def write(datasetDict, out_file, metadata=None, ref_file=None, compression=None):
""" Write one file.
Parameters: datasetDict : dict of dataset, with key = datasetName and value = 2D/3D array, e.g.:
{'height' : np.ones(( 200,300), dtype=np.int16),
'incidenceAngle': np.ones(( 200,300), dtype=np.float32),
'bperp' : np.ones((80,200,300), dtype=np.float32),
...}
out_file : str, output file name
metadata : dict of attributes
ref_file : str, reference file to get auxliary info
compression : str, compression while writing to HDF5 file, None, "lzf", "gzip"
Returns: out_file : str
Examples: dsDict = dict()
dsDict['velocity'] = np.ones((200,300), dtype=np.float32)
write(datasetDict=dsDict, out_file='velocity.h5', metadata=atr)
"""
# copy metadata to meta
if metadata:
meta = {key: value for key, value in metadata.items()}
elif ref_file:
meta = readfile.read_attribute(ref_file)
else:
raise ValueError('No metadata or reference file input.')
# convert ndarray input into dict type
if isinstance(datasetDict, np.ndarray):
data = np.array(datasetDict, datasetDict.dtype)
datasetDict = dict()
datasetDict[meta['FILE_TYPE']] = data
ext = os.path.splitext(out_file)[1].lower()
# HDF5 File
if ext in ['.h5', '.he5']:
if compression is None and ref_file:
compression = readfile.get_hdf5_compression(ref_file)
k = meta['FILE_TYPE']
if k == 'timeseries':
if ref_file is None:
raise Exception('Can not write {} file without reference file!'.format(k))
obj = timeseries(out_file)
obj.write2hdf5(datasetDict[k],
metadata=meta,
refFile=ref_file,
compression=compression)
else:
if os.path.isfile(out_file):
print('delete exsited file: {}'.format(out_file))
os.remove(out_file)
print('create HDF5 file: {} with w mode'.format(out_file))
with h5py.File(out_file, 'w') as f:
# 1. Write input datasets
maxDigit = max([len(i) for i in list(datasetDict.keys())])
for dsName in datasetDict.keys():
data = datasetDict[dsName]
print(('create dataset /{d:<{w}} of {t:<10} in size of {s:<20} '
'with compression={c}').format(d=dsName,
w=maxDigit,
t=str(data.dtype),
s=str(data.shape),
c=compression))
ds = f.create_dataset(dsName,
data=data,
chunks=True,
compression=compression)
# 2. Write extra/auxliary datasets from ref_file
if ref_file and os.path.splitext(ref_file)[1] in ['.h5', '.he5']:
atr_ref = readfile.read_attribute(ref_file)
shape_ref = (int(atr_ref['LENGTH']), int(atr_ref['WIDTH']))
with h5py.File(ref_file, 'r') as fr:
dsNames = [i for i in fr.keys()
if (i not in list(datasetDict.keys())
and isinstance(fr[i], h5py.Dataset)
and fr[i].shape[-2:] != shape_ref)]
maxDigit = max([len(i) for i in dsNames]+[maxDigit])
for dsName in dsNames:
ds = fr[dsName]
print(('create dataset /{d:<{w}} of {t:<10} in size of {s:<10} '
'with compression={c}').format(d=dsName,
w=maxDigit,
t=str(ds.dtype),
s=str(ds.shape),
c=compression))
f.create_dataset(dsName,
data=ds[:],
chunks=True,
compression=compression)
# 3. metadata
for key, value in meta.items():
f.attrs[key] = str(value)
print('finished writing to {}'.format(out_file))
# ISCE / ROI_PAC GAMMA / Image product
else:
key_list = list(datasetDict.keys())
data_list = []
for key in key_list:
data_list.append(datasetDict[key])
# Write Data File
print('write {}'.format(out_file))
if ext in ['.unw', '.cor', '.hgt']:
write_float32(data_list[0], out_file)
meta['DATA_TYPE'] = 'float32'
elif ext == '.dem':
write_real_int16(data_list[0], out_file)
meta['DATA_TYPE'] = 'int16'
elif ext in ['.trans']:
write_float32(data_list[0], data_list[1], out_file)
elif ext in ['.utm_to_rdc', '.UTM_TO_RDC']:
data = np.zeros(rg.shape, dtype=np.complex64)
data.real = datasetDict['rangeCoord']
data.imag = datasetDict['azimuthCoord']
data.astype('>c8').tofile(out_file)
elif ext in ['.mli', '.flt']:
write_real_float32(data_list[0], out_file)
elif ext == '.slc':
write_complex_int16(data_list[0], out_file)
elif ext == '.int':
write_complex64(data_list[0], out_file)
elif meta['DATA_TYPE'].lower() in ['float32', 'float']:
write_real_float32(data_list[0], out_file)
elif meta['DATA_TYPE'].lower() in ['int16', 'short']:
write_real_int16(data_list[0], out_file)
elif meta['DATA_TYPE'].lower() in ['byte','bool']:
write_byte(data_list[0], out_file)
else:
print('Un-supported file type: '+ext)
return 0
# write metadata file
write_roipac_rsc(meta, out_file+'.rsc', print_msg=True)
return out_file
def write(datasetDict, out_file, metadata=None, ref_file=None, compression=None, ds_unit_dict=None, print_msg=True):
""" Write one file.
