geowombat package

geowombat package#

Subpackages#

Submodules#

geowombat.config module#

class geowombat.config.update(config={'bigtiff': 'NO', 'blockxsize': 512, 'blockysize': 512, 'compress': None, 'driver': 'GTiff', 'ignore_warnings': False, 'l57_angles_path': None, 'l8_angles_path': None, 'nasa_earthdata_code': None, 'nasa_earthdata_key': None, 'nasa_earthdata_user': None, 'nodata': None, 'offset': None, 'ref_bounds': None, 'ref_crs': None, 'ref_image': None, 'ref_res': None, 'ref_tar': None, 'scale_factor': None, 'sensor': None, 'tiled': True, 'with_config': False}, **kwargs)[source]#

Bases: object

Updates the global configuration parameters. See ‘config.ini’ for parameter options and defaults.

Note that nodata is only used/applied as a value setter during array warping. I.e., the nodata argument is not the input ‘no data’ value itself. Rather, it is used to replace ‘no data’ values in the opened, warped array.

Example

>>> with gw.config.update(sensor='l8'):
>>>     with gw.open('image.tif') as ds:
>>>         print(ds.gw.config)

geowombat.handler module#

geowombat.handler.add_handler(logger)[source]#

Module contents#

class geowombat.TimeModule[source]#

Bases: object

Methods

`__call__`(w, array, band_dict)
`calculate`(data)	Calculates the user function.

abstract calculate(data)[source]#

Calculates the user function.

Parameters:

| (data (numpy.ndarray) – jax.Array | torch.Tensor | tensorflow.Tensor): The input array, shaped [time x bands x rows x columns].
data (Any) –

Return type:

Any

Returns:

numpy.ndarray | jax.Array | torch.Tensor | tensorflow.Tensor:

Shaped (time|bands x rows x columns)

class geowombat.TimeModulePipeline(module_list)[source]#

Bases: object

Methods

__call__(w, array, band_dict)

Parameters:: module_list (List[TimeModule]) –

geowombat.apply(infile, outfile, block_func, args=None, count=1, scheduler='processes', gdal_cache=512, n_jobs=4, overwrite=False, tags=None, **kwargs)[source]#

Applies a function and writes results to file.

Parameters:

infile (str) – The input file to process.
outfile (str) – The output file.
block_func (func) – The user function to apply to each block. The function should always return the window, the data, and at least one argument. The block data inside the function will be a 2d array if the input image has 1 band, otherwise a 3d array.
args (Optional[tuple]) – Additional arguments to pass to block_func.
count (Optional[int]) – The band count for the output file.
scheduler (Optional[str]) – The concurrent.futures scheduler to use. Choices are [‘threads’, ‘processes’].
gdal_cache (Optional[int]) – The GDAL cache size (in MB).
n_jobs (Optional[int]) – The number of blocks to process in parallel.
overwrite (Optional[bool]) – Whether to overwrite an existing output file.
tags (Optional[dict]) – Image tags to write to file.
kwargs (Optional[dict]) – Additional keyword arguments to pass to rasterio.open.

Returns:

None, writes to outfile

Examples

>>> import geowombat as gw
>>>
>>> # Here is a function with no arguments
>>> def my_func0(w, block, arg):
>>>     return w, block
>>>
>>> gw.apply('input.tif',
>>>          'output.tif',
>>>           my_func0,
>>>           n_jobs=8)
>>>
>>> # Here is a function with 1 argument
>>> def my_func1(w, block, arg):
>>>     return w, block * arg
>>>
>>> gw.apply('input.tif',
>>>          'output.tif',
>>>           my_func1,
>>>           args=(10.0,),
>>>           n_jobs=8)

geowombat.array_to_polygon(data, mask=None, connectivity=4, num_workers=1)#

Converts an xarray.DataArray` to a ``geopandas.GeoDataFrame

Parameters:

data (DataArray) – The xarray.DataArray to convert.
mask (Optional[str, numpy ndarray, or rasterio Band object]) – Must evaluate to bool (rasterio.bool_ or rasterio.uint8). Values of False or 0 will be excluded from feature generation. Note well that this is the inverse sense from Numpy’s, where a mask value of True indicates invalid data in an array. If source is a Numpy masked array and mask is None, the source’s mask will be inverted and used in place of mask. If mask is equal to ‘source’, then data is used as the mask.
connectivity (Optional[int]) – Use 4 or 8 pixel connectivity for grouping pixels into features.
num_workers (Optional[int]) – The number of parallel workers to send to dask.compute().

Return type:

GeoDataFrame

Returns:

geopandas.GeoDataFrame

Example

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif') as src:
>>>
>>>     # Convert the input image to a GeoDataFrame
>>>     df = gw.array_to_polygon(
>>>         src,
>>>         mask='source',
>>>         num_workers=8
>>>     )

geowombat.avi(data, nodata=None, mask=False, sensor=None, scale_factor=None)#

Calculates the advanced vegetation index

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[AVI = {(NIR \times (1.0 - red) \times (NIR - red))}^{0.3334}\]

Returns:: Data range: 0 to 1
Return type:: xarray.DataArray

geowombat.bounds_to_coords(bounds, dst_crs)#

Converts bounds from longitude and latitude to native map coordinates.

Parameters:

bounds (tuple | rasterio.coords.BoundingBox) – The lat/lon bounds to transform.
dst_crs (str, object, or DataArray) – The CRS to transform to. It can be provided as a string, a CRS instance (e.g., pyproj.crs.CRS), or a geowombat.DataArray.

Returns:

(left, bottom, right, top)

Return type:

tuple

geowombat.calc_area(data, values, op='eq', units='km2', row_chunks=None, col_chunks=None, n_workers=1, n_threads=1, scheduler='threads', n_chunks=100)#

Calculates the area of data values.

Parameters:

data (DataArray) – The xarray.DataArray to calculate area.
values (list) – A list of values.
op (Optional[str]) – The value sign. Choices are [‘gt’, ‘ge’, ‘lt’, ‘le’, ‘eq’].
units (Optional[str]) – The units to return. Choices are [‘km2’, ‘ha’].
row_chunks (Optional[int]) – The row chunk size to process in parallel.
col_chunks (Optional[int]) – The column chunk size to process in parallel.
n_workers (Optional[int]) – The number of parallel workers for scheduler.
n_threads (Optional[int]) – The number of parallel threads for dask.compute().
scheduler (Optional[str]) –
The parallel task scheduler to use. Choices are [‘processes’, ‘threads’, ‘mpool’].

mpool: process pool of workers using multiprocessing.Pool processes: process pool of workers using concurrent.futures threads: thread pool of workers using concurrent.futures
n_chunks (Optional[int]) – The chunk size of windows. If not given, equal to n_workers x 50.

Return type:

DataFrame

Returns:

pandas.DataFrame

Example

>>> import geowombat as gw
>>>
>>> # Read a land cover image with 512x512 chunks
>>> with gw.open('land_cover.tif', chunks=512) as src:
>>>
>>>     df = gw.calc_area(
>>>         src,
>>>         [1, 2, 5],        # calculate the area of classes 1, 2, and 5
>>>         units='km2',      # return area in kilometers squared
>>>         n_workers=4,
>>>         row_chunks=1024,  # iterate over larger chunks to use 512 chunks in parallel
>>>         col_chunks=1024
>>>     )

geowombat.clip(data, df, query=None, mask_data=False, expand_by=0)#

Clips a DataArray by vector polygon geometry.

