OpenJPEG and no such child: Granule errors

Optical Toolbox sen2cor
#1

Hello. I am new to using SNAP and sen2cor. My advisor suggested that I use Sentinel-2 data for my thesis work and part of it requires the use of this tool. I have a clean install on a Windows 10 desktop and consistently receive the follow errors no matter which .SAFE I select. I also have selected not to downsample 20 to 60:

image

yet in the output it says:

20 m resolution will be downsampled to 60 m

which doesn’t make sense to me, but more importantly, things seem to otherwise progress well enough until near the end and I start getting these errors:

Progress[%]: 27.64 : PID-24700, L2A_Tables: start export for 20 m resolution, elapsed time[s]: 0.005, total: 0:11:58.683000
OpenJPEG function failure.
Traceback (most recent call last):
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 2446, in exportBandList
self.glymurWrapper(filename, band)
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 2606, in glymurWrapper
*glymur.Jp2k(filename, band, *kwargs)
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\lib\site-packages\glymur\jp2k.py”, line 177, in __init__
*self._write(data, *kwargs)
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\lib\site-packages\glymur\jp2k.py”, line 539, in _write
self._write_openjp2(img_array, verbose=verbose)
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\lib\site-packages\glymur\jp2k.py”, line 783, in _write_openjp2
opj2.start_compress(codec, image, strm)
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\lib\site-packages\glymur\lib\openjp2.py”, line 1299, in start_compress
OPENJP2.opj_start_compress(codec, image, stream)
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\lib\site-packages\glymur\lib\openjp2.py”, line 594, in check_error
raise OpenJPEGLibraryError(“OpenJPEG function failure.”)
OpenJPEGLibraryError: OpenJPEG function failure.
Progress[%]: 27.65 : PID-24700, L2A_Tables: preparing downsampled export for 60 m resolution, elapsed time[s]: 0.106, total: 0:11:58.789000
Progress[%]: 27.65 : PID-24700, L2A_Tables: start export for 60 m resolution, elapsed time[s]: 0.005, total: 0:11:58.794000
no such child: Granule
Traceback (most recent call last):
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_Process.py”, line 495, in main
if tile.process() == True:
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 118, in process
if not self.process_resolution(20):
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 148, in process_resolution
return self._process()
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 192, in _process
if self.postprocess() == False:
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 263, in postprocess
self.tables.downsampleBandList_20to60_andExport()
File “C:\Users\XXXX.snap\auxdata\Sen2Cor-02.08.00-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 2187, in downsampleBandList_20to60_andExport
Granule = pi.Product_Organisation.Granule_List.Granule
File “src/lxml/lxml.objectify.pyx”, line 229, in lxml.objectify.ObjectifiedElement.__getattr__ (src\lxml\lxml.objectify.c:3835)
File “src/lxml/lxml.objectify.pyx”, line 450, in lxml.objectify._lookupChildOrRaise (src\lxml\lxml.objectify.c:6539)
AttributeError: no such child: Granule
Progress[%]: 100.00 : Application terminated with at least one error.
Finished tool execution in 724 seconds

I have attempted to uninstall and reinstall both SNAP as a whole as well as the sen2cor plugins. I have tried both 2.8.0 (what my advisor uses and suggested) and 2.9.0 (latest available to me to download). 2.9.0 fails instantly with

“wrong identifier for xml structure.
unspecific error in metadata
Syntax error in metadata, see report file for details.”

Though, it is a .SAFE and using the .xml within it as instructed.

2.8.0 gives me the best output so far, I DO actually get an output directory, though it is incomplete due to the errors mentioned above.

I would appreciate any insight on how to get beyond these issues. I have a month until the end of the semester when all my data needs to be corrected.
Thank you.

#2

I’m still at a complete loss. The errors continue without fail, no matter what I try. Any thoughts or suggestions would be greatly appreciated.

#3

What did you select as the output format? BEAM-DiMap is currently the safest.

@Amalia-Castro-Gomez could you investigate?

#4

Again, I’m new with this, so I apologize for my lack of knowledge but I don’t have any options for output in the sen2cor screen that pops up. Where do I set that?

image

image
image1152×833 24.2 KB

#5

Dear cpyywhite,

I imagine you are already doing it, but a general advice is to unzip the S2 L1C product and to not apply any other processing step to the dataset before using it as input for Sen2Cor. Then, inside the Sen2Cor tool, in I/O Parameters, you could try using as input the MTD_MSIL1C.xml file that is inside your unzipped S2 L1C product.

I am going to take a bit more time to explore this in detail.

In the meantime, could we get your advice @marpet ? What do you think is happening?

#6

Yes, the MTD_MSIL1C.xml is the file I am selecting:

image
image1157×934 38.1 KB

Should I be selecting it another way?

