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Read multiple netCDF4 using Python 3


Extract single datapoint from netCDF file in R using ndcfUsing netCDF4 Python climate algorithm?Read HDF4 data using pythonCalculating Climate Suitable Days using netCDF4 and Python?Extracting Multivalues to Points from NETCDF4 Raster using ArcPy seems imprecise?Using python and ArcPy to read multiple files, apply a function and write into new a directryHow can I use GDAL Merge with multiple files in one folder in python 2.7?Combining multiple netcdf in folder in RCan't import shapefile in Pythonpython-netcdf4: Writing file leaves CRS as 'undefined' and extent not correct






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0















I need to read a multiple netCDF4 files using python 3. The files are in different folder named 2019, 2018 with months and days. And the files have the same variables I use to read and plot it.



I can do that just for one file. How I can read all files and variable IR in all files in all folder?



path='/home/all/2019/03/25/Mmult_201903250000.nc'
nc = netCDF4.Dataset('/home/all/2019/03/25/Mmult_201903250000.nc')
IR=nc.variables['IR'][:]
plt.pcolormesh(IR)
plt.colorbar()
plt.show()









share|improve this question









New contributor




Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.


























    0















    I need to read a multiple netCDF4 files using python 3. The files are in different folder named 2019, 2018 with months and days. And the files have the same variables I use to read and plot it.



    I can do that just for one file. How I can read all files and variable IR in all files in all folder?



    path='/home/all/2019/03/25/Mmult_201903250000.nc'
    nc = netCDF4.Dataset('/home/all/2019/03/25/Mmult_201903250000.nc')
    IR=nc.variables['IR'][:]
    plt.pcolormesh(IR)
    plt.colorbar()
    plt.show()









    share|improve this question









    New contributor




    Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
    Check out our Code of Conduct.






















      0












      0








      0








      I need to read a multiple netCDF4 files using python 3. The files are in different folder named 2019, 2018 with months and days. And the files have the same variables I use to read and plot it.



      I can do that just for one file. How I can read all files and variable IR in all files in all folder?



      path='/home/all/2019/03/25/Mmult_201903250000.nc'
      nc = netCDF4.Dataset('/home/all/2019/03/25/Mmult_201903250000.nc')
      IR=nc.variables['IR'][:]
      plt.pcolormesh(IR)
      plt.colorbar()
      plt.show()









      share|improve this question









      New contributor




      Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.












      I need to read a multiple netCDF4 files using python 3. The files are in different folder named 2019, 2018 with months and days. And the files have the same variables I use to read and plot it.



      I can do that just for one file. How I can read all files and variable IR in all files in all folder?



      path='/home/all/2019/03/25/Mmult_201903250000.nc'
      nc = netCDF4.Dataset('/home/all/2019/03/25/Mmult_201903250000.nc')
      IR=nc.variables['IR'][:]
      plt.pcolormesh(IR)
      plt.colorbar()
      plt.show()






      python netcdf






      share|improve this question









      New contributor




      Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.











      share|improve this question









      New contributor




      Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.









      share|improve this question




      share|improve this question








      edited Apr 4 at 8:28









      Kadir Şahbaz

      4,60221531




      4,60221531






      New contributor




      Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.









      asked Apr 4 at 8:12









      Sarah TohamiSarah Tohami

      11




      11




      New contributor




      Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.





      New contributor





      Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.






      Sarah Tohami is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.




















          1 Answer
          1






          active

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          0














          You can use the glob.glob module to search all the nc-files in your sub-folder like this (taken from https://stackoverflow.com/questions/14798220/how-can-i-search-sub-folders-using-glob-glob-module):



          import glob

          list_of_paths = glob.glob('C:/Users/sam/Desktop/myfolder/**/*.nc', recursive=True)


          Then, if there is a dimension in your netcdfs that is unlimited, you can open all the files in one line like this:



          import netCDF4

          nc = netCDF4.MFDataset(list_of_paths)


          After this you will probably want to be carefull, because doing:



          IR=nc.variables['IR'][:]


          will load the 'IR'-data from ALL your nc-files into your memory at once, which could crash you computer. So it's probably better to load small parts at a time by replacing [:] with, for example, [0:2].






          share|improve this answer























          • thanks u but what mean [0:2] my problem that i have a simple application wxpython when i have button this button for select file in directory netcdf file i want to open so after open i want plot it so i will try ... but please what mean [0:2] ? exist method to open the file i want and plot it ?

