Merge remote-tracking branch 'origin/main' into documentation

# Conflicts:
#	xarray_sentinel/sentinel1.py

Author: aurghs

tests/test_10_esa_safe.py

@@ -1,5 +1,6 @@
 import pathlib
 import typing as T
+from xml.etree import ElementTree
 
 import pytest
 import xmlschema
@@ -165,6 +166,28 @@ def test_parse_annotation_filename() -> None:
         esa_safe.parse_annotation_filename("")
 
 
+def test_findtext() -> None:
+    tree = ElementTree.fromstring("<root><child>text</child></root>")
+
+    res = esa_safe.findtext(tree, ".//child")
+
+    assert res == "text"
+
+    with pytest.raises(ValueError):
+        esa_safe.findtext(tree, ".//dummy")
+
+
+def test_findall() -> None:
+    tree = ElementTree.fromstring("<root><c1>text</c1><c2></c2></root>")
+
+    res = esa_safe.findall(tree, ".//c1")
+
+    assert res == ["text"]
+
+    with pytest.raises(ValueError):
+        esa_safe.findall(tree, ".//c2")
+
+
 @pytest.mark.parametrize("product_id,expected", SENTINEL1_ATTRIBUTES.items())
 def test_parse_manifest_sentinel1(
     product_id: str, expected: T.Dict[str, T.Any]

tests/test_20_sentinel1.py

@@ -53,9 +53,12 @@
     / "measurement"
     / "s1a-s3-slc-vh-20210401t152855-20210401t152914-037258-04638e-001.tiff"
 )
-GRD_IW_VV_annotation = (
+GRD_IW = (
     DATA_FOLDER
     / "S1B_IW_GRDH_1SDV_20210401T052623_20210401T052648_026269_032297_ECC8.SAFE"
+)
+GRD_IW_VV_annotation = (
+    GRD_IW
     / "annotation"
     / "s1b-iw-grd-vv-20210401t052623-20210401t052648-026269-032297-001.xml"
 )
@@ -70,6 +73,9 @@ def test_get_fs_path() -> None:
 
     assert path == str((SLC_IW / "manifest.safe"))
 
+    with pytest.raises(TypeError):
+        sentinel1.get_fs_path("*", fs=fs, storage_options={})
+
     with pytest.raises(ValueError):
         sentinel1.get_fs_path("non-existent-path/*")
 
@@ -288,14 +294,20 @@ def test_crop_burst_dataset() -> None:
         sentinel1.crop_burst_dataset(swath_ds, burst_id=1)
 
 
+def test_mosaic_slc_iw() -> None:
+    da = sentinel1.open_sentinel1_dataset(SLC_IW_V340, group="IW1/HH")
+
+    res = sentinel1.mosaic_slc_iw(da)
+
+    assert isinstance(res, xr.Dataset)
+
+
 def test_calibrate_amplitude() -> None:
     swath_ds = sentinel1.open_sentinel1_dataset(SLC_IW, group="IW1/VH")
     burst_ds = sentinel1.crop_burst_dataset(swath_ds, burst_index=8)
-    calibration_ds = sentinel1.open_calibration_dataset(SLC_IW1_VV_calibration)
+    cal_ds = sentinel1.open_sentinel1_dataset(SLC_IW, group="IW1/VH/calibration")
 
-    res = sentinel1.calibrate_amplitude(
-        burst_ds.measurement, calibration_ds["betaNought"]
-    )
+    res = sentinel1.calibrate_amplitude(burst_ds.measurement, cal_ds["betaNought"])
 
     assert set(res.dims) == {"azimuth_time", "slant_range_time"}
     assert np.issubdtype(res.dtype, np.complex64)
@@ -304,11 +316,50 @@ def test_calibrate_amplitude() -> None:
 def test_calibrate_intensity() -> None:
     swath_ds = sentinel1.open_sentinel1_dataset(SLC_IW, group="IW1/VH")
     burst_ds = sentinel1.crop_burst_dataset(swath_ds, burst_index=8)
-    calibration_ds = sentinel1.open_calibration_dataset(SLC_IW1_VV_calibration)
+    cal_ds = sentinel1.open_sentinel1_dataset(SLC_IW, group="IW1/VH/calibration")
+
+    res = sentinel1.calibrate_intensity(burst_ds.measurement, cal_ds["betaNought"])
+
+    assert set(res.dims) == {"azimuth_time", "slant_range_time"}
+    assert np.issubdtype(res.dtype, np.float32)
+
+    cal_ds["betaNought"].attrs.pop("long_name")
 
