py eddy tracker multifile analysis about py-eddy-tracker

[AntSimi]

Hi, I am not sure to understand your request. What did you mean by multiple file format? Could you explain more about your work? Antoine

[abhijithpkurian]

i mean time series AVISO data and that to only for a particular region from global dataset. I am not able to use the xarray function for selecting (slicing) th region. It would be great if you can share a sample code. Thank you Kurian

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On Thu, Mar 12, 2020 at 1:46 PM AntSimi ***@***.***> wrote: Hi, I am not sure to understand your request. What did you mean by multiple file format? Could you explain more about your work? Antoine Le mer. 11 mars 2020 à 07:02, abhijithpkurian ***@***.***> a écrit : > Dear Sir > > I wish to use py-eddy-tracker for the arabian sea. I wish to know how to > employ the same for multiple file format for time series analysis. It would > be great if you can comment upon the same with a sample code. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > < #4?email_source=notifications&email_token=AIS7AZJMIPEA67MMWGIM4N3RG4SPPA5CNFSM4LFOIVLKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IUDJFXQ >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AIS7AZLXP7PHFUNZIBZI7TTRG4SPPANCNFSM4LFOIVLA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJ3UIVYAZRYQ4WIIMS32PFDRHCK7PANCNFSM4LFOIVLA> .

[AntSimi]

Hi, Py eddy tracker is designed to detect on the whole grid which are used in input, there no tools in py eddy tracker to subset grid(you could use NCO tools for that). In my mind it's better to use on whole grid (global or not): 1. if you reduce area you will have filter artefact near the bounds 2. Eddies on the bounds of your area will be more accurate I think it's better to detect on the whole grid, and subset on your area after detection process.You could do that with EddySubSetter tools (which are provide in pet module). Antoine

[abhijithpkurian]

I sincerely thankyou for the time you spend and request your support in long run Thank you Kurian

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On Thu, Mar 12, 2020 at 5:21 PM AntSimi ***@***.***> wrote: Hi, Py eddy tracker is designed to detect on the whole grid which are used in input, there no tools in py eddy tracker to subset grid(you could use NCO tools for that). In my mind it's better to use on whole grid (global or not): 1. if you reduce area you will have filter artefact near the bounds 2. Eddies on the bounds of your area will be more accurate I think it's better to detect on the whole grid, and subset on your area after detection process.You could do that with EddySubSetter tools (which are provide in pet module). Antoine Le jeu. 12 mars 2020 à 10:31, abhijithpkurian ***@***.***> a écrit : > i mean time series AVISO data and that to only for a particular region from > global dataset. I am not able to use the xarray function for selecting > (slicing) th region. It would be great if you can share a sample code. > Thank you > > Kurian > > On Thu, Mar 12, 2020 at 1:46 PM AntSimi ***@***.***> wrote: > > > Hi, > > I am not sure to understand your request. > > What did you mean by multiple file format? > > Could you explain more about your work? > > > > Antoine > > > > Le mer. 11 mars 2020 à 07:02, abhijithpkurian < ***@***.***> > a > > écrit : > > > > > Dear Sir > > > > > > I wish to use py-eddy-tracker for the arabian sea. I wish to know how > to > > > employ the same for multiple file format for time series analysis. It > > would > > > be great if you can comment upon the same with a sample code. > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub > > > < > > > #4?email_source=notifications&email_token=AIS7AZJMIPEA67MMWGIM4N3RG4SPPA5CNFSM4LFOIVLKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IUDJFXQ > > >, > > > or unsubscribe > > > < > > > https://github.com/notifications/unsubscribe-auth/AIS7AZLXP7PHFUNZIBZI7TTRG4SPPANCNFSM4LFOIVLA > > > > > > . > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > < > #4 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AJ3UIVYAZRYQ4WIIMS32PFDRHCK7PANCNFSM4LFOIVLA > > > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > < #4 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AIS7AZPDUBYLTLS3FAS54ETRHCTYPANCNFSM4LFOIVLA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJ3UIV3AQUHWZCLEKMG6FGTRHDEDZANCNFSM4LFOIVLA> .

[abhijithpkurian]

Dear Sir It would be great if you can give an example(script) of a 10 day data analysis script since the provided in the github is a single day analysis example script. Thank you Kurian On Thu, Mar 12, 2020 at 5:19 PM Abhijith Kurian <[email protected]> wrote:

