2D telemac output

[eroome]

Hi,
Does opendrift work with a 2D telemac (selafin) output?

cheers,
Ed

[knutfrode]

Hi,

There is a reader for Telemac/Selafin, which I believe was originally made by @Boorhin
https://github.com/OpenDrift/opendrift/blob/74f61eb68830ca91cca5b901796112ae1ac16824/opendrift/readers/reader_telemac_selafin.py

There is a example script in the gallery, but the output is not shown, as it needs a Selafin package which is not included in OpenDrift distribution:
https://opendrift.github.io/gallery/example_long_selafin.html#sphx-glr-gallery-example-long-selafin-py

I dont know if this reader will work with 2D data, but it can proably be adapted to work.

[eroome]

Hi,

Thanks for the quick reply, I have been working on adapting the reader today but I am new to the structure of opendirft and python in general. Do you have any pointers as to what would need changing, I assume its a case of removing the depth related varaibles?

cheers,
Ed

[eroome]

Hi @knutfrode @Boorhin ,

Have either of you had recent success running the example script and reading the Telemac-3D file.
I can't get it to read the seawater_velocity data.

Maybe it is a new issue which has arisen due to a python update or something?

cheers,
Ed

[Boorhin]

Hi, The reader use the script from telemac (that is easy to replicate to be honest). The number of layers is of course read so that is not an issue. If I have an example of a 2D file I could check for compatibility but I don't think it would be an issue. Did you try it? Cheers

…

On Mon, 29 Apr 2024, 16:11 eroome, ***@***.***> wrote: Hi, Thanks for the quick reply, I have been working on adapting the reader today but I am new to the structure of opendirft and python in general. Do you have any pointers as to what would need changing, I assume its a case of removing the depth related varaibles? cheers, Ed — Reply to this email directly, view it on GitHub <#1293 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACJCEFWQZZ3NJ7CAQS2UX5TY7ZPJBAVCNFSM6AAAAABG2LKFY6VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TENRUGE4DE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[eroome]

Hi @Boorhin ,

I did check for compatibility by adapting your example script (shown below). However, OceanDrift runs but it fails to read any values for x_seawater_velocity and y_seawater_velocity. Is your script designed to be compatible with 2D files?

from datetime import timedelta, datetime
from os import sep
from pyproj import Proj
from opendrift.readers import reader_telemac_selafin
from opendrift.models.oceandrift import OceanDrift

o = OceanDrift(loglevel=0)

filename='C:\Users\edroo\Desktop\PhillipinesAtmosTest_xy.slf'

proj="+proj=utm +zone=51 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"

start_time= datetime(2021,11,25,00,00)
selafin = reader_telemac_selafin.Reader(filename=filename,proj4 = proj, start_time=start_time)
o.add_reader(selafin)

o.set_config('general:coastline_action', 'previous')

time_step = timedelta(hours=0.5)
length= timedelta(hours=(3524))
num_steps = ((3548)+1)

lon,lat = 123.7716, 10.2259
o.seed_elements(lon=lon, lat=lat, radius=20, number= 200,
time= start_time)
o.run(time_step=timedelta(hours=0.5), duration=timedelta(1/24))

[Boorhin]

I cannot see an error message so it is difficult to judge. You can probe the variables in your file with the reader. Did you use the telemac script to see what's in your file first? Cheers

…

On Tue, 30 Apr 2024, 09:52 eroome, ***@***.***> wrote: Hi @Boorhin <https://github.com/Boorhin> , I did check for compatibility by adapting your example script (shown below). However, OceanDrift runs but it fails to read any values for x_seawater_velocity and y_seawater_velocity. Is your script designed to be compatible with 2D files? from datetime import timedelta, datetime from os import sep from pyproj import Proj from opendrift.readers import reader_telemac_selafin from opendrift.models.oceandrift import OceanDrift o = OceanDrift(loglevel=0) log level: Use a value of 20 to get only a minimum of information, or a value of 50 for no output at all. filename='C:\Users\edroo\Desktop\PhillipinesAtmosTest_xy.slf' #Lambert North proj = "+proj=latlon +ellps=WGS84 +lat_1=0 +lat_0=0 +lon_0=0 +a=6378137.0 rf=298.257223563" proj="+proj=utm +zone=51 +ellps=WGS84 +datum=WGS84 +units=m +no_defs" start_time= datetime(2021,11,25,00,00) selafin = reader_telemac_selafin.Reader(filename=filename,proj4 = proj, start_time=start_time) o.add_reader(selafin) #%% o.set_config('general:coastline_action', 'previous') start_time = selafin.start_time generally wrong time_step = timedelta(hours=0.5) length= timedelta(hours=(35 *24)) num_steps = ((35*48)+1) center seeds in the middle #x,y = (selafin.x.max()-selafin.x.min())/2+selafin.x.min(),\ (selafin.y.max()-selafin.y.min())/2+selafin.y.min() lon,lat = 123.7716, 10.2259 o.seed_elements(lon=lon, lat=lat, radius=20, number= 200, time= start_time) o.run(time_step=timedelta(hours=0.5), duration=timedelta(1/24)) — Reply to this email directly, view it on GitHub <#1293 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACJCEFVURBLEJGSDF47WMYDY75LVPAVCNFSM6AAAAABG2LKFY6VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TENZSGU2DE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[eroome]