#7

Hi cpyywhite,

There is already a version 2.10 available. It is available here: Sen2Cor – STEP (esa.int)

Using BEAM-DIMAP as output format is not working.
Sen2Cor is an external tool and does not use the SNAP functionality. SNAP is only providing a way to invoke the tool via a graphical user interface. Sen2Cor writes its own format. It is like the SAFE format.

This issue has been reported already multiple times:
Search results for ‘AttributeError: no such child: Granule’ - STEP Forum (esa.int)

For the latest version 2.10.1 there seems to be an issue in the source code, respectively there is a library missing. At least the following threads are indicating this

It seems that it works in some cases and in others not. Otherwise, there would have been more reports.

I think the sen2cor teams need to have a look at it.

In the meantime, cppywhite, you can try to call sen2cor directly from the command line. This removes the tool wrapper and thereby one source of possible errors.

#8

Thank you. I did read the manual and saw the command line section but found it a little hard to follow and understand what the correct syntax was that I needed.

#9

Yes, I know. It is not simple to use.

#10

I was able to get the command line version to work but I am getting the same errors. I tried both 2.10 as well as the most recent version, 2.11:

Sen2Cor. Version: 02.10.01, created: 2021.12.13, supporting Level-1C product version 14.2 - 14.9 started …
Product version: 14.6
Operation mode: TOOLBOX
Processing baseline: 99.99
Progress[%]: 0.00 : Generating datastrip metadata
L2A datastrip successfully generated
No resolution specified, will process 20 and 10 m resolution
20 m resolution will be downsampled to 60 m
Progress[%]: 0.07 : PID-27904, L2A_ProcessTile: processing with resolution 20 m, elapsed time[s]: 1.720, total: 0:00:12.220000
Progress[%]: 0.07 : PID-27904, L2A_ProcessTile: start of pre processing, elapsed time[s]: 0.003, total: 0:00:12.223000
Progress[%]: 0.07 : PID-27904, L2A_Tables: start import, elapsed time[s]: 0.048, total: 0:00:12.271000
Progress[%]: 0.09 : PID-27904, L2A_Tables: band B01 imported, elapsed time[s]: 0.436, total: 0:00:12.707000
Progress[%]: 0.51 : PID-27904, L2A_Tables: band B02 imported, elapsed time[s]: 10.829, total: 0:00:23.536000
Progress[%]: 0.96 : PID-27904, L2A_Tables: band B03 imported, elapsed time[s]: 11.354, total: 0:00:34.890000
Progress[%]: 1.39 : PID-27904, L2A_Tables: band B04 imported, elapsed time[s]: 11.176, total: 0:00:46.066000
Progress[%]: 1.52 : PID-27904, L2A_Tables: band B05 imported, elapsed time[s]: 3.259, total: 0:00:49.325000
Progress[%]: 1.65 : PID-27904, L2A_Tables: band B06 imported, elapsed time[s]: 3.128, total: 0:00:52.453000
Progress[%]: 1.78 : PID-27904, L2A_Tables: band B07 imported, elapsed time[s]: 3.475, total: 0:00:55.928000
Progress[%]: 1.91 : PID-27904, L2A_Tables: band B8A imported, elapsed time[s]: 3.395, total: 0:00:59.323000
Progress[%]: 1.94 : PID-27904, L2A_Tables: band B09 imported, elapsed time[s]: 0.664, total: 0:00:59.987000
Progress[%]: 1.97 : PID-27904, L2A_Tables: band B10 imported, elapsed time[s]: 0.669, total: 0:01:00.656000
Progress[%]: 2.10 : PID-27904, L2A_Tables: band B11 imported, elapsed time[s]: 3.514, total: 0:01:04.170000
Progress[%]: 2.24 : PID-27904, L2A_Tables: band B12 imported, elapsed time[s]: 3.330, total: 0:01:07.500000
Progress[%]: 2.24 : PID-27904, L2A_Tables: AUX_CAMS* file not found., elapsed time[s]: 0.020, total: 0:01:07.520000
Progress[%]: 2.24 : PID-27904, L2A_Tables: No L1C AUX_DATA for aerosol optical thickness @ 550nm information, elapsed time[s]: 0.004, total: 0:01:07.524000
Progress[%]: 2.24 : PID-27904, L2A_Tables: CAMS ncfile: not present, elapsed time[s]: 0.005, total: 0:01:07.529000
Progress[%]: 2.24 : PID-27904, L2A_ProcessTile: start of Scene Classification, elapsed time[s]: 0.006, total: 0:01:07.535000
Progress[%]: 2.26 : PID-27904, L2A_Tables: band B02 must be resampled, elapsed time[s]: 0.696, total: 0:01:08.231000
Progress[%]: 2.41 : PID-27904, Pre process , elapsed time[s]: 3.721, total: 0:01:11.952000
Progress[%]: 2.41 : PID-27904, L2A_Tables: band B01 must be resampled, elapsed time[s]: 0.014, total: 0:01:11.966000
Progress[%]: 2.66 : PID-27904, L2A_Tables: band B03 must be resampled, elapsed time[s]: 6.361, total: 0:01:18.327000
