def _add_band(self, idx, ds, bidx):
""" Add a band to VRT
Args:
idx (int): Index of band in VRT
ds (RasterReader): `rasterio` dataset
bidx (int): Band index of `ds`
"""
band = SubElement(self.root, 'VRTRasterBand')
band.set('dataType', dtypes._gdal_typename(ds.dtypes[bidx - 1]))
band.set('band', str(idx + 1))
# Color interpretation
ci = SubElement(band, 'ColorInterp')
ci.text = COLOR_INTERP[idx]
# Add NoDataValue
if ds.nodatavals:
ndv = SubElement(band, 'NoDataValue')
ndv.text = str(ds.nodatavals[bidx - 1])
# Add SimpleSource
source = SubElement(band, 'SimpleSource')
source_path = SubElement(source, 'SourceFilename')
source_path.text = os.path.abspath(ds.name)
source_props = SubElement(source, 'SourceProperties')
source_props.set('RasterXSize', str(ds.width))
source_props.set('RasterYSize', str(ds.height))
source_props.set('DataType', dtypes._gdal_typename(ds.dtypes[bidx - 1]))
source_props.set('BlockXSize', str(ds.block_shapes[bidx - 1][1]))
source_props.set('BlockYSize', str(ds.block_shapes[bidx - 1][0]))
return source
def add_band(self,
dtype,
band_idx,
color_interp,
nodata=None,
hidenodata=False):
vrtrasterband = ET.SubElement(self.vrtdataset, 'VRTRasterBand')
dtype = dtype if isinstance(dtype, str) else dtype.name
vrtrasterband.attrib['dataType'] = _gdal_typename(
dtype) if check_dtype(dtype) else dtype
vrtrasterband.attrib['band'] = str(band_idx)
if nodata is not None:
nodatavalue = ET.SubElement(vrtrasterband, 'NoDataValue')
nodatavalue.text = str(nodata)
if hidenodata:
hidenodatavalue = ET.SubElement(vrtrasterband,
'HideNoDataValue')
hidenodatavalue.text = "1" if hidenodata else "0"
colorinterp = ET.SubElement(vrtrasterband, 'ColorInterp')
colorinterp.text = color_interp.capitalize()
return vrtrasterband
def _setup_band_simplesource(self, simplesource, band_idx, dtype, relative_to_vrt, file_name,
rasterxsize, rasterysize, blockxsize, blockysize, nodata):
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "1" if relative_to_vrt else "0"
sourcefilename.text = vsi_path(parse_path(file_name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = str(band_idx)
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(rasterxsize)
sourceproperties.attrib['RasterYSize'] = str(rasterysize)
if blockxsize is not None and blockysize is not None:
sourceproperties.attrib['BlockXSize'] = str(blockxsize)
sourceproperties.attrib['BlockYSize'] = str(blockysize)
dtype = dtype if isinstance(dtype, str) else dtype.name
sourceproperties.attrib['DataType'] = _gdal_typename(dtype) if check_dtype(dtype) else dtype
def resize_array(
data: numpy.ndarray,
height: int,
width: int,
resampling_method: Resampling = "nearest",
) -> numpy.ndarray:
"""resize array to a given height and width."""
