Generating GeoJSON to support NowCoast team

saeed-moghimi-noaa commented 1 year ago

@Erin-nagel @agibbons-NOAA @josephzhang8 @cuill @feiye-vims @moghimis @gseroka @yangz888

Jul 19, 2022 | STOFS 3D GeoJSON Attendees: Adam Gibbons - NOAA Affiliate Erin Nagel - NOAA Affiliate Fei Ye John Kelley - NOAA Federal Linlin Cui Saeed Moghimi - NOAA Federal Y. Joseph Zhang Zizang Yang - NOAA Federal

Action items

Generating GeoJSON for STOFS3D

GeoJSON for Max disturbance
For max elev to add when that max value happened for specific
Include the start and end time of the forecast A set of hourly water surface elevation GeoJSON (2nd priority)

Metadata to GeoJSON

Valid time in GeoJson
Include rgb value + elevation value
Other metadata
When you click on a polygon what would you like to see?

Time stamp: hourly 2D outputs (STOFS-3D Atlantic) (2nd priority)
Adding current at 4.5m (3rd priority)

1st priority: Add above mention information to current max elev GeoJSON file

2nd: Then work on generating hourly GeoJSON files

Hi Saeed,

Thank you for reviewing the max water level STOFS3D web map service. Adam is currently working on the map interaction feature to query the service, however the GeoJSON only contains RGBA values rather than water level values and we would like to request some modifications to the current GeoJSON to include some additional attributes. Besides adding water level values is there any additional information your team would like to include?

Moving forward we would like to add an hourly STOFS3D service and I have included some general requirements and additional metadata for the GeoJSON files your team produces, please pass the requirements along to your team and let me know if you have any questions.

GeoJSON STOFS3D Product Requirements for nowCOAST:

Format: The filename must include the valid cycle time of the forecast for the first timestamp and the valid hourly forecast time or forecast time of the maximum water level disturbance for the second timestamp depending on the product Each feature-level object must include the following property names: "id","maxWaterLevel", "minWaterLevel", "verticalDatum", "units", "rgba" Example:

 properties": {
  "id": 1,
  "maxVal": 0.1,
  "minVal": 0.4,
  "verticalDatum": "NAVD88",
  "unit": "meters",
  "rgba": "#000080"
 }

Note: If there is only one water level elevation value per polygon, then include the property name "waterLevel" instead of "minWaterLevel" and "maxWaterLevel", but this attribute should be consistent for each product All property names must use the "camelCase" naming convention "id","maxWaterLevel", "minWaterLevel" properties must be encoded as true numeric values (i.e. not enclosed with quotes) and each feature-level object must have a unique id The top-level object should contain a coordinate reference system property Example:

"crs": { "type": "name", "properties": { "name": "EPSG:4326" } Polygons and MultiPolygons should follow the right-hand rule, as follows: The exterior ring should be counterclockwise. Interior rings should be clockwise. Example: The Shapely User Manual — Shapely 1.8.2 documentation All Polygons and MultiPolygons must be checked for validity and may not possess any overlapping exterior or interior rings, self intersections, duplicate nodes, sliver polygons, or gaps between polygons 1) Max Water Level Forecast Product

Suggested Product Path and Filename Format: s3://noaa-nos-stofs3d-pds/yyyymmdd/system_region_product_YYYYMMDDtHHz_YYYYMMDDtHHz.json

Example: s3://noaa-nos-stofs3d-pds/20220430/stofs3d_atlantic_maxwldisturbance 20220430t12z_20220430t23z .json

Note: Filename must include the valid cycle time of the forecast for the first timestamp (e.g 20220430T12Z) and the valid forecast time of the maximum water level disturbance for the second timestamp (e.g 20220430t23z)

2) Hourly Water Level Forecast Product

Suggested Product Path and Filename Format: s3://noaa-nos-stofs3d-pds/yyyymmdd/forecast_cycle/region/system_region_fcst_YYYYMMDDtHHz_YYYYMMDDtHHz.json :

Examples:

s3://noaa-nos-stofs3d-pds/20220430/12/atlantic/stofs3d_atlantic_f001_20220430t12z_20220430t13z.json
s3://noaa-nos-stofs3d-pds/20220430/12/atlantic/stofs3d_atlantic_f002_20220430t12z_20220430t14z.json
s3://noaa-nos-stofs3d-pds/20220430/12/atlantic/stofs3d_atlantic_f003_20220430t12z_20220430t15z.json
s3://noaa-nos-stofs3d-pds/20220430/12/atlantic/stofs3d_atlantic_f004_20220430t12z_20220430t16z.json
s3://noaa-nos-stofs3d-pds/20220430/12/atlantic/stofs3d_atlantic_f005_20220430t12z_20220430t17z.json
s3://noaa-nos-stofs3d-pds/20220430/12/atlantic/stofs3d_atlantic_f006_20220430t12z_20220430t18z.json

Note: Filename must include the cycle time of the forecast for the first timestamp (e.g. 20220430t12z) and the valid hourly forecast time for the second timestamp (e.g 20220430t18z)

Thank you,

nowCOAST Team

Erin Nagel - NOAA Affiliate

Fri, Jul 8, 10:24 AM (11 days ago)

to me, John, Adam

saeed-moghimi-noaa commented 1 year ago

@JohnGWKelley @erin-nagel @agibbons-NOAA @josephzhang8 @cuill @feiye-vims @moghimis @gseroka @yangz888

Nice website: https://www.gdacs.org/

yangz888 commented 1 year ago

Thanks, Saeed! - Zizang

On Wed, Jul 20, 2022 at 11:23 AM Saeed Moghimi @.***> wrote:

@JohnGWKelley https://github.com/JohnGWKelley @erin-nagel https://github.com/erin-nagel @agibbons-NOAA https://github.com/agibbons-NOAA @josephzhang8 https://github.com/josephzhang8 @cuill https://github.com/cuill @feiye-vims https://github.com/feiye-vims @moghimis https://github.com/moghimis @gseroka https://github.com/gseroka @yangz888 https://github.com/yangz888

Nice website: https://www.gdacs.org/

— Reply to this email directly, view it on GitHub https://github.com/schism-dev/pyschism/issues/44#issuecomment-1190424493, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP7TWSG2VI4MXY7BYFKRQOTVVAKW5ANCNFSM54BFEXFA . You are receiving this because you were mentioned.Message ID: @.***>

josephzhang8 commented 1 year ago

Thx Saeed; nice landing page.

