Error in Correct Troposphere step

[engelb...@gmail.com]

Dear Yunjun,

I hope you are well. I am experiencing problems in the the execution of the step "Correct_toposphere". The reanalysis dataset is ERA5 which appers to be downloading correctly. The program fails with a KeyError: 'Y_UNIT'. I add the error details below. The interferograms are Sentinel-1 scenes with preprocessing in SNAP. Any guidance would be appreciated.

******************** step - correct_troposphere ********************

Input data seems to be geocoded. Lookup file not needed.

Atmospheric correction using Weather Re-analysis dataset (PyAPS, Jolivet et al., 2011)

Weather Re-analysis dataset: ERA5

tropo_pyaps3.py -f /home/jengelbrecht/working/EB_S1_mintpy/AOI1_3/timeseries.h5 --model ERA5 -g /home/jengelbrecht/working/EB_S1_mintpy/AOI1_3/inputs/geometryGeo.h5 -w /home/jengelbrecht/weather_data/

weather model: ERA5 - dry (hydrostatic) and wet delay

weather directory: /home/jengelbrecht/weather_data

output tropospheric delay file: /home/jengelbrecht/working/EB_S1_mintpy/AOI1_3/inputs/ERA5.h5

output corrected time-series file: /home/jengelbrecht/working/EB_S1_mintpy/AOI1_3/timeseries_ERA5.h5

read dates/time info from file: /home/jengelbrecht/working/EB_S1_mintpy/AOI1_3/timeseries.h5

time of cloest available product: 23:00 UTC

Traceback (most recent call last):

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 1256, in <module>

    main(sys.argv[1:])

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 1238, in main

    app.run(steps=inps.runSteps)

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 1053, in run

    self.run_tropospheric_delay_correction(sname)

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 809, in run_tropospheric_delay_correction

    tropo_pyaps3.main(iargs)

  File "/home/jengelbrecht/MintPy/mintpy/tropo_pyaps3.py", line 784, in main

    get_grib_info(inps)

  File "/home/jengelbrecht/MintPy/mintpy/tropo_pyaps3.py", line 266, in get_grib_info

    inps.snwe = get_snwe(inps.atr, geom_file=inps.geom_file)

  File "/home/jengelbrecht/MintPy/mintpy/tropo_pyaps3.py", line 393, in get_snwe

    lat0, lat1, lon0, lon1 = get_bounding_box(meta, geom_file=geom_file)

  File "/home/jengelbrecht/MintPy/mintpy/tropo_pyaps3.py", line 457, in get_bounding_box

    if not meta['Y_UNIT'].lower().startswith('deg'):

KeyError: 'Y_UNIT'

All the best,

Jeanine

[Zhang Yunjun]

Hi Jeanine,

This bug has been reported and fixed. 

Cheers,

Yunjun

[engelb...@gmail.com]

Wonderful, thank you Yunjun, I have updated the installation and the ERA5.h5 input is now successfully created. However, the process now get's stuck on calculating the absolute delay.  The interferograms are Sentinel-1 scenes with preprocessing in SNAP.  The error is detailed below. I would appreciate any additional guidance.

--------------------------------------------------

create HDF5 file: /home/jengelbrecht/working/EB_S1_mintpy/AOI1_test3/inputs/ERA5.h5 with w mode

create dataset  : date       of |S8                       in size of (34,)                with compression = None

create dataset  : timeseries of <class 'numpy.float32'>   in size of (34, 902, 934)       with compression = None

close  HDF5 file: /home/jengelbrecht/working/EB_S1_mintpy/AOI1_test3/inputs/ERA5.h5

------------------------------------------------------------------------------

calculating absolute delay for each date using PyAPS (Jolivet et al., 2011; 2014) ...

number of grib files used: 34

Traceback (most recent call last):

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 1281, in <module>

    main(sys.argv[1:])

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 1263, in main

    app.run(steps=inps.runSteps)

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 1054, in run

    self.run_tropospheric_delay_correction(sname)

  File "/home/jengelbrecht/MintPy/mintpy/smallbaselineApp.py", line 810, in run_tropospheric_delay_correction

    tropo_pyaps3.main(iargs)

  File "/home/jengelbrecht/MintPy/mintpy/tropo_pyaps3.py", line 841, in main

    calc_delay_timeseries(inps)

  File "/home/jengelbrecht/MintPy/mintpy/tropo_pyaps3.py", line 769, in calc_delay_timeseries

    tropo_data = get_delay(grib_file,

  File "/home/jengelbrecht/MintPy/mintpy/tropo_pyaps3.py", line 636, in get_delay

    aps_obj = pa.PyAPS(grib_file,

  File "/home/jengelbrecht/PyAPS/pyaps3/objects.py", line 121, in __init__

    self.minlon = np.nanmin(self.lon[np.nonzero(self.mask)]) - self.bufspc

  File "<__array_function__ internals>", line 5, in nanmin

  File "/home/jengelbrecht/miniconda3/lib/python3.8/site-packages/numpy/lib/nanfunctions.py", line 319, in nanmin

    res = np.fmin.reduce(a, axis=axis, out=out, **kwargs)

ValueError: zero-size array to reduction operation fmin which has no identity

[Zhang Yunjun]

Hi Jeanine,

Hmm..., I can not see the cause from your error message above. 

If you could send me (yunju...@gmail.com) the "inputs/geometryGeo.h5" and "timeseries.h5" files, I could take a further look. 

Yunjun

[Emre baydoğan]

hi everyone, ı have a problem. how can ı solve this problem ? 

20 Ekim 2021 Çarşamba tarihinde saat 08:43:40 UTC+3 itibarıyla Zhang Yunjun şunları yazdı:

[Emre Havazlı]

Hi Emre,

Please delete your ERA5.h5 file and try running the tropospheric correction again. 

It looks like the ERA5.h5 is empty, please ensure the corrections are downloaded and written to the file without an issue.

Kolay gelsin

Emre Havazli