Progress[%]: 2.81 : PID-27904, L2A_Tables: band B04 must be resampled, elapsed time[s]: 3.874, total: 0:01:22.201000
Progress[%]: 2.98 : PID-27904, L2A_Tables: band B09 must be resampled, elapsed time[s]: 4.191, total: 0:01:26.392000
Progress[%]: 3.17 : PID-27904, L2A_Tables: band B10 must be resampled, elapsed time[s]: 4.866, total: 0:01:31.258000
Progress[%]: 3.37 : PID-27904, L2A_SC init , elapsed time[s]: 5.156, total: 0:01:36.414000
Progress[%]: 3.40 : PID-27904, L2A_CSND_1_1 , elapsed time[s]: 0.703, total: 0:01:37.117000
Progress[%]: 3.42 : PID-27904, L2A_CSND_1_2 , elapsed time[s]: 0.692, total: 0:01:37.809000
Progress[%]: 3.43 : PID-27904, L2A_CSND_2_0 , elapsed time[s]: 0.199, total: 0:01:38.008000
Progress[%]: 3.46 : PID-27904, L2A_CSND_2_1 , elapsed time[s]: 0.664, total: 0:01:38.672000
Progress[%]: 3.47 : PID-27904, L2A_CSND_2_1_2, elapsed time[s]: 0.340, total: 0:01:39.012000
Progress[%]: 3.48 : PID-27904, L2A_CSND_2_2 , elapsed time[s]: 0.274, total: 0:01:39.286000
Progress[%]: 3.50 : PID-27904, L2A_CSND_2_3 , elapsed time[s]: 0.376, total: 0:01:39.662000
Progress[%]: 3.52 : PID-27904, L2A_CSND_2_4 , elapsed time[s]: 0.645, total: 0:01:40.307000
Progress[%]: 3.56 : PID-27904, L2A_CSND_2_5 , elapsed time[s]: 0.986, total: 0:01:41.293000
Progress[%]: 3.56 : PID-27904, L2A_SnowPostProcessingCCI , elapsed time[s]: 0.005, total: 0:01:41.298000
Progress[%]: 3.61 : PID-27904, L2A_CSND_3 , elapsed time[s]: 1.130, total: 0:01:42.428000
Progress[%]: 3.64 : PID-27904, L2A_CSND_5_1 , elapsed time[s]: 0.922, total: 0:01:43.350000
Progress[%]: 3.70 : PID-27904, L2A_CSND_5_2 , elapsed time[s]: 1.553, total: 0:01:44.903000
Progress[%]: 3.74 : PID-27904, L2A_CSND_6 , elapsed time[s]: 1.070, total: 0:01:45.973000
Progress[%]: 3.77 : PID-27904, L2A_CSND_6_2 , elapsed time[s]: 0.724, total: 0:01:46.697000
Progress[%]: 3.81 : PID-27904, L2A_CSND_7 , elapsed time[s]: 0.892, total: 0:01:47.589000
Progress[%]: 3.84 : PID-27904, DV recovery , elapsed time[s]: 0.920, total: 0:01:48.509000
Progress[%]: 3.88 : PID-27904, WP recovery , elapsed time[s]: 1.015, total: 0:01:49.524000
Progress[%]: 3.88 : PID-27904, WP recovery with CCI Water Bodies at 150m , elapsed time[s]: 0.005, total: 0:01:49.529000
Progress[%]: 3.93 : PID-27904, Snow recovery , elapsed time[s]: 1.095, total: 0:01:50.624000
Progress[%]: 4.07 : PID-27904, SnowSoilBorders, elapsed time[s]: 3.576, total: 0:01:54.200000
Progress[%]: 4.09 : PID-27904, Soil recovery , elapsed time[s]: 0.533, total: 0:01:54.733000
Progress[%]: 4.09 : PID-27904, Cirrus recovery with B10 , elapsed time[s]: 0.005, total: 0:01:54.738000
Progress[%]: 4.09 : PID-27904, Urban and Bare pixel recovery with CCI Land Cover Map at 300 m , elapsed time[s]: 0.004, total: 0:01:54.742000
Progress[%]: 4.41 : PID-27904, Bright pixels Hollstein Fmask, elapsed time[s]: 8.232, total: 0:02:02.974000
Cloud heights processed in 0:00:10.441000 seconds
Progress[%]: 6.03 : PID-27904, L2A_SHD , elapsed time[s]: 41.253, total: 0:02:44.227000
Progress[%]: 6.03 : PID-27904, WP recovery with CCI Water Bodies at 150m , elapsed time[s]: 0.005, total: 0:02:44.232000
Progress[%]: 6.07 : PID-27904, Topographic casted shadow Pixels post processing, elapsed time[s]: 1.146, total: 0:02:45.378000
Progress[%]: 6.18 : PID-27904, Post process , elapsed time[s]: 2.761, total: 0:02:48.139000
Progress[%]: 6.18 : PID-27904, L2A_ProcessTile: start of Atmospheric Correction, elapsed time[s]: 0.058, total: 0:02:48.197000
Progress[%]: 6.22 : PID-27904, L2A_AtmCorr: end of calculation terrain maps, elapsed time[s]: 0.852, total: 0:02:49.049000
Progress[%]: 6.22 : PID-27904, L2A_AtmCorr: start of AOT retrieval at 550nm, elapsed time[s]: 0.004, total: 0:02:49.053000
Progress[%]: 6.35 : PID-27904, L2A_AtmCorr: end of internal classification, elapsed time[s]: 3.386, total: 0:02:52.439000
Progress[%]: 6.36 : PID-27904, L2A_AtmCorr: end of interpolation LUTs, elapsed time[s]: 0.311, total: 0:02:52.750000
Progress[%]: 6.80 : PID-27904, L2A_AtmCorr: end retrieving reference pixels for dark areas, elapsed time[s]: 11.164, total: 0:03:03.914000
Progress[%]: 7.86 : PID-27904, L2A_AtmCorr: end of check for negative reflectance pixels, elapsed time[s]: 27.042, total: 0:03:30.956000