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I sincerely thankyou for the time you spend and request your support in long run Thank you Kurian On Thu, Mar 12, 2020 at 5:21 PM AntSimi ***@***.***> wrote: > Hi, > Py eddy tracker is designed to detect on the whole grid which are used in > input, there no tools in py eddy tracker to subset grid(you could use NCO > tools for that). > In my mind it's better to use on whole grid (global or not): > > 1. if you reduce area you will have filter artefact near the bounds > 2. Eddies on the bounds of your area will be more accurate > > I think it's better to detect on the whole grid, and subset on your area > after detection process.You could do that with EddySubSetter tools (which > are provide in pet module). > > Antoine > > > > Le jeu. 12 mars 2020 à 10:31, abhijithpkurian ***@***.***> > a > écrit : > > > i mean time series AVISO data and that to only for a particular region > from > > global dataset. I am not able to use the xarray function for selecting > > (slicing) th region. It would be great if you can share a sample code. > > Thank you > > > > Kurian > > > > On Thu, Mar 12, 2020 at 1:46 PM AntSimi ***@***.***> > wrote: > > > > > Hi, > > > I am not sure to understand your request. > > > What did you mean by multiple file format? > > > Could you explain more about your work? > > > > > > Antoine > > > > > > Le mer. 11 mars 2020 à 07:02, abhijithpkurian < > ***@***.***> > > a > > > écrit : > > > > > > > Dear Sir > > > > > > > > I wish to use py-eddy-tracker for the arabian sea. I wish to know > how > > to > > > > employ the same for multiple file format for time series analysis. > It > > > would > > > > be great if you can comment upon the same with a sample code. > > > > > > > > — > > > > You are receiving this because you are subscribed to this thread. > > > > Reply to this email directly, view it on GitHub > > > > < > > > > > > #4?email_source=notifications&email_token=AIS7AZJMIPEA67MMWGIM4N3RG4SPPA5CNFSM4LFOIVLKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IUDJFXQ > > > >, > > > > or unsubscribe > > > > < > > > > > > https://github.com/notifications/unsubscribe-auth/AIS7AZLXP7PHFUNZIBZI7TTRG4SPPANCNFSM4LFOIVLA > > > > > > > > . > > > > > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub > > > < > > > #4 (comment) > > >, > > > or unsubscribe > > > < > > > https://github.com/notifications/unsubscribe-auth/AJ3UIVYAZRYQ4WIIMS32PFDRHCK7PANCNFSM4LFOIVLA > > > > > > . > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub > > < > #4 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AIS7AZPDUBYLTLS3FAS54ETRHCTYPANCNFSM4LFOIVLA > > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#4 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AJ3UIV3AQUHWZCLEKMG6FGTRHDEDZANCNFSM4LFOIVLA> > . >

[AntSimi]

Hi,
I don't know the exact format or your file.
But when i need to do that i wrote a bash script, in the actual version of py-eddy-tracker there no direct command to do that.
Or you could use a python script like that with some correction on varname and filename and date:

from glob import glob
filenames =glob('.......')

for filename in filenames:
    from datetime import datetime
    h = RegularGridDataset(filename, lon_name, lat_name)
    h.bessel_high_filter('adt', 500, order=3)
    date = datetime(2019, 2, 23)
    a, c = h.eddy_identification(
        'adt', 'ugos', 'vgos', # Variables used for identification
        date, # Date of identification
        0.002, # step between two isolines of detection (m)
        pixel_limit=(5, 2000), # Min and max pixel count for valid contour
        shape_error=55, # Error max (%) between ratio of circle fit and contour
        )
    with Dataset(date.strftime('share/Anticyclonic_%Y%m%d.nc'), 'w') as h:
        a.to_netcdf(h)
    with Dataset(date.strftime('share/Cyclonic_%Y%m%d.nc'), 'w') as h:
        c.to_netcdf(h)

Antoine

[abhijithpkurian]

Dear Sir I am using a similar format but I am not able to sort out with the date as i have to deal daily netCDF4 files for one year how can Ichange the date on each iteration. Thank you Kurian

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On Mon, Mar 16, 2020 at 2:20 PM AntSimi ***@***.***> wrote: Hi, I don't know the exact format or your file. But when i need to do that i wrote a bash script, in the actual version of py-eddy-tracker there no direct command to do that. Or you could use a python script like that with some correction on varname and filename and date: from glob import glob filenames =glob('.......') for filename in filenames: from datetime import datetime h = RegularGridDataset(filename, lon_name, lat_name) h.bessel_high_filter('adt', 500, order=3) date = datetime(2019, 2, 23) a, c = h.eddy_identification( 'adt', 'ugos', 'vgos', # Variables used for identification date, # Date of identification 0.002, # step between two isolines of detection (m) pixel_limit=(5, 2000), # Min and max pixel count for valid contour shape_error=55, # Error max (%) between ratio of circle fit and contour ) with Dataset(date.strftime('share/Anticyclonic_%Y%m%d.nc'), 'w') as h: a.to_netcdf(h) with Dataset(date.strftime('share/Cyclonic_%Y%m%d.nc'), 'w') as h: c.to_netcdf(h) Antoine — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJ3UIV6ON3TSE24J4ADK5CTRHXR4HANCNFSM4LFOIVLA> .

[AntSimi]

Maybe, you could do with:

from datetime import datetime
for filename in filenames:
     date = datetime.strptime('...blabla_20180101.nc', '...blabla_%Y%m%d.nc')

Antoine

[abhijithpkurian]

Dear Sir Thank you for your cooperation. I will get back to you after making a check. Thank you Kurian

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On Mon, Mar 16, 2020 at 3:31 PM AntSimi ***@***.***> wrote: Maybe, you could do with: from datetime import datetimefor filename in filenames: date = datetime.strptime('...blabla_20180101.nc', '...blabla_%Y%m%d.nc') Antoine — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJ3UIV5UPPL7AQ4KQT7FRITRHX2GRANCNFSM4LFOIVLA> .

