Repository: corteva/rioxarray

Issue:
merge_arrays: ignores CF conventions all versions >0.15.5 are affected
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#### Code Sample, a copy-pastable example if possible

This example uses MODIS in HDF4 data, available on request.

```python
import numpy as np 
import xarray as xr 
from rioxarray.merge import merge_arrays

filename = "MYD21A2.A2020289.h12v11.061.2020349230516.hdf"
modis_tile = xr.open_dataset(filename, engine='rasterio').squeeze(drop=True)
tile = modis_tile['LST_Day_1KM']
data = merge_arrays([tile], nodata=np.nan)
print(np.unique(data))
# [13744. 13805. 13931. ... 20096. 20116.   nan]  <= WRONG
 
tile = 1.0*modis_tile['LST_Day_1KM']   # applies CF conventions before merge_array
data = merge_arrays([tile], nodata=np.nan) 
print(np.unique(data))
# [274.88   276.1    278.62   ... 401.91998 402.31998      nan]   <= CORRECT
```
#### Problem description

After updating to rioxarray from >0.15.5 to any later version, `merge_arrays` fails to apply CF conventions. Both 0.16.x and 0.17.x are affected.

This is the only thing which looks relevant, could it be the culprit here?

https://github.com/corteva/rioxarray/compare/0.15.5...0.15.6#diff-a5cbac5348d8946289580aa7cc146328084dc0ae31e6ed5b970d1484757fff5bL52


#### Expected Output

In both examples, the output should be the same:
```
# [274.88   276.1    278.62   ... 401.91998 402.31998      nan]
```

#### Environment Information

```
rioxarray (0.15.6) deps:
rasterio: 1.4.1
xarray: 2024.7.0
GDAL: 3.8.4
GEOS: 3.12.1
PROJ: 9.4.0
PROJ DATA: /home/USER/.local/share/proj:/usr/share/proj
GDAL DATA: None

Other python deps:
scipy: 1.12.0
pyproj: 3.6.1

System:
python: 3.10.4 (main, Jan 11 2023, 11:01:58) [GCC 11.3.0]
executable: /home/USER/.pyenv/versions/default/bin/python
machine: Linux-6.8.0-45-generic-x86_64-with-glibc2.39
```

Discussion:
@snowman2: Thanks for the report :+1:. See #817@jparal: Thank you for your help!

Solution patch:
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index ea2e41c6..76d0c0a4 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -40,7 +40,7 @@ jobs:
         gdal-version: ['3.8.2']
         include:
           - python-version: '3.10'
-            rasterio-version: ''
+            rasterio-version: '==1.3'
             xarray-version: '==2024.7.0'
             numpy-version: '<2'
             run-with-scipy: 'YES'
diff --git a/docs/history.rst b/docs/history.rst
index 7c458ab7..5aa1959b 100644
--- a/docs/history.rst
+++ b/docs/history.rst
@@ -3,6 +3,7 @@ History
 
 Latest
 ------
+- BUG:merge: Fix merging masked and scaled data (issue #814)
 
 0.17.0
 ------
diff --git a/rioxarray/_io.py b/rioxarray/_io.py
index 9e628828..3de2895e 100644
--- a/rioxarray/_io.py
+++ b/rioxarray/_io.py
@@ -328,7 +328,7 @@ def __init__(
             )
             if self._unsigned_dtype is not None and self._fill_value is not None:
                 self._fill_value = self._unsigned_dtype.type(self._fill_value)
-            if self._unsigned_dtype is None and dtype.kind not in ("i", "u"):
+            if self._unsigned_dtype is None:
                 warnings.warn(
                     f"variable {name!r} has _Unsigned attribute but is not "
                     "of integer type. Ignoring attribute.",
diff --git a/rioxarray/merge.py b/rioxarray/merge.py
index 397a5185..58d483b7 100644
--- a/rioxarray/merge.py
+++ b/rioxarray/merge.py
@@ -2,7 +2,6 @@
 This module allows you to merge xarray Datasets/DataArrays
 geospatially with the `rasterio.merge` module.
 """
-
 from collections.abc import Sequence
 from typing import Callable, Optional, Union
 
@@ -12,6 +11,7 @@
 from rasterio.merge import merge as _rio_merge
 from xarray import DataArray, Dataset
 