            – Sarah Tohami
            Apr 4 at 9:44











          • i have question we can use loop for and loop for for variables keys ?

            – Sarah Tohami
            Apr 4 at 9:49











          • that is imformations about my variable IR in file netCDF4._netCDF4.Variable'> int16 IR_108(ny, nx) Offset : radiance = offset + CN x slope: -10.456819486590666 Slope : radiance = offset + CN x slope: 0.2050356762076601 unlimited dimensions: current shape = (3712, 3712) filling on

            – Sarah Tohami
            Apr 4 at 11:33











          • when i do : import numpy as np import netCDF4 import matplotlib.pyplot as plt import glob list_of_paths = glob.glob('/home/all/2019/03/25/*.nc', recursive=True)nc = netCDF4.MFDataset(list_of_paths) IR=nc.variables['IR'][0:1] i had error like : name 'nc' is not defined In [15]: nc = netCDF4.MFDataset(list_of_paths) --------------------------------------------------------------------------- OSError: dataset /homm/all/msg04/all/2019/03/25/Mmulti_201903252000.nc does not have a aggregation dimension

            – Sarah Tohami
            Apr 5 at 7:15











          • ok then you'll have to use "netCDF4.Dataset" instead of "netCDF4.MFDataset" and load a single nc-file at a time. So you need to make a for-loop on the list_of_paths

            – Bert Coerver
            Apr 5 at 7:30











          Your Answer








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          1 Answer
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          active

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          0














          You can use the glob.glob module to search all the nc-files in your sub-folder like this (taken from https://stackoverflow.com/questions/14798220/how-can-i-search-sub-folders-using-glob-glob-module):



          import glob

          list_of_paths = glob.glob('C:/Users/sam/Desktop/myfolder/**/*.nc', recursive=True)


          Then, if there is a dimension in your netcdfs that is unlimited, you can open all the files in one line like this:



          import netCDF4

          nc = netCDF4.MFDataset(list_of_paths)


          After this you will probably want to be carefull, because doing:



          IR=nc.variables['IR'][:]


          will load the 'IR'-data from ALL your nc-files into your memory at once, which could crash you computer. So it's probably better to load small parts at a time by replacing [:] with, for example, [0:2].






          share|improve this answer























          • thanks u but what mean [0:2] my problem that i have a simple application wxpython when i have button this button for select file in directory netcdf file i want to open so after open i want plot it so i will try ... but please what mean [0:2] ? exist method to open the file i want and plot it ?

            – Sarah Tohami
            Apr 4 at 9:44











          • i have question we can use loop for and loop for for variables keys ?

            – Sarah Tohami
            Apr 4 at 9:49











          • that is imformations about my variable IR in file netCDF4._netCDF4.Variable'> int16 IR_108(ny, nx) Offset : radiance = offset + CN x slope: -10.456819486590666 Slope : radiance = offset + CN x slope: 0.2050356762076601 unlimited dimensions: current shape = (3712, 3712) filling on

            – Sarah Tohami
            Apr 4 at 11:33











          • when i do : import numpy as np import netCDF4 import matplotlib.pyplot as plt import glob list_of_paths = glob.glob('/home/all/2019/03/25/*.nc', recursive=True)nc = netCDF4.MFDataset(list_of_paths) IR=nc.variables['IR'][0:1] i had error like : name 'nc' is not defined In [15]: nc = netCDF4.MFDataset(list_of_paths) --------------------------------------------------------------------------- OSError: dataset /homm/all/msg04/all/2019/03/25/Mmulti_201903252000.nc does not have a aggregation dimension

            – Sarah Tohami
            Apr 5 at 7:15











          • ok then you'll have to use "netCDF4.Dataset" instead of "netCDF4.MFDataset" and load a single nc-file at a time. So you need to make a for-loop on the list_of_paths

            – Bert Coerver
            Apr 5 at 7:30















          0














          You can use the glob.glob module to search all the nc-files in your sub-folder like this (taken from https://stackoverflow.com/questions/14798220/how-can-i-search-sub-folders-using-glob-glob-module):



          import glob

          list_of_paths = glob.glob('C:/Users/sam/Desktop/myfolder/**/*.nc', recursive=True)


          Then, if there is a dimension in your netcdfs that is unlimited, you can open all the files in one line like this:



          import netCDF4

          nc = netCDF4.MFDataset(list_of_paths)


          After this you will probably want to be carefull, because doing:



          IR=nc.variables['IR'][:]


          will load the 'IR'-data from ALL your nc-files into your memory at once, which could crash you computer. So it's probably better to load small parts at a time by replacing [:] with, for example, [0:2].






          share|improve this answer























          • thanks u but what mean [0:2] my problem that i have a simple application wxpython when i have button this button for select file in directory netcdf file i want to open so after open i want plot it so i will try ... but please what mean [0:2] ? exist method to open the file i want and plot it ?

