CRS not found when process Sentinel-1 product with SNAP gpt. #69

TK12331 · 2022-12-02T09:02:38Z

TK12331
Dec 2, 2022

I want to change the process in EOReader to produce Calibration product, thus I comment Terrain-Correction and LinearToFromdB in grd_s1_preprocess_default.xml and change the sourceProduct refid to Calibration . Finally, my xml is as followes:

<graph id="Graph">
  <version>1.0</version>
  <node id="Read">
    <operator>Read</operator>
    <sources/>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <file>${file}</file>
    </parameters>
  </node>
  <node id="Apply-Orbit-File">
    <operator>Apply-Orbit-File</operator>
    <sources>
      <sourceProduct refid="Read"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <orbitType>Sentinel Precise (Auto Download)</orbitType>
      <polyDegree>3</polyDegree>
      <continueOnFail>true</continueOnFail>
    </parameters>
  </node>
 <node id="ThermalNoiseRemoval">
    <operator>ThermalNoiseRemoval</operator>
    <sources>
      <sourceProduct refid="Apply-Orbit-File"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <selectedPolarisations/>
      <removeThermalNoise>true</removeThermalNoise>
      <reIntroduceThermalNoise>false</reIntroduceThermalNoise>
    </parameters>
  </node>
  <node id="Remove-GRD-Border-Noise">
    <operator>Remove-GRD-Border-Noise</operator>
    <sources>
      <sourceProduct refid="ThermalNoiseRemoval"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <selectedPolarisations/>
      <borderLimit>500</borderLimit>
      <trimThreshold>0.5</trimThreshold>
    </parameters>
  </node>
  <node id="Calibration">
    <operator>Calibration</operator>
    <sources>
      <sourceProduct refid="Remove-GRD-Border-Noise"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <sourceBands/>
      <auxFile>Latest Auxiliary File</auxFile>
      <externalAuxFile/>
      <outputImageInComplex>false</outputImageInComplex>
      <outputImageScaleInDb>false</outputImageScaleInDb>
      <createGammaBand>false</createGammaBand>
      <createBetaBand>false</createBetaBand>
      <selectedPolarisations>${calib_pola}</selectedPolarisations>
      <outputSigmaBand>true</outputSigmaBand>
      <outputGammaBand>false</outputGammaBand>
      <outputBetaBand>false</outputBetaBand>
    </parameters>
  </node>
  <!-- <node id="Terrain-Correction">
    <operator>Terrain-Correction</operator>
    <sources>
      <sourceProduct refid="Calibration"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <sourceBands/>
      <demName>${dem_name}</demName>
      <externalDEMFile>${dem_path}</externalDEMFile>
      <externalDEMNoDataValue>0.0</externalDEMNoDataValue>
      <externalDEMApplyEGM>true</externalDEMApplyEGM>
      <demResamplingMethod>BILINEAR_INTERPOLATION</demResamplingMethod>
      <imgResamplingMethod>BILINEAR_INTERPOLATION</imgResamplingMethod>
      <pixelSpacingInMeter>${res_m}</pixelSpacingInMeter>
      <pixelSpacingInDegree>${res_deg}</pixelSpacingInDegree>
      <mapProjection>${crs}</mapProjection>
      <alignToStandardGrid>false</alignToStandardGrid>
      <standardGridOriginX>0.0</standardGridOriginX>
      <standardGridOriginY>0.0</standardGridOriginY>
      <nodataValueAtSea>false</nodataValueAtSea>
      <saveDEM>false</saveDEM>
      <saveLatLon>false</saveLatLon>
      <saveIncidenceAngleFromEllipsoid>false</saveIncidenceAngleFromEllipsoid>
      <saveLocalIncidenceAngle>false</saveLocalIncidenceAngle>
      <saveProjectedLocalIncidenceAngle>false</saveProjectedLocalIncidenceAngle>
      <saveSelectedSourceBand>true</saveSelectedSourceBand>
      <applyRadiometricNormalization>false</applyRadiometricNormalization>
      <saveSigmaNought>false</saveSigmaNought>
      <saveGammaNought>false</saveGammaNought>
      <saveBetaNought>false</saveBetaNought>
      <incidenceAngleForSigma0>Use projected local incidence angle from DEM</incidenceAngleForSigma0>
      <incidenceAngleForGamma0>Use projected local incidence angle from DEM</incidenceAngleForGamma0>
      <auxFile>Latest Auxiliary File</auxFile>
      <externalAuxFile/>
    </parameters>
  </node>
  <node id="LinearToFromdB">
    <operator>LinearToFromdB</operator>
    <sources>
      <sourceProduct refid="Calibration"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <sourceBands/>
    </parameters>
  </node> -->
  <node id="Write">
    <operator>Write</operator>
    <sources>
      <sourceProduct refid="Calibration"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <file>${out}</file>
      <formatName>BEAM-DIMAP</formatName>
    </parameters>
  </node>
  <applicationData id="Presentation">
    <Description/>
    <node id="Read">
            <displayPosition x="37.0" y="35.0"/>
    </node>
    <node id="Apply-Orbit-File">
      <displayPosition x="30.0" y="76.0"/>
    </node>
    <node id="ThermalNoiseRemoval">
      <displayPosition x="24.0" y="125.0"/>
    </node>
    <node id="Remove-GRD-Border-Noise">
      <displayPosition x="27.0" y="175.0"/>
    </node>
    <node id="Calibration">
      <displayPosition x="96.0" y="222.0"/>
    </node>
    <!-- <node id="Terrain-Correction">
      <displayPosition x="284.0" y="259.0"/>
    </node>
    <node id="LinearToFromdB">
      <displayPosition x="138.0" y="263.0"/>
    </node> -->
    <node id="Write">
            <displayPosition x="522.0" y="264.0"/>
    </node>
  </applicationData>
</graph>