Deprecated since version 2.1.7: Use geowombat.clip_by_polygon().

Parameters:

data (DataArray) – The xarray.DataArray to subset.
df (GeoDataFrame or str) – The geopandas.GeoDataFrame or filename to clip to.
query (Optional[str]) – A query to apply to df.
mask_data (Optional[bool]) – Whether to mask values outside of the df geometry envelope.
expand_by (Optional[int]) – Expand the clip array bounds by expand_by pixels on each side.

Return type:

DataArray

Returns:

xarray.DataArray

Examples

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif') as ds:
>>>     ds = gw.clip(ds, df, query="Id == 1")
>>>
>>> # or
>>>
>>> with gw.open('image.tif') as ds:
>>>     ds = ds.gw.clip(df, query="Id == 1")

geowombat.clip_by_polygon(data, df, query=None, mask_data=False, expand_by=0)#

Clips a DataArray by vector polygon geometry.

Parameters:

data (DataArray) – The xarray.DataArray to subset.
df (GeoDataFrame or str) – The geopandas.GeoDataFrame or filename to clip to.
query (Optional[str]) – A query to apply to df.
mask_data (Optional[bool]) – Whether to mask values outside of the df geometry envelope.
expand_by (Optional[int]) – Expand the clip array bounds by expand_by pixels on each side.

Return type:

DataArray

Returns:

xarray.DataArray

Examples

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif') as ds:
>>>     ds = gw.clip_by_polygon(ds, df, query="Id == 1")

geowombat.coords_to_indices(x, y, transform)#

Converts map coordinates to array indices.

Parameters:

x (float or 1d array) – The x coordinates.
y (float or 1d array) – The y coordinates.
transform (object) – The affine transform.

Returns:

(col_index, row_index)

Return type:

tuple

Example

>>> import geowombat as gw
>>> from geowombat.core import coords_to_indices
>>>
>>> with gw.open('image.tif') as src:
>>>     j, i = coords_to_indices(x, y, src)

geowombat.coregister(target, reference, band_names_reference=None, band_names_target=None, wkt_version=None, **kwargs)#

Co-registers an image, or images, using AROSICS.

While the required inputs are DataArrays, the intermediate results are stored as NumPy arrays. Therefore, memory usage is constrained to the size of the input data. Dask is not used for any of the computation in this function.

Parameters:

target (DataArray or str) – The target xarray.DataArray or file name to co-register to reference.
reference (DataArray or str) – The reference xarray.DataArray or file name used to co-register target.
band_names_reference (Optional[list | tuple]) – Band names to open for the reference data.
band_names_target (Optional[list | tuple]) – Band names to open for the target data.
wkt_version (Optional[str]) – The WKT version to use with to_wkt().
kwargs (Optional[dict]) – Keyword arguments passed to arosics.

Return type:

DataArray

Reference:: https://pypi.org/project/arosics

Return type:

DataArray

Returns:

xarray.DataArray

Parameters:

target (str | Path | DataArray) –
reference (str | Path | DataArray) –
band_names_reference (Sequence[str] | None) –
band_names_target (Sequence[str] | None) –
wkt_version (str | None) –

Example

>>> import geowombat as gw
>>>
>>> # Co-register a single image to a reference image
>>> with gw.open('target.tif') as tar, gw.open('reference.tif') as ref:
>>>     results = gw.coregister(
>>>         tar, ref, q=True, ws=(512, 512), max_shift=3, CPUs=4
>>>     )
>>>
>>> # or
>>>
>>> results = gw.coregister(
>>>     'target.tif',
>>>     'reference.tif',
>>>     q=True,
>>>     ws=(512, 512),
>>>     max_shift=3,
>>>     CPUs=4
>>> )

geowombat.evi(data, nodata=None, mask=False, sensor=None, scale_factor=None)#

Calculates the enhanced vegetation index

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[EVI = 2.5 \times \frac{NIR - red}{NIR + 6 \times red - 7.5 \times blue + 1}\]

Returns:: Data range: 0 to 1
Return type:: xarray.DataArray

geowombat.evi2(data, nodata=None, mask=False, sensor=None, scale_factor=None)#

Calculates the two-band modified enhanced vegetation index

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[EVI2 = 2.5 \times \frac{NIR - red}{NIR + 1 + 2.4 \times red}\]

Reference:: See [JHDM08]

Returns:: Data range: 0 to 1
Return type:: xarray.DataArray

geowombat.extract(data, aoi, bands=None, time_names=None, band_names=None, frac=1.0, min_frac_area=None, all_touched=False, id_column='id', time_format='%Y%m%d', mask=None, n_jobs=8, verbose=0, n_workers=1, n_threads=-1, use_client=False, address=None, total_memory=24, processes=False, pool_kwargs=None, **kwargs)#

Extracts data within an area or points of interest. Projections do not need to match, as they are handled ‘on-the-fly’.

Parameters:

data (DataArray) – The xarray.DataArray to extract data from.
aoi (str or GeoDataFrame) – A file or geopandas.GeoDataFrame to extract data frame.
bands (Optional[int or 1d array-like]) – A band or list of bands to extract. If not given, all bands are used. Bands should be GDAL-indexed (i.e., the first band is 1, not 0).
band_names (Optional[list]) – A list of band names. Length should be the same as bands.
time_names (Optional[list]) – A list of time names.
frac (Optional[float]) – A fractional subset of points to extract in each polygon feature.
min_frac_area (Optional[int | float]) – A minimum polygon area to use frac. Otherwise, use all samples within a polygon.
all_touched (Optional[bool]) – The all_touched argument is passed to rasterio.features.rasterize().
id_column (Optional[str]) – The id column name.
time_format (Optional[str]) – The datetime conversion format if time_names are datetime objects.
mask (Optional[GeoDataFrame or Shapely Polygon]) – A shapely.geometry.Polygon mask to subset to.
n_jobs (Optional[int]) – The number of features to rasterize in parallel.
verbose (Optional[int]) – The verbosity level.
n_workers (Optional[int]) – The number of process workers. Only applies when use_client = True.
n_threads (Optional[int]) – The number of thread workers. Only applies when use_client = True.
use_client (Optional[bool]) – Whether to use a dask client.
address (Optional[str]) – A cluster address to pass to client. Only used when use_client = True.
total_memory (Optional[int]) – The total memory (in GB) required when use_client = True.
processes (Optional[bool]) – Whether to use process workers with the dask.distributed client. Only applies when use_client = True.
pool_kwargs (Optional[dict]) – Keyword arguments passed to multiprocessing.Pool().imap().
kwargs (Optional[dict]) – Keyword arguments passed to dask.compute().

Return type:

GeoDataFrame

Returns:

geopandas.GeoDataFrame

Examples

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif') as src:
>>>     df = gw.extract(src, 'poly.gpkg')
>>>
>>> # On a cluster
>>> # Use a local cluster
>>> with gw.open('image.tif') as src:
>>>     df = gw.extract(src, 'poly.gpkg', use_client=True, n_threads=16)
>>>
>>> # Specify the client address with a local cluster
>>> with LocalCluster(
>>>     n_workers=1,
>>>     threads_per_worker=8,
>>>     scheduler_port=0,
>>>     processes=False,
>>>     memory_limit='4GB'
>>> ) as cluster:
>>>
>>>     with gw.open('image.tif') as src:
>>>         df = gw.extract(
>>>             src,
>>>             'poly.gpkg',
>>>             use_client=True,
>>>             address=cluster
>>>         )

geowombat.indices_to_coords(col_index, row_index, transform)#

Converts array indices to map coordinates.

