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Categories » BEAM Toolbox Usage » RE: Operating with netCDF MERIS files. Trying to use gpt for ICOL correctio
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RE: Operating with netCDF MERIS files. Trying to use gpt for ICOL correctio
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Operating with netCDF MERIS files. Trying to use gpt for ICOL correction.
11/6/13 5:47 PM
Hello!

I am currently operating with MERIS netCDF files and would like to apply ICOL correction to them in gpt. Unfortunately I wasn' t able to make correct changes in this XML (attached to this message) and it didn't accept my netCDF files. All my source files are in netCDF format and conversion into N1 format isn't a good option because at the end I will need netCDF format again.

So, I would be very thankful for some hints and advice how to change that script!

Regards,
Evelin
Attachments: icol.xml (1.5k)
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RE: Operating with netCDF MERIS files. Trying to use gpt for ICOL correctio
11/7/13 6:34 PM as a reply to Evelin Kangro.
Dear Evelin,

could you please provide an example of your netCDF products? Then we can check this here and modify your graph xml accordingly. - Your target products shall be in netCDF as well, is that correct?

Thanks and best regards,
Olaf
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RE: Operating with netCDF MERIS files. Trying to use gpt for ICOL correctio
11/8/13 5:21 PM as a reply to Olaf Danne.
Hello!

Thank You for Your reply! Actually I still need to operate with N1 images and basically if I will cut the image smaller the source product will be in Dimap format.Also I would like to process this new ICOL corrected image with C2R processor but the test script with N1 images (not cutted) I wrote doesn't seem to work, giving me Error:null. Still at the end I will need the whole data in netCDF format in order to remap the images for another scripting. But I thought that if I will have the Level2 C2R processed image I should be able to save it or export the raster data as netCDF format. Also there probably a script that does this conversion as well.

To make it more clear what I would like to achive:
-I have MERIS L1b images in N1/Dimap format
-I have MERIS L1b images in N1/Dimap format
-I need to run the ICOL script on them
-the output file of ICOL is then Dimap again
-in turn the output should be the input for C2R script which gives L2 MERIS Dimap image as an output. At the moment this script is a test version for N1 format.
-Then this ouput of L2 image needs to be converted into netCDF format

Added attachments include: ICOL and C2R XML scripts. MERIS images from these pages: http://www.upload.ee/files/3693385/subset_0_of_MER_FRS_1PNPDK20110607_093341_000002143103_00180_48470_6575.dim.html and data file http://www.upload.ee/files/3693379/subset_0_of_MER_FRS_1PNPDK20110607_093341_000002143103_00180_48470_6575.data.tar.gz.html

The command I used (also a test version creating a N1 file): gpt.sh icol.xml -Pn1TargetFile=/users/pmlvis/pmlvis15/scratch-network/L1_subset_0_of_MER_FRS_1PNPDK20110607_093341_000002143103_00180_48470_6575.N1 -Sn1Product= users/pmlvis/pmlvis15/scratch-network/L1_subset_0_of_MER_FRS_1PNPDK20110607_093341_000002143103_00180_48470_6575.N1

The command contains N1 file altough it is the same subset image that is in the attachments, but I tried to run the script with one N1 image which wasn't cutted.

I really would appreciate if You could help me with the gpt and the scripts!

Regards,
Evelin
Attachments: case2r.xml (1.6k), icol.xml (1.3k)
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RE: Operating with netCDF MERIS files. Trying to use gpt for ICOL correctio
11/12/13 4:00 PM as a reply to Evelin Kangro.
Dear Evelin,

to illustrate the rules how to do this task, please find attached graph XMLs for:
- ICOL with DIMAP or N1 input, DIMAP or NetCDF output: icol_dimap_netcdf.xml
- ICOL with N1 input, patched N1 output: icol_patch_N1.xml
- C2R with DIMAP or N1 input, DIMAP or NetCDF output: case2r.xml
- ICOL and C2R with DIMAP or N1 input, DIMAP or NetCDF output: icol_c2r_netcdf.xml

I used as example product 'MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959.N1'.
Then, assuming that scripts and source product are in the same directory, the command line calls would be:

DIMAP output:
- gpt.sh icol_dimap_netcdf.xml -SsourceProduct=./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959.N1 -t ./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959_ICOL.dim

NetCDF output:
- gpt.sh icol_dimap_netcdf.xml -SsourceProduct=./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959.N1 -f NetCDF-CF -t ./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959_ICOL.nc

patched N1 output:
- gpt.sh icol_patch_N1.xml -SsourceProduct=./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959.N1 -PpatchedFile=./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959_ICOL.N1

All three output products can be used as input for Case2R, such as
- gpt.sh case2r.xml -SsourceProduct=./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959_ICOL.dim -f NetCDF-CF -t ./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959_C2R.nc
to generate NetCDF output.

However, if I understand correctly, the most convenient way for you would be to do everything in one step with the graph XML icol_c2r_netcdf.xml. In this case, your command would simply be:
- gpt.sh icol_c2r_netcdf.xml -SsourceProduct=./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959.N1 -f NetCDF-CF -t ./MER_RR__1PPBCM20100314_095819_000000542087_00380_42017_0959_C2R.nc

If you have further questions, let us know. In any case of problems, please refer also to the BEAM GPF help documentation:
gpt.sh -h (general)
gpt.sh -h <processor>, e.g.: gpt.sh -h icol.Meris

Best regards,
Olaf
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RE: Operating with netCDF MERIS files. Trying to use gpt for ICOL correctio
11/12/13 5:33 PM as a reply to Olaf Danne.
Hi!

Thank You very much for Your reply!! I now have many opportunities how to operate with different formats. Very good! Thank You again! However, it seems to me that You forgot to forward these graph xml files?? I wasn' t able to find them in Your letter.

Cheers,
Evelin
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RE: Operating with netCDF MERIS files. Trying to use gpt for ICOL correctio
11/13/13 3:02 PM as a reply to Evelin Kangro.
Hi Evelin,

oh, I'm very sorry for that, something must have gone wrong! I'll try again now, I hope the attachments will reach you this time.

Cheers,
Olaf
Attachments: case2r.xml (1.2k), icol_c2r_netcdf.xml (2.2k), icol_dimap_netcdf.xml (1.0k), icol_patch_N1.xml (1.5k)
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