Yes, I checked that, the variables are being read correctly by the reader. The error arises in the later part, when ocean drift needs to interpolate the velocity values from the selafin file. The error message is as follows...

argmin of an empty sequence
Traceback (most recent call last):
File "C:\Users\edroo\opendrift\opendrift\models\basemodel\environment.py", line 646, in get_environment
reader.get_variables_interpolated(
File "C:\Users\edroo\opendrift\opendrift\readers\basereader\variables.py", line 898, in get_variables_interpolated
env, env_profiles = self.get_variables_interpolated_xy(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\edroo\opendrift\opendrift\readers\basereader\variables.py", line 764, in get_variables_interpolated_xy
env, env_profiles = self.get_variables_interpolated(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\edroo\opendrift\opendrift\readers\basereader\unstructured.py", line 61, in get_variables_interpolated
env = self.get_variables(variables, time, reader_x, reader_y, z)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\edroo\opendrift\opendrift\readers\reader_telemac_selafin.py", line 231, in get_variables
idx_layer = np.abs(pm - z).argmin(axis=0)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: attempt to get argmin of an empty sequence

[Boorhin]

Is it possible to have an extract of the file? Not sure what the empty sequence means. Sounds like new python jargon. I can adapt the reader to the 2D example if that's the issue. Personally, I don't really like slf files, they are from another century ;) I transform them to xarray zarr archives. It is easier to understand what's in it. I have a repo with a script to do that if you are interested. I still don't really know what's in your file, all kinds of things can be stored in these Fortran files and I have had access to only few of them. Cheers

…

On Tue, 30 Apr 2024, 13:03 eroome, ***@***.***> wrote: Yes, I checked that, the variables are being read correctly by the reader. The error arises in the later part, when ocean drift needs to interpolate the velocity values from the selafin file. The error message is as follows... argmin of an empty sequence Traceback (most recent call last): File "C:\Users\edroo\opendrift\opendrift\models\basemodel\environment.py", line 646, in get_environment reader.get_variables_interpolated( File "C:\Users\edroo\opendrift\opendrift\readers\basereader\variables.py", line 898, in get_variables_interpolated env, env_profiles = self.get_variables_interpolated_xy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\edroo\opendrift\opendrift\readers\basereader\variables.py", line 764, in get_variables_interpolated_xy env, env_profiles = self.*get_variables_interpolated*( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\edroo\opendrift\opendrift\readers\basereader\unstructured.py", line 61, in *get_variables_interpolated* env = self.get_variables(variables, time, reader_x, reader_y, z) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\edroo\opendrift\opendrift\readers\reader_telemac_selafin.py", line 231, in get_variables idx_layer = np.abs(pm - z).argmin(axis=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: attempt to get argmin of an empty sequence — Reply to this email directly, view it on GitHub <#1293 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACJCEFXHB6LMXHHSBSE627TY76CCHAVCNFSM6AAAAABG2LKFY6VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TENZUGYZTI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[eroome]

I get the same error code with that reader, they look very similar.
Does that reader work for you (with the example)?

[Boorhin]

So I investigated your 3D example, it does not contain an elevation variable (Z) so the reader will not manage to index the layers. What version of Telemac are you using?
This is using the telemac python interface, notice that you only have the velocities but no topology.

It could be that they changed the way the Fortran files are coded but I really doubt it. So maybe it is a matter of exporting Z ? The 3D files I have contain much more variables including 'ELEVATION Z '

[eroome]

I am using a very recent release TELEMAC/v8p5r0-issue981. I need to use this because it has a new atmospheric forcing method.
In my last post I was reffering to you example (https://opendrift.github.io/gallery/example_long_selafin.html) - this still does not work for me.

In reader_telemac_selafin, I change the path to this.... pytel = os.path.join('C:\Users\edroo\opendrift', 'scripts', 'python3') -- (in line 29)
This shouldn't cause any issues right?

[eroome]

I will re-run my example case now - outputting Z.

[Boorhin]

I went through the 2D file and it is possible to make some reader out of it if I think about it. Should be relatively easy,
For the 3D file I see that there are 2 layers but I am unable to place them in space with what's in the file.