[abhijithpkurian]

Dear Sir Will it be possible to use the same code as mentioned to be used for a particular region. Is there any options which can be incorporated into the script for a regional analysis(Example: Arabian Sea). Can something be done in the eddy_identification.yaml or within the script itself. Thank you Kurian On Mon, Mar 16, 2020 at 3:22 PM Abhijith Kurian <[email protected]> wrote:

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Dear Sir Thank you for your cooperation. I will get back to you after making a check. Thank you Kurian On Mon, Mar 16, 2020 at 3:31 PM AntSimi ***@***.***> wrote: > Maybe, you could do with: > > from datetime import datetimefor filename in filenames: > date = datetime.strptime('...blabla_20180101.nc', '...blabla_%Y%m%d.nc') > > Antoine > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#4 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AJ3UIV5UPPL7AQ4KQT7FRITRHX2GRANCNFSM4LFOIVLA> > . >

[abhijithpkurian]

Is there any way that I can limit it to a basin range either the identification or tracking. On Tue, Mar 17, 2020 at 10:05 AM Abhijith Kurian <[email protected]> wrote:

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Dear Sir Will it be possible to use the same code as mentioned to be used for a particular region. Is there any options which can be incorporated into the script for a regional analysis(Example: Arabian Sea). Can something be done in the eddy_identification.yaml or within the script itself. Thank you Kurian On Mon, Mar 16, 2020 at 3:22 PM Abhijith Kurian ***@***.***> wrote: > Dear Sir > > Thank you for your cooperation. I will get back to you after making a > check. Thank you > > Kurian > > > On Mon, Mar 16, 2020 at 3:31 PM AntSimi ***@***.***> wrote: > >> Maybe, you could do with: >> >> from datetime import datetimefor filename in filenames: >> date = datetime.strptime('...blabla_20180101.nc', '...blabla_%Y%m%d.nc') >> >> Antoine >> >> — >> You are receiving this because you authored the thread. >> Reply to this email directly, view it on GitHub >> <#4 (comment)>, >> or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AJ3UIV5UPPL7AQ4KQT7FRITRHX2GRANCNFSM4LFOIVLA> >> . >> >

[abhijithpkurian]

Dear Sir A humble request my study is confined to bay of bengal will it be possible to limit the identification and tracking within the basinal scale. It would be great if you can help me sort out with this. Thanking you kurian On Tue, Mar 17, 2020 at 10:52 AM Abhijith Kurian <[email protected]> wrote:

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Is there any way that I can limit it to a basin range either the identification or tracking. On Tue, Mar 17, 2020 at 10:05 AM Abhijith Kurian < ***@***.***> wrote: > Dear Sir > > Will it be possible to use the same code as mentioned to be used for a > particular region. Is there any options which can be incorporated into the > script for a regional analysis(Example: Arabian Sea). Can something be done > in the eddy_identification.yaml or within the script itself. Thank you > > Kurian > > On Mon, Mar 16, 2020 at 3:22 PM Abhijith Kurian < > ***@***.***> wrote: > >> Dear Sir >> >> Thank you for your cooperation. I will get back to you after making a >> check. Thank you >> >> Kurian >> >> >> On Mon, Mar 16, 2020 at 3:31 PM AntSimi ***@***.***> >> wrote: >> >>> Maybe, you could do with: >>> >>> from datetime import datetimefor filename in filenames: >>> date = datetime.strptime('...blabla_20180101.nc', '...blabla_%Y%m%d.nc') >>> >>> Antoine >>> >>> — >>> You are receiving this because you authored the thread. >>> Reply to this email directly, view it on GitHub >>> <#4 (comment)>, >>> or unsubscribe >>> <https://github.com/notifications/unsubscribe-auth/AJ3UIV5UPPL7AQ4KQT7FRITRHX2GRANCNFSM4LFOIVLA> >>> . >>> >>

[evanmason]

One way to do this is to make subsets of the input files (you can use NCO tools for example: http://nco.sourceforge.net/) focusing on the region you are interested in. But as pointed out above, we recommend using the full grid and then the EddySubSetter tools module.

[abhijithpkurian]

But can the subsetting be done for the entire dataset from 1993 to recent.after the complete detection and tracking. And is there any sample code on subsetting since it is not provided in the documentation. Thank you

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On Tue, Mar 17, 2020 at 2:28 PM evanmason ***@***.***> wrote: One way to do this is to make subsets of the input files (you can use NCO tools for example: http://nco.sourceforge.net/) focusing on the region you are interested in. But as pointed out above, we recommend using the full grid and then the EddySubSetter tools module. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJ3UIV3C4HGQZEMC22AWTPLRH43UXANCNFSM4LFOIVLA> .