How to Process multiple files using C2RCC

snap
#19

Where have you stored the processDataset.bash?

In your first case, the error

zsh: processDataset.bash: command not found…
zsh: command not found: processDataset.bash

tells you that the command (the file is not found). Your working directory seems to be /snap/bin.
You can save the file there. or you change the current working directory to the folder where the bash file is already located. Then the command should work.

In your second case you call gpt. But the parameters do not match the expected values.

#20

Dear marpet,

in first case, i put the file “processDataset.bash” , "resample_s2.xml " and “resample_20m.properties” stored in “snap/bin” thanks

Best

Binbin

#21

Maybe the file is not marked as executable.

How to Make Bash Script Executable Using Chmod (linoxide.com)
Have a look at step 4.

#22

try to follow your suggestion.

(binbin2) [bjiang@viz3]~/snap/bin% chmod u+x processDataset.bash resample_s2.xml resample_20m.properties “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/orgin” “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/orgin/S2A_MSIL1C_20160106T153632_N0201_R111_T19TCJ_20160106T153739.SAFE/C2RCC” resampled20m
chmod: cannot access ‘resampled20m’: No such file or directory
(binbin2) [bjiang@viz3]~/snap/bin% chmod u+x processDataset.bash
(binbin2) [bjiang@viz3]~/snap/bin% processDataset.bash resample_s2.xml resample_20m.properties “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/orgin” “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/orgin/S2A_MSIL1C_20160106T153632_N0201_R111_T19TCJ_20160106T153739.SAFE/C2RCC” resampled20m
zsh: processDataset.bash: command not found…
zsh: command not found: processDataset.bash

#23

by the way, i fix the “processDataset.bash” for my gpt path, like below,

adapt this path to your needs

export PATH=~/home/bjiang/snap/bin:$PATH
gptPath=“gpt”

is that right? when i try it again, the error like this below
(binbin2) [bjiang@viz3]~/snap/bin% ./processDataset.bash resample_s2.xml resample_20m.properties “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/orgin” “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/orgin/S2A_MSIL1C_20160106T153632_N0201_R111_T19TCJ_20160106T153739.SAFE/C2RCC” resampled20m
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
./processDataset.bash: line 53: gpt: command not found
(binbin2) [bjiang@viz3]~/snap/bin%

Best

Binbin

#24

It looks like works. thank you all. any suggestion for c2rcc atmospheric correction?

Best

Binbin

(binbin2) [bjiang@viz3]~/snap/bin% ./processDataset.bash resample_s2.xml resample_20m.properties “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/trytryorgin” “/home/bjiang/Sentinel2/getOC-master-3/2016woodram/C2RCCtry” resampled20m
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: GDAL 3.0.2 found on system. JNI driver will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 3.0.2 set to be used by SNAP.
Native library load failed.
java.lang.UnsatisfiedLinkError: /nfs3-home/bjiang/.snap/auxdata/gdal/gdal-3-0-X-jni/libgdalalljni.so: libgdal.so.26: cannot open shared object file: No such file or directory
SEVERE: org.esa.s2tbx.dataio.gdal.GDALLoader: Failed to initialize GDAL native drivers. GDAL readers and writers were disabled.java.lang.reflect.InvocationTargetException
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 3.0.2 set to be used by SNAP.
Executing processing graph
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32619
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [granuleidentifier] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
…10%…20%…30%…40%…50%…60%…70%…80%…90% done.
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: GDAL 3.0.2 found on system. JNI driver will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 3.0.2 set to be used by SNAP.
Native library load failed.
java.lang.UnsatisfiedLinkError: /nfs3-home/bjiang/.snap/auxdata/gdal/gdal-3-0-X-jni/libgdalalljni.so: libgdal.so.26: cannot open shared object file: No such file or directory
SEVERE: org.esa.s2tbx.dataio.gdal.GDALLoader: Failed to initialize GDAL native drivers. GDAL readers and writers were disabled.java.lang.reflect.InvocationTargetException
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 3.0.2 set to be used by SNAP.
Executing processing graph
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32619
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [granuleidentifier] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
…10%…20%…30%…40%…50%…60%…70%…80%…90% done.
(binbin2) [bjiang@viz3]~/snap/bin%

#25

Good that it now works.

But the chmod command should actually look like:

chmod u+x processDataset.bash

Not more. Afterwards it can be invoked the normal way.