            – Sarah Tohami
            Apr 4 at 9:44











          • i have question we can use loop for and loop for for variables keys ?

            – Sarah Tohami
            Apr 4 at 9:49











          • that is imformations about my variable IR in file netCDF4._netCDF4.Variable'> int16 IR_108(ny, nx) Offset : radiance = offset + CN x slope: -10.456819486590666 Slope : radiance = offset + CN x slope: 0.2050356762076601 unlimited dimensions: current shape = (3712, 3712) filling on

            – Sarah Tohami
            Apr 4 at 11:33











          • when i do : import numpy as np import netCDF4 import matplotlib.pyplot as plt import glob list_of_paths = glob.glob('/home/all/2019/03/25/*.nc', recursive=True)nc = netCDF4.MFDataset(list_of_paths) IR=nc.variables['IR'][0:1] i had error like : name 'nc' is not defined In [15]: nc = netCDF4.MFDataset(list_of_paths) --------------------------------------------------------------------------- OSError: dataset /homm/all/msg04/all/2019/03/25/Mmulti_201903252000.nc does not have a aggregation dimension

            – Sarah Tohami
            Apr 5 at 7:15











          • ok then you'll have to use "netCDF4.Dataset" instead of "netCDF4.MFDataset" and load a single nc-file at a time. So you need to make a for-loop on the list_of_paths

            – Bert Coerver
            Apr 5 at 7:30













          0












          0








          0







          You can use the glob.glob module to search all the nc-files in your sub-folder like this (taken from https://stackoverflow.com/questions/14798220/how-can-i-search-sub-folders-using-glob-glob-module):



          import glob

          list_of_paths = glob.glob('C:/Users/sam/Desktop/myfolder/**/*.nc', recursive=True)


          Then, if there is a dimension in your netcdfs that is unlimited, you can open all the files in one line like this:



          import netCDF4

          nc = netCDF4.MFDataset(list_of_paths)


          After this you will probably want to be carefull, because doing:



          IR=nc.variables['IR'][:]


          will load the 'IR'-data from ALL your nc-files into your memory at once, which could crash you computer. So it's probably better to load small parts at a time by replacing [:] with, for example, [0:2].






          share|improve this answer













          You can use the glob.glob module to search all the nc-files in your sub-folder like this (taken from https://stackoverflow.com/questions/14798220/how-can-i-search-sub-folders-using-glob-glob-module):



          import glob

          list_of_paths = glob.glob('C:/Users/sam/Desktop/myfolder/**/*.nc', recursive=True)


          Then, if there is a dimension in your netcdfs that is unlimited, you can open all the files in one line like this:



          import netCDF4

          nc = netCDF4.MFDataset(list_of_paths)


          After this you will probably want to be carefull, because doing:



          IR=nc.variables['IR'][:]


          will load the 'IR'-data from ALL your nc-files into your memory at once, which could crash you computer. So it's probably better to load small parts at a time by replacing [:] with, for example, [0:2].







          share|improve this answer












          share|improve this answer



          share|improve this answer










          answered Apr 4 at 8:52









          Bert CoerverBert Coerver

          708310




          708310












          • thanks u but what mean [0:2] my problem that i have a simple application wxpython when i have button this button for select file in directory netcdf file i want to open so after open i want plot it so i will try ... but please what mean [0:2] ? exist method to open the file i want and plot it ?

            – Sarah Tohami
            Apr 4 at 9:44











          • i have question we can use loop for and loop for for variables keys ?