out_shape: Union[Tuple[int, int], Tuple[int, int, int]]
if len(data.shape) == 2:
count = 1
h = data.shape[0]
w = data.shape[1]
out_shape = (height, width)
else:
count = data.shape[0]
h = data.shape[1]
w = data.shape[2]
out_shape = (count, height, width)
# We are using GDAL MEM driver to create a new dataset from the numpy array
# ref: https://github.com/rasterio/rasterio/blob/master/rasterio/_io.pyx#L1946-L1955
info = {
"DATAPOINTER": data.__array_interface__["data"][0],
"PIXELS": w,
"LINES": h,
"BANDS": count,
"DATATYPE": _gdal_typename(data.dtype.name),
}
dataset_options = ",".join(f"{name}={val}" for name, val in info.items())
datasetname = f"MEM:::{dataset_options}"
with rasterio.open(datasetname, "r+") as src:
# if a 2D array is passed, using indexes=1 makes sure we return an 2D array
indexes = 1 if len(data.shape) == 2 else None
return src.read(
out_shape=out_shape,
indexes=indexes,
resampling=Resampling[resampling_method],
)
def _make_band(root, source_band, vrt_bidx, description=None, vrt_ndv=None):
# Create <VRTRasterBand>
band = ET.SubElement(root, 'VRTRasterBand')
band.set('dataType', _gdal_typename(source_band.dtype))
band.set('band', str(vrt_bidx))
# Optional subelements
# TODO: ColorTable, GDALRasterAttributeTable, UnitType,
# Offset, Scale, CategoryNames
colorinterp = gdal.GetColorInterpretationName(
source_band.colorinterp.value)
_make_subelement(band, 'ColorInterp', colorinterp)
# Output band NDV defaults to source NDV
vrt_ndv = vrt_ndv if vrt_ndv is not None else source_band.nodata
if vrt_ndv is not None:
_make_subelement(band, 'NoDataValue', str(vrt_ndv))
description = description or source_band.description
if description:
band.set('Description', description)
return band
def _make_source_props(xml_parent, source_band):
"""Creates <SourceProperties ... /> tag
Parameters
----------
xml_parent : xml.etree.Element.SubElement
Parent XML element, like a "ComplexSource" or "SimpleSource"
source_band : VRTSourceBand
The source band
Returns
-------
xml.etree.Element.SubElement
"SourceProperties" subelement
"""
ele = ET.SubElement(xml_parent, 'SourceProperties')
ele.set('RasterXSize', str(source_band.width))
ele.set('RasterYSize', str(source_band.height))
ele.set('DataType', _gdal_typename(source_band.dtype))
ele.set('BlockXSize', str(source_band.blockxsize))
ele.set('BlockYSize', str(source_band.blockysize))
return ele
def _boundless_vrt_doc(src_dataset,
nodata=None,
background=None,
hidenodata=False,
width=None,
height=None,
transform=None):
"""Make a VRT XML document.
Parameters
----------
src_dataset : Dataset
The dataset to wrap.
background : Dataset, optional
A dataset that provides the optional VRT background. NB: this dataset
must have the same number of bands as the src_dataset.
Returns
-------
bytes
An ascii-encoded string (an ElementTree detail)
"""
nodata = nodata or src_dataset.nodata
width = width or src_dataset.width
height = height or src_dataset.height
transform = transform or src_dataset.transform
vrtdataset = ET.Element('VRTDataset')
vrtdataset.attrib['rasterYSize'] = str(height)
vrtdataset.attrib['rasterXSize'] = str(width)
srs = ET.SubElement(vrtdataset, 'SRS')
srs.text = src_dataset.crs.wkt if src_dataset.crs else ""
geotransform = ET.SubElement(vrtdataset, 'GeoTransform')
geotransform.text = ','.join([str(v) for v in transform.to_gdal()])
for bidx, ci, block_shape, dtype in zip(src_dataset.indexes,
src_dataset.colorinterp,
src_dataset.block_shapes,
src_dataset.dtypes):
vrtrasterband = ET.SubElement(vrtdataset, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = _gdal_typename(dtype)
vrtrasterband.attrib['band'] = str(bidx)
if nodata is not None:
nodatavalue = ET.SubElement(vrtrasterband, 'NoDataValue')
nodatavalue.text = str(nodata)
if hidenodata:
hidenodatavalue = ET.SubElement(vrtrasterband,
'HideNoDataValue')
hidenodatavalue.text = "1"
colorinterp = ET.SubElement(vrtrasterband, 'ColorInterp')
colorinterp.text = ci.name.capitalize()
if background is not None:
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(background.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(background.width)
srcrect.attrib['ySize'] = str(background.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = '0'
dstrect.attrib['yOff'] = '0'
dstrect.attrib['xSize'] = str(width)
dstrect.attrib['ySize'] = str(height)
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str(
(src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str(
(src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width *
src_dataset.transform.a / transform.a)
dstrect.attrib['ySize'] = str(src_dataset.height *
src_dataset.transform.e / transform.e)
if src_dataset.nodata is not None:
nodata_elem = ET.SubElement(simplesource, 'NODATA')
nodata_elem.text = str(src_dataset.nodata)
if all(MaskFlags.per_dataset in flags
for flags in src_dataset.mask_flag_enums):
maskband = ET.SubElement(vrtdataset, 'MaskBand')
vrtrasterband = ET.SubElement(maskband, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = 'Byte'
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = 'mask,1'
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = 'Byte'
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str(
(src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str(
(src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width)
dstrect.attrib['ySize'] = str(src_dataset.height)
return ET.tostring(vrtdataset)
def test_gdal_name(dtype, name):
assert _gdal_typename(dtype) == name
def test_gdal_name():
assert _gdal_typename(ubyte) == 'Byte'
assert _gdal_typename(np.uint8) == 'Byte'
assert _gdal_typename(np.uint16) == 'UInt16'
def _boundless_vrt_doc(src_dataset,
nodata=None,
background=None,
hidenodata=False,
width=None,
height=None,
transform=None,
masked=False):
"""Make a VRT XML document.
