gdalwarp - Unable to warp HDF5 files

I have numerous HDF5 files(.nc) which I need to batch process warp using one of the gdal utilities gdalwarp. When I tried to warp the files an error occurred:

INPUT:

gdalwarp -geoloc -te 109.975 3.475 135.025 25.025 HDF5:"@file"://geophysical_data/chlor_a %out_path%\@fname.tif"

RESULT:

ERROR 1: Unable to compute a GEOLOC_ARRAY based transformation between pixel/lin e and georeferenced coordinates for HDF5:A2015045060500.L2_LAC_OC.nc://geophysical _data/chlor_a.

Update1:

Just to make it clear, do you mean in lat.vrt, lon.vrt and chlor.vrt I should remove the GCP Id's and MDI key and insert this section:

     
     oc-long.vrt  

     1  
     oc-lat.vrt  
     1  
     0  
     0  
     1  
     1  
   

in between this section?

  ###### metadata section here #######

 
    
      HDF5:A2015194044000.L2_LAC.SeAHABS.nc://geophysical_data/chlor_a
      1
      
      

      
    
  

Answer

After some testing, I think that the geoloc is not working properly. So I used the alternative method using manually created vrt files:

1. Create a file named lon.vrt:

  GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9108"]],AUTHORITY["EPSG","4326"]]
  
    
      HDF5:A2015045060000.L2_LAC_OC.nc://navigation_data/longitude
      1
      
      
      
    

  

2. Same for the latitudes in lat.vrt:

  GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9108"]],AUTHORITY["EPSG","4326"]]
  

    
      HDF5:A2015045060000.L2_LAC_OC.nc://navigation_data/latitude
      1
      
      
      
    
  

3. and for the data chlor.vrt:

         
         lon.vrt  
         1  
         lat.vrt  
         1  

         0  
         0  
         1  
         1  
          
         
    
      HDF5:A2015045060000.L2_LAC_OC.nc://geophysical_data/chlor_a
      1
      

      
      
    
  

4. Do the warping with:

gdalwarp -geoloc -t_srs EPSG:4326 chlor.vrt chlor-out.tif

and the result fits to the shorelines around Borneo:

---

Alternatively to creating the vrts manually, you can create them with GDAL:

gdal_translate -of VRT HDF5:A2015045060000.L2_LAC_OC.nc://navigation_data/longitude lon.vrt
gdal_translate -of VRT HDF5:A2015045060000.L2_LAC_OC.nc://navigation_data/latitude lat.vrt
gdal_translate -of VRT HDF5:A2015045060000.L2_LAC_OC.nc://geophysical_data/chlor_a chlor.vrt

With a good text editor, remove the GCP lists from all of them, and insert only into the chlor.vrt this section instead:

     
     lon.vrt  
     1  
     lat.vrt  
     1  
     0  
     0  
     1  
     1  

    

Then run

gdalwarp -geoloc -t_srs EPSG:4326 -overwrite chlor.vrt chlor-vrt.tif 

to get the same picture as above.

---

Another solution, working with manually edited GCP points, can be found in my answer for Using GDALwarp for reprojecting netCDF file?