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scientific functions to compute radar or geophysical parameters from satellite images over ocean

Home Page: https://cyclobs.ifremer.fr/static/sarwing_datarmor/xsarsea

License: MIT License

Python 100.00%

dask datatree ocean ocean-sciences oceanography python radar research science waves

xsarsea's Introduction

xsarsea

CMOD, sigma0 detrend, and others sar processing tools over ocean.

Installation

xsarsea is supposed to use [xsar](https://github.com/umr-lops/xsar) objects to map SAR products into xarray Datasets.

now you can install xsarsea

conda activate xsar

for user:

pip install git+https://github.com/umr-lops/xsarsea.git

for development:

pip install git+https://github.com/umr-lops/xsarsea.git
cd xsarsea
pip install -r requirements.txt
pip install -e .

Documentation and examples

https://cyclobs.ifremer.fr/static/sarwing_datarmor/xsarsea

xsarsea's People

Contributors

Stargazers

Watchers

Forkers

oarcher agrouaze lanougue hellokaito vincelhx c-core-labs

xsarsea's Issues

problem in cross-spectra calculation

Hi! I'm a new learner in wave related subjects. I'm confused about 'sar_slc/processing.py' line 776, cross-spectra is caculated by intensity(L2)*np.conj(intensity) , the question is why 'df' is multiplied?
looking to your reply.

cross spectrum on IW SLC products is for now hard coded for VV polarization

see

xsarsea/src/xsarsea/sar_slc/processing.py

Line 69 in 4fdc585

 burst = crop_burst(dt['measurement'].ds, dt['bursts'].ds, burst_number=b, valid=True).sel(pol='VV') 

documentation notebook level 1

not entirely working

[windspeed] lut format and resolutions for cmod and gmfs

Currently, lut are loaded from sarwing lut files, or dynamically generated from gmfs.

It will be a good thing to have a xsarsea format (like netcdf) ti store luts.

A question that we want to study is the stepping of the luts.

Currently, luts are stored and generated with

inc_step=0.1
wspd_step=0.1
phi_step=1.

Those tiny steps produce huge luts, inducing IO issue and cpu time.

Can we try to reduce the lut size ? For example, CMOD7 lut have the following steps:

wspd_step = 0.2
inc_step = 1
phi_step = 2.5

( so the official cmod7 size is 3.6Mb, and the sarwing cmod7 lut size is 346Mb)

cross spectrum from IW SLC intra and inter burst are not always same 'line' size

The overlap size from burst to burst in intra and inter burst is not constant.
Limiting the nperseg 'line' size to a low value is not always sufficient.
Different solutions have to be investigating:

parsing all the bursts to find the lowest nperseg line value.
keeping separate all the xspectrum of a subswath using datatree
interpolating the xspectrum on a common grid.

Documentation issue

This issue is a placeholder for PR and problems about documentation

Problem when doing .compute() on windspeed variables

Performing inversion this way :

windspeed_co, windspeed_dual = windspeed.invert_from_model(
        dataset_1000m.incidence,
        dataset_1000m.sigma0_ocean.isel(pol=0),
        dataset_1000m.sigma0_ocean.isel(pol=1),
        #ancillary_wind=-np.conj(xsar_obj_1000m.dataset['ancillary_wind']),
        ancillary_wind=-dataset_1000m['ancillary_wind'],
        dsig_cr = dsig_cr,
        model=('cmod5n',GMF_VH_NAME))

dataset_1000m["windspeed_co"] = np.abs(windspeed_co)
dataset_1000m["windspeed_co"].attrs["comment"] = dataset_1000m["windspeed_co"].attrs["comment"].replace("wind speed and direction","wind speed")
dataset_1000m["windspeed_dual"] = np.abs(windspeed_dual)
dataset_1000m["windspeed_dual"].attrs["comment"] = dataset_1000m["windspeed_dual"].attrs["comment"].replace("wind speed and direction","wind speed")

dataset_1000m["windspeed_co"].compute() leads to :

HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 9:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found

BUT looks to work

there is no method in xsarsea to match with sigma0 denoised values provided by ESA in Level-2 products

Currently there is no specific methods in xsarsea to get a NRCS (aka sigma0 denoised) value from a Sentinel-1 product as a Level-2 like. For instance, WV products computing the average value of xsar sigma0 values lead to values up to 3 dB below compare to the value provided in official ESA Level-2 product (oswNrcsNezCorr variable).
Looking at the ESA processor it seems that some steps are potentially* missing in xsarsea.
Typically what ESA processor do to compute the sigma0 is:

read digital number
apply calibration (dividing by the sigma0_lut²)
low pass filter the image
keep intensity multiplying by <abs(image)²>
remove platform (I suppose it is related to https://en.wikipedia.org/wiki/Apodization technics.
final average sigma0 value is mean((image* np.conj(image)).real)

I don't know if we need to be able to reproduce the sigma0 given by ESA

gradients and streaks analysis

xsarsea needs a gradients analysis toolbox to retrieve streaks direction.
It should be implemented from Koch(2004)