Parameters
----------
src_dataset : Dataset
The dataset to wrap.
background : int or float, optional
The background fill value for the boundless VRT.
masked : bool
If True, the src_dataset is replaced by its valid data mask.
Returns
-------
str
An XML text string.
"""
nodata = nodata or src_dataset.nodata
width = width or src_dataset.width
height = height or src_dataset.height
transform = transform or src_dataset.transform
vrtdataset = ET.Element('VRTDataset')
vrtdataset.attrib['rasterYSize'] = str(height)
vrtdataset.attrib['rasterXSize'] = str(width)
srs = ET.SubElement(vrtdataset, 'SRS')
srs.text = src_dataset.crs.wkt if src_dataset.crs else ""
geotransform = ET.SubElement(vrtdataset, 'GeoTransform')
geotransform.text = ','.join([str(v) for v in transform.to_gdal()])
for bidx, ci, block_shape, dtype in zip(src_dataset.indexes,
src_dataset.colorinterp,
src_dataset.block_shapes,
src_dataset.dtypes):
vrtrasterband = ET.SubElement(vrtdataset, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = _gdal_typename(dtype)
vrtrasterband.attrib['band'] = str(bidx)
if background is not None or nodata is not None:
nodatavalue = ET.SubElement(vrtrasterband, 'NoDataValue')
nodatavalue.text = str(background or nodata)
if hidenodata:
hidenodatavalue = ET.SubElement(vrtrasterband,
'HideNoDataValue')
hidenodatavalue.text = "1"
colorinterp = ET.SubElement(vrtrasterband, 'ColorInterp')
colorinterp.text = ci.name.capitalize()
complexsource = ET.SubElement(vrtrasterband, 'ComplexSource')
sourcefilename = ET.SubElement(complexsource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.attrib["shared"] = "0"
sourcefilename.text = parse_path(src_dataset.name).as_vsi()
sourceband = ET.SubElement(complexsource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(complexsource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(complexsource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(complexsource, 'DstRect')
dstrect.attrib['xOff'] = str(
(src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str(
(src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width *
src_dataset.transform.a / transform.a)
dstrect.attrib['ySize'] = str(src_dataset.height *
src_dataset.transform.e / transform.e)
if src_dataset.nodata is not None:
nodata_elem = ET.SubElement(complexsource, 'NODATA')
nodata_elem.text = str(src_dataset.nodata)
if src_dataset.options is not None:
openoptions = ET.SubElement(complexsource, 'OpenOptions')
for ookey, oovalue in src_dataset.options.items():
ooi = ET.SubElement(openoptions, 'OOI')
ooi.attrib['key'] = str(ookey)
ooi.text = str(oovalue)
# Effectively replaces all values of the source dataset with
# 255. Due to GDAL optimizations, the source dataset will not
# be read, so we get a performance improvement.
if masked:
scaleratio = ET.SubElement(complexsource, 'ScaleRatio')
scaleratio.text = '0'
scaleoffset = ET.SubElement(complexsource, 'ScaleOffset')
scaleoffset.text = '255'
if all(MaskFlags.per_dataset in flags
for flags in src_dataset.mask_flag_enums):
maskband = ET.SubElement(vrtdataset, 'MaskBand')
vrtrasterband = ET.SubElement(maskband, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = 'Byte'
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.attrib["shared"] = "0"
sourcefilename.text = parse_path(src_dataset.name).as_vsi()
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = 'mask,1'
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = 'Byte'
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str(
(src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str(
(src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width)
dstrect.attrib['ySize'] = str(src_dataset.height)
return ET.tostring(vrtdataset).decode('ascii')
def test_gdal_name():
assert _gdal_typename(ubyte) == 'Byte'
assert _gdal_typename(np.uint8) == 'Byte'
assert _gdal_typename(np.uint16) == 'UInt16'
def _boundless_vrt_doc(src_dataset, nodata=None, width=None, height=None, transform=None):
"""Make a VRT XML document."""