     res = sentinel1.calibrate_intensity(
-        burst_ds.measurement, calibration_ds["betaNought"]
+        burst_ds.measurement, cal_ds["betaNought"], as_db=True
     )
 
     assert set(res.dims) == {"azimuth_time", "slant_range_time"}
     assert np.issubdtype(res.dtype, np.float32)
+
+    res = sentinel1.calibrate_intensity(
+        burst_ds.measurement,
+        cal_ds["betaNought"],
+        as_db=True,
+        min_db=None,
+    )
+
+    assert np.issubdtype(res.dtype, np.float32)
+
+
+def test_slant_range_time_to_ground_range() -> None:
+    swath_ds = sentinel1.open_sentinel1_dataset(SLC_IW, group="IW1/VV")
+    swath = swath_ds.measurement[:1000, :1000]
+    cc_ds = sentinel1.open_sentinel1_dataset(
+        GRD_IW, group="IW/VV/coordinate_conversion"
+    )
+
+    res = sentinel1.slant_range_time_to_ground_range(
+        swath.azimuth_time, swath.slant_range_time, cc_ds
+    )
+
+    assert isinstance(res, xr.DataArray)
+
+
+def test_do_override_product_files() -> None:
+    template = "{dirname}/{prefix}{swath}-{polarization}{ext}"
+    _, product_files = esa_safe.parse_manifest_sentinel1(SLC_S3 / "manifest.safe")
+
+    res = sentinel1.do_override_product_files(template, product_files)
+
+    assert "./annotation/s3-vv.xml" in res

tests/test_40_reformat_netcdf4.py

@@ -13,9 +13,11 @@
 def test_to_group_netcdf(tmpdir: T.Any) -> None:
     product_path = (
         DATA_FOLDER
-        / "S1B_IW_SLC__1SDV_20210401T052622_20210401T052650_026269_032297_EFA4.SAFE"
+        / "S1B_IW_GRDH_1SDV_20210401T052623_20210401T052648_026269_032297_ECC8.SAFE"
     )
     tmp_path = str(tmpdir.join("tmp.nc"))
-    groups = {"IW1/VV/gcp": "IW1/VV/gcp", "IW2/VH/attitude": "IW2/VH/attitude"}
+    groups = {"IW/VV/gcp": "IW/VV/gcp", "IW/VH/attitude": "IW/VH/attitude"}
 
     reformat.to_group_netcdf(product_path, tmp_path, groups, engine="netcdf4")
+
+    reformat.to_group_netcdf(product_path, tmp_path, engine="netcdf4")

tests/test_40_reformat_zarr.py

@@ -13,9 +13,11 @@
 def test_to_group_zarr(tmpdir: T.Any) -> None:
     product_path = (
         DATA_FOLDER
-        / "S1B_IW_SLC__1SDV_20210401T052622_20210401T052650_026269_032297_EFA4.SAFE"
+        / "S1B_IW_GRDH_1SDV_20210401T052623_20210401T052648_026269_032297_ECC8.SAFE"
     )
     tmp_path = str(tmpdir.join("tmp.zarr"))
-    groups = {"IW1/VV/gcp": "IW1/VV/gcp", "IW2/VH/attitude": "IW2/VH/attitude"}
+    groups = {"IW/VV/gcp": "IW/VV/gcp", "IW/VH/attitude": "IW/VH/attitude"}
 
     reformat.to_group_zarr(product_path, tmp_path, groups)
+
+    reformat.to_group_zarr(product_path, tmp_path)