Parameters:

col_index (float or 1d array) – The column index.
row_index (float or 1d array) – The row index.
transform (Affine, DataArray, or tuple) – The affine transform.

Returns:

(x, y)

Return type:

tuple

Example

>>> import geowombat as gw
>>> from geowombat.core import indices_to_coords
>>>
>>> with gw.open('image.tif') as src:
>>>     x, y = indices_to_coords(j, i, src)

geowombat.kndvi(data, nodata=None, mask=False, sensor=None, scale_factor=None)#

Calculates the kernel normalized difference vegetation index

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[kNDVI = tanh({NDVI}^2)\]

Reference:: See [CVCTMMartinez+21]

Returns:: Data range: -1 to 1
Return type:: xarray.DataArray

geowombat.load(image_list, time_names, band_names, chunks=512, nodata=65535, in_range=None, out_range=None, data_slice=None, num_workers=1, src=None, scheduler='ray')[source]#

Loads data into memory using xarray.open_mfdataset() and ray. This function does not check data alignments and CRSs. It assumes each image in image_list has the same y and x dimensions and that the coordinates align.

The load function cannot be used if dataclasses was pip installed.

Parameters:

image_list (list) – The list of image file paths.
time_names (list) – The list of image datetime objects.
band_names (list) – The list of bands to open.
chunks (Optional[int]) – The dask chunk size.
nodata (Optional[float | int]) – The ‘no data’ value.
in_range (Optional[tuple]) – The input (min, max) range. If not given, defaults to (0, 10000).
out_range (Optional[tuple]) – The output (min, max) range. If not given, defaults to (0, 1).
data_slice (Optional[tuple]) – The slice object to read, given as (time, bands, rows, columns).
num_workers (Optional[int]) – The number of threads.
scheduler (Optional[str]) – The distributed scheduler. Currently not implemented.

Returns:

Datetime list, array of (time x bands x rows x columns)

Return type:

list, numpy.ndarray

Example

>>> import datetime
>>> import geowombat as gw
>>>
>>> image_names = ['LT05_L1TP_227082_19990311_20161220_01_T1.nc',
>>>                'LT05_L1TP_227081_19990311_20161220_01_T1.nc',
>>>                'LT05_L1TP_227082_19990327_20161220_01_T1.nc']
>>>
>>> image_dates = [datetime.datetime(1999, 3, 11, 0, 0),
>>>                datetime.datetime(1999, 3, 11, 0, 0),
>>>                datetime.datetime(1999, 3, 27, 0, 0)]
>>>
>>> data_slice = (slice(0, None), slice(0, None), slice(0, 64), slice(0, 64))
>>>
>>> # Load data into memory
>>> dates, y = gw.load(image_names,
>>>                    image_dates,
>>>                    ['red', 'nir'],
>>>                    chunks=512,
>>>                    nodata=65535,
>>>                    data_slice=data_slice,
>>>                    num_workers=4)

geowombat.lonlat_to_xy(lon, lat, dst_crs)#

Converts from longitude and latitude to native map coordinates.

Parameters:

lon (float) – The longitude to convert.
lat (float) – The latitude to convert.
dst_crs (str, object, or DataArray) – The CRS to transform to. It can be provided as a string, a CRS instance (e.g., pyproj.crs.CRS), or a geowombat.DataArray.

Returns:

(x, y)

Return type:

tuple

Example

>>> import geowombat as gw
>>> from geowombat.core import lonlat_to_xy
>>>
>>> lon, lat = -55.56822206, -25.46214220
>>>
>>> with gw.open('image.tif') as src:
>>>     x, y = lonlat_to_xy(lon, lat, src)

geowombat.mask(data, dataframe, query=None, keep='in')#

Masks a DataArray by vector polygon geometry.

Parameters:

data (DataArray) – The xarray.DataArray to mask.
dataframe (GeoDataFrame or str) – The geopandas.GeoDataFrame or filename to use for masking.
query (Optional[str]) – A query to apply to dataframe.
keep (Optional[str]) – If keep = ‘in’, mask values outside of the geometry (keep inside). Otherwise, if keep = ‘out’, mask values inside (keep outside).

Return type:

DataArray

Returns:

xarray.DataArray

Examples

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif') as ds:
>>>     ds = ds.gw.mask(df)

geowombat.moving(data, stat='mean', perc=50, w=3, nodata=None, weights=False)#

Applies a moving window function over Dask array blocks.

Parameters:

data (DataArray) – The xarray.DataArray to process.
stat (Optional[str]) – The statistic to compute. Choices are [‘mean’, ‘std’, ‘var’, ‘min’, ‘max’, ‘perc’].
perc (Optional[int]) – The percentile to return if stat = ‘perc’.
w (Optional[int]) – The moving window size (in pixels).
nodata (Optional[int or float]) – A ‘no data’ value to ignore.
weights (Optional[bool]) – Whether to weight values by distance from window center.

Return type:

DataArray

Returns:

xarray.DataArray

Examples

>>> import geowombat as gw
>>>
>>> # Calculate the mean within a 5x5 window
>>> with gw.open('image.tif') as src:
>>>     res = gw.moving(ds, stat='mean', w=5, nodata=32767.0)
>>>
>>> # Calculate the 90th percentile within a 15x15 window
>>> with gw.open('image.tif') as src:
>>>     res = gw.moving(stat='perc', w=15, perc=90, nodata=32767.0)
>>>     res.data.compute(num_workers=4)

geowombat.nbr(data, nodata=None, mask=False, sensor=None, scale_factor=None)#

Calculates the normalized burn ratio

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[NBR = \frac{NIR - SWIR2}{NIR + SWIR2}\]

Returns:: Data range: -1 to 1
Return type:: xarray.DataArray

geowombat.ndvi(data, nodata=None, mask=False, sensor=None, scale_factor=None)#

Calculates the normalized difference vegetation index

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[NDVI = \frac{NIR - red}{NIR + red}\]

Returns:: Data range: -1 to 1
Return type:: xarray.DataArray

geowombat.norm_diff(data, b1, b2, sensor=None, nodata=None, mask=False, scale_factor=None)#

Calculates the normalized difference band ratio

Parameters:

data (DataArray) – The xarray.DataArray to process.
b1 (str) – The band name of the first band.
b2 (str) – The band name of the second band.
sensor (Optional[str]) – sensor (Optional[str]): The data’s sensor. If None, the band names should reflect the index being calculated.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[{norm}_{diff} = \frac{b2 - b1}{b2 + b1}\]

Returns:: Data range: -1 to 1
Return type:: xarray.DataArray

class geowombat.open(filename, band_names=None, time_names=None, stack_dim='time', bounds=None, bounds_by='reference', resampling='nearest', persist_filenames=False, netcdf_vars=None, mosaic=False, overlap='max', nodata=None, scale_factor=None, offset=None, dtype=None, scale_data=False, num_workers=1, **kwargs)[source]#

Bases: object

Opens one or more raster files.