-Joseph

Joseph Zhang Office: (804) 684 7466 Web: schism.wiki

From: Saeed Moghimi @.> Sent: Wednesday, July 20, 2022 11:23 AM To: schism-dev/pyschism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/pyschism] Generating GeoJSON to support NowCoast team (Issue #44)

[EXTERNAL to VIMS received message]

Nice website: https://www.gdacs.org/https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.gdacs.org%2F&data=05%7C01%7Cyjzhang%40vims.edu%7C4dec1fdd782d45f9400e08da6a63cb3d%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C637939274084835039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=urvQtObFBCALh15aU0IqCdUGNltkyuApP2dF3yJt%2BWg%3D&reserved=0

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saeed-moghimi-noaa commented 1 year ago

Hi @cuill

Any update on this issue?

Thanks, -Saeed

@feiye-vims @moghimis @gseroka @yangz888 @erin-nagel @agibbons-NOAA @josephzhang8

cuill commented 1 year ago

Hi Saeed,

The script to generate max disturbance was revised and added to the postprocessing workflow on Frontera. However, the STOFS3D forecast on Frontera was paused because of the texascale event this week.

I will let you know when the data is available on the S3 bucket next week.

Best, Linlin

saeed-moghimi-noaa commented 1 year ago

Hi @cuill

Thanks for the quick update.

Hi @yangz888 We may need to include this on the operational workflow as well.

Thanks, -Saeed

FYI @erin-nagel

yangz888 commented 1 year ago

Hi @cuill https://github.com/cuill & Saeed, Let's talk about it at the bi-weekly meeting next Tuesday. Thanks!

Zizang

On Thu, Jul 28, 2022 at 5:49 PM Saeed Moghimi @.***> wrote:

Hi @cuill https://github.com/cuill

Thanks for the quick update.

Hi @yangz888 https://github.com/yangz888 We may need to include this on the operational workflow as well.

Thanks, -Saeed

FYI @erin-nagel https://github.com/erin-nagel

— Reply to this email directly, view it on GitHub https://github.com/schism-dev/pyschism/issues/44#issuecomment-1198665863, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP7TWSDGUMFGY3JXECPCBYLVWL54ZANCNFSM54BFEXFA . You are receiving this because you were mentioned.Message ID: @.***>

cuill commented 1 year ago

@yangz888

Sounds good! -Linlin

saeed-moghimi-noaa commented 1 year ago

Thanks to Linlin:

Update the script to add the TACC ssystem. However the TACC system is not working so there is no new GeoJSON
@cuill to share a sample GeoJSON with @erin-nagel

Rethink the disturbance to have more physical understandable (to public) definition: @josephzhang8

Maximum disturbance
- Colors over land mean water height above ground.
- Colors over water mean water height above NAVD88.

@yangz888

To include GeoJSON script to the WCOSS2 to have the files generated
@yangz888 will inform the team when the scripts implemented and the GeoJSON is being uploaded to S3 bucket.

cuill commented 1 year ago

GeoJSON files for max and hourly disturbance are available on S3 bucket:

https://noaa-nos-stofs3d-pds.s3.amazonaws.com/index.html#STOFS3D-Atl-VIMS/20220801/

stofs3d_atlantic_disturbance20220731t00z*.json stofs3d_atlantic_max_disturbance_20220731t01z_20220803t00z.json

saeed-moghimi-noaa commented 1 year ago

@erin-nagel @agibbons-NOAA @josephzhang8 @cuill @feiye-vims @moghimis @gseroka @yangz888

All,

First of all please make sure to communicate through this github issue for follow ups and updates:

Recent Email

STOFS3D Max Disturbance and Hourly GeoJSON Review
18 messages
________________________________________
Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>   Tue, Aug 30, 2022 at 12:38 PM
To: Linlin Cui <lcui@vims.edu>
Cc: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Linlin,

Thank you for making the changes to STOFS3D GeoJSON content and adding the hourly forecast. After reviewing the max disturbance and hourly GeoJSON outputs and comparing it to the services provided by LSU displayed on the CERA website https://cera.coastalrisk.live/, it appears the GeoJSON is missing data, which is captured in the image below comparing the GeoJSON displayed in QGIS on the left and the LSU STOFS3D service on the right. 

So it may be possible that we are losing data during the mesh to contour conversion or possibly we need to use the data range from the model output, rather than a set data range of 0.5m to 2.9m, for the levels used to create the contours. 

The data range shown in the legend of LSU's STOFS3D service is < 0m to > 3m, do you know how the LSU team is creating their STOFS3D max disturbance service? Are they using the ADCIRC NetCDF output your team has generated to produce polygons? 

Let me know if you need any additional information and if you can look into this discrepancy.

Thank you,

Erin

-- 

Erin Nagel
Software Engineer, ERT
NOAA/NOS/OCS/CSDL

________________________________________
Linlin Cui <lcui@vims.edu>  Tue, Aug 30, 2022 at 1:16 PM
To: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>
Cc: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Erin,

So it may be possible that we are losing data during the mesh to contour conversion or possibly we need to use the data range from the model output, rather than a set data range of 0.5m to 2.9m, for the levels used to create the contours. 

Originally, we used Folium to generate maxelev html file. However, the html file was too large, then we specified the ranges (0.5-3.0) to show. I think this causes nodata areas. I can add model ranges back into GeoJSON file.

The data range shown in the legend of LSU's STOFS3D service is < 0m to > 3m, do you know how the LSU team is creating their STOFS3D max disturbance service? Are they using the ADCIRC NetCDF output your team has generated to produce polygons? 

LSU team are using ADCIRC NetCDF files we generated.

Best,
Linlin

From: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>
Date: Tuesday, August 30, 2022 at 12:39 PM
To: Linlin Cui <lcui@vims.edu>
Cc: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Subject: STOFS3D Max Disturbance and Hourly GeoJSON Review

[EXTERNAL to VIMS received message] 

Hi Linlin, 

Thank you for making the changes to STOFS3D GeoJSON content and adding the hourly forecast. After reviewing the max disturbance and hourly GeoJSON outputs and comparing it to the services provided by LSU displayed on the CERA website https://cera.coastalrisk.live/, it appears the GeoJSON is missing data, which is captured in the image below comparing the GeoJSON displayed in QGIS on the left and the LSU STOFS3D service on the right.  

[Quoted text hidden]

________________________________________
Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>   Tue, Aug 30, 2022 at 2:31 PM
To: Linlin Cui <lcui@vims.edu>, Carola Kaiser <ckaiser@cct.lsu.edu>
Cc: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Linlin

I think CERA uses netcdf file to determine the range and does not use a set range. I cc here @Carola Kaiser  to chime in.