However, the error CRS not found is raised as followes:

Executing processing graph
version = 3.2
....10%....20%....30%....40%....50%....60%....70%....80%....90% done.
C:\Users\10992\.conda\envs\DL1\lib\site-packages\rioxarray\_io.py:1111: NotGeoreferencedWarning: Dataset has no geotransform, gcps, or rpcs. The identity matrix will be returned.
  warnings.warn(str(rio_warning.message), type(rio_warning.message))  # type: ignore
C:\Users\10992\.conda\envs\DL1\lib\site-packages\rasterio\__init__.py:342: NotGeoreferencedWarning: The given matrix is equal to Affine.identity or its flipped counterpart. GDAL may ignore this matrix and save no geotransform without raising an error. This behavior is somewhat driver-specific.
  dataset = writer(
Traceback (most recent call last):
  File "e:\SAR_DATA\eoreader-main\K.py", line 21, in <module>
    bands = s1_prod.load([VH])
  File "e:\SAR_DATA\eoreader-main\eoreader\products\product.py", line 900, in load
    band_dict = self._load(unique_bands, resolution, size, **kwargs)
  File "e:\SAR_DATA\eoreader-main\eoreader\products\sar\sar_product.py", line 681, in _load
    bands = self._load_bands(band_list, resolution=resolution, size=size, **kwargs)
  File "e:\SAR_DATA\eoreader-main\eoreader\products\sar\sar_product.py", line 624, in _load_bands
    band_arrays[band_name] = self._read_band(
  File "e:\SAR_DATA\eoreader-main\eoreader\products\sar\sar_product.py", line 582, in _read_band
    return utils.read(
  File "e:\SAR_DATA\eoreader-main\eoreader\utils.py", line 169, in read
    return rasters.read(
  File "C:\Users\10992\.conda\envs\DL1\lib\site-packages\sertit\rasters_rio.py", line 132, in path_or_arr_or_dst_wrapper
    out = function(dst, *args, **kwargs)
  File "C:\Users\10992\.conda\envs\DL1\lib\site-packages\sertit\rasters.py", line 700, in read
    xda = xda.rio.reproject(
  File "C:\Users\10992\.conda\envs\DL1\lib\site-packages\rioxarray\raster_array.py", line 444, in reproject
    raise MissingCRS(
rioxarray.exceptions.MissingCRS: CRS not found. Please set the CRS with 'rio.write_crs()'. Data variable: 20200308T121318_S1_VV_VH_IW_GRD_VH

I have spent a long time to deal with it but failed, can u help me?

In additon, what <applicationData id="Presentation"> in XML means?

Answered by remi-braun

Dec 2, 2022

You must keep the terrain correction step in your graph otherwise your image remains in sensor CRS (and thus not georeferenced).

Don't bother about <applicationData id="Presentation">, it's not important 😉

View full answer

TK12331 · 2022-12-02T09:33:59Z

TK12331
Dec 2, 2022
Author

This is the message that cmd outputs when running grd_s1_preprocess_default.xml, which is very different from that of the output when I run my XML...

Executing processing graph
version = 3.2
.Copernicus_DSM_COG_10_N26_00_E086_00_DEM.tif
Copernicus_DSM_COG_10_N26_00_E087_00_DEM.tif
.Copernicus_DSM_COG_10_N26_00_E088_00_DEM.tif
Copernicus_DSM_COG_10_N26_00_E089_00_DEM.tif
..10%....20%....30%..Copernicus_DSM_COG_10_N25_00_E086_00_DEM.tif
.Copernicus_DSM_COG_10_N25_00_E087_00_DEM.tif
Copernicus_DSM_COG_10_N25_00_E088_00_DEM.tif
.Copernicus_DSM_COG_10_N25_00_E089_00_DEM.tif
40%....50%....60%....70%....80%Copernicus_DSM_COG_10_N24_00_E086_00_DEM.tif
.Copernicus_DSM_COG_10_N24_00_E087_00_DEM.tif
Copernicus_DSM_COG_10_N24_00_E088_00_DEM.tif
.Copernicus_DSM_COG_10_N24_00_E089_00_DEM.tif
..90% done.

0 replies

remi-braun · 2022-12-02T09:34:56Z

remi-braun
Dec 2, 2022
Maintainer

You must keep the terrain correction step in your graph otherwise your image remains in sensor CRS (and thus not georeferenced).

Don't bother about <applicationData id="Presentation">, it's not important 😉

0 replies

TK12331 · 2022-12-02T11:14:07Z

TK12331
Dec 2, 2022
Author

I keep the terrain correction step, but the same error raised, while the calibration tif is saved. Can I keep the calibration tif with no error for the execution of subsequent code? Now the only difference between default and my XML is the <sourceProduct refid="Calibration"/> .

  <node id="Write">
    <operator>Write</operator>
    <sources>
      <sourceProduct refid="Calibration"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <file>${out}</file>
      <formatName>BEAM-DIMAP</formatName>
    </parameters>
  </node>

2 replies

remi-braun Dec 2, 2022
Maintainer

Here your graph says to write on disk after the calibration step, so anything else written on the graph won't be done.

TK12331 Dec 5, 2022
Author

Got it. Thank you!

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CRS not found when process Sentinel-1 product with SNAP gpt. #69

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