Update the HRPT reader to latest satpy api #1531

mraspaud · 2021-02-03T20:44:02Z

This PR adapts the HRPT reader to dask, xarray and latest pygac

Closes Cannot read AVHRR in HRPT format (geoloc dtype error) #175
Tests added
Passes flake8 satpy
Fully documented

codecov · 2021-02-03T20:51:30Z

Codecov Report

Merging #1531 (8ca02e5) into master (e0f1fb8) will increase coverage by 0.36%.
The diff coverage is 99.53%.

@@            Coverage Diff             @@
##           master    #1531      +/-   ##
==========================================
+ Coverage   91.65%   92.02%   +0.36%     
==========================================
  Files         248      249       +1     
  Lines       36172    36309     +137     
==========================================
+ Hits        33155    33413     +258     
+ Misses       3017     2896     -121

Flag	Coverage Δ
behaviourtests	`4.34% <0.00%> (-0.02%)`	⬇️
unittests	`92.56% <99.53%> (+0.36%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
satpy/readers/hrpt.py	`98.62% <98.80%> (+92.60%)`	⬆️
satpy/tests/reader_tests/test_avhrr_l0_hrpt.py	`100.00% <100.00%> (ø)`
satpy/tests/reader_tests/test_avhrr_l1b_gaclac.py	`99.64% <100.00%> (+<0.01%)`	⬆️
satpy/readers/viirs_compact.py	`64.12% <0.00%> (-0.77%)`	⬇️

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ghost · 2021-02-03T21:47:19Z

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howff

Thanks very much for the quick PR!
But I think in hrpt.py get_dataset is treating key as a dict but it's a tuple so instead of key['name'] you need to use key.name (and same for key.calibration).

mraspaud · 2021-02-04T12:01:28Z

@howff the key is in principle an instance of a DataID. The recommended way to access its fields now is with ['name'].

howff · 2021-02-04T16:06:01Z

The tuple problem was probably me patching hrpt.py into a version of satpy older than master. But when I use this branch I can confirm that the data loads ok and the built-in composites also work, so thank you very much :)

mraspaud · 2021-02-04T16:30:49Z

You are very welcome, it was high time to update this reader! So thank you for poking us.

mraspaud · 2021-02-05T10:38:37Z

@howff I think I'm happy with this PR now. Any further comments?

gerritholl · 2021-02-05T15:30:35Z

I'm getting an error message with our files.

from satpy import Scene
sc = Scene(["/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf"], reader="avhrr_l1b_hrpt")
sc.load(["4"])
sc.show("4")

gives:

[DEBUG: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Reading ('/home/gholl/checkouts/satpy/satpy/etc/readers/avhrr_l1b_hrpt.yaml',)
[DEBUG: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Assigning to avhrr_l1b_hrpt: ['/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf']
[DEBUG: 2021-02-05 16:30:00 : satpy.composites.config_loader] Looking for composites config file avhrr-2.yaml
[DEBUG: 2021-02-05 16:30:00 : satpy.composites.config_loader] No composite config found called avhrr-2.yaml
[DEBUG: 2021-02-05 16:30:00 : satpy.composites.config_loader] Looking for composites config file avhrr-3.yaml
[DEBUG: 2021-02-05 16:30:00 : satpy.composites.config_loader] Looking for composites config file visir.yaml
[DEBUG: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] No coordinates found for DataID(name='longitude', resolution=1050, modifiers=())
[WARNING: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Failed to load DataID(name='longitude', resolution=1050, modifiers=()) from <HRPTFile: '/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf'>
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 687, in _load_dataset
    projectable = fh.get_dataset(dsid, ds_info)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 161, in get_dataset
    attrs['platform_name'] = self.platform_name
  File "/data/gholl/miniconda3/envs/py38b/lib/python3.8/functools.py", line 967, in __get__
    val = self.func(instance)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 156, in platform_name
    return spacecrafts[(self._data["id"]["id"][0] >> 3) & 15]
KeyError: 2
[ERROR: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Could not load dataset 'DataID(name='longitude', resolution=1050, modifiers=())': "Could not load DataID(name='longitude', resolution=1050, modifiers=()) from any provided files"
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 829, in _load_dataset_with_area
    ds = self._load_dataset_data(file_handlers, dsid, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 711, in _load_dataset_data
    proj = self._load_dataset(dsid, ds_info, file_handlers, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 696, in _load_dataset
    raise KeyError(
KeyError: "Could not load DataID(name='longitude', resolution=1050, modifiers=()) from any provided files"
[DEBUG: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] No coordinates found for DataID(name='latitude', resolution=1050, modifiers=())
[WARNING: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Failed to load DataID(name='latitude', resolution=1050, modifiers=()) from <HRPTFile: '/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf'>
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 687, in _load_dataset
    projectable = fh.get_dataset(dsid, ds_info)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 161, in get_dataset
    attrs['platform_name'] = self.platform_name
  File "/data/gholl/miniconda3/envs/py38b/lib/python3.8/functools.py", line 967, in __get__
    val = self.func(instance)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 156, in platform_name
    return spacecrafts[(self._data["id"]["id"][0] >> 3) & 15]
KeyError: 2
[ERROR: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Could not load dataset 'DataID(name='latitude', resolution=1050, modifiers=())': "Could not load DataID(name='latitude', resolution=1050, modifiers=()) from any provided files"
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 829, in _load_dataset_with_area
    ds = self._load_dataset_data(file_handlers, dsid, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 711, in _load_dataset_data
    proj = self._load_dataset(dsid, ds_info, file_handlers, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 696, in _load_dataset
    raise KeyError(
KeyError: "Could not load DataID(name='latitude', resolution=1050, modifiers=()) from any provided files"
[WARNING: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Failed to load coordinates for 'DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=())'
[WARNING: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Failed to load DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=()) from <HRPTFile: '/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf'>
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 687, in _load_dataset
    projectable = fh.get_dataset(dsid, ds_info)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 161, in get_dataset
    attrs['platform_name'] = self.platform_name
  File "/data/gholl/miniconda3/envs/py38b/lib/python3.8/functools.py", line 967, in __get__
    val = self.func(instance)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 156, in platform_name
    return spacecrafts[(self._data["id"]["id"][0] >> 3) & 15]
KeyError: 2
[ERROR: 2021-02-05 16:30:00 : satpy.readers.yaml_reader] Could not load dataset 'DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=())': "Could not load DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=()) from any provided files"
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 829, in _load_dataset_with_area
    ds = self._load_dataset_data(file_handlers, dsid, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 711, in _load_dataset_data
    proj = self._load_dataset(dsid, ds_info, file_handlers, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 696, in _load_dataset
    raise KeyError(
KeyError: "Could not load DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=()) from any provided files"
[WARNING: 2021-02-05 16:30:00 : satpy.scene] The following datasets were not created and may require resampling to be generated: DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=())
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/dataset/data_dict.py", line 169, in __getitem__
    return super(DatasetDict, self).__getitem__(item)
KeyError: '4'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "test-hrpt.py", line 5, in <module>
    sc.show("4")
  File "/home/gholl/checkouts/satpy/satpy/scene.py", line 819, in show
    img = get_enhanced_image(self[dataset_id].squeeze(), overlay=overlay)
  File "/home/gholl/checkouts/satpy/satpy/scene.py", line 644, in __getitem__
    return self._datasets[key]
  File "/home/gholl/checkouts/satpy/satpy/dataset/data_dict.py", line 171, in __getitem__
    key = self.get_key(item)
  File "/home/gholl/checkouts/satpy/satpy/dataset/data_dict.py", line 158, in get_key
    return get_key(match_key, self.keys(), num_results=num_results,
  File "/home/gholl/checkouts/satpy/satpy/dataset/data_dict.py", line 107, in get_key
    raise KeyError("No dataset matching '{}' found".format(str(key)))
KeyError: "No dataset matching 'DataQuery(name='4')' found"

TAlonglong · 2021-02-05T15:36:27Z

Do you need https://github.com/pytroll/python-geotiepoints for that?

gerritholl · 2021-02-05T15:37:27Z

Same problem after installing the latest pyorbital and pygac:

[DEBUG: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Reading ('/home/gholl/checkouts/satpy/satpy/etc/readers/avhrr_l1b_hrpt.yaml',)
[DEBUG: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Assigning to avhrr_l1b_hrpt: ['/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf']
[DEBUG: 2021-02-05 16:36:41 : satpy.composites.config_loader] Looking for composites config file avhrr-3.yaml
[DEBUG: 2021-02-05 16:36:41 : satpy.composites.config_loader] Looking for composites config file visir.yaml
[DEBUG: 2021-02-05 16:36:41 : satpy.composites.config_loader] Looking for composites config file avhrr-2.yaml
[DEBUG: 2021-02-05 16:36:41 : satpy.composites.config_loader] No composite config found called avhrr-2.yaml
[DEBUG: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] No coordinates found for DataID(name='longitude', resolution=1050, modifiers=())
[WARNING: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Failed to load DataID(name='longitude', resolution=1050, modifiers=()) from <HRPTFile: '/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf'>
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 687, in _load_dataset
    projectable = fh.get_dataset(dsid, ds_info)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 161, in get_dataset
    attrs['platform_name'] = self.platform_name
  File "/data/gholl/miniconda3/envs/py38b/lib/python3.8/functools.py", line 967, in __get__
    val = self.func(instance)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 156, in platform_name
    return spacecrafts[(self._data["id"]["id"][0] >> 3) & 15]
KeyError: 2
[ERROR: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Could not load dataset 'DataID(name='longitude', resolution=1050, modifiers=())': "Could not load DataID(name='longitude', resolution=1050, modifiers=()) from any provided files"
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 829, in _load_dataset_with_area
    ds = self._load_dataset_data(file_handlers, dsid, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 711, in _load_dataset_data
    proj = self._load_dataset(dsid, ds_info, file_handlers, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 696, in _load_dataset
    raise KeyError(
KeyError: "Could not load DataID(name='longitude', resolution=1050, modifiers=()) from any provided files"
[DEBUG: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] No coordinates found for DataID(name='latitude', resolution=1050, modifiers=())
[WARNING: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Failed to load DataID(name='latitude', resolution=1050, modifiers=()) from <HRPTFile: '/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf'>
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 687, in _load_dataset
    projectable = fh.get_dataset(dsid, ds_info)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 161, in get_dataset
    attrs['platform_name'] = self.platform_name
  File "/data/gholl/miniconda3/envs/py38b/lib/python3.8/functools.py", line 967, in __get__
    val = self.func(instance)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 156, in platform_name
    return spacecrafts[(self._data["id"]["id"][0] >> 3) & 15]
KeyError: 2
[ERROR: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Could not load dataset 'DataID(name='latitude', resolution=1050, modifiers=())': "Could not load DataID(name='latitude', resolution=1050, modifiers=()) from any provided files"
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 829, in _load_dataset_with_area
    ds = self._load_dataset_data(file_handlers, dsid, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 711, in _load_dataset_data
    proj = self._load_dataset(dsid, ds_info, file_handlers, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 696, in _load_dataset
    raise KeyError(
KeyError: "Could not load DataID(name='latitude', resolution=1050, modifiers=()) from any provided files"
[WARNING: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Failed to load coordinates for 'DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=())'
[WARNING: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Failed to load DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=()) from <HRPTFile: '/media/nas/x21308/scratch/20210205141010_NOAA_19.hmf'>
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 687, in _load_dataset
    projectable = fh.get_dataset(dsid, ds_info)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 161, in get_dataset
    attrs['platform_name'] = self.platform_name
  File "/data/gholl/miniconda3/envs/py38b/lib/python3.8/functools.py", line 967, in __get__
    val = self.func(instance)
  File "/home/gholl/checkouts/satpy/satpy/readers/hrpt.py", line 156, in platform_name
    return spacecrafts[(self._data["id"]["id"][0] >> 3) & 15]
KeyError: 2
[ERROR: 2021-02-05 16:36:41 : satpy.readers.yaml_reader] Could not load dataset 'DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=())': "Could not load DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=()) from any provided files"
Traceback (most recent call last):
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 829, in _load_dataset_with_area
    ds = self._load_dataset_data(file_handlers, dsid, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 711, in _load_dataset_data
    proj = self._load_dataset(dsid, ds_info, file_handlers, **kwargs)
  File "/home/gholl/checkouts/satpy/satpy/readers/yaml_reader.py", line 696, in _load_dataset
    raise KeyError(
KeyError: "Could not load DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=()) from any provided files"
[WARNING: 2021-02-05 16:36:41 : satpy.scene] The following datasets were not created and may require resampling to be generated: DataID(name='4', wavelength=WavelengthRange(min=10.3, central=10.8, max=11.3, unit='µm'), resolution=1050, calibration=<calibration.brightness_temperature>, modifiers=())
Traceback (most recent call last):
  File "test-hrpt.py", line 7, in <module>
    ls.save_datasets(filename=str(plotdir() / "{start_time:%Y%m%d%H%M}-{platform_name:s}-{name:s}.tif"))
  File "/home/gholl/checkouts/satpy/satpy/scene.py", line 1001, in save_datasets
    raise RuntimeError("None of the requested datasets have been "
RuntimeError: None of the requested datasets have been generated or could not be loaded. Requested composite inputs may need to have matching dimensions (eg. through resampling).

from conda list:

pygac                     1.4.0                    pypi_0    pypi
pyorbital                 1.6.0+11.gf1e50fc          pypi_0    pypi
satpy                     0.25.2.dev50+g905197a3           dev_0    <develop>

mraspaud · 2021-02-05T15:37:35Z

@TAlonglong yes, and pyorbital and pygac

mraspaud · 2021-02-05T15:38:02Z

@gerritholl do you have python-geotiepoints installed?

gerritholl · 2021-02-05T15:51:21Z

It was probably a corrupted file. With other files I do get an image, but many lines are misplaced:

20210202124445_NOAA_18.hmf:

20210205041432_NOAA_19.hmf:

20210205091618_NOAA_19.hmf:

I don't remember having seen this before. Maybe AAPP has some error checking to remove those lines?

mraspaud · 2021-02-05T15:54:02Z

@gerritholl fun! I guess some consistancy check is in order...

gerritholl · 2021-02-05T15:56:44Z

Both 20210205091618_NOAA_19.hmf files, projected on eurol, channel 4 without any other corrections.

With the avhrr_l1b_aapp reader pre-processed by AAPP:

With the avhrr_l1b_hrpt reader, no processing by AAPP:

howff · 2021-02-05T16:09:04Z

Some misplaced scanlines is to be expected if the timestamps have been corrupted due to noisy data.
The KeyError is possibly also the same cause, if the spacecraft id in the data has been corrupted by a bit flip.
Adding a filter for this is probably something I could contribute but it's not a bug in satpy.

mraspaud · 2021-02-05T16:13:22Z

@howff, yes, corrupted timestamps are probably the issue. I was thinking of trying to fit the timestamps to a line to correct the outliers, but how would you do it?

gerritholl · 2021-02-05T16:37:00Z

I agree that it's not a bug in Satpy, rather a missing feature — but as long as the data quality reading directly is worse than when pre-processing it with AAPP, users are going to keep AAPP in their pipelines despite the additional overhead.

gerritholl · 2021-02-05T16:38:04Z

Doesn't pygac have a lot of experience in filtering the dozens of things that can go wrong with data? Could that help here? There's already a pygac dependency anyway...

mraspaud · 2021-02-05T18:24:19Z

@gerritholl indeed: https://github.com/pytroll/pygac/blob/c86b67ed6f3b76b27cdcfd0f352b6b22bba7fe1a/pygac/reader.py#L757

mraspaud · 2021-02-05T19:00:22Z

ah no that won't work as HRPT doesn't have line numbers

howff · 2021-02-08T09:32:11Z

I would be happy to have this PR merged, to get the new API working, and leave the handling of dirty data to a different PR.

mraspaud · 2021-02-08T09:46:54Z

ok, great, I will merge this one then. @howff do you want to take a shot at that new PR for filter or fixing erroneous timestamps?

Update hrpt reader

7b0a86d

mraspaud self-assigned this Feb 3, 2021

mraspaud mentioned this pull request Feb 3, 2021

Cannot read AVHRR in HRPT format (geoloc dtype error) #175

Closed

Add a test file for hrpt

4257b68

mraspaud added bug component:readers labels Feb 4, 2021

Add tests for hrpt reader

0373de8

howff suggested changes Feb 4, 2021

View reviewed changes

mraspaud added 2 commits February 4, 2021 13:22

Add tests for hrpt reader 3a/3b splitting

d2822e8

Start refactoring the hrpt reader

bfb56d7

Test hrpt's navigation functions

6732116

mraspaud marked this pull request as ready for review February 5, 2021 10:36

mraspaud requested a review from djhoese as a code owner February 5, 2021 10:36

mraspaud requested a review from pnuu February 5, 2021 15:15

Making the platform name and frame sync check more robust

7ef6de0

mraspaud merged commit 5200840 into pytroll:master Feb 8, 2021

mraspaud deleted the fix-hrpt branch February 8, 2021 09:47

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Update the HRPT reader to latest satpy api #1531

Update the HRPT reader to latest satpy api #1531

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Update the HRPT reader to latest satpy api #1531

Update the HRPT reader to latest satpy api #1531

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