Parameters:

filename (str or list) – The file name, search string, or a list of files to open.
band_names (Optional[1d array-like]) – A list of band names if bounds is given or window is given. Default is None.
time_names (Optional[1d array-like]) – A list of names to give the time dimension if bounds is given. Default is None.
stack_dim (Optional[str]) – The stack dimension. Choices are [‘time’, ‘band’].
bounds (Optional[1d array-like]) – A bounding box to subset to, given as [minx, maxy, miny, maxx]. Default is None.
bounds_by (Optional[str]) –
How to concatenate the output extent if filename is a list and mosaic = False. Choices are [‘intersection’, ‘union’, ‘reference’]. * reference: Use the bounds of the reference image. If a ref_image is not given, the first image in

the filename list is used.
- intersection: Use the intersection (i.e., minimum extent) of all the image bounds
- union: Use the union (i.e., maximum extent) of all the image bounds
resampling (Optional[str]) – The resampling method if filename is a list. Choices are [‘average’, ‘bilinear’, ‘cubic’, ‘cubic_spline’, ‘gauss’, ‘lanczos’, ‘max’, ‘med’, ‘min’, ‘mode’, ‘nearest’].
persist_filenames (Optional[bool]) – Whether to persist the filenames list with the xarray.DataArray attributes. By default, persist_filenames=False to avoid storing large file lists.
netcdf_vars (Optional[list]) – NetCDF variables to open as a band stack.
mosaic (Optional[bool]) – If filename is a list, whether to mosaic the arrays instead of stacking.
overlap (Optional[str]) – The keyword that determines how to handle overlapping data if filenames is a list. Choices are [‘min’, ‘max’, ‘mean’].
nodata (Optional[float | int]) –
A ‘no data’ value to set. Default is None. If nodata is None, the ‘no data’ value is set from the file metadata. If nodata is given, then the file ‘no data’ value is overridden. See docstring examples for use of nodata in geowombat.config.update.
Note

The geowombat.config.update overrides this argument. Thus, preference is always given in the following order:
1. geowombat.config.update(nodata not None)
2. open(nodata not None)
3. file ‘no data’ value from metadata ‘_FillValue’ or ‘nodatavals’
scale_factor (Optional[float | int]) –
A scale value to apply to the opened data. The same rules used in nodata apply. I.e.,
Note

The geowombat.config.update overrides this argument. Thus, preference is always given in the following order:
1. geowombat.config.update(scale_factor not None)
2. open(scale_factor not None)
3. file scale value from metadata ‘scales’
offset (Optional[float | int]) –
An offset value to apply to the opened data. The same rules used in nodata apply. I.e.,
Note

The geowombat.config.update overrides this argument. Thus, preference is always given in the following order:
1. geowombat.config.update(offset not None)
2. open(offset not None)
3. file offset value from metadata ‘offsets’
dtype (Optional[str]) – A data type to force the output to. If not given, the data type is extracted from the file.
scale_data (Optional[bool]) –
Whether to apply scaling to the opened data. Default is False. Scaled data are returned as:

scaled = data * gain + offset

See the arguments nodata, scale_factor, and offset for rules regarding how scaling is applied.
num_workers (Optional[int]) – The number of parallel workers for Dask if bounds is given or window is given. Default is 1.
kwargs (Optional[dict]) – Keyword arguments passed to the file opener.

Returns:

xarray.DataArray or xarray.Dataset

Examples

>>> import geowombat as gw
>>>
>>> # Open an image
>>> with gw.open('image.tif') as ds:
>>>     print(ds)
>>>
>>> # Open a list of images, stacking along the 'time' dimension
>>> with gw.open(['image1.tif', 'image2.tif']) as ds:
>>>     print(ds)
>>>
>>> # Open all GeoTiffs in a directory, stack along the 'time' dimension
>>> with gw.open('*.tif') as ds:
>>>     print(ds)
>>>
>>> # Use a context manager to handle images of difference sizes and projections
>>> with gw.config.update(ref_image='image1.tif'):
>>>     # Use 'time' names to stack and mosaic non-aligned images with identical dates
>>>     with gw.open(['image1.tif', 'image2.tif', 'image3.tif'],
>>>
>>>         # The first two images were acquired on the same date
>>>         #   and will be merged into a single time layer
>>>         time_names=['date1', 'date1', 'date2']) as ds:
>>>
>>>         print(ds)
>>>
>>> # Mosaic images across space using a reference
>>> #   image for the CRS and cell resolution
>>> with gw.config.update(ref_image='image1.tif'):
>>>     with gw.open(['image1.tif', 'image2.tif'], mosaic=True) as ds:
>>>         print(ds)
>>>
>>> # Mix configuration keywords
>>> with gw.config.update(ref_crs='image1.tif', ref_res='image1.tif', ref_bounds='image2.tif'):
>>>     # The ``bounds_by`` keyword overrides the extent bounds
>>>     with gw.open(['image1.tif', 'image2.tif'], bounds_by='union') as ds:
>>>         print(ds)
>>>
>>> # Resample an image to 10m x 10m cell size
>>> with gw.config.update(ref_crs=(10, 10)):
>>>     with gw.open('image.tif', resampling='cubic') as ds:
>>>         print(ds)
>>>
>>> # Open a list of images at a window slice
>>> from rasterio.windows import Window
>>> # Stack two images, opening band 3
>>> with gw.open(
>>>     ['image1.tif', 'image2.tif'],
>>>     band_names=['date1', 'date2'],
>>>     num_workers=8,
>>>     indexes=3,
>>>     window=Window(row_off=0, col_off=0, height=100, width=100),
>>>     dtype='float32'
>>> ) as ds:
>>>     print(ds)
>>>
>>> # Scale data upon opening, using the image metadata to get scales and offsets
>>> with gw.open('image.tif', scale_data=True) as ds:
>>>     print(ds)
>>>
>>> # Scale data upon opening, specifying scales and overriding metadata
>>> with gw.open('image.tif', scale_data=True, scale_factor=1e-4) as ds:
>>>     print(ds)
>>>
>>> # Scale data upon opening, specifying scales and overriding metadata
>>> with gw.config.update(scale_factor=1e-4):
>>>     with gw.open('image.tif', scale_data=True) as ds:
>>>         print(ds)
>>>
>>> # Open a NetCDF variable, specifying a NetCDF prefix and variable to open
>>> with gw.open('netcdf:image.nc:blue') as src:
>>>     print(src)
>>>
>>> # Open a NetCDF image without access to transforms by providing full file path
>>> # NOTE: This will be faster than the above method
>>> # as it uses ``xarray.open_dataset`` and bypasses CRS checks.
>>> # NOTE: The chunks must be provided by the user.
>>> # NOTE: Providing band names will ensure the correct order when reading from a NetCDF dataset.
>>> with gw.open(
>>>     'image.nc',
>>>     chunks={'band': -1, 'y': 256, 'x': 256},
>>>     band_names=['blue', 'green', 'red', 'nir', 'swir1', 'swir2'],
>>>     engine='h5netcdf'
>>> ) as src:
>>>     print(src)
>>>
>>> # Open multiple NetCDF variables as an array stack
>>> with gw.open('netcdf:image.nc', netcdf_vars=['blue', 'green', 'red']) as src:
>>>     print(src)

Methods

close

close()[source]#

geowombat.polygon_to_array(polygon, col=None, data=None, cellx=None, celly=None, band_name=None, row_chunks=512, col_chunks=512, src_res=None, fill=0, default_value=1, all_touched=True, dtype='uint8', sindex=None, tap=False, bounds_by='intersection')#

Converts a polygon geometry to an xarray.DataArray.

