I have problem about extracting multiple NetCDF files with multiple stations of interest

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chonlada33
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I have problem about extracting multiple NetCDF files with multiple stations of interest

by chonlada33 » Mon Dec 20, 2021 7:07 am America/New_York

I have downloaded chlorophyll_a from https://oceancolor.gsfc.nasa.gov/l3/
I have got the daily data (366 netCDF files).
I want to extract chlorophyll a from multiple netCDF files in each day (365 days) with multiple stations (about 3627 stations which prepared the area of interest in CSV file)

I have seen several tutorials about combining and extracting netCDF files and in all of the tutorials, netCDF files contain "time" coordinated with lat and long. But my netCDF files do not have time!
One file is one day's value. Chlorophyll a, lat, long, and palette are all contained within a single file (e.g. dict_keys(['chlor_a', 'lat', 'lon', 'palette']).

I have applied some code in python from the tutorials.
I tried to apply the file name to be the date variable but it did not work!!
This is file name example : A2020001.L3m_DAY_CHL.x_chlor_a.nc. at 1st January 2020.
I have got an empty csv table when I exported it.

Has anyone done it? Please help to advise me about python code.

I am looking forward to hearing some suggestions!

Thanks in advance

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OB.DAAC - amscott
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by OB.DAAC - amscott » Mon Dec 20, 2021 2:40 pm America/New_York

Using SeaDAS, I find a time parameter under Bands > chlor_a. If you view the image and mouseover an area of interest on the image, you see the time populate on the pixel info to the right.

chonlada33
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by chonlada33 » Mon Dec 20, 2021 9:15 pm America/New_York

So, how do I use seaDAS to combine all 365 files and extract all stations at once?
If you have, could you kindly let me know if you have any tutorial links or documentation on how to combine and extract? It would be extremely helpful.

Thanks in advance!

OB SeaDAS - knowles
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by OB SeaDAS - knowles » Tue Dec 21, 2021 9:49 am America/New_York

There's a tool called Pixel Extraction in SeaDAS. I think it's a bit hidden, but you can find it by typing "Extract Pixel Values" in the search area of the SeaDAS GUI (top right corner of SeaDAS). The Pixel Extraction tool let's you enter the input files, and specify the coordinates for your stations either directly or via a CVS file, and it let's you specify whether you want to restrict extraction by date, as well as pixel aggregation and other features.

I don't know if 366 files will cause a memory issue in this tool, but if it does you can do it in smaller chunks of files and then combine the resulting text files of the extracted values.

The command line version of this Pixel Extraction tool is a gpt tool called PixEx. However the command line gpt tools are not yet operational as of SeaDAS 8.1.0. This same tool is in the software SNAP. SeaDAS and SNAP share a lot of the same underlying code and tools. So if you wish to do this at the command line then you will want to use SNAP for the moment until SeaDAS supports this feature at the command line.
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gnwiii
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by gnwiii » Wed Dec 22, 2021 10:24 pm America/New_York

chonlada33 wrote: Mon Dec 20, 2021 9:15 pm America/New_York So, how do I use seaDAS to combine all 365 files and extract all stations at once?
If you have, could you kindly let me know if you have any tutorial links or documentation on how to combine and extract? It would be extremely helpful.
SeaDAS focuses on the specific needs of ocean color processing. Once you have level-3 mapped files in NetCDF4-CF format there are tools that support multiple disciplines beyond just ocean color. I have used NCO <https://github.com/nco/nco> and CDO <https://mpimet.mpg.de/cdo>. Both are often available in linux distros or macports. They are command-line programs suitable for large scale batch processing, but the learning curve is long and steep.

For CDO you add times to the individual files and then use "mergetime" to combine them into one or more (depending on your system capacity) larger files.

chonlada33
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by chonlada33 » Sun Dec 26, 2021 8:34 pm America/New_York

Thank you very much for your kind helping.
I have tried to extract in R already. It is solved now!!

gnwiii
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by gnwiii » Mon Dec 27, 2021 10:46 am America/New_York

Glad you found success. I assume you have previous experience with R. For the benefit of the next person with the same question, it might be helpful to provide a brief outline of your workflow.

chonlada33
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by chonlada33 » Mon Dec 27, 2021 11:08 pm America/New_York

I attempted to utilize seaDAS at first, but because of my laptop's window operating system, I was unable to use the extraction feature.
I followed the instructions, which stated that I should connect to the server first.
But the procedure was too difficult for me, so I went my own way.
It's weird and appears to be a manual process.

Actually, I have applied R code from my friend.
For my data, However, the date and time variables were absent from my netCDF file.
To begin, I must create 366 file names from January 1 to December 31 of the same year.

Actually, after extracting, I wanted to utilize the filename as a single variable name, but I didn't know how.
Because when I download the entire year's amount of netCDF files, some days are missing.
I addressed the problem by creating a new netCDF file in Python and replacing the missing file with this.

##############Python code for making empty netCDF file##############
import netCDF4 as nc
import numpy as np
import xarray as xr

ncfile = nc.Dataset("A2020001.L3m_DAY_CHL.x_chlor_a.nc",'r+')
lu_index = ncfile.variables['chlor_a'][:]
lu_index = 0
ncfile.variables['chlor_a'][:] = lu_index
chl_a1 = ncfile.variables['chlor_a'][:]
print(chl_a1)

ncfile.close()


##################### R code for extracting data ###################
rm(list=ls(all=T))

#Define directory

workdir<-"C:/Users/nanae/Documents/R/R_extract"
class(workdir)
setwd(workdir)
getwd()

#Import library
library(rasterVis)
library(RColorBrewer)
library(pals)
library(ncdf4)
library(rworldmap)
library(rworldxtra)
library(raster)
library(plotly)

# Read chl-a data
raster_stack = list.files('C:/Users/nanae/Documents/R/R_extract/',pattern='*.nc',full.names=TRUE) #
class(raster_stack)
chl_aqa <- raster::stack(raster_stack, varname = 'chlor_a')
names(chl_aqa)<-seq(as.Date("2020-01-01"), by = "day", length.out = 366) #create each file name (start date is 2020-01-01, and end date is 2020-12-31)

#Import station of interest using csv
station_data<-read.csv("stations.csv",header = TRUE)
station_data<- SpatialPoints(coords=station_data, proj4string = CRS("+proj=longlat +datum=WGS84"))

#Extract
extract_value<-extract(chl_aqa,station_data)
extract_value<-t(rasValues)
extract_value

#export
write.csv(extract_value, file ="extract_chlor_a.csv")


I hope this solution could help.
If someone finds an error or maybe something that can be improved, kindly advise, please.

gnwiii
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Re: I have problem about extracting multiple NetCDF files with multiple stations of interest

by gnwiii » Tue Dec 28, 2021 10:55 am America/New_York

chonlada33 wrote: Mon Dec 27, 2021 11:08 pm America/New_York I attempted to utilize seaDAS at first, but because of my laptop's window operating system, I was unable to use the extraction feature.
Thanks for the additional detail. I think pixel extraction should work in the SeaDAS GUI, but a laptop may not have the capacity (mainly RAM) to process many files at once. Linux excels at running the same program repeatedly to apply the same process to a list of files.

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