def coherence_masking(input_gdal_dataset: Dataset, coherence_file_path: str,
coherence_thresh: float) -> None:
"""
Perform coherence masking on raster in-place.
Based on gdal_calc formula provided by Nahidul:
gdal_calc.py -A 20151127-20151209_VV_8rlks_flat_eqa.cc.tif
-B 20151127-20151209_VV_8rlks_eqa.unw.tif
--outfile=test_v1.tif --calc="B*(A>=0.8)-999*(A<0.8)"
--NoDataValue=-999
"""
coherence_ds = gdal.Open(coherence_file_path, gdalconst.GA_ReadOnly)
coherence_band = coherence_ds.GetRasterBand(1)
src_band = input_gdal_dataset.GetRasterBand(1)
ndv = np.nan
coherence = coherence_band.ReadAsArray()
src = src_band.ReadAsArray()
var = {"coh": coherence, "src": src, "t": coherence_thresh, "ndv": ndv}
formula = "where(coh>=t, src, ndv)"
res = ne.evaluate(formula, local_dict=var)
src_band.WriteArray(res)
# update metadata
input_gdal_dataset.GetRasterBand(1).SetNoDataValue(ndv)
input_gdal_dataset.FlushCache() # write on the disc
log.info(f"Applied coherence masking using coh file {coherence_file_path}")
def prepare_geotif_data(geotiff_handle: gdal.Dataset,
rows: int,
cols: int,
amp=False,
cleanup=False) -> np.ndarray:
"""Load in and clean the GeoTIFF for calculating the color thresholds
Args:
geotiff_handle: gdal Dataset for the GeoTIFF to prepare
rows: number of data rows to read in
cols: number of data columns to read in
amp: input TIF is in amplitude and not power
cleanup: Cleanup artifacts using a -48 db power threshold
Returns:
data: A numpy array containing the prepared GeoTIFF data
"""
data = np.nan_to_num(
geotiff_handle.GetRasterBand(1).ReadAsArray()[:rows, :cols])
threshold = cleanup_threshold(amp, cleanup)
data[data < threshold] = 0.0
if amp: # to power
data *= data
return data
def test_initial_pixel_values_all_zero_in_band(gdal_dataset: gdal.Dataset, band_index: int):
band_number = band_index + 1
band_pixels = gdal_dataset.GetRasterBand(band_number).ReadAsArray()
assert np.array_equal(band_pixels, np.array([[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]]))
def _pixel_sz_trans(ds: gdal.Dataset, ps: float) -> gdal.Dataset:
""" Resize the image by pixel size. """
ds_trans = ds.GetGeoTransform()
factor = ds_trans[1] / ps
if list(ds_trans)[:2] == [0.0, 1.0] or round(factor, 2) == 1:
return ds
ds_proj = ds.GetProjection()
ds_dtype = ds.GetRasterBand(1).DataType
width, height = ds.RasterXSize, ds.RasterYSize
ts_trans = list(ds_trans)
ts_trans[1] = ps
ts_trans[5] = -ps
mem_drv = gdal.GetDriverByName('MEM')
dst_ds = mem_drv.Create('', int(width * factor), int(height * factor),
ds.RasterCount, ds_dtype)
dst_ds.SetProjection(ds_proj)
dst_ds.SetGeoTransform(ts_trans)
gdal.ReprojectImage(ds, dst_ds, ds_proj, ds_proj,
gdalconst.GRA_CubicSpline)
return dst_ds
def set_nodata(ds: gdal.Dataset, nodata: int):
'''Sets and fills NoDataValue in RasterBand(s)'''
logging.info('setting nodata values in raster across all bands')
for idx in range(0, ds.RasterCount):
idx += 1
band = ds.GetRasterBand(idx)
band.Fill(nodata)
band.SetNoDataValue(nodata)
def save_array(raster: gdal.Dataset, result: List[int], offset: int = 0):
'''
Store the array into a raster file
Parameters:
raster: raster file to save data into
result: array of pixels to store
offset: location to begin storing array
'''
logging.info(f'saving raster results')
band = raster.GetRasterBand(1)
band.WriteArray(result, 0, offset)
band = None
def __calculate(self, ds: gdal.Dataset, out: gdal.Dataset):
'''Calculates resulting raster'''
# chunk rasters for memory efficiency
chunk = math.floor(self.yres / self.const['chunk'])
for o in range(0, self.yres, chunk):
arr = []
for idx in range(ds.RasterCount):
idx += 1
band = ds.GetRasterBand(idx)
arr.append(read_band(band, False, o, chunk))
# calculate chunk
result = self.calc(self.const, arr, self.region,
self.chart == 'cpmed')
result = set_mask(self.const, result, arr, self.need_dummy)
save_array(out, result, o)
result = None
def __init__(self,
raster: gdal.Dataset,
width: float,
distance: float,
inverse: bool = False,
modify: bool = False,
average: int = None):
self.raster = raster
self.width = width
self.average = average
self.inverse = inverse
self.modify = modify
self.distance = distance
self.no_data_value = raster.GetRasterBand(1).GetNoDataValue()
if modify and not distance:
logger.warning('Warning: modify option used with zero distance.')
