S-1 subset using geographical coordinates with snappy

development python
#1

Dear All,

I am trying to subset a S-1 image with Snappy . I used the code proposed in :https://github.com/ec-everest/e-learning-modules/blob/885da29f323658567614d444de9f4bf2493d2446/src/main/resources/e-learning/02%20Plot%20Sentinel-1%20subset.ipynb and it worked fine.

Now I am tryng to subset putting the lat/long coordinates of a four corners polygon but without any success.
Do you have an idea on how to solve it?

Kind regards

Fabiano

#2

Did you look at the snappy examples in the snappy installation directory?

#3

Thank you very much for the answer,
.Right now I am running the following code but it produce a void output file:
SAR_path=‘my_path’
image_name=“my_image_name”
SAR_image = ProductIO.readProduct(SAR_path)

wkt=“POLYGON((7.62 81.585, 7.62 81.699, 7.465 81.699, 7.465 81.585,7.62 81.585 ))”
geom = WKTReader().read(wkt)
HashMap = jpy.get_type(‘java.util.HashMap’)
GPF.getDefaultInstance().getOperatorSpiRegistry().loadOperatorSpis()
parameters = HashMap()
parameters.put(‘copyMetadata’, True)
parameters.put(‘geoRegion’, geom)
SAR_image_subset = GPF.createProduct(‘Subset’, parameters, SAR_image)
ProductIO.writeProduct(SAR_image_subset, image_name+’_subset’, ‘BEAM-DIMAP’)

Kind Regards

Fabiano

1 Like
#4

Your code looks good.
You say you get a void output file. Does it mean that the right region is written but there is just no data?
Or is also the wrong region extracted?

#5

Thank you very much I solved it ! I just had to restart the PC

Fabiano

#6

Dear All,

I’m quietly newbie in snappy and I am trying to subset a S-1 image with Snappy . I have tried with different images, but i only I trained myself with error:

band.readPixels(0, 0, w, h, band_data)
RuntimeError: java.lang.RuntimeException: javax.imageio.IIOException: I/O error reading image metadata!

The source code as follows:

import sys
sys.path.append(’/home/dani-ifca/.snap/snap-python/’)
from snappy import ProductIO
from snappy import jpy
from snappy import GPF
from snappy import HashMap

import numpy as np
import matplotlib.pylab as plt

pathS1=’/home/dani-ifca/Escritorio/image sentinel/S1B_IW_GRDH_1SDV_20161111T061637_20161111T061702_002907_004EEF_B9BC.SAFE’

p = ProductIO.readProduct(pathS1)
width = p.getSceneRasterWidth()
height = p.getSceneRasterHeight()
name = p.getName()
band_names = p.getBandNames()

print(“Product name: %s. Size = %d x %d pixels” % (name, width, height))
print(“Bands: %s” % (list(band_names)))

x = 18727
y = 15438
width = 2872
height = 3459

HashMap = jpy.get_type(‘java.util.HashMap’)
GPF.getDefaultInstance().getOperatorSpiRegistry().loadOperatorSpis()
parameters = HashMap()
parameters.put(‘copyMetadata’, True)
parameters.put(‘region’, “%s,%s,%s,%s” % (x, y, width, height))
subset = GPF.createProduct(‘Subset’, parameters, p)

band = subset.getBand(‘Amplitude_VV’)

w = band.getRasterWidth()
h = band.getRasterHeight()
band_data = np.zeros(w * h, np.float32)
band.readPixels(0, 0, w, h, band_data)

Thank you in advance.

#7

Is this thread of any help for you?

A search reveals that the error is reported several times. It seems to be a memory issue.

#8

I am having trouble with creating the Subset Sentinel-2, but I assume the Topic is entirely the same so I would like to ask the question in here.