nodata = nodata or src_dataset.nodata
width = width or src_dataset.width
height = height or src_dataset.height
transform = transform or src_dataset.transform
vrtdataset = ET.Element('VRTDataset')
vrtdataset.attrib['rasterYSize'] = str(height)
vrtdataset.attrib['rasterXSize'] = str(width)
srs = ET.SubElement(vrtdataset, 'SRS')
srs.text = src_dataset.crs.wkt
geotransform = ET.SubElement(vrtdataset, 'GeoTransform')
geotransform.text = ','.join([str(v) for v in transform.to_gdal()])
for bidx, ci, block_shape, dtype in zip(src_dataset.indexes, src_dataset.colorinterp, src_dataset.block_shapes, src_dataset.dtypes):
vrtrasterband = ET.SubElement(vrtdataset, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = _gdal_typename(dtype)
vrtrasterband.attrib['band'] = str(bidx)
if nodata is not None:
nodatavalue = ET.SubElement(vrtrasterband, 'NoDataValue')
nodatavalue.text = str(nodata)
colorinterp = ET.SubElement(vrtrasterband, 'ColorInterp')
colorinterp.text = ci.name.capitalize()
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str((src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str((src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width)
dstrect.attrib['ySize'] = str(src_dataset.height)
if src_dataset.nodata is not None:
nodata_elem = ET.SubElement(simplesource, 'NODATA')
nodata_elem.text = str(src_dataset.nodata)
if all(MaskFlags.per_dataset in flags for flags in src_dataset.mask_flag_enums):
maskband = ET.SubElement(vrtdataset, 'MaskBand')
vrtrasterband = ET.SubElement(maskband, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = 'Byte'
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = 'mask,1'
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = 'Byte'
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str((src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str((src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width)
dstrect.attrib['ySize'] = str(src_dataset.height)
return ET.tostring(vrtdataset)
def _boundless_vrt_doc(
src_dataset, nodata=None, background=None, hidenodata=False,
width=None, height=None, transform=None, masked=False):
"""Make a VRT XML document.
Parameters
----------
src_dataset : Dataset
The dataset to wrap.
background : int or float, optional
The background fill value for the boundless VRT.
masked : book
If True, the src_dataset is replaced by its valid data mask.
Returns
-------
str
An XML text string.
"""
nodata = nodata or src_dataset.nodata
width = width or src_dataset.width
height = height or src_dataset.height
transform = transform or src_dataset.transform
vrtdataset = ET.Element('VRTDataset')
vrtdataset.attrib['rasterYSize'] = str(height)
vrtdataset.attrib['rasterXSize'] = str(width)
srs = ET.SubElement(vrtdataset, 'SRS')
srs.text = src_dataset.crs.wkt if src_dataset.crs else ""
geotransform = ET.SubElement(vrtdataset, 'GeoTransform')
geotransform.text = ','.join([str(v) for v in transform.to_gdal()])
for bidx, ci, block_shape, dtype in zip(src_dataset.indexes, src_dataset.colorinterp, src_dataset.block_shapes, src_dataset.dtypes):
vrtrasterband = ET.SubElement(vrtdataset, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = _gdal_typename(dtype)
vrtrasterband.attrib['band'] = str(bidx)
if nodata is not None:
nodatavalue = ET.SubElement(vrtrasterband, 'NoDataValue')
nodatavalue.text = str(nodata)
if hidenodata:
hidenodatavalue = ET.SubElement(vrtrasterband, 'HideNoDataValue')
hidenodatavalue.text = "1"
colorinterp = ET.SubElement(vrtrasterband, 'ColorInterp')
colorinterp.text = ci.name.capitalize()
if background is not None:
complexsource = ET.SubElement(vrtrasterband, 'ComplexSource')
sourcefilename = ET.SubElement(complexsource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = '1'