Best,
-Saeed

______________________________________________________
Saeed Moghimi, PhD
NOS Storm Surge Modeling Team Lead
Coastal Marine Modeling Branch, Coast Survey Development Laboratory, Office of Coast Survey at NOAA National Ocean Service.
Address: 1315 East West Hwy, Room 6607, Silver Spring, Maryland  20910 
Phone: ‪(302) 827-3986

The contents of this message are mine personally and do not necessarily reflect any position of NOAA.

[Quoted text hidden]

________________________________________
Carola Kaiser <ckaiser@cct.lsu.edu> Wed, Aug 31, 2022 at 11:51 AM
To: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Linlin Cui <lcui@vims.edu>
Cc: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi All,

Yes, CERA uses the netcdf file to read the data. The range is not set to a fixed range with regard to the min/max values.

Carola

~~~~~~~~~~~~~~~~~~~~~~~~~~
Carola Kaiser, IT Consultant & GIS Web Development
Center for Computation & Technology
Louisiana State University
e-mail: ckaiser@cct.lsu.edu
CERA: https://cera.coastalrisk.live
[Quoted text hidden]

________________________________________
Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>   Wed, Aug 31, 2022 at 1:11 PM
To: Carola Kaiser <ckaiser@cct.lsu.edu>
Cc: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Linlin Cui <lcui@vims.edu>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Carola,

Thanks for clarifying and how is your team using the ADCIRC grid netCDF file to display STOFS3D maximum disturbance and maximum water height in CERA?
Thank you,

Erin
[Quoted text hidden]

________________________________________
Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>   Wed, Aug 31, 2022 at 2:09 PM
To: Carola Kaiser <ckaiser@cct.lsu.edu>
Cc: Linlin Cui <lcui@vims.edu>, Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Linlin and Erin,

Perhaps we can do the same on the GeoJSON side. For instance, determine the range based on the data (mn and max over all) for each run cycle and keep it the same across all GeoJSONS for that specific run cycle. 

Since we have in the meta data it can be used to generate a new legend for each run cycle.

Does this make sense?

Thanks,
-Saeed 

______________________________________________________
Saeed Moghimi, PhD
NOS Storm Surge Modeling Team Lead
Coastal Marine Modeling Branch, Coast Survey Development Laboratory, Office of Coast Survey at NOAA National Ocean Service.
Address: 1315 East West Hwy, Room 6607, Silver Spring, Maryland  20910 
Phone: ‪(302) 827-3986

The contents of this message are mine personally and do not necessarily reflect any position of NOAA.

On Wed, Aug 31, 2022 at 11:51 AM Carola Kaiser <ckaiser@cct.lsu.edu> wrote:
[Quoted text hidden]

________________________________________
Linlin Cui <lcui@vims.edu>  Wed, Aug 31, 2022 at 5:25 PM
To: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Carola Kaiser <ckaiser@cct.lsu.edu>
Cc: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Saeed,

We may need to mask the data first to remove very large values on land boundary then calculate (min, max). I’ll take a look at the script. 

Best,
Linlin
[Quoted text hidden]

________________________________________
Carola Kaiser <ckaiser@cct.lsu.edu> Thu, Sep 1, 2022 at 10:47 AM
To: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>
Cc: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Linlin Cui <lcui@vims.edu>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Erin, 
We are currently using a static classification with 32 levels. The levels have set intervals of 0.3 m. However, the minimum class contains all values < 0.3m and the maximum class all values > 10 ft. With that, we get map legend that stay the same for all runs, so that the runs can be easily compared to each other.

Regards, Carola
~~~~~~~~~~~~~~~~~~~~~~~~~~
Carola Kaiser, IT Consultant & GIS Web Development
Center for Computation & Technology
Louisiana State University
e-mail: ckaiser@cct.lsu.edu
CERA: https://cera.coastalrisk.live

From: Erin Nagel - NOAA Affiliate [mailto:erin.nagel@noaa.gov] 
Sent: Wednesday, August 31, 2022 12:12 PM
To: Carola Kaiser <ckaiser@cct.lsu.edu>
[Quoted text hidden]
[Quoted text hidden]

________________________________________
Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>   Thu, Sep 1, 2022 at 11:41 AM
To: Carola Kaiser <ckaiser@cct.lsu.edu>
Cc: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Linlin Cui <lcui@vims.edu>, John Kelley - NOAA Federal <john.kelley@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Carola,

Thanks for the information and are you reading and displaying the data directly from the ADCIRC NetCDF or are you converting the ADCIRC NetCDF data into another format like ESRI Shapefile, to display max disturbance?

Erin 
[Quoted text hidden]

________________________________________
John Kelley - NOAA Federal <john.kelley@noaa.gov>   Wed, Sep 7, 2022 at 3:52 PM
To: Linlin Cui <lcui@vims.edu>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>
Cc: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Linlin and Saeed,

Do you have an estimate on when we might have a new geoJSON file to test?

John

[Quoted text hidden]

________________________________________
Linlin Cui <lcui@vims.edu>  Wed, Sep 7, 2022 at 4:06 PM
To: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>
Cc: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi John,

Sorry for the delay in getting new geoJSON files. I have been tied up with other tasks. I will work on it the rest of the week. 

Before starting, I would like to know how many levels would your group like to be included in geoJSON files.  For reference, CERA has 32 levels. And let you know, increasing levels will increase file size accordingly.

Best,
Linlin
[Quoted text hidden]

________________________________________
John Kelley - NOAA Federal <john.kelley@noaa.gov>   Wed, Sep 7, 2022 at 6:22 PM
To: Linlin Cui <lcui@vims.edu>
Cc: Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
LinLin,

Let's go with 32 levels as well.

We appreciate you working on this important task.

John

[Quoted text hidden]

________________________________________
Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>   Wed, Sep 7, 2022 at 6:32 PM
To: Linlin Cui <lcui@vims.edu>
Cc: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Linlin,

Thanks for working on this, to handle the increased file size if possible can you use a different output file driver preferably a geopackage or shapefile.

Thank you,

Erin
[Quoted text hidden]

________________________________________
Linlin Cui <lcui@vims.edu>  Thu, Sep 8, 2022 at 1:54 PM
To: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>
Cc: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Erin,

Thanks for suggesting with a different output driver. I have generated three types (json, gpkg, and shp) of dataset for your test. You can download data here:

http://ccrm.vims.edu/yinglong/Cui/nowCOAST/

There are 32 polygons, with the first one covering data less than 0, and the last one covering greater than 3.0 m and less than model’s maximum. The interval is 0.1 m.

One method to further reduce the file size is to decrease decimals. But it seems to change the geometry type from “MultiPolygon” to “FeatureCollection” after doing make_valid. I am not sure if this will work on your end. 