+from rioxarray._io import open_rasterio
 from rioxarray.rioxarray import _get_nonspatial_coords, _make_coords
 
 
@@ -31,13 +31,25 @@ def __init__(self, xds: DataArray):
         self.count = int(xds.rio.count)
         self.dtypes = [xds.dtype]
         self.name = xds.name
-        self.nodatavals = [xds.rio.nodata]
+        if xds.rio.encoded_nodata is not None:
+            self.nodatavals = [xds.rio.encoded_nodata]
+        else:
+            self.nodatavals = [xds.rio.nodata]
         res = xds.rio.resolution(recalc=True)
         self.res = (abs(res[0]), abs(res[1]))
         self.transform = xds.rio.transform(recalc=True)
-        # profile is only used for writing to a file.
-        # This never happens with rioxarray merge.
-        self.profile: dict = {}
+        self.profile: dict = {
+            "crs": self.crs,
+            "nodata": self.nodatavals[0],
+        }
+        self._scale_factor = self._xds.encoding.get("scale_factor", 1.0)
+        self._add_offset = self._xds.encoding.get("add_offset", 0.0)
+        self._mask_and_scale = (
+            self._xds.rio.encoded_nodata is not None
+            or self._scale_factor != 1
+            or self._add_offset != 0
+            or self._xds.encoding.get("_Unsigned") is not None
+        )
 
     def colormap(self, *args, **kwargs) -> None:
         """
@@ -54,7 +66,15 @@ def read(self, *args, **kwargs) -> numpy.ma.MaskedArray:
         with MemoryFile() as memfile:
             self._xds.rio.to_raster(memfile.name)
             with memfile.open() as dataset:
-                return dataset.read(*args, **kwargs)
+                if self._mask_and_scale:
+                    kwargs["masked"] = True
+                out = dataset.read(*args, **kwargs)
+                if self._mask_and_scale:
+                    if self._scale_factor != 1:
+                        out = out * self._scale_factor
+                    if self._add_offset != 0:
+                        out = out + self._add_offset
+                return out
 
 
 def merge_arrays(
@@ -132,41 +152,28 @@ def merge_arrays(
             rioduckarrays.append(RasterioDatasetDuck(dataarray))
 
     # use rasterio to merge
-    merged_data, merged_transform = _rio_merge(
-        rioduckarrays,
-        **{key: val for key, val in input_kwargs.items() if val is not None},
-    )
     # generate merged data array
     representative_array = rioduckarrays[0]._xds
-    if parse_coordinates:
-        coords = _make_coords(
-            src_data_array=representative_array,
-            dst_affine=merged_transform,
-            dst_width=merged_data.shape[-1],
-            dst_height=merged_data.shape[-2],
+    with MemoryFile() as memfile:
+        _rio_merge(
+            rioduckarrays,
+            **{key: val for key, val in input_kwargs.items() if val is not None},
+            dst_path=memfile.name,
         )
-    else:
-        coords = _get_nonspatial_coords(representative_array)
-
-    # make sure the output merged data shape is 2D if the
-    # original data was 2D. this can happen if the
-    # xarray datasarray was squeezed.
-    if len(merged_data.shape) == 3 and len(representative_array.shape) == 2:
-        merged_data = merged_data.squeeze()
-
-    xda = DataArray(
-        name=representative_array.name,
-        data=merged_data,
-        coords=coords,
-        dims=tuple(representative_array.dims),
-        attrs=representative_array.attrs,
-    )
-    xda.rio.write_nodata(
-        nodata if nodata is not None else representative_array.rio.nodata, inplace=True
-    )
-    xda.rio.write_crs(representative_array.rio.crs, inplace=True)
-    xda.rio.write_transform(merged_transform, inplace=True)
-    return xda
+        with open_rasterio(  # type: ignore
+            memfile.name,
+            parse_coordinates=parse_coordinates,
+            mask_and_scale=rioduckarrays[0]._mask_and_scale,
+        ) as xda:
+            xda = xda.load()
+        xda.coords.update(
+            {
+                coord: value
+                for coord, value in _get_nonspatial_coords(representative_array).items()
+                if coord not in xda.coords
+            }
+        )
+    return xda  # type: ignore
 