sourcefilename.text = 'dummy.tif' # vsi_path(parse_path(background.name))
sourceband = ET.SubElement(complexsource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(complexsource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(complexsource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = '1' # str(background.width)
srcrect.attrib['ySize'] = '1' # str(background.height)
dstrect = ET.SubElement(complexsource, 'DstRect')
dstrect.attrib['xOff'] = '0'
dstrect.attrib['yOff'] = '0'
dstrect.attrib['xSize'] = '1' # str(width)
dstrect.attrib['ySize'] = '1' # str(height)
scaleratio = ET.SubElement(complexsource, 'ScaleRatio')
scaleratio.text = '0'
scaleoffset = ET.SubElement(complexsource, 'ScaleOffset')
scaleoffset.text = str(background)
complexsource = ET.SubElement(vrtrasterband, 'ComplexSource')
sourcefilename = ET.SubElement(complexsource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(complexsource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(complexsource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(complexsource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(complexsource, 'DstRect')
dstrect.attrib['xOff'] = str((src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str((src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width * src_dataset.transform.a / transform.a)
dstrect.attrib['ySize'] = str(src_dataset.height * src_dataset.transform.e / transform.e)
if src_dataset.nodata is not None:
nodata_elem = ET.SubElement(complexsource, 'NODATA')
nodata_elem.text = str(src_dataset.nodata)
# Effectively replaces all values of the source dataset with
# 255. Due to GDAL optimizations, the source dataset will not
# be read, so we get a performance improvement.
if masked:
scaleratio = ET.SubElement(complexsource, 'ScaleRatio')
scaleratio.text = '0'
scaleoffset = ET.SubElement(complexsource, 'ScaleOffset')
scaleoffset.text = '255'
if all(MaskFlags.per_dataset in flags for flags in src_dataset.mask_flag_enums):
maskband = ET.SubElement(vrtdataset, 'MaskBand')
vrtrasterband = ET.SubElement(maskband, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = 'Byte'
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = 'mask,1'
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = 'Byte'
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str((src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str((src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width)
dstrect.attrib['ySize'] = str(src_dataset.height)
return ET.tostring(vrtdataset).decode('ascii')
def stack(_input,
output,
tile_x_size,
tile_y_size,
config=None,
attrs=None,
bbox=None):
with rasterio.open(_input) as src:
profile = src.profile
trans = Affine.to_gdal(src.transform)
dt = np.dtype(src.dtypes[0]) # read first band data type
# read initial image metadata
profile['driver'] = 'TileDB'
profile['blockxsize'] = tile_x_size
profile['blockysize'] = tile_y_size
if 'tiled' in profile:
del profile['tiled']
arr = xr.open_rasterio(_input, chunks={'x': tile_x_size, 'y': tile_y_size})
if bbox is None:
w = profile['width']
h = profile['height']
bbox = (0, 0, w, h)
else:
w = bbox[2] - bbox[0]
h = bbox[3] - bbox[1]
nBlocksX = math.ceil(w / (tile_x_size * 1.0))
nBlocksY = math.ceil(h / (tile_y_size * 1.0))
# GDAL TileDB driver writes/reads blocks so bypass rasterio
dom = tiledb.Domain(
tiledb.Dim(name='BANDS', domain=(0, profile['count'] - 1), tile=1),
tiledb.Dim(name='Y',
domain=(0, (nBlocksY * tile_y_size) - 1),
tile=tile_y_size,
dtype=np.uint64),
tiledb.Dim(name='X',
domain=(0, (nBlocksX * tile_x_size) - 1),
tile=tile_x_size,
dtype=np.uint64))
cfg = tiledb.Config(config)
ctx = tiledb.Ctx(config=cfg)
schema = tiledb.ArraySchema(
domain=dom,
sparse=False,
attrs=[tiledb.Attr(name="TDB_VALUES", dtype=dt)],