I have tried to run The snappy example from GitHub

But got this error:

python snappy_subset.py /workdir/S2A_MSIL2A_20200515T045701_N0214_R119_T44PLU_20200515T093525.zip "POLYGON((79.6500 12.3000,79.7500 12.3000,79.7500 12.2000,79.6500 12.2000,79.6500 12.3000))"
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
SEVERE: org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller: The environment variable LD_LIBRARY_PATH is not set. It must contain the current folder '.'.
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
Reading...
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32644
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
WARNING: org.esa.s2tbx.dataio.s2.ortho.Sentinel2OrthoProductReader: Warning: missing file /workdir/S2A_MSIL2A_20200515T045701_N0214_R119_T44PLU_20200515T093525.zip/S2A_MSIL2A_20200515T045701_N0214_R119_T44PLU_20200515T093525.SAFE/GRANULE/L2A_T44PLU_A025570_20200515T051007/QI_DATA/L2A_T44PLU_20200515T045701_DDV_20m.jp2

WARNING: org.esa.s2tbx.dataio.s2.ortho.Sentinel2OrthoProductReader: Warning: no image files found for band quality_dense_dark_vegetation

Traceback (most recent call last):
File "snappy_subset.py", line 27, in <module>
    sub_product = op.getTargetProduct()
RuntimeError: java.lang.NullPointerException

It is possible that this error is also related to s2tbx.GDALInstaller error as I have tried to use gpt tool with same Sentinel-2 product and WKT geoRegion and got this error instead:

gpt Subset -Ssource=/workdir/S2A_MSIL2A_20200515T045701_N0214_R119_T44PLU_20200515T093525.zip -PcopyMetadata=true -PgeoRegion="POLYGON((79.6500 12.3000,79.7500 12.3000,79.7500 12.2000,79.6500 12.2000,79.6500 12.3000))"
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
SEVERE: org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller: The environment variable LD_LIBRARY_PATH is not set. It must contain the current folder '.'.
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32644
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.s2tbx.dataio.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
WARNING: org.esa.s2tbx.dataio.s2.ortho.Sentinel2OrthoProductReader: Warning: missing file /workdir/S2A_MSIL2A_20200515T045701_N0214_R119_T44PLU_20200515T093525.zip/S2A_MSIL2A_20200515T045701_N0214_R119_T44PLU_20200515T093525.SAFE/GRANULE/L2A_T44PLU_A025570_20200515T051007/QI_DATA/L2A_T44PLU_20200515T045701_DDV_20m.jp2

WARNING: org.esa.s2tbx.dataio.s2.ortho.Sentinel2OrthoProductReader: Warning: no image files found for band quality_dense_dark_vegetation

java.lang.NullPointerException
        at org.esa.snap.core.gpf.common.SubsetOp.initialize(SubsetOp.java:210)
        at org.esa.snap.core.gpf.internal.OperatorContext.initializeOperator(OperatorContext.java:486)
        at org.esa.snap.core.gpf.internal.OperatorContext.getTargetProduct(OperatorContext.java:273)
        at org.esa.snap.core.gpf.Operator.getTargetProduct(Operator.java:387)
        at org.esa.snap.core.gpf.main.CommandLineTool.runOperator(CommandLineTool.java:306)
        at org.esa.snap.core.gpf.main.CommandLineTool.runGraphOrOperator(CommandLineTool.java:284)
        at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:188)
        at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:121)
        at org.esa.snap.core.gpf.main.GPT.run(GPT.java:54)
        at org.esa.snap.core.gpf.main.GPT.main(GPT.java:34)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.esa.snap.runtime.Launcher.lambda$run$0(Launcher.java:55)
        at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189)
        at org.esa.snap.runtime.Launcher.run(Launcher.java:51)
        at org.esa.snap.runtime.Launcher.main(Launcher.java:31)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:65)
        at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

Error: java.lang.NullPointerException

@marpet if you have a moment, would you be willing to look into it with me? I noticed that the last commit to snappy_subset.py example has failed jenkins tests.

This is where I got so far:
If I run the code line by line in Jupyter Lab, I can open the product and work with it. The code always hangs on the same line

sub_product = op.getTargetProduct()
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-19-03cefc25ad88> in <module>
----> 1 sub_product = op.getTargetProduct()

RuntimeError: java.lang.NullPointerException

Most strangely, if I resample the product first

product = ProductIO.readProduct(file)

parameters = HashMap()
parameters.put('targetResolution',10)
result = snappy.GPF.createProduct('Resample', parameters, product)

op = SubsetOp()
op.setSourceProduct(result )
op.setGeoRegion(geom)
op.setCopyMetadata(True)

sub_product = op.getTargetProduct()

Everything just works! Can anyone make sense of it? Thanks for any help.