Progress[%]: 7.92 : PID-27904, L2A_AtmCorr: the rescaling of path radiance in blue band has been disabled by configuration, elapsed time[s]: 1.582, total: 0:03:32.538000
Progress[%]: 8.57 : PID-27904, L2A_AtmCorr: end of visibility index calculation, elapsed time[s]: 16.372, total: 0:03:48.910000
Progress[%]: 8.57 : PID-27904, L2A_AtmCorr: end of AOT retrieval at 550nm, elapsed time[s]: 0.005, total: 0:03:48.915000
Progress[%]: 8.57 : PID-27904, L2A_AtmCorr: start of water vapour retrieval, elapsed time[s]: 0.003, total: 0:03:48.918000
Progress[%]: 8.59 : PID-27904, L2A_AtmCorr: end of water vapour retrieval preparation, elapsed time[s]: 0.679, total: 0:03:49.597000
Progress[%]: 12.01 : PID-27904, L2A_AtmCorr: end of water vapour retrieval, elapsed time[s]: 87.263, total: 0:05:16.860000
Progress[%]: 12.01 : PID-27904, L2A_AtmCorr: preparation of surface reflectance retrieval, elapsed time[s]: 0.006, total: 0:05:16.866000
Progress[%]: 12.13 : PID-27904, L2A_AtmCorr: end of surface reflectance retrieval preparation, elapsed time[s]: 2.891, total: 0:05:19.757000
Progress[%]: 12.13 : PID-27904, L2A_AtmCorr: start of surface reflectance retrieval, elapsed time[s]: 0.004, total: 0:05:19.761000
Progress[%]: 16.86 : PID-27904, L2A_AtmCorr: end of surface reflectance retrieval, elapsed time[s]: 120.766, total: 0:07:20.527000
Progress[%]: 16.86 : PID-27904, L2A_AtmCorr: start of rho retrieval step 2, elapsed time[s]: 0.007, total: 0:07:20.534000
Progress[%]: 18.77 : PID-27904, L2A_AtmCorr: end of rho retrieval step 2, elapsed time[s]: 48.515, total: 0:08:09.049000
Progress[%]: 18.77 : PID-27904, L2A_ProcessTile: start of post processing, elapsed time[s]: 0.021, total: 0:08:09.070000
Progress[%]: 18.80 : PID-27904, L2A_Tables: start export for 20 m resolution, elapsed time[s]: 0.734, total: 0:08:09.804000
OpenJPEG function failure.
Traceback (most recent call last):
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 3457, in exportBandList
self.glymurWrapper(filename, band)
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 3617, in glymurWrapper
glymur.Jp2k(filename, band, **kwargs)
File “E:\Software\Sen2Cor-02.10.01-win64\lib\site-packages\glymur\jp2k.py”, line 177, in __init__
self._write(data, **kwargs)
File “E:\Software\Sen2Cor-02.10.01-win64\lib\site-packages\glymur\jp2k.py”, line 539, in _write
self._write_openjp2(img_array, verbose=verbose)
File “E:\Software\Sen2Cor-02.10.01-win64\lib\site-packages\glymur\jp2k.py”, line 783, in _write_openjp2
opj2.start_compress(codec, image, strm)
File “E:\Software\Sen2Cor-02.10.01-win64\lib\site-packages\glymur\lib\openjp2.py”, line 1299, in start_compress
OPENJP2.opj_start_compress(codec, image, stream)
File “E:\Software\Sen2Cor-02.10.01-win64\lib\site-packages\glymur\lib\openjp2.py”, line 594, in check_error
raise OpenJPEGLibraryError(“OpenJPEG function failure.”)
OpenJPEGLibraryError: OpenJPEG function failure.
Progress[%]: 18.89 : PID-27904, L2A_Tables: preparing downsampled export for 60 m resolution, elapsed time[s]: 2.282, total: 0:08:12.086000
Progress[%]: 18.89 : PID-27904, L2A_Tables: start export for 60 m resolution, elapsed time[s]: 0.005, total: 0:08:12.091000
no such child: Granule
Traceback (most recent call last):
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_Process.py”, line 692, in main
if tile.process() == True:
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 117, in process
if not self.process_resolution(20):
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 147, in process_resolution
return self._process()
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 197, in _process
if self.postprocess() == False:
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 273, in postprocess
res = self.tables.downsampleBandList_20to60_andExport()
File “E:\Software\Sen2Cor-02.10.01-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 3096, in downsampleBandList_20to60_andExport
Granule = pi.Product_Organisation.Granule_List.Granule
File “src/lxml/lxml.objectify.pyx”, line 229, in lxml.objectify.ObjectifiedElement.__getattr__ (src\lxml\lxml.objectify.c:3835)
File “src/lxml/lxml.objectify.pyx”, line 450, in lxml.objectify._lookupChildOrRaise (src\lxml\lxml.objectify.c:6539)
AttributeError: no such child: Granule
Progress[%]: 100.00 : Application terminated with at least one error.