[eroome]

Hi Julien, I no longer need a 2D file reader. From now onwards I will just run my model in 3D. But I am still having trouble running your example with the 3D reader. Sent from Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Julien Moreau ***@***.***> Sent: Monday, May 6, 2024 8:05:44 PM To: OpenDrift/opendrift ***@***.***> Cc: Edward Roome (Staff) ***@***.***>; Author ***@***.***> Subject: Re: [OpenDrift/opendrift] 2D telemac output (Discussion #1293) I went through the 2D file and it is possible to make some reader out of it if I think about it. Should be relatively easy, For the 3D file I see that there are 2 layers but I am unable to place them in space with what's in the file. — Reply to this email directly, view it on GitHub<#1293 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BEJBZYCI4AMEQVHHJLJGHYTZA7IARAVCNFSM6AAAAABG2LKFY6VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TGMZTGM3DI>. You are receiving this because you authored the thread.Message ID: ***@***.***> Mae croeso i chi gysylltu gyda'r Brifysgol yn Gymraeg neu Saesneg. Ni fydd gohebu yn Gymraeg yn arwain at oedi. You are welcome to contact the University in Welsh or English. Corresponding in Welsh will not lead to delay. Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

[Boorhin]

I am using a very recent release TELEMAC/v8p5r0-issue981. I need to use this because it has a new atmospheric forcing method. In my last post I was reffering to you example (https://opendrift.github.io/gallery/example_long_selafin.html) - this still does not work for me.

In reader_telemac_selafin, I change the path to this.... pytel = os.path.join('C:\Users\edroo\opendrift', 'scripts', 'python3') -- (in line 29) This shouldn't cause any issues right?

Hi, you have a configuration problem, you should not specifically change this line, you should create an environmental variable called HOMETEL as per specification of Telemac installation. In your case it should be 'C:\Users\edroo\opendrift'
Then pytel will work and thus the reader
Please tell me when you have a file, I will then try to see if there are more issues
cheers

[eroome]

So I made the HOMETEL variable and outputted 'Z' - the reader is getting x vel and y vel values now, thanks !

[Boorhin]

Glad it works!
in my to-do list I need to make a test if HOMETEL exists.

[eroome]

Yep, it works fine so far! Thinking about it, I think I will need a 2D reader to get variables such as Depth, Wind X Y and Stokes Drift from my 2D mesh. I think there could be a easier work around though by using this xarray-selafin · PyPI<https://pypi.org/project/xarray-selafin/> But my python skills are not good enough to clearly see how you can input the xarray dataset into open drift. Ed

…

________________________________ From: Julien Moreau ***@***.***> Sent: 07 May 2024 11:03 To: OpenDrift/opendrift ***@***.***> Cc: Edward Roome (Staff) ***@***.***>; Author ***@***.***> Subject: Re: [OpenDrift/opendrift] 2D telemac output (Discussion #1293) Glad it works! in my to-do list I need to make a test if HOMETEL exists. — Reply to this email directly, view it on GitHub<#1293 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BEJBZYHGZWTOPJ5SM3LGDJ3ZBCRFXAVCNFSM6AAAAABG2LKFY6VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TGMZZGY2DC>. You are receiving this because you authored the thread.Message ID: ***@***.***> Mae croeso i chi gysylltu gyda'r Brifysgol yn Gymraeg neu Saesneg. Ni fydd gohebu yn Gymraeg yn arwain at oedi. You are welcome to contact the University in Welsh or English. Corresponding in Welsh will not lead to delay. Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

[Boorhin]

yes I did something similar a long time ago
https://github.com/Boorhin/Telemac3D_to_xarray
But you can map any variable with the current reader, if you give me a list of what you want, it is not complicated to do
Again an example file is the easiest, I did based on the Telemac doc but they don't list the variables properly so I don't have an exhaustive list of all the potential variables. I then have to convert them into something that OD can read aka CF-compliant

[Boorhin]

My fork of opendrift contains a reader for xarray that never made it to the master branch of Opendrift. I am a bit tired of fighting the CI-CC system of the devs so I gave up but you can try it.
https://github.com/Boorhin/opendrift/blob/master/opendrift/readers/reader_xarray_CF_unstructured.py

[knutfrode]

Probably better than making a specific reader for Xarray, is to update the generic unstructured reader to accept an Xarray dataset, as alternative to providing filename or URL.
This approach is already used for the generic structured reader and the ROMS reader.
https://github.com/OpenDrift/opendrift/blob/master/opendrift/readers/reader_netCDF_CF_generic.py
https://github.com/OpenDrift/opendrift/blob/master/opendrift/readers/reader_ROMS_native.py

However, this would require that the Telemac data structure is the same as expected in the generic unstructured reader, which I guess is to some degree adapted to FVCOM:
https://github.com/OpenDrift/opendrift/blob/master/opendrift/readers/reader_netCDF_CF_unstructured.py