Parameters:

polygon (GeoDataFrame | str) – The geopandas.DataFrame or file with polygon geometry.
col (Optional[str]) – The column in polygon you want to assign values from. If not set, creates a binary raster.
data (Optional[DataArray]) – An xarray.DataArray to use as a reference for rasterizing.
cellx (Optional[float]) – The output cell x size.
celly (Optional[float]) – The output cell y size.
band_name (Optional[list]) – The xarray.DataArray band name.
row_chunks (Optional[int]) – The dask row chunk size.
col_chunks (Optional[int]) – The dask column chunk size.
(Optional[tuple] (src_res) – A source resolution to align to.
fill (Optional[int]) – Used as fill value for all areas not covered by input geometries to rasterio.features.rasterize.
default_value (Optional[int]) – Used as value for all geometries, if not provided in shapes to rasterio.features.rasterize.
all_touched (Optional[bool]) – If True, all pixels touched by geometries will be burned in. If false, only pixels whose center is within the polygon or that are selected by Bresenham’s line algorithm will be burned in. The all_touched value for rasterio.features.rasterize().
dtype (Optional[str | numpy data type]) – The output data type for rasterio.features.rasterize().
sindex (Optional[object]) – An instanced of geopandas.GeoDataFrame.sindex.
tap (Optional[bool]) – Whether to target align pixels.
bounds_by (Optional[str]) –
How to concatenate the output extent. Choices are [‘intersection’, ‘union’, ‘reference’].
- reference: Use the bounds of the reference image
- intersection: Use the intersection (i.e., minimum extent) of all the image bounds
- union: Use the union (i.e., maximum extent) of all the image bounds
src_res (Sequence[float] | None) –

Return type:

DataArray

Returns:

xarray.DataArray

Example

>>> import geowombat as gw
>>> import geopandas as gpd
>>>
>>> df = gpd.read_file('polygons.gpkg')
>>>
>>> # 100x100 cell size
>>> data = gw.polygon_to_array(df, 100.0, 100.0)
>>>
>>> # Align to an existing image
>>> with gw.open('image.tif') as src:
>>>     data = gw.polygon_to_array(df, data=src)

geowombat.polygons_to_points(data, df, frac=1.0, min_frac_area=None, all_touched=False, id_column='id', n_jobs=1, **kwargs)#

Converts polygons to points.

Parameters:

data (DataArray or Dataset) – The xarray.DataArray or xarray.Dataset.
df (GeoDataFrame) – The geopandas.GeoDataFrame containing the geometry to rasterize.
frac (Optional[float]) – A fractional subset of points to extract in each feature.
min_frac_area (Optional[int | float]) – A minimum polygon area to use frac. Otherwise, use all samples within a polygon.
all_touched (Optional[bool]) – The all_touched argument is passed to rasterio.features.rasterize.
id_column (Optional[str]) – The ‘id’ column.
n_jobs (Optional[int]) – The number of features to rasterize in parallel.
kwargs (Optional[dict]) – Keyword arguments passed to multiprocessing.Pool().imap.

Returns:

geopandas.GeoDataFrame

geowombat.recode(data, polygon, to_replace, num_workers=1)#

Recodes a DataArray with polygon mappings.

Parameters:

data (DataArray) – The xarray.DataArray to recode.
polygon (GeoDataFrame | str) – The geopandas.DataFrame or file with polygon geometry.
to_replace (dict) –
How to find the values to replace. Dictionary mappings should be given as {from: to} pairs. If to_replace is an integer/string mapping, the to string should be ‘mode’.

{1: 5}:
recode values of 1 to 5

{1: ‘mode’}:
recode values of 1 to the polygon mode
num_workers (Optional[int]) – The number of parallel Dask workers (only used if to_replace has a ‘mode’ mapping).

Return type:

DataArray

Returns:

xarray.DataArray

Example

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif', chunks=512) as ds:
>>>     # Recode 1 with 5 within a polygon
>>>     res = gw.recode(ds, 'poly.gpkg', {1: 5})

geowombat.replace(data, to_replace)#

Replace values given in to_replace with value.

Parameters:

data (DataArray) – The xarray.DataArray to recode.
to_replace (dict) –
How to find the values to replace. Dictionary mappings should be given as {from: to} pairs. If to_replace is an integer/string mapping, the to string should be ‘mode’.

{1: 5}:
recode values of 1 to 5

{1: ‘mode’}:
recode values of 1 to the polygon mode

Return type:

DataArray

Returns:

xarray.DataArray

Example

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif', chunks=512) as ds:
>>>     # Replace 1 with 5
>>>     res = gw.replace(ds, {1: 5})

geowombat.sample(data, method='random', band=None, n=None, strata=None, spacing=None, min_dist=None, max_attempts=10, num_workers=1, verbose=1, **kwargs)#

Generates samples from a raster.

Parameters:

data (DataArray) – The xarray.DataArray to extract data from.
method (Optional[str]) – The sampling method. Choices are [‘random’, ‘systematic’].
band (Optional[int or str]) – The band name to extract from. Only required if method = ‘random’ and strata is given.
n (Optional[int]) – The total number of samples. Only required if method = ‘random’.
strata (Optional[dict]) –
The strata to sample within. The dictionary key–>value pairs should be {‘conditional,value’: sample size}.

E.g.,

strata = {‘==,1’: 0.5, ‘>=,2’: 0.5} … would sample 50% of total samples within class 1 and 50% of total samples in class >= 2.

strata = {‘==,1’: 10, ‘>=,2’: 20} … would sample 10 samples within class 1 and 20 samples in class >= 2.
spacing (Optional[float]) – The spacing (in map projection units) when method = ‘systematic’.
min_dist (Optional[float or int]) – A minimum distance allowed between samples. Only applies when method = ‘random’.
max_attempts (Optional[int]) – The maximum numer of attempts to sample points > min_dist from each other.
num_workers (Optional[int]) – The number of parallel workers for dask.compute().
verbose (Optional[int]) – The verbosity level.
kwargs (Optional[dict]) – Keyword arguments passed to geowombat.extract.

Return type:

GeoDataFrame

Returns:

geopandas.GeoDataFrame

Examples

>>> import geowombat as gw
>>>
>>> # Sample 100 points randomly across the image
>>> with gw.open('image.tif') as src:
>>>     df = gw.sample(src, n=100)
>>>
>>> # Sample points systematically (with 10km spacing) across the image
>>> with gw.open('image.tif') as src:
>>>     df = gw.sample(src, method='systematic', spacing=10000.0)
>>>
>>> # Sample 50% of 100 in class 1 and 50% in classes >= 2
>>> strata = {'==,1': 0.5, '>=,2': 0.5}
>>> with gw.open('image.tif') as src:
>>>     df = gw.sample(src, band=1, n=100, strata=strata)
>>>
>>> # Specify a per-stratum minimum allowed point distance of 1,000 meters
>>> with gw.open('image.tif') as src:
>>>     df = gw.sample(src, band=1, n=100, min_dist=1000, strata=strata)

geowombat.save(data, filename, mode='w', nodata=None, overwrite=False, client=None, compute=True, tags=None, compress='none', compression=None, num_workers=1, log_progress=True, tqdm_kwargs=None, bigtiff=None)[source]#

Saves a DataArray to raster using rasterio/dask.