_______________________________________________________________________

Sen2Cor. Version: 02.11.00, created: 2022.10.20, supporting Level-1C product version 14.2 - 14.9 started …
Product version: 14.6
Operation mode: TOOLBOX
Processing baseline: 99.99
Progress[%]: 0.00 : Generating datastrip metadata
L2A datastrip successfully generated
No resolution specified, will process 20 and 10 m resolution
20 m resolution will be downsampled to 60 m
Progress[%]: 0.13 : PID-13576, L2A_ProcessTile: processing with resolution 20 m, elapsed time[s]: 3.241, total: 0:00:14.892000
Progress[%]: 0.13 : PID-13576, L2A_ProcessTile: start of pre processing, elapsed time[s]: 0.004, total: 0:00:14.896000
Progress[%]: 0.15 : PID-13576, L2A_Tables: start import, elapsed time[s]: 0.488, total: 0:00:15.384000
Progress[%]: 0.18 : PID-13576, L2A_Tables: band B01 imported, elapsed time[s]: 0.800, total: 0:00:16.184000
Progress[%]: 0.62 : PID-13576, L2A_Tables: band B02 imported, elapsed time[s]: 11.211, total: 0:00:27.395000
Progress[%]: 1.11 : PID-13576, L2A_Tables: band B03 imported, elapsed time[s]: 12.685, total: 0:00:40.080000
Progress[%]: 1.63 : PID-13576, L2A_Tables: band B04 imported, elapsed time[s]: 13.032, total: 0:00:53.112000
Progress[%]: 1.78 : PID-13576, L2A_Tables: band B05 imported, elapsed time[s]: 3.906, total: 0:00:57.018000
Progress[%]: 1.93 : PID-13576, L2A_Tables: band B06 imported, elapsed time[s]: 3.759, total: 0:01:00.777000
Progress[%]: 2.09 : PID-13576, L2A_Tables: band B07 imported, elapsed time[s]: 4.158, total: 0:01:04.935000
Progress[%]: 2.26 : PID-13576, L2A_Tables: band B8A imported, elapsed time[s]: 4.262, total: 0:01:09.197000
Progress[%]: 2.28 : PID-13576, L2A_Tables: band B09 imported, elapsed time[s]: 0.680, total: 0:01:09.877000
Progress[%]: 2.31 : PID-13576, L2A_Tables: band B10 imported, elapsed time[s]: 0.772, total: 0:01:10.649000
Progress[%]: 2.49 : PID-13576, L2A_Tables: band B11 imported, elapsed time[s]: 4.453, total: 0:01:15.102000
Progress[%]: 2.65 : PID-13576, L2A_Tables: band B12 imported, elapsed time[s]: 4.191, total: 0:01:19.293000
Progress[%]: 2.66 : PID-13576, L2A_Tables: AUX_CAMS* file not found., elapsed time[s]: 0.214, total: 0:01:19.507000
Progress[%]: 2.66 : PID-13576, L2A_Tables: No L1C AUX_DATA for aerosol optical thickness @ 550nm information, elapsed time[s]: 0.004, total: 0:01:19.511000
Progress[%]: 2.66 : PID-13576, L2A_Tables: CAMS ncfile: not present, elapsed time[s]: 0.006, total: 0:01:19.517000
Progress[%]: 2.66 : PID-13576, L2A_ProcessTile: start of Scene Classification, elapsed time[s]: 0.006, total: 0:01:19.523000
Progress[%]: 2.87 : PID-13576, L2A_Tables: band B02 must be resampled, elapsed time[s]: 5.280, total: 0:01:24.803000
Progress[%]: 3.02 : PID-13576, Pre process , elapsed time[s]: 3.736, total: 0:01:28.539000
Progress[%]: 3.02 : PID-13576, L2A_Tables: band B01 must be resampled, elapsed time[s]: 0.015, total: 0:01:28.554000
Progress[%]: 3.29 : PID-13576, L2A_Tables: band B03 must be resampled, elapsed time[s]: 6.918, total: 0:01:35.472000
Progress[%]: 3.43 : PID-13576, L2A_Tables: band B04 must be resampled, elapsed time[s]: 3.705, total: 0:01:39.177000
Progress[%]: 3.60 : PID-13576, L2A_Tables: band B09 must be resampled, elapsed time[s]: 4.257, total: 0:01:43.434000
Progress[%]: 3.79 : PID-13576, L2A_Tables: band B10 must be resampled, elapsed time[s]: 4.969, total: 0:01:48.403000
Progress[%]: 4.00 : PID-13576, L2A_SC init , elapsed time[s]: 5.214, total: 0:01:53.617000
Progress[%]: 4.03 : PID-13576, L2A_CSND_1_1 , elapsed time[s]: 0.760, total: 0:01:54.377000
Progress[%]: 4.06 : PID-13576, L2A_CSND_1_2 , elapsed time[s]: 0.780, total: 0:01:55.157000
Progress[%]: 4.13 : PID-13576, L2A_CSND_2_0 , elapsed time[s]: 1.711, total: 0:01:56.868000
Progress[%]: 4.16 : PID-13576, L2A_CSND_2_1 , elapsed time[s]: 0.746, total: 0:01:57.614000
