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Multispectral tools: convert data to float32 dtype before doing calcu…
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…lations (#755)

* convert to f4 dtype before doing calculations

* add tests
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@thuydotm
thuydotm authored Feb 16, 2023
1 parent b0c87a9 commit 68aa763
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Showing 2 changed files with 138 additions and 12 deletions.
32 changes: 20 additions & 12 deletions xrspatial/multispectral.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,9 @@ def arvi(nir_agg: xr.DataArray,
cupy_func=_arvi_cupy,
dask_cupy_func=_arvi_dask_cupy)

out = mapper(red_agg)(nir_agg.data, red_agg.data, blue_agg.data)
out = mapper(red_agg)(
nir_agg.data.astype('f4'), red_agg.data.astype('f4'), blue_agg.data.astype('f4')
)

return DataArray(out,
name=name,
Expand Down Expand Up @@ -311,8 +313,10 @@ def evi(nir_agg: xr.DataArray,
cupy_func=_evi_cupy,
dask_cupy_func=_evi_dask_cupy)

out = mapper(red_agg)(nir_agg.data, red_agg.data, blue_agg.data, c1, c2,
soil_factor, gain)
out = mapper(red_agg)(
nir_agg.data.astype('f4'), red_agg.data.astype('f4'), blue_agg.data.astype('f4'),
c1, c2, soil_factor, gain
)

return DataArray(out,
name=name,
Expand Down Expand Up @@ -431,7 +435,7 @@ def gci(nir_agg: xr.DataArray,
cupy_func=_gci_cupy,
dask_cupy_func=_gci_dask_cupy)

out = mapper(nir_agg)(nir_agg.data, green_agg.data)
out = mapper(nir_agg)(nir_agg.data.astype('f4'), green_agg.data.astype('f4'))

return DataArray(out,
name=name,
Expand Down Expand Up @@ -510,7 +514,7 @@ def nbr(nir_agg: xr.DataArray,
dask_cupy_func=_run_normalized_ratio_dask_cupy,
)

out = mapper(nir_agg)(nir_agg.data, swir2_agg.data)
out = mapper(nir_agg)(nir_agg.data.astype('f4'), swir2_agg.data.astype('f4'))

return DataArray(out,
name=name,
Expand Down Expand Up @@ -594,7 +598,7 @@ def nbr2(swir1_agg: xr.DataArray,
dask_cupy_func=_run_normalized_ratio_dask_cupy,
)

out = mapper(swir1_agg)(swir1_agg.data, swir2_agg.data)
out = mapper(swir1_agg)(swir1_agg.data.astype('f4'), swir2_agg.data.astype('f4'))

return DataArray(out,
name=name,
Expand Down Expand Up @@ -671,7 +675,7 @@ def ndvi(nir_agg: xr.DataArray,
dask_cupy_func=_run_normalized_ratio_dask_cupy,
)

out = mapper(nir_agg)(nir_agg.data, red_agg.data)
out = mapper(nir_agg)(nir_agg.data.astype('f4'), red_agg.data.astype('f4'))

return DataArray(out,
name=name,
Expand Down Expand Up @@ -753,7 +757,7 @@ def ndmi(nir_agg: xr.DataArray,
dask_cupy_func=_run_normalized_ratio_dask_cupy,
)

out = mapper(nir_agg)(nir_agg.data, swir1_agg.data)
out = mapper(nir_agg)(nir_agg.data.astype('f4'), swir1_agg.data.astype('f4'))

return DataArray(out,
name=name,
Expand Down Expand Up @@ -937,7 +941,7 @@ def savi(nir_agg: xr.DataArray,
cupy_func=_savi_cupy,
dask_cupy_func=_savi_dask_cupy)

out = mapper(red_agg)(nir_agg.data, red_agg.data, soil_factor)
out = mapper(red_agg)(nir_agg.data.astype('f4'), red_agg.data.astype('f4'), soil_factor)

return DataArray(out,
name=name,
Expand Down Expand Up @@ -1071,7 +1075,9 @@ def sipi(nir_agg: xr.DataArray,
cupy_func=_sipi_cupy,
dask_cupy_func=_sipi_dask_cupy)

out = mapper(red_agg)(nir_agg.data, red_agg.data, blue_agg.data)
out = mapper(red_agg)(
nir_agg.data.astype('f4'), red_agg.data.astype('f4'), blue_agg.data.astype('f4')
)

return DataArray(out,
name=name,
Expand Down Expand Up @@ -1238,7 +1244,9 @@ def ebbi(red_agg: xr.DataArray,
cupy_func=_ebbi_cupy,
dask_cupy_func=_ebbi_dask_cupy)