Please let me know which data format you would prefer. Then I’ll add the revision to VIMS forecast workflow.
[Quoted text hidden]

________________________________________
Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>   Fri, Sep 9, 2022 at 9:51 AM
To: Linlin Cui <lcui@vims.edu>
Cc: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Linlin,

Thank you for the quick turnaround and including all the requested outputs, we prefer a GeoPackage format for all outputs, and below is the visualized GeoPackage max disturbance output with a random color ramp applied, the output contains all of the data and attributes requested. 

However, the filename for the max disturbance output contains the start and end time of the forecast cycle (e.g stofs3d_atlantic_max_disturbance_20220807t01z_20220808t00z.gpkg) rather than the valid forecast time for when the maximum water level disturbance occurs within the forecast cycle. Let me know if it is possible to add that information to the filename, if this is not possible, I suggest only generating a water level GeoPackage file for each hour for the full forecast, instead of generating both the hourly water level and the max disturbance outputs.

Thank you,

Erin 

[Quoted text hidden]

________________________________________
Linlin Cui <lcui@vims.edu>  Fri, Sep 9, 2022 at 10:18 AM
To: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>
Cc: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Erin,

The time for max disturbance is spatially varying. We calculate max disturbance at each node based on its timeseries during forecast cycle. It is not possible to be included in the filename. 

Best,
Linlin

From: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>
Date: Friday, September 9, 2022 at 9:52 AM
To: Linlin Cui <lcui@vims.edu>
Cc: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Subject: Re: STOFS3D Max Disturbance and Hourly GeoJSON Review
Hi Linlin, 

Thank you for the quick turnaround and including all the requested outputs, we prefer a GeoPackage format for all outputs, and below is the visualized GeoPackage max disturbance output with a random color ramp applied, the output contains all of the data and attributes requested. 

However, the filename for the max disturbance output contains the start and end time of the forecast cycle (e.g stofs3d_atlantic_max_disturbance_20220807t01z_20220808t00z.gpkg) rather than the valid forecast time for when the maximum water level disturbance occurs within the forecast cycle. Let me know if it is possible to add that information to the filename, if this is not possible, I suggest only generating a water level GeoPackage file for each hour for the full forecast, instead of generating both the hourly water level and the max disturbance outputs.

Thank you,

Erin 
[Quoted text hidden]

________________________________________
Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>   Fri, Sep 9, 2022 at 11:19 AM
To: Linlin Cui <lcui@vims.edu>
Cc: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Linlin,

Thanks for clarifying, let's move forward with the hourly water level geopackage files only. Let me know when the sample hourly files are available on http://ccrm.vims.edu/yinglong/Cui/nowCOAST/.

Thank you,

Erin
[Quoted text hidden]

________________________________________
Linlin Cui <lcui@vims.edu>  Fri, Sep 9, 2022 at 12:01 PM
To: Erin Nagel - NOAA Affiliate <erin.nagel@noaa.gov>
Cc: John Kelley - NOAA Federal <john.kelley@noaa.gov>, Saeed Moghimi - NOAA Federal <saeed.moghimi@noaa.gov>, Adam Gibbons - NOAA Affiliate <adam.m.gibbons@noaa.gov>
Hi Erin,

The sample files are ready on
http://ccrm.vims.edu/yinglong/Cui/nowCOAST/
[Quoted text hidden]

saeed-moghimi-noaa commented 1 year ago

@erin-nagel @agibbons-NOAA @josephzhang8 @cuill @feiye-vims @moghimis @gseroka @yangz888

Hi Erin,

Please let @cuill and @yangz888 know about the status of your testing and if you need any changes regrading GeoJSON and GeoPackage. We are working closely with NOAA/NCO to finalize python requirement and we need to provide final python script to them asap.

Thanks, -Saeed

erin-nagel commented 1 year ago

@cuill @yangz888 @agibbons-NOAA @josephzhang8 @cuill @feiye-vims @moghimis @gseroka @yangz888

STOFS3D Team,

For the max disturbance files would it be possible to add two additional attributes to the GeoPackage file for each polygon containing a minimum datetime and a maximum datetime, to capture the time range for when the spatially varying max disturbance occurs during the forecast cycle?

Otherwise we have no additional changes and please go ahead with posting the STOFS3D hourly disturbance GeoPackage files for the full forecast period (e.g. 72 hours) to the noaa-nos-stofs3d-pds S3 bucket.

Thank you, Erin

saeed-moghimi-noaa commented 1 year ago

@cuill @yangz888 @agibbons-NOAA @josephzhang8 @cuill @feiye-vims @moghimis @gseroka @yangz888

Erin, Thanks for your prompt response.

I will let @cuill to comment on the datetime request.

Best, -Saeed

cuill commented 1 year ago

@erin-nagel @saeed-moghimi-noaa

I'll send the revised script for generating hourly GeoPackage files to Dan and Zizang. Meanwhile, I will think about how to add datetime information to the max disturbance file.

Thanks, Linlin

cuill commented 1 year ago

@yangz888 Hi Zizang,

You can find the revised script here (on Frontera): /work2/07933/cuivims/ICOGS3D/Forecast/PostP/NewIO/gen_geojson.py

The command line to run it is the same as the old one. The only difference is it will generate gpkg files. Dan already tested it on Frontera. The runtime (~40 min on Frontera) is longer than the old one because more polygons are generated.

Let me know if you have any issues accessing the file or running it.

Thanks, Linlin

saeed-moghimi-noaa commented 1 year ago

Thanks @cuill for prompt response. Highly appreciated. -Saeed

yangz888 commented 1 year ago

Thanks, Linlin! I'll keep the progress posted! - Zizang

On Wed, Sep 21, 2022 at 2:18 PM cuill @.***> wrote:

@yangz888 https://github.com/yangz888 Hi Zizang,

You can find the revised script here (on Frontera): /work2/07933/cuivims/ICOGS3D/Forecast/PostP/NewIO/gen_geojson.py

The command line to run it is the same as the old one. The only difference is it will generate gpkg files. Dan already tested it on Frontera. The runtime (~40 min on Frontera) is longer than the old one because more polygons are generated.

Let me know if you have any issues accessing the file or running it.

Thanks, Linlin

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yangz888 commented 1 year ago

Dear Help Team,

FYI, I see the following on Acorn:

@.:/lfs/h1> pwd /lfs/h1 @.:/lfs/h1> ls -l total 0

Thanks, Zizang

yangz888 commented 1 year ago

Hi Linlin,

FYI that Acorn won’t be available until the end of this week. I’ll be able to test your new python code afterwards. I’ll keep you updated on the process.

