Batch processing using GPT, Export Pixels (PixEx)

snap
#1

Hello all.
I want to export specific pixels from a S2 image . I have a shapefile with specific points that I need.
In the PixEx description it says to input a files that have geo-coordinates. But I assume, that it is not a shapefile.
So I exported attribute table with longitude and latitude of that shapefile to .txt (in the graph file it is named Ex_attrb).
I attach the .txt file with PixEx code info. PixEx.txt (900 Bytes)

And that’s the gpt line that I call and what I get:

gpt re_ide.xml -Pfile="/shared/Sentinel-2/Level_1C/S2A_OPER_PRD_MSIL1C_PDMC_20160427T183742_R136_V20160427T093037_20160427T093037.SAFE/GRANULE/S2A_OPER_MSI_L1C_TL_SGS__20160427T133230_A004423_T34UFF_N02.01/"
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.snap.core.gpf.descriptor.ToolAdapterOperatorDescriptor: Adapter META-INF has been automatically converted to the new format
SEVERE: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Failed to register module Sen2Cor. Problem: org.esa.snap.core.gpf.descriptor.SimpleSourceProductDescriptor : org.esa.snap.core.gpf.descriptor.SimpleSourceProductDescriptor
---- Debugging information ----
message : org.esa.snap.core.gpf.descriptor.SimpleSourceProductDescriptor
cause-exception : com.thoughtworks.xstream.mapper.CannotResolveClassException
cause-message : org.esa.snap.core.gpf.descriptor.SimpleSourceProductDescriptor
class : [Lorg.esa.snap.core.gpf.descriptor.DefaultSourceProductDescriptor;
required-type : [Lorg.esa.snap.core.gpf.descriptor.DefaultSourceProductDescriptor;
converter-type : com.thoughtworks.xstream.converters.collections.ArrayConverter
path : /operator/sourceProductDescriptors/org.esa.snap.core.gpf.descriptor.SimpleSourceProductDescriptor
line number : 94
class[1] : org.esa.snap.core.gpf.descriptor.ToolAdapterOperatorDescriptor
converter-type[1] : com.thoughtworks.xstream.converters.reflection.ReflectionConverter
version : 1.4.8

SEVERE: org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller: The environment variable LD_LIBRARY_PATH is not set. It must contain the current folder ‘.’.
Executing processing graph
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32634
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
No subsampling of 20.0 m product necessary to access 50 m water mask
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Checking for ‘/home/rus/.snap/auxdata/watermask/50m.zip’ …
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Found ‘50m.zip’.
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Checking for ‘/home/rus/.snap/auxdata/watermask/150m.zip’ …
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Found ‘150m.zip’.
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Checking for ‘/home/rus/.snap/auxdata/watermask/GC_water_mask.zip’ …
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Found ‘GC_water_mask.zip’.
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Checking for ‘/home/rus/.snap/auxdata/watermask/MODIS_north_water_mask.zip’ …
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Found ‘MODIS_north_water_mask.zip’.
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Checking for ‘/home/rus/.snap/auxdata/watermask/MODIS_south_water_mask.zip’ …
INFO: org.esa.snap.watermask.operator.WatermaskUtils: Found ‘MODIS_south_water_mask.zip’.
done.

Error: [NodeId: PixEx] Operator ‘PixExOp’: ‘double’ cannot be converted to a double.

Thanks for any help.

PixEx in gpt
#2

In the xml file you can remove the sources tag.

  <sources>
    <sourceProducts refid="Import-Vector"/>
  </sources>

But the error is caused by the coordinates tag.

    <coordinates>
      <coordinate>
        <name>Ex_attrb</name>
        <latitude>double</latitude>
        <longitude>double</longitude>
      </coordinate>
    </coordinates>

Replace the ‘double’ by the specific latitude/longitude values.

For specifying a file with the list of coordinates use the tag

 <coordinatesFile>file</coordinatesFile>

and specify the path to the file.
For information about the file format please see the help in SNAP Desktop.

From the log output I guess that you are still using SNAP 5. It would be good that you update to version 6.

#3

Hello.
Actually the reason why it was not working was that it has to be “sourceProduct refid=“Import-Vector”” and not "
"sourceProducts refid=“Import-Vector”. But it does have this “s” in the documentation.
And yes, I indeed, forgot to update snap in my virtual machine (I had it updated in my dektop pc). Thanks for noticing. :slight_smile: