fix: mosaic nan #323
fix: mosaic nan #323
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| @@ -76,91 +76,91 @@ def _check_config_globals( | |||
| bounds_by (str) | |||
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Only formatting changse
| @@ -191,6 +191,11 @@ def mask_nodata(self) -> xr.DataArray: | |||
| ``xarray.DataArray`` | |||
| """ | |||
| nodata_value = self._obj.gw.nodataval | |||
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| if np.isnan(nodata_value): | |||
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skip replacing nodata with nan if already nodata is already nan
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This could be dropped but might speed up things
added test.py by accident
| srtm30m_bounding_boxes = str(p / "srtm30m_bounding_boxes.gpkg") | ||
| wrs2 = str(p / "wrs2.tar.gz") | ||
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| l8_224077_20200518_B2_nan = str(p / "l8_224077_20200518_B2_nan.tif") |
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added version with nan for missing data values
| ), | ||
| ) | ||
| ) | ||
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| def test_mosaic_max_nan(self): |
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added tests specific to union and nan
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@jgrss I have resolved the problems with mosaicing - but I am getting a new error with h5netcdf tests, I tried pining h5netcdf versions 1.1 and 1.2 but that didn't resolve it. Just wondering if you have any thoughts here. On reading and writing its thowing: ======================================================================
FAIL: test_to_netcdf (tests.test_write.TestWrite.test_to_netcdf)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/runner/work/geowombat/geowombat/tests/test_write.py", line 29, in test_to_netcdf
.gw.to_netcdf(filename=out_path, overwrite=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/geowombat/core/geoxarray.py", line 731, in to_netcdf
to_netcdf(self._obj, filename, *args, **kwargs)
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/geowombat/core/io.py", line 663, in to_netcdf
ds.to_netcdf(
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/xarray/core/dataset.py", line 2327, in to_netcdf
return to_netcdf( # type: ignore # mypy cannot resolve the overloads:(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/xarray/backends/api.py", line 1337, in to_netcdf
dump_to_store(
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/xarray/backends/api.py", line 1384, in dump_to_store
store.store(variables, attrs, check_encoding, writer, unlimited_dims=unlimited_dims)
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/xarray/backends/common.py", line 366, in store
self.set_dimensions(variables, unlimited_dims=unlimited_dims)
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/xarray/backends/common.py", line 443, in set_dimensions
self.set_dimension(dim, length, is_unlimited)
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/xarray/backends/h5netcdf_.py", line 260, in set_dimension
self.ds.dimensions[name] = length
~~~~~~~~~~~~~~~~~~^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/h5netcdf/dimensions.py", line 29, in __setitem__
self._objects[name] = Dimension(self._group, name, size, create_h5ds=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/h5netcdf/dimensions.py", line 91, in __init__
self._create_scale()
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/h5netcdf/dimensions.py", line 211, in _create_scale
if not self._root._h5py.h5ds.is_scale(self._h5ds.id):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5ds.pyx", line 35, in h5py.h5ds.is_scale
File "h5py/defs.pyx", line 4505, in h5py.defs.H5DSis_scale
RuntimeError: Unspecified error in H5DSis_scale (return value <0) |
| @@ -513,6 +513,18 @@ def __init__( | |||
| w = src.block_window(1, 0, 0) | |||
| kwargs["chunks"] = (band_chunks, w.height, w.width) | |||
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| # kw = { | |||
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I would like to send a note to the user if they have config updates when using mosaic or stacking multiple images - since updates to res, etc don't get used since open_warp isn't called -
However when _check_config_globals is run its breaking all the tests and I am not sure why.
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@jgrss This is ready to merge. |
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@jgrss I am happy to report I finally figured out how to update the ml scikit-learn to the newest version! Can you take a look through? |
I'll take a look (after a long delay). |
What is this PR changing?
This resolves issues with nan's in arrays during mosaics.
Closes #322
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