Thanks, Zizang

---------- Forwarded message ---------From: Rick Beam - NOAA Affiliate < @.> Date: Wed, Sep 21, 2022 at 4:51 PM Subject: Acorn system still unavailable To: Davin Chan - NOAA Affiliate @.>

The Acorn system is still unavailable for job runs until Saturday 9/24/2022 We will send an email out when it is ready, If you attempt to run jobs that may fail or get deleted. We are preparing image updates and testing for new compilers etc...

On Wed, Sep 21, 2022 at 2:26 PM Saeed Moghimi @.***> wrote:

Thanks @cuill https://github.com/cuill for prompt response. Highly appreciated. -Saeed

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cuill commented 1 year ago

@yangz888 Thanks for the updates.

saeed-moghimi-noaa commented 1 year ago

@erin-nagel @agibbons-NOAA @josephzhang8 @cuill @feiye-vims @moghimis @gseroka @yangz888

Linlin, Thanks a lot for your work on this topic. Highly appreciated.

Following conversation with Zizang, would you please place the latest geojson/package (please see the following on Frontera: /work2/07542/tknzyang/frontera/NPool/test_geoPkg/ dir_gpkg/*gpkg) somewher at the VIMS ftp site for Erin to test and provide feedback?

Thanks, -Saeed

erin-nagel commented 1 year ago

Saeed,

GeoPackage files have been posted to noaa-nos-stofs3d-pds AWS S3 bucket since 9/24, I began testing nowCOAST@AWS operations for STOFS3D hourly product on 9/26, after making some adjustments on our end we were able to successfully process and display all 72 hour forecasts. We will let your team know when the service is available for review on one of our prototype map viewers, but here are two initial images during Hurricane Ian.

STOFS3D_sample1

STOFS3D_sample2

saeed-moghimi-noaa commented 1 year ago

Hi @erin-nagel

@yangz888 was suggesting to do a final check before we pass the scripts to NCO to be included to the operational workflow.

@cuill Are there any changes to these files in comparison with the ones you passed to @erin-nagel before? If they are the same then we may not need to pass them to Erin for testing, right?

Thanks, -Saeed

cuill commented 1 year ago

@erin-nagel @saeed-moghimi-noaa @yangz888

The python script Zizang is using is the same as VIMS' version. So there are no changes to these files.

Maybe check if the file size is consistent with VIMS' version.

yangz888 commented 1 year ago

Hi Erin,

Just to clarify, there are the following two sets of STOFS-3D-Atl run output on AWS S3: (1) https://noaa-nos-stofs3d-pds.s3.amazonaws.com/index.html#STOFS3D-Atl- VIMS/ The VIMS run, run cycle hour is t00z. (2) https://noaa-gestofs-pds.s3.amazonaws.com/index.html#_stofs-3D-Atlantic/ This directory contains outputs from the NOAA set up, run cycle hour is t12z; there are no gpkg files here yet.

I am running Linlin's updated gen_geopkg python script. I'll be able to place sample outputs on AWS S3 for you to test early next week. If they seem to be ok, we'll contact the NCEP NCO to start creating the gpkg files and make them available in (2).

Thanks, Zizang

On Fri, Oct 7, 2022 at 10:17 AM Erin Nagel @.***> wrote:

Saeed,

GeoPackage files have been posted to noaa-nos-stofs3d-pds AWS S3 bucket since 9/24, I began testing @.*** operations for STOFS3D hourly product on 9/26, after making some adjustments on our end we were able to successfully process and display all 72 hour forecasts. We will let your team know when the service is available for review on one of our prototype map viewers, but here are two initial images during Hurricane Ian.

[image: STOFS3D_sample1] https://user-images.githubusercontent.com/51652109/194574860-82147e58-a661-46ad-ab8a-e163c73cc1cc.JPG

[image: STOFS3D_sample2] https://user-images.githubusercontent.com/51652109/194574895-19baef76-fc06-4618-8c88-949c11289356.jpg

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erin-nagel commented 1 year ago

Hi Zizang,

Thanks for clarifying, we currently only subscribe to the noaa-nos-stofs3d-pds bucket and process the VIMS run, so once you post the sample outputs to noaa-gestofs-pds, we can subscribe to that bucket and test the NOAA run, we will also deploy a map viewer next week so we can all review the hourly STOFS3D Atlantic web map service before you hand off the code to NCO.

Thanks everyone,

Erin

yangz888 commented 1 year ago

Sounds great! Thank you, Erin. - Zizang

On Fri, Oct 7, 2022 at 2:50 PM Erin Nagel @.***> wrote:

Hi Zizang,

Thanks for clarifying, we currently only subscribe to the noaa-nos-stofs3d-pds bucket and process the VIMS run, so once you post the sample outputs to noaa-gestofs-pds, we can subscribe to that bucket and test the NOAA run, we will also deploy a map viewer next week so we can all review the hourly STOFS3D Atlantic web map service before you hand off the code to NCO.

Thanks everyone,

Erin

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yangz888 commented 1 year ago

Hi Erin and John,

Please see the following sample input (netCDF) files and the created gpk files at the AWS S3: https://noaa-gestofs-pds.s3.amazonaws.com/index.html#_stofs-3D-Atlantic/stofs_3d_atl_sample_gpkg/, where source_data_to_create_pkg.nc.gz is the input file to Linlin's python script and the gpkg.gz files (total 72 files) are the outputs.

Please let me know if you have any questions.

Thanks, Zizang

On Fri, Oct 7, 2022 at 2:56 PM Zizang Yang - NOAA Federal < @.***> wrote:

Sounds great! Thank you, Erin. - Zizang

On Fri, Oct 7, 2022 at 2:50 PM Erin Nagel @.***> wrote:

Hi Zizang,

Thanks for clarifying, we currently only subscribe to the noaa-nos-stofs3d-pds bucket and process the VIMS run, so once you post the sample outputs to noaa-gestofs-pds, we can subscribe to that bucket and test the NOAA run, we will also deploy a map viewer next week so we can all review the hourly STOFS3D Atlantic web map service before you hand off the code to NCO.

Thanks everyone,

Erin

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erin-nagel commented 1 year ago

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/, this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

yangz888 commented 1 year ago

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/, this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

[image: image] https://user-images.githubusercontent.com/51652109/195416881-8b199851-5700-4dc0-ad01-bd0395ef786e.png

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agibbons-NOAA commented 1 year ago

Hi Zizang,

As to the animation issue, unfortunately this demo is using a somewhat rough prototype of the viewer. The speed of the service in its current state is also prohibiting faster animation. We intend to improve on this.

What should at least work reliably right now is clicking various times on the slider and seeing the data for those times. (Provided you wait long enough for the data to load before clicking again a new time). Your best bet at animating in this demo will be to lower the animation speed. You can do this by clicking the menu immediately to the right of the time slider where you will find another slider which allows you to lower the animation speed. Hopefully that is helpful.