ctx=ctx)
tiledb.DenseArray.create(output, schema)
with tiledb.DenseArray(output, 'w', ctx=ctx) as arr_output:
arr[:, bbox[0]:bbox[2],
bbox[1]:bbox[3]].data.to_tiledb(arr_output, storage_options=config)
# write the GDAL metadata file from the source profile
vfs = tiledb.VFS()
meta = f"{output}/{os.path.basename(output)}.tdb.aux.xml"
try:
f = vfs.open(meta, "w")
root = ET.Element('PAMDataset')
geo = ET.SubElement(root, 'GeoTransform')
geo.text = ', '.join(map(str, trans))
meta = ET.SubElement(root, 'Metadata')
meta.set('domain', 'IMAGE_STRUCTURE')
t = ET.SubElement(meta, 'MDI')
t.set('key', 'DATA_TYPE')
t.text = _gdal_typename(np.complex128)
nbits = ET.SubElement(meta, 'MDI')
nbits.set('key', 'NBITS')
nbits.text = str(dt.itemsize * 8)
xsize = ET.SubElement(meta, 'MDI')
xsize.set('key', 'X_SIZE')
xsize.text = str(w)
ysize = ET.SubElement(meta, 'MDI')
ysize.set('key', 'Y_SIZE')
ysize.text = str(h)
vfs.write(f, ET.tostring(root))
finally:
vfs.close(f)
def add_mask_band(self, dtype):
maskband = ET.SubElement(self.vrtdataset, 'MaskBand')
vrtrasterband = ET.SubElement(maskband, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = _gdal_typename(dtype) if check_dtype(dtype) else dtype
return vrtrasterband
def _boundless_vrt_doc(
src_dataset, nodata=None, background=None, hidenodata=False,
width=None, height=None, transform=None):
"""Make a VRT XML document.
Parameters
----------
src_dataset : Dataset
The dataset to wrap.
background : Dataset, optional
A dataset that provides the optional VRT background. NB: this dataset
must have the same number of bands as the src_dataset.
Returns
-------
bytes
An ascii-encoded string (an ElementTree detail)
"""
nodata = nodata or src_dataset.nodata
width = width or src_dataset.width
height = height or src_dataset.height
transform = transform or src_dataset.transform
vrtdataset = ET.Element('VRTDataset')
vrtdataset.attrib['rasterYSize'] = str(height)
vrtdataset.attrib['rasterXSize'] = str(width)
srs = ET.SubElement(vrtdataset, 'SRS')
srs.text = src_dataset.crs.wkt if src_dataset.crs else ""
geotransform = ET.SubElement(vrtdataset, 'GeoTransform')
geotransform.text = ','.join([str(v) for v in transform.to_gdal()])
for bidx, ci, block_shape, dtype in zip(src_dataset.indexes, src_dataset.colorinterp, src_dataset.block_shapes, src_dataset.dtypes):
vrtrasterband = ET.SubElement(vrtdataset, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = _gdal_typename(dtype)
vrtrasterband.attrib['band'] = str(bidx)
if nodata is not None:
nodatavalue = ET.SubElement(vrtrasterband, 'NoDataValue')
nodatavalue.text = str(nodata)
if hidenodata:
hidenodatavalue = ET.SubElement(vrtrasterband, 'HideNoDataValue')
hidenodatavalue.text = "1"
colorinterp = ET.SubElement(vrtrasterband, 'ColorInterp')
colorinterp.text = ci.name.capitalize()
if background is not None:
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(background.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(background.width)
srcrect.attrib['ySize'] = str(background.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = '0'
dstrect.attrib['yOff'] = '0'
dstrect.attrib['xSize'] = str(width)
dstrect.attrib['ySize'] = str(height)
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = str(bidx)
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = _gdal_typename(dtype)
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str((src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str((src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width * src_dataset.transform.a / transform.a)
dstrect.attrib['ySize'] = str(src_dataset.height * src_dataset.transform.e / transform.e)
if src_dataset.nodata is not None:
nodata_elem = ET.SubElement(simplesource, 'NODATA')
nodata_elem.text = str(src_dataset.nodata)