out = mapper(red_agg)(red_agg.data, swir_agg.data, tir_agg.data)
out = mapper(red_agg)(
red_agg.data.astype('f4'), swir_agg.data.astype('f4'), tir_agg.data.astype('f4')
)

return DataArray(out,
name=name,
Expand Down Expand Up @@ -1298,7 +1306,7 @@ def _normalize_data(agg, pixel_max, c, th):
dask_func=_normalize_data_dask,
cupy_func=_normalize_data_cupy,
dask_cupy_func=_normalize_data_dask_cupy)
out = mapper(agg)(agg.data, pixel_max, c, th)
out = mapper(agg)(agg.data.astype('f4'), pixel_max, c, th)
return out


Expand Down
118 changes: 118 additions & 0 deletions xrspatial/tests/test_multispectral.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -281,6 +281,60 @@ def qgis_ebbi():
return result


@pytest.fixture
def data_uint_dtype_normalized_ratio(dtype):
# test data for input data array of uint dtype
# normalized ratio is applied with different bands for NBR, NBR2, NDVI, NDMI.
band1 = xr.DataArray(np.array([[1, 1], [1, 1]], dtype=dtype))
band2 = xr.DataArray(np.array([[0, 2], [1, 2]], dtype=dtype))
result = np.array([[1, -0.33333334], [0, -0.33333334]], dtype=np.float32)
return band1, band2, result


@pytest.fixture
def data_uint_dtype_arvi(dtype):
nir = xr.DataArray(np.array([[1, 1], [1, 1]], dtype=dtype))
red = xr.DataArray(np.array([[0, 1], [0, 2]], dtype=dtype))
blue = xr.DataArray(np.array([[0, 2], [1, 2]], dtype=dtype))
result = np.array([[1, 0.2], [1, -0.14285715]], dtype=np.float32)
return nir, red, blue, result


@pytest.fixture
def data_uint_dtype_evi(dtype):
nir = xr.DataArray(np.array([[1, 1], [1, 1]], dtype=dtype))
red = xr.DataArray(np.array([[0, 1], [0, 2]], dtype=dtype))
blue = xr.DataArray(np.array([[0, 2], [1, 2]], dtype=dtype))
result = np.array([[1.25, 0.], [-0.45454547, 2.5]], dtype=np.float32)
return nir, red, blue, result


@pytest.fixture
def data_uint_dtype_savi(dtype):
nir = xr.DataArray(np.array([[1, 1], [1, 1]], dtype=dtype))
red = xr.DataArray(np.array([[0, 1], [0, 2]], dtype=dtype))
result = np.array([[0.25, 0.], [0.25, -0.125]], dtype=np.float32)
return nir, red, result


@pytest.fixture
def data_uint_dtype_sipi(dtype):
nir = xr.DataArray(np.array([[1, 1], [1, 1]], dtype=dtype))
red = xr.DataArray(np.array([[0, 0], [0, 2]], dtype=dtype))
blue = xr.DataArray(np.array([[0, 2], [1, 2]], dtype=dtype))
result = np.array([[1, -1], [0, 1]], dtype=np.float32)
return nir, red, blue, result


@pytest.fixture
def data_uint_dtype_ebbi(dtype):
red = xr.DataArray(np.array([[0, 0], [0, 2]], dtype=dtype))
swir = xr.DataArray(np.array([[1, 1], [1, 1]], dtype=dtype))
tir = xr.DataArray(np.array([[0, 2], [1, 2]], dtype=dtype))
result = np.array([[0.1, 0.05773503], [0.07071068, -0.05773503]], dtype=np.float32)
return red, swir, tir, result