Thanks,

Adam

On Wed, Oct 12, 2022 at 3:04 PM yangz888 @.***> wrote:

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/, this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

[image: image] < https://user-images.githubusercontent.com/51652109/195416881-8b199851-5700-4dc0-ad01-bd0395ef786e.png

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yangz888 commented 1 year ago

Hi Adam,

Thank you very much for the prompt reply and the detailed explanations to my questions! It works very well.

Best, Zizang

On Wed, Oct 12, 2022 at 3:19 PM Adam Gibbons @.***> wrote:

Hi Zizang,

As to the animation issue, unfortunately this demo is using a somewhat rough prototype of the viewer. The speed of the service in its current state is also prohibiting faster animation. We intend to improve on this.

What should at least work reliably right now is clicking various times on the slider and seeing the data for those times. (Provided you wait long enough for the data to load before clicking again a new time). Your best bet at animating in this demo will be to lower the animation speed. You can do this by clicking the menu immediately to the right of the time slider where you will find another slider which allows you to lower the animation speed. Hopefully that is helpful.

Thanks,

Adam

On Wed, Oct 12, 2022 at 3:04 PM yangz888 @.***> wrote:

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/, this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

[image: image] <

https://user-images.githubusercontent.com/51652109/195416881-8b199851-5700-4dc0-ad01-bd0395ef786e.png

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yangz888 commented 1 year ago

Hi Erin and the team,

Just a follow up about the geoPackage files from the NOAA's testing STOFS-3D-Alt runs. We understand that you have successfully implemented the wonderful demo (available at https://137.75.94.147/gateway/).

We are writing to check/confirm: are there any issues about the files we provides, e.g., their format, file and the included variable names, meta data, etc. that we need to take care of? If it is ok with the nowCOAST team, we'll proceed with the NOAA/NCEP to include generating geoPackage files in its parallel test.

Thank you, Zizang

On Wed, Oct 12, 2022 at 3:34 PM Zizang Yang - NOAA Federal < @.***> wrote:

Hi Adam,

Thank you very much for the prompt reply and the detailed explanations to my questions! It works very well.

Best, Zizang

On Wed, Oct 12, 2022 at 3:19 PM Adam Gibbons @.***> wrote:

Hi Zizang,

As to the animation issue, unfortunately this demo is using a somewhat rough prototype of the viewer. The speed of the service in its current state is also prohibiting faster animation. We intend to improve on this.

What should at least work reliably right now is clicking various times on the slider and seeing the data for those times. (Provided you wait long enough for the data to load before clicking again a new time). Your best bet at animating in this demo will be to lower the animation speed. You can do this by clicking the menu immediately to the right of the time slider where you will find another slider which allows you to lower the animation speed. Hopefully that is helpful.

Thanks,

Adam

On Wed, Oct 12, 2022 at 3:04 PM yangz888 @.***> wrote:

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/, this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

[image: image] <

https://user-images.githubusercontent.com/51652109/195416881-8b199851-5700-4dc0-ad01-bd0395ef786e.png

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JohnGWKelley commented 1 year ago

Zizang,

I saw the following strange features when I zoomed in:

1) high water disturbances along the coast, for example in south coast of MA (red, orange, green artifacts)

[image: image.png]

2) inundation of coastal areas (0 - 0.5 m?) along the coast

[image: image.png]

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Thu, Oct 13, 2022 at 1:41 PM yangz888 @.***> wrote:

Hi Erin and the team,

Just a follow up about the geoPackage files from the NOAA's testing STOFS-3D-Alt runs. We understand that you have successfully implemented the wonderful demo (available at https://137.75.94.147/gateway/).

We are writing to check/confirm: are there any issues about the files we provides, e.g., their format, file and the included variable names, meta data, etc. that we need to take care of? If it is ok with the nowCOAST team, we'll proceed with the NOAA/NCEP to include generating geoPackage files in its parallel test.

Thank you, Zizang

On Wed, Oct 12, 2022 at 3:34 PM Zizang Yang - NOAA Federal < @.***> wrote:

Hi Adam,

Thank you very much for the prompt reply and the detailed explanations to my questions! It works very well.

Best, Zizang

On Wed, Oct 12, 2022 at 3:19 PM Adam Gibbons @.***> wrote:

Hi Zizang,

As to the animation issue, unfortunately this demo is using a somewhat rough prototype of the viewer. The speed of the service in its current state is also prohibiting faster animation. We intend to improve on this.

What should at least work reliably right now is clicking various times on the slider and seeing the data for those times. (Provided you wait long enough for the data to load before clicking again a new time). Your best bet at animating in this demo will be to lower the animation speed. You can do this by clicking the menu immediately to the right of the time slider where you will find another slider which allows you to lower the animation speed. Hopefully that is helpful.

Thanks,

Adam

On Wed, Oct 12, 2022 at 3:04 PM yangz888 @.***> wrote:

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/, this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

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yangz888 commented 1 year ago

Hi John,

Good catch! We'll have the rouine STOFS-3D-meeting with the VIMS team at 4:00 pm today. I've just invited you as optional. Please feel free to join the discussion.

Thanks, Zizang

On Thu, Oct 13, 2022 at 1:52 PM John G.W. Kelley @.***> wrote:

Zizang,

I saw the following strange features when I zoomed in:

1) high water disturbances along the coast, for example in south coast of MA (red, orange, green artifacts)

[image: image.png]

2) inundation of coastal areas (0 - 0.5 m?) along the coast

[image: image.png]

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Thu, Oct 13, 2022 at 1:41 PM yangz888 @.***> wrote:

Hi Erin and the team,

Just a follow up about the geoPackage files from the NOAA's testing STOFS-3D-Alt runs. We understand that you have successfully implemented the wonderful demo (available at https://137.75.94.147/gateway/).

We are writing to check/confirm: are there any issues about the files we provides, e.g., their format, file and the included variable names, meta data, etc. that we need to take care of? If it is ok with the nowCOAST team, we'll proceed with the NOAA/NCEP to include generating geoPackage files in its parallel test.

Thank you, Zizang

On Wed, Oct 12, 2022 at 3:34 PM Zizang Yang - NOAA Federal < @.***> wrote:

Hi Adam,

Thank you very much for the prompt reply and the detailed explanations to my questions! It works very well.

Best, Zizang

On Wed, Oct 12, 2022 at 3:19 PM Adam Gibbons @.***> wrote:

Hi Zizang,

As to the animation issue, unfortunately this demo is using a somewhat rough prototype of the viewer. The speed of the service in its current state is also prohibiting faster animation. We intend to improve on this.