if all(MaskFlags.per_dataset in flags for flags in src_dataset.mask_flag_enums):
maskband = ET.SubElement(vrtdataset, 'MaskBand')
vrtrasterband = ET.SubElement(maskband, 'VRTRasterBand')
vrtrasterband.attrib['dataType'] = 'Byte'
simplesource = ET.SubElement(vrtrasterband, 'SimpleSource')
sourcefilename = ET.SubElement(simplesource, 'SourceFilename')
sourcefilename.attrib['relativeToVRT'] = "0"
sourcefilename.text = vsi_path(parse_path(src_dataset.name))
sourceband = ET.SubElement(simplesource, 'SourceBand')
sourceband.text = 'mask,1'
sourceproperties = ET.SubElement(simplesource, 'SourceProperties')
sourceproperties.attrib['RasterXSize'] = str(width)
sourceproperties.attrib['RasterYSize'] = str(height)
sourceproperties.attrib['dataType'] = 'Byte'
sourceproperties.attrib['BlockYSize'] = str(block_shape[0])
sourceproperties.attrib['BlockXSize'] = str(block_shape[1])
srcrect = ET.SubElement(simplesource, 'SrcRect')
srcrect.attrib['xOff'] = '0'
srcrect.attrib['yOff'] = '0'
srcrect.attrib['xSize'] = str(src_dataset.width)
srcrect.attrib['ySize'] = str(src_dataset.height)
dstrect = ET.SubElement(simplesource, 'DstRect')
dstrect.attrib['xOff'] = str((src_dataset.transform.xoff - transform.xoff) / transform.a)
dstrect.attrib['yOff'] = str((src_dataset.transform.yoff - transform.yoff) / transform.e)
dstrect.attrib['xSize'] = str(src_dataset.width)
dstrect.attrib['ySize'] = str(src_dataset.height)
return ET.tostring(vrtdataset)
def close(self):
from lxml.builder import ElementMaker
logger.debug("%s new entries in %s", self.new_entries, self)
if not self._new:
logger.debug("no entries to write")
return
# combine existing and new entries
all_entries = {**self._existing, **self._new}
logger.debug("writing a total of %s entries", len(all_entries))
# get VRT attributes
vrt_affine, vrt_shape = raster.tiles_to_affine_shape(
list(all_entries.keys()))
vrt_dtype = _gdal_typename(self._output.profile()["dtype"])
vrt_nodata = self._output.output_params["nodata"]
# build XML
E = ElementMaker()
vrt = E.VRTDataset(
E.SRS(self._tp.crs.wkt),
E.GeoTransform(", ".join(map(str, vrt_affine.to_gdal()))),
*[
E.VRTRasterBand(
E.NoDataValue(str(vrt_nodata)),
E.ColorInterp("Gray"),
*[
E.ComplexSource(
E.SourceFilename(
_tile_path(orig_path=path, for_gdal=True)
if path_is_remote(path) else relative_path(
path=path,
base_dir=os.path.split(self.path)[0]),
relativeToVRT="0"
if path_is_remote(path) else "1"),
E.SourceBand(str(b_idx)),
E.SourceProperties(
RasterXSize=str(tile.shape.width),
RasterYSize=str(tile.shape.height),
DataType=vrt_dtype,
BlockXSize=str(self._output.profile().get(
"blockxsize", self._tp.tile_size)),
BlockYSize=str(self._output.profile().get(
"blockysize", self._tp.tile_size)),
),
E.SrcRect(
xOff="0",
yOff="0",
xSize=str(tile.shape.width),
ySize=str(tile.shape.height),
),
E.DstRect(
xOff=str(
list(
raster.bounds_to_ranges(
out_bounds=tile.bounds,
in_affine=vrt_affine,
in_shape=vrt_shape))[2]),
yOff=str(
list(
raster.bounds_to_ranges(
out_bounds=tile.bounds,
in_affine=vrt_affine,
in_shape=vrt_shape))[0]),
xSize=str(tile.shape.width),
ySize=str(tile.shape.height),
), E.NODATA(str(vrt_nodata)))
for tile, path in sorted(all_entries.items(),
key=operator.itemgetter(1))
],
dataType=vrt_dtype,
band=str(b_idx))
for b_idx in range(1,
self._output.profile()["count"] + 1)
],
rasterXSize=str(vrt_shape.width),
rasterYSize=str(vrt_shape.height),
)
# generate pretty XML and write
xmlstr = minidom.parseString(ET.tostring(vrt)).toprettyxml(indent=" ")
if self._bucket:
key = "/".join(self.path.split("/")[3:])
logger.debug("upload %s", key)
self.bucket_resource.put_object(Key=key, Body=xmlstr)
else:
logger.debug("write to %s", self.path)
with open(self.path, "w") as dst:
dst.write(xmlstr)