def write(ds: gdal.Dataset,
data: np.ndarray,
col_off: int = 0,
row_off: int = 0,
band: int = 1) -> int:
"""
Write a chip of data to the given data set and band.
Args:
ds: gdal data set to write to
data: data to write
col_off: column offset to start writing data
row_off: row offset to start writing data
band: which band if it is a tiff-stack
Returns:
0 if successfull
"""
return ds.GetRasterBand(band).WriteArray(data, col_off, row_off)
def set_median_ct_colours(const: dict, ds: gdal.Dataset):
'''Set the Median Concentration colours'''
band = ds.GetRasterBand(1)
# set colors
logging.info('setting median ct colors')
colors = gdal.ColorTable()
colors.SetColorEntry(const['water'], (150, 200, 255))
colors.CreateColorRamp(1, (140, 255, 160), 3, (140, 255, 160))
colors.CreateColorRamp(4, (255, 255, 0), 6, (255, 255, 0))
colors.CreateColorRamp(7, (255, 125, 7), 8, (255, 125, 7))
colors.CreateColorRamp(9, (255, 0, 0), 10, (255, 0, 0))
colors.SetColorEntry(11, (150, 150, 150))
colors.SetColorEntry(const['land'], (211, 181, 141))
colors.SetColorEntry(const['nodata'], (255, 255, 255))
band.SetRasterColorTable(colors)
band.SetRasterColorInterpretation(gdal.GCI_PaletteIndex)
ds = None
def set_frequency_colours(const: dict, ds: gdal.Dataset):
'''Set the Frequency colours'''
band = ds.GetRasterBand(1)
# set colors
logging.info('setting frequency colors')
colors = gdal.ColorTable()
colors.SetColorEntry(const['water'], (150, 200, 255))
colors.CreateColorRamp(1, (255, 242, 0), 15, (255, 242, 0))
colors.CreateColorRamp(16, (255, 200, 0), 33, (255, 200, 0))
colors.CreateColorRamp(34, (255, 125, 3), 50, (255, 125, 3))
colors.CreateColorRamp(51, (255, 0, 112), 66, (255, 0, 112))
colors.CreateColorRamp(67, (204, 0, 184), 84, (204, 0, 184))
colors.CreateColorRamp(85, (0, 0, 255), 99, (0, 0, 255))
colors.SetColorEntry(100, (75, 75, 75))
colors.SetColorEntry(const['land'], (211, 181, 141))
colors.SetColorEntry(const['nodata'], (255, 255, 255))
band.SetRasterColorTable(colors)
band.SetRasterColorInterpretation(gdal.GCI_PaletteIndex)
ds = None
def set_median_predom_colours(const: dict, ds: gdal.Dataset):
'''Set the Median Predominance colours'''
band = ds.GetRasterBand(1)
# set colors
logging.info('setting median predominance colors')
colors = gdal.ColorTable()
colors.SetColorEntry(const['water'], (150, 200, 255))
colors.SetColorEntry(1, (240, 210, 250))
colors.SetColorEntry(4, (135, 60, 215))
colors.SetColorEntry(5, (220, 80, 215))
colors.SetColorEntry(6, (255, 255, 0))
colors.SetColorEntry(7, (155, 210, 0))
colors.SetColorEntry(10, (0, 200, 20))
colors.SetColorEntry(11, (0, 120, 0))
colors.SetColorEntry(12, (180, 100, 50))
colors.SetColorEntry(const['land'], (211, 181, 141))
colors.SetColorEntry(const['nodata'], (255, 255, 255))
band.SetRasterColorTable(colors)
band.SetRasterColorInterpretation(gdal.GCI_PaletteIndex)
ds = None
def _create_blank_raster(
in_data_set: gdal.Dataset,
out_raster_path: Path,
nr_bands: int = 1,
no_data: float = np.nan,
e_type: int = 6,
):
"""Takes input data set and creates new raster. It copies input data set size, projection and geo info."""