This issue is here to track PR and discussions.

unit tests

Unable to detrend with dask and tcp cluster

When using dask on a tcp cluster, detrend fail:

import xsar
import xsarsea
from dask.distributed import Client, LocalCluster
cluster = LocalCluster(protocol='tcp://') # works without tcp
client = Client(cluster)
ds_L1 = xsar.open_dataset('/S1A_IW_GRDH_1SDV_20210710T054447_20210710T054512_038711_04916F_5179.SAFE', resolution = '200m')
ds_L1['sigma0_detrend'] = xsarsea.sigma0_detrend(ds_L1['sigma0'], ds_L1['incidence'])

[...]
File ~/anaconda3/envs/xsar/lib/python3.9/site-packages/cloudpickle/cloudpickle_fast.py:633, in CloudPickler.dump(self, obj)
    631 def dump(self, obj):
    632     try:
--> 633         return Pickler.dump(self, obj)
    634     except RuntimeError as e:
    635         if "recursion" in e.args[0]:

PicklingError: Can't pickle <ufunc 'gmf_cmodifr2'>: attribute lookup gmf_cmodifr2 on __main__ failed

That's because gmf_cmodifr2 is not picklable, because it's not defined in __main__ (ie top level).
From https://docs.python.org/3/library/pickle.html#what-can-be-pickled-and-unpickled:

functions (built-in and user-defined) accessible from the top level of a module (using def, not lambda);

problem to install `xsar` and `xsarsea` python3.10

Following the installation documentation: https://cyclobs.ifremer.fr/static/sarwing_datarmor/xsarsea/installing.html
An error occur with openCV and numpy:

Collecting opencv-python
  Downloading opencv_python-4.5.5.64-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (60.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.5/60.5 MB 12.6 MB/s eta 0:00:00
  Downloading opencv_python-4.5.5.62-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (60.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 MB 10.0 MB/s eta 0:00:00
  Downloading opencv_python-4.5.4.60-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (60.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.3/60.3 MB 10.0 MB/s eta 0:00:00
  Downloading opencv_python-4.5.4.58-cp310-cp310-manylinux2014_x86_64.whl (60.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.3/60.3 MB 6.4 MB/s eta 0:00:00
  Downloading opencv-python-4.5.3.56.tar.gz (89.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.2/89.2 MB 8.4 MB/s eta 0:00:00
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [927 lines of output]
      Ignoring numpy: markers 'python_version == "3.6" and platform_machine != "aarch64" and platform_machine != "arm64"' don't match your environment
      Ignoring numpy: markers 'python_version >= "3.6" and sys_platform == "linux" and platform_machine == "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version >= "3.6" and sys_platform == "darwin" and platform_machine == "arm64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.7" and platform_machine != "aarch64" and platform_machine != "arm64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and platform_machine != "aarch64" and platform_machine != "arm64"' don't match your environment
      Collecting setuptools
        Downloading setuptools-65.5.1-py3-none-any.whl (1.2 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 13.0 MB/s eta 0:00:00
      Collecting wheel
        Downloading wheel-0.38.4-py3-none-any.whl (36 kB)
      Collecting scikit-build
        Downloading scikit_build-0.16.2-py3-none-any.whl (78 kB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.1/78.1 kB 4.8 MB/s eta 0:00:00
      Collecting cmake
        Downloading cmake-3.25.0-py2.py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23.7 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.7/23.7 MB 25.6 MB/s eta 0:00:00
      Collecting pip
        Downloading pip-22.3.1-py3-none-any.whl (2.1 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 30.9 MB/s eta 0:00:00
      Collecting numpy==1.19.3
        Downloading numpy-1.19.3.zip (7.3 MB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 37.8 MB/s eta 0:00:00
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'done'
      Collecting packaging
        Downloading packaging-21.3-py3-none-any.whl (40 kB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 2.0 MB/s eta 0:00:00
      Collecting distro
        Downloading distro-1.8.0-py3-none-any.whl (20 kB)
      Collecting pyparsing!=3.0.5,>=2.0.2
        Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
           ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 7.0 MB/s eta 0:00:00
      Building wheels for collected packages: numpy
        Building wheel for numpy (pyproject.toml): started
        Building wheel for numpy (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error
      
        × Building wheel for numpy (pyproject.toml) did not run successfully.
        │ exit code: 1
        ╰─> [877 lines of output]
            setup.py:67: RuntimeWarning: NumPy 1.19.3 may not yet support Python 3.10.
              warnings.warn(
            Running from numpy source directory.

possible explanations to investigate are:

'jinja2<=3.0.3', in xsar/setup.py
'numpy<=1.21', # numba needs numpy<=1.21 in xsarsea/setup.py

copol
crosspol
dualpol

Also

nesz flattening
read ancillary ecmwf file (0.1deg@1h)

For the moment, we won't:

improve denoising quality
read all ecmwf ancillary files formats

cc: @vincelhx

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