Parameters: datasetDict - dict of dataset, with key = datasetName and value = 2D/3D array, e.g.:
{'height' : np.ones(( 200,300), dtype=np.int16),
'incidenceAngle': np.ones(( 200,300), dtype=np.float32),
'bperp' : np.ones((80,200,300), dtype=np.float32),
...}
out_file - str, output file name
metadata - dict of attributes
ref_file - str, reference file to get auxliary info
compression - str, compression while writing to HDF5 file, None, "lzf", "gzip"
ds_unit_dict - dict, dataset unit definition
{dname : dunit,
dname : dunit,
...
}
Returns: out_file - strs
Examples: dsDict = dict()
dsDict['velocity'] = np.ones((200,300), dtype=np.float32)
write(datasetDict=dsDict, out_file='velocity.h5', metadata=atr)
"""
vprint = print if print_msg else lambda *args, **kwargs: None
# copy metadata to meta
if metadata:
meta = {key: value for key, value in metadata.items()}
elif ref_file:
meta = readfile.read_attribute(ref_file)
else:
raise ValueError('No metadata or reference file input.')
# convert ndarray input into dict type
if isinstance(datasetDict, np.ndarray):
data = np.array(datasetDict, datasetDict.dtype)
datasetDict = dict()
datasetDict[meta['FILE_TYPE']] = data
# file extension
fbase, fext = os.path.splitext(out_file)
# ignore certain meaningless file extensions
while fext in ['.geo', '.rdr', '.full', '.wgs84']:
fbase, fext = os.path.splitext(fbase)
if not fext:
fext = fbase
fext = fext.lower()
# output file info
out_dir = os.path.dirname(os.path.abspath(out_file))
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
vprint('create directory: {}'.format(out_dir))
# HDF5 File
if fext in ['.h5', '.he5']:
# grab info from reference h5 file
if ref_file and os.path.splitext(ref_file)[1] in ['.h5', '.he5']:
# compression
if compression is None:
compression = readfile.get_hdf5_compression(ref_file)
# list of auxiliary datasets
shape2d = (int(meta['LENGTH']), int(meta['WIDTH']))
with h5py.File(ref_file, 'r') as fr:
auxDsNames = [i for i in fr.keys()
if (i not in list(datasetDict.keys())
and isinstance(fr[i], h5py.Dataset)
and fr[i].shape[-2:] != shape2d)]
else:
auxDsNames = []
# check required datasets
dsNames = list(datasetDict.keys()) + auxDsNames
if meta['FILE_TYPE'] in ['timeseries', 'ifgramStack']:
if 'date' not in dsNames:
raise Exception("Can not write {} file without 'date' dataset!".format(meta['FILE_TYPE']))
# remove existing file
if os.path.isfile(out_file):
os.remove(out_file)
vprint('delete exsited file: {}'.format(out_file))
# writing
print('create HDF5 file: {} with w mode'.format(out_file))
maxDigit = max([len(i) for i in dsNames])
with h5py.File(out_file, 'w') as f:
# 1. write input datasets
for dsName in datasetDict.keys():
data = datasetDict[dsName]
vprint(('create dataset /{d:<{w}} of {t:<10} in size of {s:<20} '
'with compression={c}').format(d=dsName,
w=maxDigit,
t=str(data.dtype),
s=str(data.shape),
c=compression))
ds = f.create_dataset(dsName,
data=data,
chunks=True,
compression=compression)
# 2. Write extra/auxliary datasets from ref_file
if len(auxDsNames) > 0:
with h5py.File(ref_file, 'r') as fr:
for dsName in auxDsNames:
ds = fr[dsName]
vprint(('create dataset /{d:<{w}} of {t:<10} in size of {s:<10} '
'with compression={c}').format(d=dsName,
w=maxDigit,
t=str(ds.dtype),
s=str(ds.shape),
c=compression))
f.create_dataset(dsName,
data=ds[:],
chunks=True,
compression=compression)
# 3. metadata
for key, value in meta.items():