            – Sarah Tohami
            Apr 4 at 9:49











          • that is imformations about my variable IR in file netCDF4._netCDF4.Variable'> int16 IR_108(ny, nx) Offset : radiance = offset + CN x slope: -10.456819486590666 Slope : radiance = offset + CN x slope: 0.2050356762076601 unlimited dimensions: current shape = (3712, 3712) filling on

            – Sarah Tohami
            Apr 4 at 11:33











          • when i do : import numpy as np import netCDF4 import matplotlib.pyplot as plt import glob list_of_paths = glob.glob('/home/all/2019/03/25/*.nc', recursive=True)nc = netCDF4.MFDataset(list_of_paths) IR=nc.variables['IR'][0:1] i had error like : name 'nc' is not defined In [15]: nc = netCDF4.MFDataset(list_of_paths) --------------------------------------------------------------------------- OSError: dataset /homm/all/msg04/all/2019/03/25/Mmulti_201903252000.nc does not have a aggregation dimension

            – Sarah Tohami
            Apr 5 at 7:15











          • ok then you'll have to use "netCDF4.Dataset" instead of "netCDF4.MFDataset" and load a single nc-file at a time. So you need to make a for-loop on the list_of_paths

            – Bert Coerver
            Apr 5 at 7:30

















          • thanks u but what mean [0:2] my problem that i have a simple application wxpython when i have button this button for select file in directory netcdf file i want to open so after open i want plot it so i will try ... but please what mean [0:2] ? exist method to open the file i want and plot it ?

            – Sarah Tohami
            Apr 4 at 9:44











          • i have question we can use loop for and loop for for variables keys ?

            – Sarah Tohami
            Apr 4 at 9:49











          • that is imformations about my variable IR in file netCDF4._netCDF4.Variable'> int16 IR_108(ny, nx) Offset : radiance = offset + CN x slope: -10.456819486590666 Slope : radiance = offset + CN x slope: 0.2050356762076601 unlimited dimensions: current shape = (3712, 3712) filling on

            – Sarah Tohami
            Apr 4 at 11:33











          • when i do : import numpy as np import netCDF4 import matplotlib.pyplot as plt import glob list_of_paths = glob.glob('/home/all/2019/03/25/*.nc', recursive=True)nc = netCDF4.MFDataset(list_of_paths) IR=nc.variables['IR'][0:1] i had error like : name 'nc' is not defined In [15]: nc = netCDF4.MFDataset(list_of_paths) --------------------------------------------------------------------------- OSError: dataset /homm/all/msg04/all/2019/03/25/Mmulti_201903252000.nc does not have a aggregation dimension

            – Sarah Tohami
            Apr 5 at 7:15











          • ok then you'll have to use "netCDF4.Dataset" instead of "netCDF4.MFDataset" and load a single nc-file at a time. So you need to make a for-loop on the list_of_paths

            – Bert Coerver
            Apr 5 at 7:30
















          thanks u but what mean [0:2] my problem that i have a simple application wxpython when i have button this button for select file in directory netcdf file i want to open so after open i want plot it so i will try ... but please what mean [0:2] ? exist method to open the file i want and plot it ?

          – Sarah Tohami
          Apr 4 at 9:44





          thanks u but what mean [0:2] my problem that i have a simple application wxpython when i have button this button for select file in directory netcdf file i want to open so after open i want plot it so i will try ... but please what mean [0:2] ? exist method to open the file i want and plot it ?

          – Sarah Tohami
          Apr 4 at 9:44













          i have question we can use loop for and loop for for variables keys ?

          – Sarah Tohami
          Apr 4 at 9:49





          i have question we can use loop for and loop for for variables keys ?

          – Sarah Tohami
          Apr 4 at 9:49













          that is imformations about my variable IR in file netCDF4._netCDF4.Variable'> int16 IR_108(ny, nx) Offset : radiance = offset + CN x slope: -10.456819486590666 Slope : radiance = offset + CN x slope: 0.2050356762076601 unlimited dimensions: current shape = (3712, 3712) filling on

          – Sarah Tohami
          Apr 4 at 11:33





          that is imformations about my variable IR in file netCDF4._netCDF4.Variable'> int16 IR_108(ny, nx) Offset : radiance = offset + CN x slope: -10.456819486590666 Slope : radiance = offset + CN x slope: 0.2050356762076601 unlimited dimensions: current shape = (3712, 3712) filling on

          – Sarah Tohami
          Apr 4 at 11:33













          when i do : import numpy as np import netCDF4 import matplotlib.pyplot as plt import glob list_of_paths = glob.glob('/home/all/2019/03/25/*.nc', recursive=True)nc = netCDF4.MFDataset(list_of_paths) IR=nc.variables['IR'][0:1] i had error like : name 'nc' is not defined In [15]: nc = netCDF4.MFDataset(list_of_paths) --------------------------------------------------------------------------- OSError: dataset /homm/all/msg04/all/2019/03/25/Mmulti_201903252000.nc does not have a aggregation dimension