Parameters:

filename (str | Path) – The output file name to write to.
overwrite (Optional[bool]) – Whether to overwrite an existing file. Default is False.
mode (Optional[str]) – The file storage mode. Choices are [‘w’, ‘r+’].
nodata (Optional[float | int]) – The ‘no data’ value. If None (default), the ‘no data’ value is taken from the DataArray metadata.
client (Optional[Client object]) – A dask.distributed.Client client object to persist data. Default is None.
compute (Optinoal[bool]) – Whether to compute and write to filename. Otherwise, return the dask task graph. If True, compute and write to filename. If False, return the dask task graph. Default is True.
tags (Optional[dict]) – Metadata tags to write to file. Default is None.
compress (Optional[str]) – The file compression type. Default is ‘none’, or no compression.
compression (Optional[str]) –
The file compression type. Default is ‘none’, or no compression.

Deprecated since version 2.1.4: Use ‘compress’ – ‘compression’ will be removed in >=2.2.0.
num_workers (Optional[int]) – The number of dask workers (i.e., chunks) to write concurrently. Default is 1.
log_progress (Optional[bool]) – Whether to log the progress bar during writing. Default is True.
tqdm_kwargs (Optional[dict]) – Keyword arguments to pass to tqdm.
bigtiff (Optional[str]) – A GDAL BIGTIFF flag. Choices are [“YES”, “NO”, “IF_NEEDED”, “IF_SAFER”].
data (DataArray) –

Returns:

None, writes to filename

Example

>>> import geowombat as gw
>>>
>>> with gw.open('file.tif') as src:
>>>     result = ...
>>>     gw.save(result, 'output.tif', compress='lzw', num_workers=8)
>>>
>>> # Create delayed write tasks and compute later
>>> tasks = [gw.save(array, 'output.tif', compute=False) for array in array_list]
>>> # Write and close files
>>> dask.compute(tasks, num_workers=8)

class geowombat.series(filenames, time_names=None, band_names=None, transfer_lib='jax', crs=None, res=None, bounds=None, resampling='nearest', nodata=0, warp_mem_limit=256, num_threads=1, window_size=None, padding=None)[source]#

Bases: BaseSeries

A class for time series concurrent processing on a GPU.

Parameters:

filenames (list) – The list of filenames to open.
band_names (Optional[list]) – The band associated names.
transfer_lib (Optional[str]) – The library to transfer data to. Choices are [‘jax’, ‘keras’, ‘numpy’, ‘pytorch’, ‘tensorflow’].
crs (Optional[str]) – The coordinate reference system.
res (Optional[list | tuple]) – The cell resolution.
bounds (Optional[object]) – The coordinate bounds.
resampling (Optional[str]) – The resampling method.
nodata (Optional[float | int]) – The ‘no data’ value.
warp_mem_limit (Optional[int]) – The rasterio warping memory limit (in MB).
num_threads (Optional[int]) – The number of rasterio warping threads.
window_size (Optional[int | list | tuple]) – The concurrent processing window size (height, width) or -1 (i.e., entire array).
padding (Optional[list | tuple]) – Padding for each window. padding should be given as a tuple of (left pad, bottom pad, right pad, top pad). If padding is given, the returned list will contain a tuple of rasterio.windows.Window objects as (w1, w2), where w1 contains the normal window offsets and w2 contains the padded window offsets.
time_names (list) –

Requirement:: > # CUDA 11.1 > pip install –upgrade “jax[cuda111]” -f https://storage.googleapis.com/jax-releases/jax_releases.html

Attributes:

band_dict
blockxsize
blockysize
count
crs
height
nchunks
nodata
transform
width

Parameters:

filenames (list) –
time_names (list) –
band_names (list) –
transfer_lib (str) –
crs (str) –
res (list | tuple) –
bounds (BoundingBox | list | tuple) –
resampling (str) –
nodata (float | int) –
warp_mem_limit (int) –
num_threads (int) –
window_size (int | list | tuple) –
padding (list | tuple) –

Methods

`apply`(func, bands[, gain, offset, ...])	Applies a function concurrently over windows.
`group_dates`(data, image_dates, band_names)	Groups data by dates.
`read`(bands[, window, gain, offset, pool, ...])	Reads a window.

ndarray_to_darray
open
warp

apply(func, bands, gain=1.0, offset=0.0, processes=False, num_workers=1, monitor_progress=True, outfile=None, bigtiff='NO', kwargs={})[source]#

Applies a function concurrently over windows.

Parameters:

func (object | str | list | tuple) – The function to apply. If func is a string, choices are [‘cv’, ‘max’, ‘mean’, ‘min’].
bands (list | int) – The bands to read.
gain (Optional[float]) – A gain factor to apply.
offset (Optional[float | int]) – An offset factor to apply.
processes (Optional[bool]) – Whether to use process workers, otherwise use threads.
num_workers (Optional[int]) – The number of concurrent workers.
monitor_progress (Optional[bool]) – Whether to monitor progress with a tqdm bar.
outfile (Optional[Path | str]) – The output file.
bigtiff (Optional[str]) – Whether to create a BigTIFF file. Choices are [‘YES’, ‘NO’,”IF_NEEDED”, “IF_SAFER”]. Default is ‘NO’.
kwargs (Optional[dict]) – Keyword arguments passed to rasterio open profile.

Returns:

Window, array, [datetime, …] If outfile is not None:

None, writes to outfile

Return type:

If outfile is None

Example

>>> import itertools
>>> import geowombat as gw
>>> import rasterio as rio
>>>
>>> # Import an image with 3 bands
>>> from geowombat.data import l8_224078_20200518
>>>
>>> # Create a custom class
>>> class TemporalMean(gw.TimeModule):
>>>
>>>     def __init__(self):
>>>         super(TemporalMean, self).__init__()
>>>
>>>     # The main function
>>>     def calculate(self, array):
>>>
>>>         sl1 = (slice(0, None), slice(self.band_dict['red'], self.band_dict['red']+1), slice(0, None), slice(0, None))
>>>         sl2 = (slice(0, None), slice(self.band_dict['green'], self.band_dict['green']+1), slice(0, None), slice(0, None))
>>>
>>>         vi = (array[sl1] - array[sl2]) / ((array[sl1] + array[sl2]) + 1e-9)
>>>
>>>         return vi.mean(axis=0).squeeze()
>>>
>>> with rio.open(l8_224078_20200518) as src:
>>>     res = src.res
>>>     bounds = src.bounds
>>>     nodata = 0
>>>
>>> # Open many files, each with 3 bands
>>> with gw.series([l8_224078_20200518]*100,
>>>                band_names=['blue', 'green', 'red'],
>>>                crs='epsg:32621',
>>>                res=res,
>>>                bounds=bounds,
>>>                nodata=nodata,
>>>                num_threads=4,
>>>                window_size=(1024, 1024)) as src:
>>>
>>>     src.apply(TemporalMean(),
>>>               bands=-1,             # open all bands
>>>               gain=0.0001,          # scale from [0,10000] -> [0,1]
>>>               processes=False,      # use threads
>>>               num_workers=4,        # use 4 concurrent threads, one per window
>>>               outfile='vi_mean.tif')
>>>
>>> # Import a single-band image
>>> from geowombat.data import l8_224078_20200518_B4
>>>
>>> # Open many files, each with 1 band
>>> with gw.series([l8_224078_20200518_B4]*100,
>>>                band_names=['red'],
>>>                crs='epsg:32621',
>>>                res=res,
>>>                bounds=bounds,
>>>                nodata=nodata,
>>>                num_threads=4,
>>>                window_size=(1024, 1024)) as src:
>>>
>>>     src.apply('mean',               # built-in function over single-band images
>>>               bands=1,              # open all bands
>>>               gain=0.0001,          # scale from [0,10000] -> [0,1]
>>>               num_workers=4,        # use 4 concurrent threads, one per window
>>>               outfile='red_mean.tif')
>>>
>>> with gw.series([l8_224078_20200518_B4]*100,
>>>                band_names=['red'],
>>>                crs='epsg:32621',
>>>                res=res,
>>>                bounds=bounds,
>>>                nodata=nodata,
>>>                num_threads=4,
>>>                window_size=(1024, 1024)) as src:
>>>
>>>     src.apply(['mean', 'max', 'cv'],    # calculate multiple statistics
>>>               bands=1,                  # open all bands
>>>               gain=0.0001,              # scale from [0,10000] -> [0,1]
>>>               num_workers=4,            # use 4 concurrent threads, one per window
>>>               outfile='stack_mean.tif')