# NDVI -------------
def test_ndvi_data_contains_valid_values():
_x = np.mgrid[1:0:21j]
Expand Down Expand Up @@ -310,6 +364,13 @@ def test_ndvi_cpu_against_qgis(nir_data, red_data, qgis_ndvi):
general_output_checks(nir_data, result, qgis_ndvi, verify_dtype=True)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_ndvi_uint_dtype(data_uint_dtype_normalized_ratio):
nir_data, red_data, result_ndvi = data_uint_dtype_normalized_ratio
result = ndvi(nir_data, red_data)
general_output_checks(nir_data, result, result_ndvi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_ndvi_gpu(nir_data, red_data, qgis_ndvi):
Expand All @@ -325,6 +386,7 @@ def test_savi_zero_soil_factor_cpu_against_qgis(nir_data, red_data, qgis_ndvi):
general_output_checks(nir_data, qgis_savi, qgis_ndvi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_savi_zero_soil_factor_gpu(nir_data, red_data, qgis_ndvi):
# savi should be same as ndvi at soil_factor=0
Expand All @@ -339,6 +401,13 @@ def test_savi_cpu_against_qgis(nir_data, red_data, qgis_savi):
general_output_checks(nir_data, result, qgis_savi)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_savi_uint_dtype(data_uint_dtype_savi):
nir_data, red_data, result_savi = data_uint_dtype_savi
result = savi(nir_data, red_data)
general_output_checks(nir_data, result, result_savi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_savi_gpu(nir_data, red_data, qgis_savi):
Expand All @@ -354,6 +423,13 @@ def test_arvi_cpu_against_qgis(nir_data, red_data, blue_data, qgis_arvi):
general_output_checks(nir_data, result, qgis_arvi)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_arvi_uint_dtype(data_uint_dtype_arvi):
nir_data, red_data, blue_data, result_arvi = data_uint_dtype_arvi
result = arvi(nir_data, red_data, blue_data)
general_output_checks(nir_data, result, result_arvi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_arvi_gpu(nir_data, red_data, blue_data, qgis_arvi):
Expand All @@ -368,6 +444,13 @@ def test_evi_cpu_against_qgis(nir_data, red_data, blue_data, qgis_evi):
general_output_checks(nir_data, result, qgis_evi)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_evi_uint_dtype(data_uint_dtype_evi):
nir_data, red_data, blue_data, result_evi = data_uint_dtype_evi
result = evi(nir_data, red_data, blue_data)
general_output_checks(nir_data, result, result_evi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_evi_gpu(nir_data, red_data, blue_data, qgis_evi):
Expand Down Expand Up @@ -396,6 +479,13 @@ def test_sipi_cpu_against_qgis(nir_data, red_data, blue_data, qgis_sipi):
general_output_checks(nir_data, result, qgis_sipi)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_sipi_uint_dtype(data_uint_dtype_sipi):
nir_data, red_data, blue_data, result_sipi = data_uint_dtype_sipi
result = sipi(nir_data, red_data, blue_data)
general_output_checks(nir_data, result, result_sipi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_sipi_gpu(nir_data, red_data, blue_data, qgis_sipi):
Expand All @@ -410,6 +500,13 @@ def test_nbr_cpu_against_qgis(nir_data, swir2_data, qgis_nbr):
general_output_checks(nir_data, result, qgis_nbr)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_nbr_uint_dtype(data_uint_dtype_normalized_ratio):
nir_data, red_data, result_nbr = data_uint_dtype_normalized_ratio
result = nbr(nir_data, red_data)
general_output_checks(nir_data, result, result_nbr, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_nbr_gpu(nir_data, swir2_data, qgis_nbr):
Expand All @@ -424,6 +521,13 @@ def test_nbr2_cpu_against_qgis(swir1_data, swir2_data, qgis_nbr2):
general_output_checks(swir1_data, result, qgis_nbr2)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_nbr2_uint_dtype(data_uint_dtype_normalized_ratio):
nir_data, red_data, result_nbr2 = data_uint_dtype_normalized_ratio
result = nbr2(nir_data, red_data)
general_output_checks(nir_data, result, result_nbr2, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_nbr2_gpu(swir1_data, swir2_data, qgis_nbr2):
Expand All @@ -438,6 +542,13 @@ def test_ndmi_cpu_against_qgis(nir_data, swir1_data, qgis_ndmi):
general_output_checks(nir_data, result, qgis_ndmi)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_ndmi_uint_dtype(data_uint_dtype_normalized_ratio):
nir_data, red_data, result_ndmi = data_uint_dtype_normalized_ratio
result = ndmi(nir_data, red_data)
general_output_checks(nir_data, result, result_ndmi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_ndmi_gpu(nir_data, swir1_data, qgis_ndmi):
Expand All @@ -452,6 +563,13 @@ def test_ebbi_cpu_against_qgis(red_data, swir1_data, tir_data, qgis_ebbi):
general_output_checks(red_data, result, qgis_ebbi)


@pytest.mark.parametrize("dtype", ["uint8", "uint16"])
def test_ebbi_uint_dtype(data_uint_dtype_ebbi):
red_data, swir_data, tir_data, result_ebbi = data_uint_dtype_ebbi
result = ebbi(red_data, swir_data, tir_data)
general_output_checks(red_data, result, result_ebbi, verify_dtype=True)


@cuda_and_cupy_available
@pytest.mark.parametrize("backend", ["cupy", "dask+cupy"])
def test_ebbi_gpu(red_data, swir1_data, tir_data, qgis_ebbi):
Expand Down

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