try:
f.attrs[key] = str(value)
except:
f.attrs[key] = str(value.encode('utf-8'))
# write attributes in dataset level
if ds_unit_dict is not None:
for key, value in ds_unit_dict.items():
if value is not None:
f[key].attrs['UNIT'] = value
vprint(f'add /{key:<{maxDigit}} attribute: UNIT = {value}')
vprint('finished writing to {}'.format(out_file))
# ISCE / ROI_PAC GAMMA / Image product
else:
# basic info
key_list = list(datasetDict.keys())
data_list = list(datasetDict.values())
meta['BANDS'] = len(key_list)
meta['INTERLEAVE'] = meta.get('INTERLEAVE', 'BIL').upper()
# data type
meta['DATA_TYPE'] = meta.get('DATA_TYPE', 'float32').lower()
DATA_TYPE_DICT = {'float' : 'float32',
'short' : 'int16',
'byte' : 'int8'}
if meta['DATA_TYPE'] in DATA_TYPE_DICT.keys():
meta['DATA_TYPE'] = DATA_TYPE_DICT[meta['DATA_TYPE']]
# adjust for pre-defined files determined by fext
if fext in ['.unw']:
meta['DATA_TYPE'] = 'float32'
meta['INTERLEAVE'] = 'BIL'
if key_list != ['magnitude', 'phase']:
data_list = [data_list[0], data_list[0]]
elif fext in ['.cor', '.hgt']:
meta['DATA_TYPE'] = 'float32'
meta['INTERLEAVE'] = 'BIL'
if meta.get('PROCESSOR', 'isce') == 'roipac':
data_list = [data_list[0], data_list[0]]
elif fext == '.dem':
meta['DATA_TYPE'] = 'int16'
elif fext in ['.trans']:
# ROI_PAC lookup table
meta['DATA_TYPE'] = 'float32'
meta['INTERLEAVE'] = 'BIL'
elif fext in ['.utm_to_rdc']:
# Gamma lookup table
meta['BANDS'] = 2
meta['DATA_TYPE'] = 'float32'
meta['INTERLEAVE'] = 'BIP'
elif fext in ['.mli', '.flt']:
meta['DATA_TYPE'] = 'float32'
elif fext == '.slc':
# SLC: complex 64 or 32
meta['BANDS'] = 1
elif fext == '.int':
# wrapped interferogram: complex 64
meta['BANDS'] = 1
meta['DATA_TYPE'] = 'complex64'
if key_list == ['magnitude', 'phase']:
data_list[0] = data_list[0] * np.exp(1j * data_list[1])
elif fext == '.msk':
meta['DATA_TYPE'] = 'int8'
data_types = ['bool', 'int8', 'int16', 'float32', 'float64', 'complex32', 'complex64', 'complex128']
if meta['DATA_TYPE'] not in data_types:
msg = 'Un-supported file type "{}" with data type "{}"!'.format(fext, meta['DATA_TYPE'])
msg += '\nSupported data type list: {}'.format(data_types)
raise ValueError(msg)
# write binary file
write_binary(data_list, out_file, data_type=meta['DATA_TYPE'], interleave=meta['INTERLEAVE'])
vprint('write file: {}'.format(out_file))
# write metadata file
write_roipac_rsc(meta, out_file+'.rsc', print_msg=print_msg)
return out_file
def write(datasetDict,
out_file,
metadata=None,
ref_file=None,
compression=None):
""" Write one file.
Parameters: datasetDict : dict of dataset, with key = datasetName and value = 2D/3D array, e.g.:
{'height' : np.ones(( 200,300), dtype=np.int16),
'incidenceAngle': np.ones(( 200,300), dtype=np.float32),
'bperp' : np.ones((80,200,300), dtype=np.float32),
...}
out_file : str, output file name
metadata : dict of attributes
ref_file : str, reference file to get auxliary info
compression : str, compression while writing to HDF5 file, None, "lzf", "gzip"
Returns: out_file : str
Examples: dsDict = dict()
dsDict['velocity'] = np.ones((200,300), dtype=np.float32)
write(datasetDict=dsDict, out_file='velocity.h5', metadata=atr)
"""
# copy metadata to meta
if metadata:
meta = {key: value for key, value in metadata.items()}
elif ref_file:
meta = readfile.read_attribute(ref_file)
else:
raise ValueError('No metadata or reference file input.')