read(bands, window=None, gain=1.0, offset=0.0, pool=None, num_workers=None, tqdm_obj=None)[source]#

Reads a window.

Return type:

Any

Parameters:

bands (int | list) –
window (Window | None) –
gain (float) –
offset (float | int) –
pool (Any | None) –
num_workers (int | None) –
tqdm_obj (Any | None) –

geowombat.subset(data, left=None, top=None, right=None, bottom=None, rows=None, cols=None, center=False, mask_corners=False)#

Subsets a DataArray.

Parameters:

data (DataArray) – The xarray.DataArray to subset.
left (Optional[float]) – The left coordinate.
top (Optional[float]) – The top coordinate.
right (Optional[float]) – The right coordinate.
bottom (Optional[float]) – The bottom coordinate.
rows (Optional[int]) – The number of output rows.
cols (Optional[int]) – The number of output rows.
center (Optional[bool]) – Whether to center the subset on left and top.
mask_corners (Optional[bool]) – Whether to mask corners (*requires pymorph).

Return type:

DataArray

Returns:

xarray.DataArray

Example

>>> import geowombat as gw
>>>
>>> with gw.open('image.tif', chunks=512) as ds:
>>>     ds_sub = gw.subset(
>>>         ds,
>>>         left=-263529.884,
>>>         top=953985.314,
>>>         rows=2048,
>>>         cols=2048
>>>     )

geowombat.tasseled_cap(data, nodata=None, sensor=None, scale_factor=None)#

Applies a tasseled cap transformation

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Return type:

DataArray

Examples

>>> import geowombat as gw
>>>
>>> with gw.config.update(sensor='qb', scale_factor=0.0001):
>>>     with gw.open('image.tif', band_names=['blue', 'green', 'red', 'nir']) as ds:
>>>         tcap = gw.tasseled_cap(ds)

Return type:

DataArray

Returns:

xarray.DataArray

Parameters:

data (DataArray) –
nodata (float | int | None) –
sensor (str | None) –
scale_factor (float | None) –

References

ASTER:: See [WS05]
CBERS2:: See [SHT11]
IKONOS:: See [Per06]
Landsat ETM+:: See [HWY+02]
Landsat OLI:: See [BZST14]
MODIS:: See [LC07]
Quickbird:: See [YEK05]
RapidEye:: See [ACG+14]

geowombat.to_netcdf(data, filename, overwrite=False, compute=True, *args, **kwargs)[source]#

Writes an Xarray DataArray to a NetCDF file.

Parameters:

data (DataArray) – The xarray.DataArray to write.
filename (str) – The output file name to write to.
overwrite (Optional[bool]) – Whether to overwrite an existing file. Default is False.
compute (Optinoal[bool]) – Whether to compute and write to filename. Otherwise, return the dask task graph. Default is True.
args (DataArray) – Additional DataArrays to stack.
kwargs (dict) – Encoding arguments.

Returns:

None, writes to filename

Examples

>>> import geowombat as gw
>>> import xarray as xr
>>>
>>> # Write a single DataArray to a .nc file
>>> with gw.config.update(sensor='l7'):
>>>     with gw.open('LC08_L1TP_225078_20200219_20200225_01_T1.tif') as src:
>>>         gw.to_netcdf(src, 'filename.nc', zlib=True, complevel=5)
>>>
>>> # Add extra layers
>>> with gw.config.update(sensor='l7'):
>>>     with gw.open(
>>>         'LC08_L1TP_225078_20200219_20200225_01_T1.tif'
>>>     ) as src, gw.open(
>>>         'LC08_L1TP_225078_20200219_20200225_01_T1_angles.tif',
>>>         band_names=['zenith', 'azimuth']
>>>     ) as ang:
>>>         src = (
>>>             xr.where(
>>>                 src == 0, -32768, src
>>>             )
>>>             .astype('int16')
>>>             .assign_attrs(**src.attrs)
>>>         )
>>>
>>>         gw.to_netcdf(
>>>             src,
>>>             'filename.nc',
>>>             ang.astype('int16'),
>>>             zlib=True,
>>>             complevel=5,
>>>             _FillValue=-32768
>>>         )
>>>
>>> # Open the data and convert to a DataArray
>>> with xr.open_dataset(
>>>     'filename.nc', engine='h5netcdf', chunks=256
>>> ) as ds:
>>>     src = ds.to_array(dim='band')

geowombat.to_raster(data, filename, readxsize=None, readysize=None, separate=False, out_block_type='gtiff', keep_blocks=False, verbose=0, overwrite=False, gdal_cache=512, scheduler='mpool', n_jobs=1, n_workers=None, n_threads=None, n_chunks=None, padding=None, tags=None, tqdm_kwargs=None, **kwargs)[source]#

Writes a dask array to a raster file.

Note

We advise using save() in place of this method.