Progress[%]: 4.17 : PID-13576, L2A_CSND_2_1_2, elapsed time[s]: 0.380, total: 0:01:57.994000
Progress[%]: 4.18 : PID-13576, L2A_CSND_2_2 , elapsed time[s]: 0.317, total: 0:01:58.311000
Progress[%]: 4.20 : PID-13576, L2A_CSND_2_3 , elapsed time[s]: 0.411, total: 0:01:58.722000
Progress[%]: 4.23 : PID-13576, L2A_CSND_2_4 , elapsed time[s]: 0.691, total: 0:01:59.413000
Progress[%]: 4.27 : PID-13576, L2A_CSND_2_5 , elapsed time[s]: 1.050, total: 0:02:00.463000
Progress[%]: 4.27 : PID-13576, L2A_SnowPostProcessingCCI , elapsed time[s]: 0.005, total: 0:02:00.468000
Progress[%]: 4.32 : PID-13576, L2A_CSND_3 , elapsed time[s]: 1.253, total: 0:02:01.721000
Progress[%]: 4.36 : PID-13576, L2A_CSND_5_1 , elapsed time[s]: 1.069, total: 0:02:02.790000
Progress[%]: 4.42 : PID-13576, L2A_CSND_5_2 , elapsed time[s]: 1.657, total: 0:02:04.447000
Progress[%]: 4.47 : PID-13576, L2A_CSND_6 , elapsed time[s]: 1.194, total: 0:02:05.641000
Progress[%]: 4.50 : PID-13576, L2A_CSND_6_2 , elapsed time[s]: 0.775, total: 0:02:06.416000
Progress[%]: 4.54 : PID-13576, L2A_CSND_7 , elapsed time[s]: 0.935, total: 0:02:07.351000
Progress[%]: 4.58 : PID-13576, DV recovery , elapsed time[s]: 0.989, total: 0:02:08.340000
Progress[%]: 4.62 : PID-13576, WP recovery , elapsed time[s]: 1.108, total: 0:02:09.448000
Progress[%]: 4.62 : PID-13576, WP recovery with CCI Water Bodies at 150m , elapsed time[s]: 0.005, total: 0:02:09.453000
Progress[%]: 4.66 : PID-13576, Snow recovery , elapsed time[s]: 1.120, total: 0:02:10.573000
Progress[%]: 4.80 : PID-13576, SnowSoilBorders, elapsed time[s]: 3.583, total: 0:02:14.156000
Progress[%]: 4.83 : PID-13576, Soil recovery , elapsed time[s]: 0.562, total: 0:02:14.718000
Progress[%]: 4.83 : PID-13576, Cirrus recovery with B10 , elapsed time[s]: 0.006, total: 0:02:14.724000
Progress[%]: 4.83 : PID-13576, Urban and Bare pixel recovery with CCI Land Cover Map at 300 m , elapsed time[s]: 0.004, total: 0:02:14.728000
Progress[%]: 5.16 : PID-13576, Bright pixels Hollstein Fmask, elapsed time[s]: 8.438, total: 0:02:23.166000
Cloud heights processed in 0:00:10.989000 seconds
Progress[%]: 6.93 : PID-13576, L2A_SHD , elapsed time[s]: 45.179, total: 0:03:08.345000
Progress[%]: 6.93 : PID-13576, WP recovery with CCI Water Bodies at 150m , elapsed time[s]: 0.006, total: 0:03:08.351000
Progress[%]: 6.97 : PID-13576, Topographic casted shadow Pixels post processing, elapsed time[s]: 1.141, total: 0:03:09.492000
Progress[%]: 7.10 : PID-13576, Post process , elapsed time[s]: 3.133, total: 0:03:12.625000
Progress[%]: 7.10 : PID-13576, L2A_ProcessTile: start of Atmospheric Correction, elapsed time[s]: 0.060, total: 0:03:12.685000
Progress[%]: 7.14 : PID-13576, L2A_AtmCorr: end of calculation terrain maps, elapsed time[s]: 0.962, total: 0:03:13.647000
Progress[%]: 7.14 : PID-13576, L2A_AtmCorr: start of AOT retrieval at 550nm, elapsed time[s]: 0.017, total: 0:03:13.664000
Progress[%]: 7.27 : PID-13576, L2A_AtmCorr: end of internal classification, elapsed time[s]: 3.358, total: 0:03:17.022000
Progress[%]: 7.28 : PID-13576, L2A_AtmCorr: end of interpolation LUTs, elapsed time[s]: 0.310, total: 0:03:17.332000
Progress[%]: 7.72 : PID-13576, L2A_AtmCorr: end retrieving reference pixels for dark areas, elapsed time[s]: 11.204, total: 0:03:28.536000
Progress[%]: 8.79 : PID-13576, L2A_AtmCorr: end of check for negative reflectance pixels, elapsed time[s]: 27.160, total: 0:03:55.696000
Progress[%]: 8.85 : PID-13576, L2A_AtmCorr: the rescaling of path radiance in blue band has been disabled by configuration, elapsed time[s]: 1.634, total: 0:03:57.330000
Progress[%]: 9.51 : PID-13576, L2A_AtmCorr: end of visibility index calculation, elapsed time[s]: 16.740, total: 0:04:14.070000
Progress[%]: 9.51 : PID-13576, L2A_AtmCorr: end of AOT retrieval at 550nm, elapsed time[s]: 0.005, total: 0:04:14.075000