          – Sarah Tohami
          Apr 5 at 7:15





          when i do : import numpy as np import netCDF4 import matplotlib.pyplot as plt import glob list_of_paths = glob.glob('/home/all/2019/03/25/*.nc', recursive=True)nc = netCDF4.MFDataset(list_of_paths) IR=nc.variables['IR'][0:1] i had error like : name 'nc' is not defined In [15]: nc = netCDF4.MFDataset(list_of_paths) --------------------------------------------------------------------------- OSError: dataset /homm/all/msg04/all/2019/03/25/Mmulti_201903252000.nc does not have a aggregation dimension

          – Sarah Tohami
          Apr 5 at 7:15













          ok then you'll have to use "netCDF4.Dataset" instead of "netCDF4.MFDataset" and load a single nc-file at a time. So you need to make a for-loop on the list_of_paths

          – Bert Coerver
          Apr 5 at 7:30





          ok then you'll have to use "netCDF4.Dataset" instead of "netCDF4.MFDataset" and load a single nc-file at a time. So you need to make a for-loop on the list_of_paths

          – Bert Coerver
          Apr 5 at 7:30










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          Romeo and Juliet ContentsCharactersSynopsisSourcesDate and textThemes and motifsCriticism and interpretationLegacyScene by sceneSee alsoNotes and referencesSourcesExternal linksNavigation menu"Consumer Price Index (estimate) 1800–"10.2307/28710160037-3222287101610.1093/res/II.5.31910.2307/45967845967810.2307/2869925286992510.1525/jams.1982.35.3.03a00050"Dada Masilo: South African dancer who breaks the rules"10.1093/res/os-XV.57.1610.2307/28680942868094"Sweet Sorrow: Mann-Korman's Romeo and Juliet Closes Sept. 5 at MN's Ordway"the original10.2307/45957745957710.1017/CCOL0521570476.009"Ram Leela box office collections hit massive Rs 100 crore, pulverises prediction"Archived"Broadway Revival of Romeo and Juliet, Starring Orlando Bloom and Condola Rashad, Will Close Dec. 8"Archived10.1075/jhp.7.1.04hon"Wherefore art thou, Romeo? To make us laugh at Navy Pier"the original10.1093/gmo/9781561592630.article.O006772"Ram-leela Review Roundup: Critics Hail Film as Best Adaptation of Romeo and Juliet"Archived10.2307/31946310047-77293194631"Romeo and Juliet get Twitter treatment""Juliet's Nurse by Lois Leveen""Romeo and Juliet: Orlando Bloom's Broadway Debut Released in Theaters for Valentine's Day"Archived"Romeo and Juliet Has No Balcony"10.1093/gmo/9781561592630.article.O00778110.2307/2867423286742310.1076/enst.82.2.115.959510.1080/00138380601042675"A plague o' both your houses: error in GCSE exam paper forces apology""Juliet of the Five O'Clock Shadow, and Other Wonders"10.2307/33912430027-4321339124310.2307/28487440038-7134284874410.2307/29123140149-661129123144728341M"Weekender Guide: Shakespeare on The Drive""balcony"UK public library membership"romeo"UK public library membership10.1017/CCOL9780521844291"Post-Zionist Critique on Israel and the Palestinians Part III: Popular Culture"10.2307/25379071533-86140377-919X2537907"Capulets and Montagues: UK exam board admit mixing names up in Romeo and Juliet paper"Istoria Novellamente Ritrovata di Due Nobili Amanti2027/mdp.390150822329610820-750X"GCSE exam error: Board accidentally rewrites Shakespeare"10.2307/29176390149-66112917639"Exam board apologises after error in English GCSE paper which confused characters in Shakespeare's Romeo and Juliet""From Mariotto and Ganozza to Romeo and Guilietta: Metamorphoses of a Renaissance Tale"10.2307/37323537323510.2307/2867455286745510.2307/28678912867891"10 Questions for Taylor Swift"10.2307/28680922868092"Haymarket Theatre""The Zeffirelli Way: Revealing Talk by Florentine Director""Michael Smuin: 1938-2007 / Prolific dance director had showy career"The Life and Art of Edwin BoothRomeo and JulietRomeo and JulietRomeo and JulietRomeo and JulietEasy Read Romeo and JulietRomeo and Julieteeecb12003684p(data)4099369-3n8211610759dbe00d-a9e2-41a3-b2c1-977dd692899302814385X313670221313670221