What should at least work reliably right now is clicking various times on the slider and seeing the data for those times. (Provided you wait long enough for the data to load before clicking again a new time). Your best bet at animating in this demo will be to lower the animation speed. You can do this by clicking the menu immediately to the right of the time slider where you will find another slider which allows you to lower the animation speed. Hopefully that is helpful.

Thanks,

Adam

On Wed, Oct 12, 2022 at 3:04 PM yangz888 @.***> wrote:

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/ , this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

[image: image] <

https://user-images.githubusercontent.com/51652109/195416881-8b199851-5700-4dc0-ad01-bd0395ef786e.png

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yangz888 commented 1 year ago

Hi John,

Somehow the images enclosed in your email didn't show up. (I know this was due to the GitHub functions.) Could you send us again directly via the email?

Thanks, Zizang

On Thu, Oct 13, 2022 at 2:10 PM Zizang Yang - NOAA Federal < @.***> wrote:

Hi John,

Good catch! We'll have the rouine STOFS-3D-meeting with the VIMS team at 4:00 pm today. I've just invited you as optional. Please feel free to join the discussion.

Thanks, Zizang

On Thu, Oct 13, 2022 at 1:52 PM John G.W. Kelley @.***> wrote:

Zizang,

I saw the following strange features when I zoomed in:

1) high water disturbances along the coast, for example in south coast of MA (red, orange, green artifacts)

[image: image.png]

2) inundation of coastal areas (0 - 0.5 m?) along the coast

[image: image.png]

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Thu, Oct 13, 2022 at 1:41 PM yangz888 @.***> wrote:

Hi Erin and the team,

Just a follow up about the geoPackage files from the NOAA's testing STOFS-3D-Alt runs. We understand that you have successfully implemented the wonderful demo (available at https://137.75.94.147/gateway/).

We are writing to check/confirm: are there any issues about the files we provides, e.g., their format, file and the included variable names, meta data, etc. that we need to take care of? If it is ok with the nowCOAST team, we'll proceed with the NOAA/NCEP to include generating geoPackage files in its parallel test.

Thank you, Zizang

On Wed, Oct 12, 2022 at 3:34 PM Zizang Yang - NOAA Federal < @.***> wrote:

Hi Adam,

Thank you very much for the prompt reply and the detailed explanations to my questions! It works very well.

Best, Zizang

On Wed, Oct 12, 2022 at 3:19 PM Adam Gibbons @.***> wrote:

Hi Zizang,

As to the animation issue, unfortunately this demo is using a somewhat rough prototype of the viewer. The speed of the service in its current state is also prohibiting faster animation. We intend to improve on this.

What should at least work reliably right now is clicking various times on the slider and seeing the data for those times. (Provided you wait long enough for the data to load before clicking again a new time). Your best bet at animating in this demo will be to lower the animation speed. You can do this by clicking the menu immediately to the right of the time slider where you will find another slider which allows you to lower the animation speed. Hopefully that is helpful.

Thanks,

Adam

On Wed, Oct 12, 2022 at 3:04 PM yangz888 @.***> wrote:

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/, this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

[image: image] <

https://user-images.githubusercontent.com/51652109/195416881-8b199851-5700-4dc0-ad01-bd0395ef786e.png

— Reply to this email directly, view it on GitHub <

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JohnGWKelley commented 1 year ago

Zizang,

Thanks. I have to leave at 415 PM, but will try to attend for the first 15 minutes.

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Thu, Oct 13, 2022 at 2:11 PM yangz888 @.***> wrote:

Hi John,

Good catch! We'll have the rouine STOFS-3D-meeting with the VIMS team at 4:00 pm today. I've just invited you as optional. Please feel free to join the discussion.

Thanks, Zizang

On Thu, Oct 13, 2022 at 1:52 PM John G.W. Kelley @.***> wrote:

Zizang,

I saw the following strange features when I zoomed in:

1) high water disturbances along the coast, for example in south coast of MA (red, orange, green artifacts)

[image: image.png]

2) inundation of coastal areas (0 - 0.5 m?) along the coast

[image: image.png]

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Thu, Oct 13, 2022 at 1:41 PM yangz888 @.***> wrote:

Hi Erin and the team,

Just a follow up about the geoPackage files from the NOAA's testing STOFS-3D-Alt runs. We understand that you have successfully implemented the wonderful demo (available at https://137.75.94.147/gateway/).

We are writing to check/confirm: are there any issues about the files we provides, e.g., their format, file and the included variable names, meta data, etc. that we need to take care of? If it is ok with the nowCOAST team, we'll proceed with the NOAA/NCEP to include generating geoPackage files in its parallel test.

Thank you, Zizang

On Wed, Oct 12, 2022 at 3:34 PM Zizang Yang - NOAA Federal < @.***> wrote:

Hi Adam,

Thank you very much for the prompt reply and the detailed explanations to my questions! It works very well.

Best, Zizang

On Wed, Oct 12, 2022 at 3:19 PM Adam Gibbons @.***> wrote:

Hi Zizang,

As to the animation issue, unfortunately this demo is using a somewhat rough prototype of the viewer. The speed of the service in its current state is also prohibiting faster animation. We intend to improve on this.

What should at least work reliably right now is clicking various times on the slider and seeing the data for those times. (Provided you wait long enough for the data to load before clicking again a new time). Your best bet at animating in this demo will be to lower the animation speed. You can do this by clicking the menu immediately to the right of the time slider where you will find another slider which allows you to lower the animation speed. Hopefully that is helpful.

Thanks,

Adam

On Wed, Oct 12, 2022 at 3:04 PM yangz888 @.***> wrote:

Hi Erin,

It looks great! Thank you very much for the quick implementation. Great job!

Quick questions: (1) Did you get chance to make a visual comparison between this set of gpk with that from the VIMS? (2) When I clicked on the "triangular" play button near the bottom of the page, sometime it displayed animated color coded fields and sometime it didn't. I guess I didn't work out the correct way of using the Website functions.

[image: image.png]

Thanks, Zizang

On Wed, Oct 12, 2022 at 2:15 PM Erin Nagel @.***> wrote:

All,

I have a STOFS3D demo available at https://137.75.94.147/gateway/ , this link will only work on the internal NOAA network. There is an opacity slider in the menu dropdown, pop up information when you select the map, and service is time enabled.