Progress[%]: 9.51 : PID-13576, L2A_AtmCorr: start of water vapour retrieval, elapsed time[s]: 0.004, total: 0:04:14.079000
Progress[%]: 9.53 : PID-13576, L2A_AtmCorr: end of water vapour retrieval preparation, elapsed time[s]: 0.658, total: 0:04:14.737000
Progress[%]: 13.02 : PID-13576, L2A_AtmCorr: end of water vapour retrieval, elapsed time[s]: 88.946, total: 0:05:43.683000
Progress[%]: 13.02 : PID-13576, L2A_AtmCorr: preparation of surface reflectance retrieval, elapsed time[s]: 0.005, total: 0:05:43.688000
Progress[%]: 13.13 : PID-13576, L2A_AtmCorr: end of surface reflectance retrieval preparation, elapsed time[s]: 2.880, total: 0:05:46.568000
Progress[%]: 13.13 : PID-13576, L2A_AtmCorr: start of surface reflectance retrieval, elapsed time[s]: 0.004, total: 0:05:46.572000
Progress[%]: 17.86 : PID-13576, L2A_AtmCorr: end of surface reflectance retrieval, elapsed time[s]: 120.400, total: 0:07:46.972000
Progress[%]: 17.86 : PID-13576, L2A_AtmCorr: start of rho retrieval step 2, elapsed time[s]: 0.012, total: 0:07:46.984000
Progress[%]: 19.76 : PID-13576, L2A_AtmCorr: end of rho retrieval step 2, elapsed time[s]: 48.670, total: 0:08:35.654000
Progress[%]: 19.77 : PID-13576, L2A_ProcessTile: start of post processing, elapsed time[s]: 0.022, total: 0:08:35.676000
Progress[%]: 19.79 : PID-13576, L2A_Tables: start export for 20 m resolution, elapsed time[s]: 0.738, total: 0:08:36.414000
OpenJPEG function failure.
Traceback (most recent call last):
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 3543, in exportBandList
self.glymurWrapper(filename, band)
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 3703, in glymurWrapper
glymur.Jp2k(filename, band, **kwargs)
File “E:\Software\Sen2Cor-02.11.00-win64\lib\site-packages\glymur\jp2k.py”, line 177, in __init__
self._write(data, **kwargs)
File “E:\Software\Sen2Cor-02.11.00-win64\lib\site-packages\glymur\jp2k.py”, line 539, in _write
self._write_openjp2(img_array, verbose=verbose)
File “E:\Software\Sen2Cor-02.11.00-win64\lib\site-packages\glymur\jp2k.py”, line 783, in _write_openjp2
opj2.start_compress(codec, image, strm)
File “E:\Software\Sen2Cor-02.11.00-win64\lib\site-packages\glymur\lib\openjp2.py”, line 1299, in start_compress
OPENJP2.opj_start_compress(codec, image, stream)
File “E:\Software\Sen2Cor-02.11.00-win64\lib\site-packages\glymur\lib\openjp2.py”, line 594, in check_error
raise OpenJPEGLibraryError(“OpenJPEG function failure.”)
OpenJPEGLibraryError: OpenJPEG function failure.
Progress[%]: 19.88 : PID-13576, L2A_Tables: preparing downsampled export for 60 m resolution, elapsed time[s]: 2.194, total: 0:08:38.608000
Progress[%]: 19.88 : PID-13576, L2A_Tables: start export for 60 m resolution, elapsed time[s]: 0.005, total: 0:08:38.613000
no such child: Granule
Traceback (most recent call last):
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_Process.py”, line 692, in main
if tile.process() == True:
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 117, in process
if not self.process_resolution(20):
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 147, in process_resolution
return self._process()
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 197, in _process
if self.postprocess() == False:
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_ProcessTileToolbox.py”, line 273, in postprocess
res = self.tables.downsampleBandList_20to60_andExport()
File “E:\Software\Sen2Cor-02.11.00-win64\Lib\site-packages\sen2cor\L2A_Tables.py”, line 3156, in downsampleBandList_20to60_andExport
Granule = pi.Product_Organisation.Granule_List.Granule
File “src/lxml/lxml.objectify.pyx”, line 229, in lxml.objectify.ObjectifiedElement.__getattr__ (src\lxml\lxml.objectify.c:3835)
File “src/lxml/lxml.objectify.pyx”, line 450, in lxml.objectify._lookupChildOrRaise (src\lxml\lxml.objectify.c:6539)
AttributeError: no such child: Granule
Progress[%]: 100.00 : Application terminated with at least one error.

