint-cli@v0.34.0...v0.35.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Draft PR for map part * Update track, curtain and linked connection logic * Add colormap type (list) for curtain * Add testing file for demo * Delete .DS_Store * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Store link state of curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] pre-commit autoupdate (#123) updates: - [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Delete .DS_Store * Add .DS_Store to .gitignore * change name of varaiable "gram_plot" to "echogram" * Update echoshader/new_version/echogram.py Co-authored-by: Wu-Jung Lee <[email protected]> * Update variable name "old_vmin" to "data_min" * Add stats part * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Create functions for repetitive code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * delete useless importing lib * Resolve conflict * Resolve conflicts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add python doc * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add docstring * Solve pre-commit issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <[email protected]> * Final-version Refactoring (#131) * Create folders for new refactoring * Add core.py, echogram.py, map.py and utils.py * Add files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add moored point in map & config in utils * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add echogram in core.py and docstring * Lined echogram and map for 2nd version * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit issue * High-order structure building * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add underlying code for hist and curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * sovle pre-commit * Add curtain, hist and table * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix little bugs ahout curtain and hist * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add subscriber about echogram * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add curtain * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add new requirements * Add bidirectional control logic * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add reset tool * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add customized opts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update file stucture * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add __init__.py * Add more docstring * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add testing demo * erase pre-commit warning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add testing files (#139) * Fix channel select bugs * Add testing files * solve pre-commit warnings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * extract out testing files * Add pytest and CI config * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Set the testing files as expected for a user * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Make the testing files to pytest format * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Improve testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add more testing cases * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Dev test ci (#142) * Adding branches for testing * renaming workflow to workflows * addign extra empty line to trigger the workflow * Put the branches into bullet points * remove test coverage * Rename test.py to test_plots.py Adding underscrore for discoverability * fixing get_data call * limit to python 3.10 * pin pandas * test with unpinned Python * Add document files (#140) * Fix channel select bugs * Add testing files * solve pre-commit warnings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * extract out testing files * Add pytest and CI config * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Set the testing files as expected for a user * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Make the testing files to pytest format * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Improve testing files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add more testing cases * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add docs for generating data * Add index and design intro page * Add index and structure intro pages * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * code blocks should have a language specified * Add data generation docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add echogram showcases * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add track and hist exampls * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add panel server setup * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve pre-commit * Improve based on feedback * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * del deprecated testing files * Add Configuration file v2 (.readthedocs.yaml) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Solve conflicts * Solve doc conflicts --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update README.md * Dev patch (#147) * Update setup_server.md removing repeating sentence from panel * splitting user and development installation instructions * removing intro.md * Update index.md adding a more general description and a note that folks can skip to the examples as this will be what most users need. Later we may reorganize the order of the sections. * language * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update _toc.yml * Update index.md Fix typo --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Dingrui Lei <[email protected]> * Fix-dev (#149) * improve dev based on feedback * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wu-Jung Lee <[email protected]> Co-authored-by: Valentina Staneva <[email protected]>

ldr426 and others added 30 commits June 5, 2023 11:17

Change importing format to comply with develop mode

2900e62

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

b1cf28b

for more information, see https://pre-commit.ci

Solve that curtain could not dynamically render

6c41175

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

4af5658

for more information, see https://pre-commit.ci

Select box correctly when not inverting y-axis

fa3bf2b

local testing

8e0b268

y-axis testing

1f3670f

Y-axis testing

02b20c3

add options for echogram

6e54923

del testing files

34af324

add options

2abe297

set y-axis inversion

6a3d8f7

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

417a6f7

for more information, see https://pre-commit.ci

Add testing files

9babf40

rename testing file

87a968c

a

9f7c23a

a

0ead50b

lasso testing

9d22f5a

add for testing

82fcfd3

06/06/2023 - testing

268a2ab

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

efd1427

for more information, see https://pre-commit.ci

Add trigram

5346214

Merge branch 'feature-refactor' into test

8948f7b

Merge branch 'OSOceanAcoustics:dev' into dev

8aa8a59

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

943753b

for more information, see https://pre-commit.ci

Delete echoshader/new_version directory

aa6c536

Add testing files

9798c0f

rename testing file

ecfaa4c

a

ec3d524

a

b7083f1

ldr426 and others added 8 commits June 14, 2023 10:51

Use Literal to solve undefined issue

d00aceb

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

26be0f5

for more information, see https://pre-commit.ci

Solve 'line too long' issues

64e5f50

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

9851bff

for more information, see https://pre-commit.ci

Solve 'line too long' issue

7ffec4a

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

64b3730

for more information, see https://pre-commit.ci

Solve "compare False should using is not"

719f9a7

Delete testing files

8b47f30

ldr426 requested a review from leewujung June 14, 2023 18:41

delete testing toy dataset

75f6bec

valentina-s reviewed Jun 15, 2023

View reviewed changes

leewujung approved these changes Jun 15, 2023

View reviewed changes

ldr426 merged commit f9ae76c into OSOceanAcoustics:dev Jun 15, 2023

ldr426 deleted the refactor-echogram branch June 15, 2023 18:52

ldr426 restored the refactor-echogram branch June 15, 2023 18:52

ldr426 deleted the refactor-echogram branch June 15, 2023 20:37

leewujung mentioned this pull request Jun 30, 2023

Refactor Echogram(s); Tricolor Echogram for Distinguishing Fish Species #82

Closed

3 tasks

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Refactor echogram and associated components using accessor #93

Refactor echogram and associated components using accessor #93

ldr426 commented Jun 12, 2023 •

edited

Loading

ldr426 commented Jun 14, 2023 •

edited

Loading

ldr426 commented Jun 14, 2023

leewujung commented Jun 14, 2023

ldr426 commented Jun 14, 2023 •

edited

Loading

leewujung commented Jun 14, 2023

valentina-s left a comment

valentina-s Jun 15, 2023

valentina-s Jun 15, 2023

valentina-s Jun 15, 2023

leewujung Jun 15, 2023

ldr426 Jun 15, 2023

valentina-s Jun 15, 2023

valentina-s Jun 15, 2023

ldr426 Jun 15, 2023

valentina-s Jun 15, 2023

ldr426 Jun 15, 2023 •

edited

Loading

valentina-s Jun 15, 2023

valentina-s commented Jun 15, 2023

valentina-s commented Jun 15, 2023

		import numpy


		def convert_to_color(ds_Sv, channel_sel, th_bottom, th_top):

Refactor echogram and associated components using accessor #93

Refactor echogram and associated components using accessor #93

Conversation

ldr426 commented Jun 12, 2023 • edited Loading

ldr426 commented Jun 14, 2023 • edited Loading

ldr426 commented Jun 14, 2023

leewujung commented Jun 14, 2023

ldr426 commented Jun 14, 2023 • edited Loading

leewujung commented Jun 14, 2023

valentina-s left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

ldr426 Jun 15, 2023 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

valentina-s commented Jun 15, 2023

valentina-s commented Jun 15, 2023

ldr426 commented Jun 12, 2023 •

edited

Loading

ldr426 commented Jun 14, 2023 •

edited

Loading

ldr426 commented Jun 14, 2023 •

edited

Loading

ldr426 Jun 15, 2023 •

edited

Loading