gtiff_driver = gdal.GetDriverByName("GTiff")
band = in_data_set.GetRasterBand(1)
x_size = band.XSize # number of columns
y_size = band.YSize # number of rows
out_ds = gtiff_driver.Create(out_raster_path.as_posix(),
xsize=x_size,
ysize=y_size,
bands=nr_bands,
eType=e_type,
options=["BIGTIFF=IF_NEEDED"])
out_ds.SetProjection(in_data_set.GetProjection())
out_ds.SetGeoTransform(in_data_set.GetGeoTransform())
out_ds.GetRasterBand(1).SetNoDataValue(no_data)
out_ds.FlushCache()
out_ds = None
def gdal_to_json(ds: gdal.Dataset):
gt = ds.GetGeoTransform(can_return_null=True)
xsize = ds.RasterXSize
ysize = ds.RasterYSize
srs = get_srs(ds)
srs = srs.ExportToProj4()
minx = gt[0] + gt[1] * 0 + gt[2] * 0
miny = gt[3] + gt[4] * 0 + gt[5] * 0
maxx = gt[0] + gt[1] * xsize + gt[2] * ysize
maxy = gt[3] + gt[4] * xsize + gt[5] * ysize
bbox = miny, minx, maxy, maxx
band_list = range(1, ds.RasterCount + 1)
data = [
ds.ReadAsArray(band_list=[bnd]).ravel().tolist() for bnd in band_list
]
ndv = [ds.GetRasterBand(i).GetNoDataValue() for i in band_list]
result = dict(bbox=bbox,
gt=gt,
srs=srs,
size=(xsize, ysize),
data=data,
ndv=ndv)
return result
def get_raster_bands(ds: gdal.Dataset) -> Iterator[gdal.Band]:
return (ds.GetRasterBand(i + 1) for i in range(ds.RasterCount))
def read_band(dataset: gdal.Dataset,
bnd_ndx: int = 1) -> Tuple[dict, 'np.array']:
"""
Read data and metadata of a rasters band based on GDAL.
:param dataset: the source raster dataset
:type dataset: gdal.Dataset
:param bnd_ndx: the index of the band (starts from 1)
:type bnd_ndx: int
:return: the band parameters and the data values
:rtype: dict of data parameters and values as a numpy.array
:raises: RasterIOException
Examples:
"""
band = dataset.GetRasterBand(bnd_ndx)
data_type = gdal.GetDataTypeName(band.DataType)
unit_type = band.GetUnitType()
stats = band.GetStatistics(False, False)
if stats is None:
dStats = dict(min=None, max=None, mean=None, std_dev=None)
else:
dStats = dict(min=stats[0],
max=stats[1],
mean=stats[2],
std_dev=stats[3])
noDataVal = band.GetNoDataValue()
nOverviews = band.GetOverviewCount()
colorTable = band.GetRasterColorTable()
if colorTable:
nColTableEntries = colorTable.GetCount()
else:
nColTableEntries = 0
# read data from band
grid_values = band.ReadAsArray()
if grid_values is None:
raise RasterIOException("Unable to read data from rasters")
# transform data into numpy array
data = np.asarray(grid_values)
# if nodatavalue exists, set null values to NaN in numpy array
if noDataVal is not None and np.isfinite(noDataVal):
data = np.where(abs(data - noDataVal) > 1e-10, data, np.NaN)
band_params = dict(dataType=data_type,
unitType=unit_type,
stats=dStats,
noData=noDataVal,
numOverviews=nOverviews,
numColorTableEntries=nColTableEntries)
return band_params, data