# convert ndarray input into dict type
if isinstance(datasetDict, np.ndarray):
data = np.array(datasetDict, datasetDict.dtype)
datasetDict = dict()
datasetDict[meta['FILE_TYPE']] = data
ext = os.path.splitext(out_file)[1].lower()
# HDF5 File
if ext in ['.h5', '.he5']:
# grab info from reference h5 file
if ref_file and os.path.splitext(ref_file)[1] in ['.h5', '.he5']:
# compression
if compression is None:
compression = readfile.get_hdf5_compression(ref_file)
# list of auxiliary datasets
shape2d = (int(meta['LENGTH']), int(meta['WIDTH']))
with h5py.File(ref_file, 'r') as fr:
auxDsNames = [
i for i in fr.keys()
if (i not in list(datasetDict.keys()) and isinstance(
fr[i], h5py.Dataset) and fr[i].shape[-2:] != shape2d)
]
else:
auxDsNames = []
# check required datasets
dsNames = list(datasetDict.keys()) + auxDsNames
if meta['FILE_TYPE'] in ['timeseries', 'ifgramStack']:
if 'date' not in dsNames:
raise Exception(
"Can not write {} file without 'date' dataset!".format(
meta['FILE_TYPE']))
# remove existing file
if os.path.isfile(out_file):
print('delete exsited file: {}'.format(out_file))
os.remove(out_file)
# writing
print('create HDF5 file: {} with w mode'.format(out_file))
maxDigit = max([len(i) for i in dsNames])
with h5py.File(out_file, 'w') as f:
# 1. write input datasets
for dsName in datasetDict.keys():
data = datasetDict[dsName]
print(
('create dataset /{d:<{w}} of {t:<10} in size of {s:<20} '
'with compression={c}').format(d=dsName,
w=maxDigit,
t=str(data.dtype),
s=str(data.shape),
c=compression))
ds = f.create_dataset(dsName,
data=data,
chunks=True,
compression=compression)
# 2. Write extra/auxliary datasets from ref_file
if len(auxDsNames) > 0:
with h5py.File(ref_file, 'r') as fr:
for dsName in auxDsNames:
ds = fr[dsName]
print((
'create dataset /{d:<{w}} of {t:<10} in size of {s:<10} '
'with compression={c}').format(d=dsName,
w=maxDigit,
t=str(ds.dtype),
s=str(ds.shape),
c=compression))
f.create_dataset(dsName,
data=ds[:],
chunks=True,
compression=compression)
# 3. metadata
for key, value in meta.items():
try:
f.attrs[key] = str(value)
except:
f.attrs[key] = str(value.encode('utf-8'))
print('finished writing to {}'.format(out_file))
# ISCE / ROI_PAC GAMMA / Image product
else:
key_list = list(datasetDict.keys())
data_list = []
for key in key_list:
data_list.append(datasetDict[key])
data_type = meta.get('DATA_TYPE', str(data_list[0].dtype)).lower()
# Write Data File
print('write {}'.format(out_file))
# determined by ext
if ext in ['.unw', '.cor', '.hgt']:
write_float32(data_list[0], out_file)
meta['DATA_TYPE'] = 'float32'
elif ext == '.dem':
write_real_int16(data_list[0], out_file)
meta['DATA_TYPE'] = 'int16'
elif ext in ['.trans']:
write_float32(data_list[0], data_list[1], out_file)
meta['DATA_TYPE'] = 'float32'
elif ext in ['.utm_to_rdc', '.UTM_TO_RDC']:
data = np.zeros(data_list[0].shape, dtype=np.complex64)
data.real = datasetDict['rangeCoord']
data.imag = datasetDict['azimuthCoord']
data.astype('>c8').tofile(out_file)
elif ext in ['.mli', '.flt']:
write_real_float32(data_list[0], out_file)
elif ext == '.slc':
write_complex_int16(data_list[0], out_file)
elif ext == '.int':
write_complex64(data_list[0], out_file)
elif ext == '.msk':
write_byte(data_list[0], out_file)
meta['DATA_TYPE'] = 'byte'
# determined by DATA_TYPE
elif data_type in ['float64']:
write_real_float64(data_list[0], out_file)
elif data_type in ['float32', 'float']:
if len(data_list) == 1:
write_real_float32(data_list[0], out_file)
elif len(data_list) == 2 and meta['scheme'] == 'BIL':