Thank you, Erin

[image: image] <

https://user-images.githubusercontent.com/51652109/195416881-8b199851-5700-4dc0-ad01-bd0395ef786e.png

— Reply to this email directly, view it on GitHub <

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cuill commented 1 year ago

Hi John,

1) high water disturbances along the coast, for example in south coast of MA (red, orange, green artifacts)

This is because STOFS3D includes watershed up to 10 meters above mean sea level, so many small rivers are included. Some of the small rivers are not connected properly due to mesh quality, which can lead to the artifacts, i.e., ponding waters. This will be fixed in the next version update, where we developed new meshing techniques.

2) inundation of coastal areas (0 - 0.5 m?) along the coast Are you referring to those deep blue areas? Those are probably dry land with an elevation value of -99999.

Linlin

erin-nagel commented 1 year ago

Linlin,

Would it be possible to remove elevation values with -99999 from the data by clipping or splitting polygons using a shoreline shapefile or by adding an additional level for elevation values with -99999?

Erin

On Thu, Oct 13, 2022 at 3:47 PM cuill @.***> wrote:

Hi John,

1) high water disturbances along the coast, for example in south coast of MA (red, orange, green artifacts)

This is because STOFS3D includes watershed up to 10 meters above mean sea level, so many small rivers are included. Some of the small rivers are not connected properly due to mesh quality, which can lead to the artifacts, i.e., ponding waters. This will be fixed in the next version update, where we developed new meshing techniques.

2) inundation of coastal areas (0 - 0.5 m?) along the coast Are you referring to those deep blue areas? Those are probably dry land with an elevation value of -99999.

Linlin

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--

Erin Nagel

Software Engineer, ERT

NOAA/NOS/OCS/CSDL

cuill commented 1 year ago

Hi Erin,

We will mask out small disturbances (<0.3 m; 1 foot) nearshore, this should resolve the issue.

Linlin

cuill commented 1 year ago

John and Erin,

Could you please check if the following result is good or not after masking? If this is okay, I'll pass the revised script to Zizang.

Screen Shot 2022-10-14 at 10 28 33 AM Screen Shot 2022-10-14 at 10 01 55 AM

Linlin

JohnGWKelley commented 1 year ago

Linlin,

I will take a look and get back to you.

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Fri, Oct 14, 2022 at 10:56 AM cuill @.***> wrote:

John and Erin,

Could you please check if the following result is good or not after masking? If this is okay, I'll pass the revised script to Zizang.

[image: Screen Shot 2022-10-14 at 10 28 33 AM] https://user-images.githubusercontent.com/6502663/195877126-741f7339-169f-4361-9fe3-2e2d6252e503.png [image: Screen Shot 2022-10-14 at 10 01 55 AM] https://user-images.githubusercontent.com/6502663/195877158-15833b4d-7a38-4ff6-9917-be9e69c9a60a.png [image: Screen Shot 2022-10-14 at 10 02 19 AM] https://user-images.githubusercontent.com/6502663/195877235-2e1979ab-d6ab-43f3-bdd4-f9d066bf9922.png

Linlin

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JohnGWKelley commented 1 year ago

Linlin,

COuld you please provide a zoomed in screenshots for NY harbor area and south coast of MA?

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Fri, Oct 14, 2022 at 10:56 AM cuill @.***> wrote:

John and Erin,

Could you please check if the following result is good or not after masking? If this is okay, I'll pass the revised script to Zizang.

[image: Screen Shot 2022-10-14 at 10 28 33 AM] https://user-images.githubusercontent.com/6502663/195877126-741f7339-169f-4361-9fe3-2e2d6252e503.png [image: Screen Shot 2022-10-14 at 10 01 55 AM] https://user-images.githubusercontent.com/6502663/195877158-15833b4d-7a38-4ff6-9917-be9e69c9a60a.png [image: Screen Shot 2022-10-14 at 10 02 19 AM] https://user-images.githubusercontent.com/6502663/195877235-2e1979ab-d6ab-43f3-bdd4-f9d066bf9922.png

Linlin

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cuill commented 1 year ago

John,

Here are zoom-in photos:

NY harbor Screen Shot 2022-10-14 at 11 11 53 AM

Buzzards Bay coast area: Screen Shot 2022-10-14 at 11 13 52 AM

Linlin

JohnGWKelley commented 1 year ago

Linlin,

The shoreline representation looks much better. However, there is still the issue with the unrealistic high values in the isolated ponding areas which we discussed during the meeting. Are you working on a potential solution for that issue?

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Fri, Oct 14, 2022 at 11:16 AM cuill @.***> wrote:

John,

Here are zoom-in photos:

NY harbor [image: Screen Shot 2022-10-14 at 11 11 53 AM] https://user-images.githubusercontent.com/6502663/195881681-b251147c-3285-4a2a-ace7-c379e9d5f2f1.png

Buzzards Bay coast area: [image: Screen Shot 2022-10-14 at 11 13 52 AM] https://user-images.githubusercontent.com/6502663/195881807-17703e3e-7469-4233-9397-165209e1e193.png

Linlin

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josephzhang8 commented 1 year ago

Hi John:

I think some of those areas are due to rainfall on higher ground.

JohnGWKelley commented 1 year ago

Joseph,

Have such occurrences of high water disturbances in isolated areas due rainfall been verified in previous hindcasts or forecasts?

I am concerned how users of STOFS3D forecast guidance maps will interpret these isolated areas of high water disturbances/inundation.

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Fri, Oct 14, 2022 at 11:38 AM Joseph Zhang @.***> wrote:

Hi John:

I think some of those areas are due to rainfall on higher ground.

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feiye-vims commented 1 year ago

Linlin mask out inundations > 2 m in the previous plots. We can try setting the threshold at 1 m if necessary.

josephzhang8 commented 1 year ago

Hi John:

See Fig. 11 of our paper: https://nhess.copernicus.org/articles/21/1703/2021/

Note that USGS HWMs are usually measured on high ground, thus the large surface elevations and the water depths (disturbances) can exceed a few meters.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: John G.W. Kelley @.> Sent: Friday, October 14, 2022 11:49 AM To: schism-dev/pyschism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/pyschism] Generating GeoJSON to support NowCoast team (Issue #44)

[EXTERNAL to VIMS received message]

Joseph,

Have such occurrences of high water disturbances in isolated areas due rainfall been verified in previous hindcasts or forecasts?

I am concerned how users of STOFS3D forecast guidance maps will interpret these isolated areas of high water disturbances/inundation.

John

John G.W. Kelley Coastal Marine Modeling Branch Coast Survey Development Laboratory NOAA/National Ocean Service NOAA-UNH Joint Hydrographic Center Durham, New Hampshire 03824 603-862-1628

On Fri, Oct 14, 2022 at 11:38 AM Joseph Zhang @.<mailto:@.>> wrote:

Hi John:

I think some of those areas are due to rainfall on higher ground.

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schism-dev / pyschism