Parameters:

data (DataArray) – The xarray.DataArray to write.
filename (str) – The output file name to write to.
readxsize (Optional[int]) – The size of column chunks to read. If not given, readxsize defaults to Dask chunk size.
readysize (Optional[int]) – The size of row chunks to read. If not given, readysize defaults to Dask chunk size.
separate (Optional[bool]) – Whether to write blocks as separate files. Otherwise, write to a single file.
out_block_type (Optional[str]) – The output block type. Choices are [‘gtiff’, ‘zarr’]. Only used if separate = True.
keep_blocks (Optional[bool]) – Whether to keep the blocks stored on disk. Only used if separate = True.
verbose (Optional[int]) – The verbosity level.
overwrite (Optional[bool]) – Whether to overwrite an existing file.
gdal_cache (Optional[int]) – The GDAL cache size (in MB).
scheduler (Optional[str]) –
The parallel task scheduler to use. Choices are [‘processes’, ‘threads’, ‘mpool’].

mpool: process pool of workers using multiprocessing.Pool processes: process pool of workers using concurrent.futures threads: thread pool of workers using concurrent.futures
n_jobs (Optional[int]) – The total number of parallel jobs.
n_workers (Optional[int]) – The number of process workers.
n_threads (Optional[int]) – The number of thread workers.
n_chunks (Optional[int]) – The chunk size of windows. If not given, equal to n_workers x 50.
overviews (Optional[bool or list]) – Whether to build overview layers.
resampling (Optional[str]) – The resampling method for overviews when overviews is True or a list. Choices are [‘average’, ‘bilinear’, ‘cubic’, ‘cubic_spline’, ‘gauss’, ‘lanczos’, ‘max’, ‘med’, ‘min’, ‘mode’, ‘nearest’].
padding (Optional[tuple]) – Padding for each window. padding should be given as a tuple of (left pad, bottom pad, right pad, top pad). If padding is given, the returned list will contain a tuple of rasterio.windows.Window objects as (w1, w2), where w1 contains the normal window offsets and w2 contains the padded window offsets.
tags (Optional[dict]) – Image tags to write to file.
tqdm_kwargs (Optional[dict]) – Additional keyword arguments to pass to tqdm.
kwargs (Optional[dict]) – Additional keyword arguments to pass to rasterio.write.

Returns:

None, writes to filename

Examples

>>> import geowombat as gw
>>>
>>> # Use 8 parallel workers
>>> with gw.open('input.tif') as ds:
>>>     gw.to_raster(ds, 'output.tif', n_jobs=8)
>>>
>>> # Use 4 process workers and 2 thread workers
>>> with gw.open('input.tif') as ds:
>>>     gw.to_raster(ds, 'output.tif', n_workers=4, n_threads=2)
>>>
>>> # Control the window chunks passed to concurrent.futures
>>> with gw.open('input.tif') as ds:
>>>     gw.to_raster(ds, 'output.tif', n_workers=4, n_threads=2, n_chunks=16)
>>>
>>> # Compress the output and build overviews
>>> with gw.open('input.tif') as ds:
>>>     gw.to_raster(ds, 'output.tif', n_jobs=8, overviews=True, compress='lzw')

geowombat.to_vrt(data, filename, overwrite=False, resampling=None, nodata=None, init_dest_nodata=True, warp_mem_limit=128)[source]#

Writes a file to a VRT file.

Parameters:

data (DataArray) – The xarray.DataArray to write.
filename (str) – The output file name to write to.
overwrite (Optional[bool]) – Whether to overwrite an existing VRT file.
resampling (Optional[object]) – The resampling algorithm for rasterio.vrt.WarpedVRT. Default is ‘nearest’.
nodata (Optional[float or int]) – The ‘no data’ value for rasterio.vrt.WarpedVRT.
init_dest_nodata (Optional[bool]) – Whether or not to initialize output to nodata for rasterio.vrt.WarpedVRT.
warp_mem_limit (Optional[int]) – The GDAL memory limit for rasterio.vrt.WarpedVRT.

Returns:

None, writes to filename

Examples

>>> import geowombat as gw
>>> from rasterio.enums import Resampling
>>>
>>> # Transform a CRS and save to VRT
>>> with gw.config.update(ref_crs=102033):
>>>     with gw.open('image.tif') as src:
>>>         gw.to_vrt(
>>>             src,
>>>             'output.vrt',
>>>             resampling=Resampling.cubic,
>>>             warp_mem_limit=256
>>>         )
>>>
>>> # Load multiple files set to a common geographic extent
>>> bounds = (left, bottom, right, top)
>>> with gw.config.update(ref_bounds=bounds):
>>>     with gw.open(
>>>         ['image1.tif', 'image2.tif'], mosaic=True
>>>     ) as src:
>>>         gw.to_vrt(src, 'output.vrt')

geowombat.transform_crs(data_src, dst_crs=None, dst_res=None, dst_width=None, dst_height=None, dst_bounds=None, src_nodata=None, dst_nodata=None, coords_only=False, resampling='nearest', warp_mem_limit=512, num_threads=1)[source]#

Transforms a DataArray to a new coordinate reference system.

Parameters:

data_src (DataArray) – The data to transform.
dst_crs (Optional[CRS | int | dict | str]) – The destination CRS.
dst_res (Optional[tuple]) – The destination resolution.
dst_width (Optional[int]) – The destination width. Cannot be used with dst_res.
dst_height (Optional[int]) – The destination height. Cannot be used with dst_res.
dst_bounds (Optional[BoundingBox | tuple]) – The destination bounds, as a rasterio.coords.BoundingBox or as a tuple of (left, bottom, right, top).
src_nodata (Optional[int | float]) – The source nodata value. Pixels with this value will not be used for interpolation. If not set, it will default to the nodata value of the source image if a masked ndarray or rasterio band, if available.
dst_nodata (Optional[int | float]) – The nodata value used to initialize the destination; it will remain in all areas not covered by the reprojected source. Defaults to the nodata value of the destination image (if set), the value of src_nodata, or 0 (GDAL default).
coords_only (Optional[bool]) – Whether to return transformed coordinates. If coords_only = True then the array is not warped and the size is unchanged. It also avoids in-memory computations.
resampling (Optional[str]) – The resampling method if filename is a list. Choices are [‘average’, ‘bilinear’, ‘cubic’, ‘cubic_spline’, ‘gauss’, ‘lanczos’, ‘max’, ‘med’, ‘min’, ‘mode’, ‘nearest’].
warp_mem_limit (Optional[int]) – The warp memory limit.
num_threads (Optional[int]) – The number of parallel threads.

Returns:

xarray.DataArray

geowombat.wi(data, nodata=None, mask=False, sensor=None, scale_factor=None)#

Calculates the woody vegetation index

Parameters:

data (DataArray) – The xarray.DataArray to process.
nodata (Optional[int or float]) – A ‘no data’ value to fill NAs with. If None, the ‘no data’ value is taken from the xarray.DataArray attributes.
mask (Optional[bool]) – Whether to mask the results.
sensor (Optional[str]) – The data’s sensor. If None, the band names should reflect the index being calculated.
scale_factor (Optional[float]) – A scale factor to apply to the data. If None, the scale value is taken from the xarray.DataArray attributes.

Equation:

\[WI = \Biggl \lbrace { 0,\text{ if } { red + SWIR1 \ge 0.5 } \atop 1 - \frac{red + SWIR1}{0.5}, \text{ otherwise } }\]

Reference:: See [LWC+13]

Returns:: Data range: 0 to 1
Return type:: xarray.DataArray

geowombat.xy_to_lonlat(x, y, dst_crs)#

Converts from native map coordinates to longitude and latitude.

Parameters:

x (float) – The x coordinate to convert.
y (float) – The y coordinate to convert.
dst_crs (str, object, or DataArray) – The CRS to transform to. It can be provided as a string, a CRS instance (e.g., pyproj.crs.CRS), or a geowombat.DataArray.

Returns:

(longitude, latitude)

Return type:

tuple

Example

>>> import geowombat as gw
>>> from geowombat.core import xy_to_lonlat
>>>
>>> x, y = 643944.6956113526, 7183104.984484519
>>>
>>> with gw.open('image.tif') as src:
>>>     lon, lat = xy_to_lonlat(x, y, src)

geowombat package

Contents

geowombat package#

Subpackages#

Submodules#

geowombat.config module#

geowombat.handler module#

Module contents#