def main():
# define input directory containing file sto be stacked
dir_in = '/...'
# define output file name
dstfile = '/.../x'
# shapefile (for stack boundaries)
shp = '/../x.shp'
# store results in separate files or one single stack file? If separate then dstfile is used as a directory.
sep = True
# list files to be resampled; those not overlapping with the shapefile geometry will excluded by function stack
srcfiles = finder(dir_in, ['S1*_VV_*norm_db.tif'])
# check whether dstfile is already a file
if os.path.isfile(dstfile):
raise IOError('dstfile already exists')
# create groups of similar time stamps for mosaicking.
# All images with a time stamp of less than 30s difference will be grouped
groups = groupbyTime(srcfiles, seconds, 30)
# final function call
# groups will be mosaicked first
# the resulting images will all have the same extent
stack(srcfiles=groups, dstfile=dstfile, resampling='bilinear',
targetres=[20, 20], srcnodata=-99, dstnodata=-99,
shapefile=shp, sortfun=seconds, separate=sep, overwrite=False)
def main():
dirs = [
"stack_savi"
] #, "stack_ndvi", "stack_msavi", "stack_reip", "stack_rvi", "stack_dvi"]
resolution = [30, 30]
# shapefile (for stack boundaries)
shp = 'F:/geodata/geo402/02_features/LADYBRAND_final_enlarged_study_area.shp'
# store results in separate files or one single stack file? If separate then dstfile is used as a directory.
sep = True
for dir in dirs:
# define input directory containing files to be stacked
dir_in = 'F:/geodata/geo402/S2/xx_S2_indices/' + dir
print(dir_in)
os.makedirs(dir_in, exist_ok=True)
# define output file name
dstfile = 'F:/geodata/geo402/S2/xx_S2_indices/mosaics/' + dir
print(dstfile)
# list files to be resampled; those not overlapping with the shapefile geometry will excluded by function stack
srcfiles = finder(dir_in, ['*'])
# check whether dstfile is already a file
if os.path.isfile(dstfile):
raise IOError('dstfile already exists')
# create groups of similar time stamps for mosaicking.
# All images with a time stamp of less than 30s difference will be grouped
groups = groupbyTime(srcfiles, seconds, 30)
# final function call
# groups will be mosaicked first
# the resulting images will all have the same extent
stack(srcfiles=groups,
dstfile=dstfile,
resampling='bilinear',
targetres=resolution,
srcnodata=-9999,
dstnodata=-9999,
shapefile=shp,
sortfun=seconds,
separate=sep,
overwrite=True)
def main():
'''
both polarisations are included in the script but are stored in different folders
'''
resolution = [30, 30]
# shapefile (for stack boundaries)
shp = 'F:/geodata/geo402/##study_area/LADYBRAND_final_enlarged_study_area.shp'
# store results in separate files or one single stack file? If separate then dstfile is used as a directory.
sep = False
# define input directory containing files to be stacked
dir_in = 'F:/geodata/geo402/S1_GRD/xx_new/GRD_VH_vrts/'
print(dir_in)
# os.makedirs(dir_in, exist_ok=True)
# define output file name
dstfile = 'F:/geodata/geo402/S1_GRD/xx_new/S1A_IW_GRD_VH_stack'
print(dstfile)
# list files to be resampled; those not overlapping with the shapefile geometry will excluded by function stack
srcfiles = finder(dir_in, ['*'])
# check whether dstfile is already a file
if os.path.isfile(dstfile):
raise IOError('dstfile already exists')
# create groups of similar time stamps for mosaicking.
# All images with a time stamp of less than 30s difference will be grouped
groups = groupbyTime(srcfiles, seconds, 30)
# final function call
# groups will be mosaicked first
# the resulting images will all have the same extent
stack(srcfiles=groups,
dstfile=dstfile,
resampling='bilinear',
targetres=resolution,
srcnodata=-99,
dstnodata=-99,
shapefile=shp,
sortfun=seconds,
separate=sep,
overwrite=True,
cores=7)
def test_stack(tmpdir, testdata):
name = testdata['tif']
outname = os.path.join(str(tmpdir), 'test')
tr = (30, 30)
# no input files provided
with pytest.raises(RuntimeError):
stack(srcfiles=[],
resampling='near',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# two files, but only one layer name
with pytest.raises(RuntimeError):
stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname,
layernames=['a'])
# targetres must be a two-entry tuple/list
with pytest.raises(RuntimeError):
stack(srcfiles=[name, name],
resampling='near',
targetres=30,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# only one file specified
with pytest.raises(RuntimeError):
stack(srcfiles=[name],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# targetres must contain two values
with pytest.raises(RuntimeError):
stack(srcfiles=[name, name],
resampling='near',
targetres=(30, 30, 30),
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# unknown resampling method
with pytest.raises(RuntimeError):
stack(srcfiles=[name, name],
resampling='foobar',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# non-existing files
with pytest.raises(RuntimeError):
stack(srcfiles=['foo', 'bar'],
resampling='near',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# create a multi-band stack
stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname,
layernames=['test1', 'test2'])
with Raster(outname) as ras:
assert ras.bands == 2
# Raster.rescale currently only supports one band
with pytest.raises(ValueError):
ras.rescale(lambda x: x * 10)
# outname exists and overwrite is False
with pytest.raises(RuntimeError):
stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=False,
srcnodata=-99,
dstnodata=-99,
dstfile=outname,
layernames=['test1', 'test2'])
# pass shapefile
outname = os.path.join(str(tmpdir), 'test2')
with Raster(name).bbox() as box:
stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname,
shapefile=box,
layernames=['test1', 'test2'])
with Raster(outname) as ras:
assert ras.bands == 2
# pass shapefile and do mosaicing
outname = os.path.join(str(tmpdir), 'test3')
with Raster(name).bbox() as box:
stack(srcfiles=[[name, name]],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname,
shapefile=box)
with Raster(outname + '.tif') as ras:
assert ras.bands == 1
assert ras.format == 'GTiff'
# projection mismatch
name2 = os.path.join(str(tmpdir), os.path.basename(name))
outname = os.path.join(str(tmpdir), 'test4')
gdalwarp(name, name2, options={'dstSRS': crsConvert(4326, 'wkt')})
with pytest.raises(RuntimeError):
stack(srcfiles=[name, name2],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# no projection found
outname = os.path.join(str(tmpdir), 'test5')
gdal_translate(name, name2, {'options': ['-co', 'PROFILE=BASELINE']})
with Raster(name2) as ras:
print(ras.projection)
with pytest.raises(RuntimeError):
stack(srcfiles=[name2, name2],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
# create separate GeoTiffs
outdir = os.path.join(str(tmpdir), 'subdir')
stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=True,
layernames=['test1', 'test2'],
srcnodata=-99,
dstnodata=-99,
dstfile=outdir,
separate=True,
compress=True)
# repeat with overwrite disabled (no error raised, just a print message)
stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=False,
layernames=['test1', 'test2'],
srcnodata=-99,
dstnodata=-99,
dstfile=outdir,
separate=True,
compress=True)
# repeat without layernames but sortfun
# bandnames not unique
outdir = os.path.join(str(tmpdir), 'subdir2')
with pytest.raises(RuntimeError):
stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=True,
sortfun=os.path.basename,
srcnodata=-99,
dstnodata=-99,
dstfile=outdir,
separate=True,
compress=True)
# repeat without layernames but sortfun
name2 = os.path.join(str(tmpdir),
os.path.basename(name).replace('VV', 'XX'))
shutil.copyfile(name, name2)
outdir = os.path.join(str(tmpdir), 'subdir2')
stack(srcfiles=[name, name2],
resampling='near',
targetres=tr,
overwrite=True,
sortfun=os.path.basename,
srcnodata=-99,
dstnodata=-99,
dstfile=outdir,
separate=True,
compress=True)
# shapefile filtering
outdir = os.path.join(str(tmpdir), 'subdir3')
files = [testdata['tif'], testdata['tif2'], testdata['tif3']]
with Raster(files[0]).bbox() as box:
stack(srcfiles=files,
resampling='near',
targetres=(30, 30),
overwrite=False,
layernames=['test1', 'test2', 'test3'],
srcnodata=-99,
dstnodata=-99,
dstfile=outdir,
separate=True,
compress=True,
shapefile=box)
# repeated run with different scene selection and only one scene after spatial filtering
stack(srcfiles=files[1:],
resampling='near',
targetres=(30, 30),
overwrite=True,
layernames=['test2', 'test3'],
srcnodata=-99,
dstnodata=-99,
dstfile=outdir,
separate=True,
compress=True,
shapefile=box)
def test_stack(tmpdir, testdata):
name = testdata['tif']
outname = os.path.join(str(tmpdir), 'test')
tr = (30, 30)
with pytest.raises(IOError):
sp.stack(srcfiles=[],
resampling='near',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
with pytest.raises(IOError):
sp.stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname,
layernames=['a'])
with pytest.raises(RuntimeError):
sp.stack(srcfiles=[name, name],
resampling='near',
targetres=30,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
with pytest.raises(IOError):
sp.stack(srcfiles=[name],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
with pytest.raises(RuntimeError):
sp.stack(srcfiles=[name, name],
resampling='near',
targetres=(30, 30, 30),
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
with pytest.raises(IOError):
sp.stack(srcfiles=[name, name],
resampling='foobar',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
with pytest.raises(RuntimeError):
sp.stack(srcfiles=[name, 'foobar'],
resampling='near',
targetres=tr,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
sp.stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=True,
srcnodata=-99,
dstnodata=-99,
dstfile=outname)
outdir = os.path.join(str(tmpdir), 'subdir')
sp.stack(srcfiles=[name, name],
resampling='near',
targetres=tr,
overwrite=True,
layernames=['test1', 'test2'],
srcnodata=-99,
dstnodata=-99,
dstfile=outdir,
separate=True,
compress=True)
with sp.Raster(outname) as ras:
assert ras.bands == 2
# Raster.rescale currently only supports one band
with pytest.raises(ValueError):
ras.rescale(lambda x: x * 10)