xarray_sentinel/esa_safe.py

@@ -70,26 +70,26 @@ def parse_tag_as_list(
 
 
 def findtext(
-    tree: ElementTree.ElementTree,
+    tree: ElementTree.Element,
     query: str,
     namespaces: T.Dict[str, str] = SENTINEL1_NAMESPACES,
 ) -> str:
     value = tree.findtext(query, namespaces=namespaces)
     if value is None:
-        raise ValueError(f"query={query} returned None")
+        raise ValueError(f"{query=} returned None")
     return value
 
 
 def findall(
-    tree: ElementTree.ElementTree,
+    tree: ElementTree.Element,
     query: str,
     namespaces: T.Dict[str, str] = SENTINEL1_NAMESPACES,
 ) -> T.List[str]:
     tags = tree.findall(query, namespaces=namespaces)
     values: T.List[str] = []
     for tag in tags:
         if tag.text is None:
-            raise ValueError(f"query={query} returned None")
+            raise ValueError(f"{query=} returned None")
         values.append(tag.text)
     return values
 
@@ -108,26 +108,26 @@ def parse_manifest_sentinel1(
     manifest_path: PathOrFileType,
 ) -> T.Tuple[T.Dict[str, T.Any], T.Dict[str, T.Tuple[str, str, str, str, str]]]:
     # We use ElementTree because we didn't find a XSD definition for the manifest
-    manifest = ElementTree.parse(manifest_path)
+    manifest = ElementTree.parse(manifest_path).getroot()
 
     family_name = findtext(manifest, ".//safe:platform/safe:familyName")
     if family_name != "SENTINEL-1":
-        raise ValueError(f"familyName={family_name} not supported")
+        raise ValueError(f"{family_name=} not supported")
 
     number = findtext(manifest, ".//safe:platform/safe:number")
     mode = findtext(manifest, ".//s1sarl1:instrumentMode/s1sarl1:mode")
     swaths = findall(manifest, ".//s1sarl1:instrumentMode/s1sarl1:swath")
 
     orbit_number = findall(manifest, ".//safe:orbitNumber")
     if len(orbit_number) != 2 or orbit_number[0] != orbit_number[1]:
-        raise ValueError(f"orbitNumber={orbit_number} not supported")
+        raise ValueError(f"{orbit_number=} not supported")
 
     relative_orbit_number = findall(manifest, ".//safe:relativeOrbitNumber")
     if (
         len(relative_orbit_number) != 2
         or relative_orbit_number[0] != relative_orbit_number[1]
     ):
-        raise ValueError(f"relativeOrbitNumber={relative_orbit_number} not supported")
+        raise ValueError(f"{relative_orbit_number=} not supported")
 
     orbit_pass = findtext(manifest, ".//s1:pass")
     if orbit_pass not in {"ASCENDING", "DESCENDING"}:

xarray_sentinel/sentinel1.py

@@ -615,16 +615,14 @@ def crop_burst_dataset(
             try:
                 burst_index = burst_ids.index(burst_id)
             except ValueError:
-                raise KeyError(
-                    f"'burst_id' {burst_id} not found in product 'burst_ids': {burst_ids}"
-                )
+                raise KeyError(f"{burst_id=} not found in product {burst_ids=}")
         else:
             raise TypeError(
                 "one keyword between 'burst_index' and 'azimuth_anx_time' must be defined"
             )
 
     if burst_index < 0 or burst_index >= pol_dataset.attrs["number_of_bursts"]:
-        raise IndexError(f"burst_index={burst_index} out of bounds")
+        raise IndexError(f"{burst_index=} out of bounds")
 
     lines_per_burst = pol_dataset.attrs["lines_per_burst"]
     ds = pol_dataset.sel(
@@ -712,7 +710,7 @@ def calibrate_intensity(
 def slant_range_time_to_ground_range(
     azimuth_time: xr.DataArray,
     slant_range_time: xr.DataArray,
-    coordinate_conversion: xr.DataArray,
+    coordinate_conversion: xr.Dataset,
 ) -> xr.DataArray:
     """
     Convert the slant range time coordinates to ground range coordinates using the coordinate conversion `sr0`