 
 def merge_datasets(


Test patch:
diff --git a/test/integration/test_integration_merge.py b/test/integration/test_integration_merge.py
index faf29f6f..53100ef1 100644
--- a/test/integration/test_integration_merge.py
+++ b/test/integration/test_integration_merge.py
@@ -51,7 +51,12 @@ def test_merge_arrays(squeeze):
         assert merged.coords["band"].values == [1]
         assert sorted(merged.coords) == ["band", "spatial_ref", "x", "y"]
         assert merged.rio.crs == rds.rio.crs
-        assert merged.attrs == rds.attrs
+        assert merged.attrs == {
+            "AREA_OR_POINT": "Area",
+            "add_offset": 0.0,
+            "scale_factor": 1.0,
+            **rds.attrs,
+        }
         assert merged.encoding["grid_mapping"] == "spatial_ref"
 
 
@@ -106,6 +111,7 @@ def test_merge__different_crs(dataset):
         assert merged.rio.crs == rds.rio.crs
         if not dataset:
             assert merged.attrs == {
+                "AREA_OR_POINT": "Area",
                 "_FillValue": -28672,
                 "add_offset": 0.0,
                 "scale_factor": 1.0,
@@ -116,9 +122,6 @@ def test_merge__different_crs(dataset):
 def test_merge_arrays__res():
     dem_test = os.path.join(TEST_INPUT_DATA_DIR, "MODIS_ARRAY.nc")
     with open_rasterio(dem_test, masked=True) as rds:
-        rds.attrs = {
-            "_FillValue": rds.rio.nodata,
-        }
         arrays = [
             rds.isel(x=slice(100), y=slice(100)),
             rds.isel(x=slice(100, 200), y=slice(100, 200)),
@@ -151,9 +154,8 @@ def test_merge_arrays__res():
         assert merged.coords["band"].values == [1]
         assert sorted(merged.coords) == ["band", "spatial_ref", "x", "y"]
         assert merged.rio.crs == rds.rio.crs
-        assert_almost_equal(merged.attrs.pop("_FillValue"), rds.attrs.pop("_FillValue"))
-        compare_attrs = dict(rds.attrs)
-        assert merged.attrs == compare_attrs
+        assert_almost_equal(merged.rio.nodata, rds.rio.nodata)
+        assert_almost_equal(merged.rio.encoded_nodata, rds.rio.encoded_nodata)
         assert merged.encoding["grid_mapping"] == "spatial_ref"
         assert_almost_equal(nansum(merged), 13760565)
 
@@ -191,7 +193,6 @@ def test_merge_datasets():
             (-4447802.078667, -10007554.677, -3335851.559, -8895604.157333),
         )
         assert merged.rio.shape == (2400, 2400)
-        assert_almost_equal(merged[data_var].sum(), 4539666606551516)
         assert_almost_equal(
             tuple(merged[data_var].rio.transform()),
             (
@@ -211,6 +212,7 @@ def test_merge_datasets():
         assert merged.rio.crs == rds.rio.crs
         assert merged.attrs == rds.attrs
         assert merged.encoding["grid_mapping"] == "spatial_ref"
+        assert_almost_equal(merged[data_var].sum(), 4539666606551516)
 
 
 @pytest.mark.xfail(os.name == "nt", reason="On windows the merged data is different.")
@@ -266,3 +268,22 @@ def test_merge_datasets__res():
         assert merged.attrs == rds.attrs
         assert merged.encoding["grid_mapping"] == "spatial_ref"
         assert_almost_equal(merged[data_var].sum(), 974566547463955)
+
+
+@pytest.mark.parametrize("mask_and_scale", [True, False])
+def test_merge_datasets__mask_and_scale(mask_and_scale):
+    test_file = os.path.join(TEST_INPUT_DATA_DIR, "tmmx_20190121.nc")
+    with open_rasterio(test_file, mask_and_scale=mask_and_scale) as rds:
+        rds = rds.to_dataset()
+        datasets = [
+            rds.isel(x=slice(100), y=slice(100)),
+            rds.isel(x=slice(100, None), y=slice(100, None)),
+            rds.isel(x=slice(100), y=slice(100, None)),
+            rds.isel(x=slice(100, None), y=slice(100)),
+        ]
+        merged = merge_datasets(datasets)
+        total = merged.air_temperature.sum()
+        if mask_and_scale:
+            assert_almost_equal(total, 133376696)
+        else:
+            assert_almost_equal(total, 10981781386)