#11

This indicates that there is some issue with sen2cor itself and not with the adapter for SNAP.

Maybe @bdpg can have a look at this?

#12

Dear user,

The issue was investigated internally and there is no error in processing the L1C product within our environment (Windows) with the latest version of Sen2Cor (2.11) fully configured.

As mentioned in point 6) of Sen2Cor FAQ, this problem may occur in Sen2Cor during processing on Windows machines when using long path pointing to the L2A destination folder.
An error in finding/writing a folder/file in the Sen2Cor Post-Processing may be the culprit of this behaviour
We recommend to keep the path_lenght for the input and output directories below 90 characters.

Cheers

@Sen2cor_dev_team

1 Like
#13

There are a few things you can try to resolve the errors you are encountering while using sen2cor in SNAP:

OpenJPEGLibraryError: OpenJPEG function failure

This error can occur for a variety of reasons, but it is often caused by a problem with the OpenJPEG library. To try to resolve this error, you can try the following:

  1. Make sure that you have the latest version of the OpenJPEG library installed.
  2. Try restarting your computer.
  3. Try running sen2cor as an administrator.
  4. Try running sen2cor from a different directory.
  5. If you are still getting the error, you can try using a different version of sen2cor.

no such child: Granule

This error can occur if the sen2cor plugin cannot find the Granule element in the SAFE metadata. To try to resolve this error, you can try the following:

  1. Make sure that you are using a valid SAFE file.
  2. Try running sen2cor with the --no-validate-metadata option.
  3. Try using a different version of sen2cor.

wrong identifier for xml structure. unspecific error in metadata Syntax error in metadata

This error can occur if the SAFE metadata is not valid. To try to resolve this error, you can try the following:

  1. Make sure that you are using a valid SAFE file.
  2. Try running sen2cor with the --no-validate-metadata option.
  3. Try opening the SAFE metadata in a text editor and checking for any errors.
  4. Try using a different version of sen2cor.

If you are still having problems after trying all of the above suggestions, you can post a question on the STEP forum or contact the sen2cor support team.

Additional tips

  • Make sure that you have enough free disk space on the computer where you are running sen2cor.
  • Try closing any other programs that you are not using.
  • If you are still having problems, you can try running sen2cor in debug mode to get more information about the error. To do this, add the --debug option to the sen2cor command line.

I hope this helps!

#14

Advertisement deleted from allan’s post. SPAM is not tolerated on this forum. Account deactivated for now, but it can be re-activated by the user.

#15

I appreciate the responses. The issues I had have semi-been resolved. I can’t state exactly what fixed it but after trying the many suggestions here, latest versions of various pieces, 4 different computers, it finally started working on my Microsoft Surface Pro (the 5th computer I tried) using sen2cor 280 and ONLY that version. Any other version just gave me the same errors as above. It definitely had nothing to do with the directory path length however. I used the same path on all the computers and even tried shorter paths (putting the data directly on the desktop for example) and I still received the above errors but it worked without any issues on the last computer (the Surface) with the original path.
I was able to start actually processing data successfully just a week or two ago.