#26

Dear marpet,

after i get the sentinel2 20m , i want to c2rcc.msi process, but it not works. Could you have some suggestions? thanks

Best

Binbin
command line:
./gpt c2rcc.msi -SsourceProduct=’/home/bjiang/Sentinel2/getOC-master-3/2016woodram/C2RCCtry’ -PoutputRpath=’/home/bjiang/Sentinel2/getOC-master-3/2016woodram/C2RCCtry/C2RCC’
error
(binbin2) [bjiang@viz3]~/snap/bin% ./gpt c2rcc.msi -SsourceProduct=’/home/bjiang/Sentinel2/getOC-master-3/2016woodram/C2RCCtry’ -PoutputRpath=’/home/bjiang/Sentinel2/getOC-master-3/2016woodram/C2RCCtry/C2RCC’
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: GDAL 3.0.2 found on system. JNI driver will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 3.0.2 set to be used by SNAP.
Native library load failed.
java.lang.UnsatisfiedLinkError: /nfs3-home/bjiang/.snap/auxdata/gdal/gdal-3-0-X-jni/libgdalalljni.so: libgdal.so.26: cannot open shared object file: No such file or directory
SEVERE: org.esa.s2tbx.dataio.gdal.GDALLoader: Failed to initialize GDAL native drivers. GDAL readers and writers were disabled.java.lang.reflect.InvocationTargetException
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 3.0.2 set to be used by SNAP.
org.esa.snap.core.gpf.OperatorException: No product reader found for ‘/nfs3-home/bjiang/Sentinel2/getOC-master-3/2016woodram/C2RCCtry’
at org.esa.snap.core.gpf.main.DefaultCommandLineContext.readProduct(DefaultCommandLineContext.java:57)
at org.esa.snap.core.gpf.main.CommandLineTool.readProduct(CommandLineTool.java:534)
at org.esa.snap.core.gpf.main.CommandLineTool.addProduct(CommandLineTool.java:479)
at org.esa.snap.core.gpf.main.CommandLineTool.getSourceProductMap(CommandLineTool.java:467)
at org.esa.snap.core.gpf.main.CommandLineTool.runOperator(CommandLineTool.java:295)
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:84)
at com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:66)
at install4j.org.esa.snap.runtime.Launcher_gpt.main(Unknown Source)

Error: No product reader found for ‘/nfs3-home/bjiang/Sentinel2/getOC-master-3/2016woodram/C2RCCtry’
(binbin2) [bjiang@viz3]~/snap/bin%

#27

The error explains it.
The path you have specified for the source product does not point to a product. But only to a directory, I guess.

#28

Dear marpet,

how could fix the problem. thanks. i have no idea about it. the “C2RCCtry” directory already has the after bash resample 20m sentinel2 data “resampled20m_S2A_MSIL1C_20160106T153632.data” and “resampled20m_S2A_MSIL1C_20160106T153632.dim” . it should works with ./gpt c2rcc.msi .

Thanks.

Binbin

#29

Have you modified the processDataset.bash file? You could compare it with the original file and maybe you see a difference.

#30

Dear marpet,

thanks for your reply fast. How could i modified the processDataset.bash? could you provide an example? thanks a lot.

Best

Binbin

#31

Sorry, but I can’t provide more help which exceeds the original guide
Bulk Processing with GPT - SNAP
Maybe you start with the basics of scripting on unix. This might help.
Shell Scripting Tutorial: How to Create Shell Script in Linux/Unix (guru99.com)

#32

A post was split to a new topic: How to get CDOM (Coloured Dissolved Organic Material) and DOC (Dissolved Organic Carbon)

#33

Hi everyone, I have processed some Sentinel 3 OLCI data with the C2RCC processor. I was wondering if there is a way to average multiple images together using snap? Thank you.

#34

Yes, you can use the mosaic processor or the binning processor.
The binning processor gives you more freedom on how the data aggregated. The mosaic only does a simple average.

#35

Hello,
I have been trying to average a few images together using the level-3 binning processor but I keep getting this as the output image. I am not sure if my parameters are incorrect or if I am trying to open the image wrong, I am using the RGB image window.
Thank you,
Chloe
Screenshot 2023-06-26 105617

Screenshot 2023-06-26 110746
Screenshot 2023-06-26 110746776×722 18.5 KB

Screenshot 2023-06-26 110807
Screenshot 2023-06-26 110807777×719 80.3 KB

Screenshot 2023-06-26 110828
Screenshot 2023-06-26 110828775×716 15.2 KB

#36

This image is also the size of very few pixels from the original images.

#37

I want to process multi MS1 scences in one go. I have exactly folowed the tutorial sent by Marco.

#38

You will have to change the Spatial Resolution because your output has right now 9.28km pixel