write_float32(data_list[0], data_list[1], out_file)
elif data_type in ['int16', 'short']:
write_real_int16(data_list[0], out_file)
elif data_type in ['int8', 'byte']:
write_byte(data_list[0], out_file)
elif data_type in ['bool']:
write_bool(data_list[0], out_file)
else:
print('Un-supported file type: ' + ext)
return 0
# write metadata file
write_roipac_rsc(meta, out_file + '.rsc', print_msg=True)
return out_file
def run_geocode(inps):
"""geocode all input files"""
start_time = time.time()
# feed the largest file for resample object initiation
ind_max = np.argmax([os.path.getsize(i) for i in inps.file])
# prepare geometry for geocoding
kwargs = dict(interp_method=inps.interpMethod,
fill_value=inps.fillValue,
nprocs=inps.nprocs,
max_memory=inps.maxMemory,
software=inps.software,
print_msg=True)
if inps.latFile and inps.lonFile:
kwargs['lat_file'] = inps.latFile
kwargs['lon_file'] = inps.lonFile
res_obj = resample(lut_file=inps.lookupFile,
src_file=inps.file[ind_max],
SNWE=inps.SNWE,
lalo_step=inps.laloStep,
**kwargs)
res_obj.open()
res_obj.prepare()
# resample input files one by one
for infile in inps.file:
print('-' * 50 + '\nresampling file: {}'.format(infile))
atr = readfile.read_attribute(infile, datasetName=inps.dset)
outfile = auto_output_filename(infile, inps)
# update_mode
if inps.updateMode:
print('update mode: ON')
if ut.run_or_skip(outfile, in_file=[infile,
inps.lookupFile]) == 'skip':
continue
## prepare output
# update metadata
if inps.radar2geo:
atr = attr.update_attribute4radar2geo(atr, res_obj=res_obj)
else:
atr = attr.update_attribute4geo2radar(atr, res_obj=res_obj)
# instantiate output file
file_is_hdf5 = os.path.splitext(outfile)[1] in ['.h5', '.he5']
if file_is_hdf5:
compression = readfile.get_hdf5_compression(infile)
writefile.layout_hdf5(outfile,
metadata=atr,
ref_file=infile,
compression=compression)
else:
dsDict = dict()
## run
dsNames = readfile.get_dataset_list(infile, datasetName=inps.dset)
maxDigit = max([len(i) for i in dsNames])
for dsName in dsNames:
if not file_is_hdf5:
dsDict[dsName] = np.zeros((res_obj.length, res_obj.width))
# loop for block-by-block IO
for i in range(res_obj.num_box):
src_box = res_obj.src_box_list[i]
dest_box = res_obj.dest_box_list[i]
# read
print('-' * 50 +
'\nreading {d:<{w}} in block {b} from {f} ...'.format(
d=dsName,
w=maxDigit,
b=src_box,
f=os.path.basename(infile)))
data = readfile.read(infile,
datasetName=dsName,
box=src_box,
print_msg=False)[0]
# resample
data = res_obj.run_resample(src_data=data, box_ind=i)
# write / save block data
if data.ndim == 3:
block = [
0, data.shape[0], dest_box[1], dest_box[3],
dest_box[0], dest_box[2]
]
else:
block = [
dest_box[1], dest_box[3], dest_box[0], dest_box[2]
]
if file_is_hdf5:
print('write data in block {} to file: {}'.format(
block, outfile))
writefile.write_hdf5_block(outfile,
data=data,
datasetName=dsName,
block=block,
print_msg=False)
else:
dsDict[dsName][block[0]:block[1], block[2]:block[3]] = data
# for binary file: ensure same data type
if not file_is_hdf5:
dsDict[dsName] = np.array(dsDict[dsName], dtype=data.dtype)
# write binary file
if not file_is_hdf5:
atr['BANDS'] = len(dsDict.keys())
writefile.write(dsDict,
out_file=outfile,
metadata=atr,
ref_file=infile)
# create ISCE XML and GDAL VRT file if using ISCE lookup table file
if inps.latFile and inps.lonFile:
writefile.write_isce_xml(atr, fname=outfile)
m, s = divmod(time.time() - start_time, 60)
print('time used: {:02.0f} mins {:02.1f} secs.\n'.format(m, s))
return outfile
