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Gaetano Raffaele authoredbf6a4132
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from TimeSeries.s2theia import *
class S2Sen2CorTilePipeline(S2TheiaTilePipeline):
# --- BEGIN SENSOR PROTOTYPE ---
NAME = 'S2-SEN2COR'
REF_TYPE = otb.ImagePixelType_uint16
MSK_TYPE = otb.ImagePixelType_uint8
PTRN_dir = 'S2*_MSIL2A*'
PTRN_ref = '_B'
B2_name = 'B02'
PTRN_10m = ['GRANULE/*/IMG_DATA/R10m/*_B02_10m.jp2',
'GRANULE/*/IMG_DATA/R10m/*_B03_10m.jp2',
'GRANULE/*/IMG_DATA/R10m/*_B04_10m.jp2',
'GRANULE/*/IMG_DATA/R10m/*_B08_10m.jp2']
PTRN_20m = ['GRANULE/*/IMG_DATA/R20m/*_B05_20m.jp2',
'GRANULE/*/IMG_DATA/R20m/*_B06_20m.jp2',
'GRANULE/*/IMG_DATA/R20m/*_B07_20m.jp2',
'GRANULE/*/IMG_DATA/R20m/*_B8A_20m.jp2',
'GRANULE/*/IMG_DATA/R20m/*_B11_20m.jp2',
'GRANULE/*/IMG_DATA/R20m/*_B12_20m.jp2']
PTRN_msk = ['GRANULE/*/IMG_DATA/R20m/*_SCL_20m.jp2']
MERG_msk = ['min']
PTRN_ful = PTRN_10m[0:3] + PTRN_20m[0:3] + [PTRN_10m[3]] + PTRN_20m[3:]
FEAT_exp = {
'B2': 'im1b1',
'B3': 'im1b2',
'B4': 'im1b3',
'B5': 'im1b4',
'B6': 'im1b5',
'B7': 'im1b6',
'B8': 'im1b7',
'B8A': 'im1b8',
'B11': 'im1b9',
'B12': 'im1b10',
'NDVI': '(im1b7-im1b3)/(im1b7+im1b3+1e-6)',
'NDWI': '(im1b2-im1b7)/(im1b2+im1b7+1e-6)',
'BRI': 'sqrt(' + '+'.join(['im1b%d*im1b%d' % (i, i) for i in range(1, 11)]) + ')',
'MNDWI': '(im1b2-im1b9)/(im1b2+im1b9+1e-6)',
'SWNDVI': '(im1b9-im1b7)/(im1b9+im1b7+1e-6)',
'NDRE': '(im1b7-im1b4)/(im1b7+im1b4+1e-6)'
}
NDT = 0
@classmethod
def _check(cls,x):
return cls.PTRN_dir.split('_')[-1].replace('*', '') in os.path.basename(x)
@classmethod
def _img_id(cls,x):
if cls._check(x):
if os.path.isdir(x) or os.path.splitext(x)[-1] == '.zip':
return '_'.join(os.path.splitext(x)[0].split('_')[-5:])
else:
return None
else:
return None
@classmethod
def _img_date(cls,x):
if cls._check(x):
if os.path.isdir(x) or os.path.splitext(x)[-1] == '.zip':
return os.path.splitext(x)[0].split('_')[-5].split('T')[0]
else:
return None
else:
return None
@classmethod
def _tile_id(cls,x):
if cls._check(x):
if os.path.isdir(x) or os.path.splitext(x)[-1] == '.zip':
return os.path.splitext(x)[0].split('_')[-2]
else:
return None
else:
return None
@classmethod
def _tile_cloud_percentage(cls, x):
if cls._check(x):
if os.path.isdir(x):
fid = open(glob.glob(os.path.join(x, '*/*/MTD_TL.xml'))[0], 'r')
mtd = fid.read()
elif os.path.splitext(x)[-1] == '.zip':
arch = zipfile.ZipFile(x)
fid = [name for name in arch.namelist() if name.endswith('MTD_TL.xml')]
mtd = arch.read(fid[0])
root = et.fromstring(mtd)
f = filter(lambda x: x.tag == "CLOUDY_PIXEL_PERCENTAGE", root.findall('*/*/*'))
r = list(f)
return float(r[0].text)
"""
def _process_mask(self, msks):
msk_pipe = [otb.Registry.CreateApplication('Superimpose')]
msk_pipe[-1].SetParameterInputImage('inr', self.pipe[-1].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterInputImage('inm', msks[0].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('interpolator', 'nn')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('BandMath'))
msk_pipe[-1].AddImageToParameterInputImageList('il', msk_pipe[-2].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('exp', 'im1b1==0 || im1b1==1 || im1b1==2 || im1b1==7 ||im1b1==3 || im1b1==8 || im1b1==9 || im1b1==10')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('BinaryMorphologicalOperation'))
msk_pipe[-1].SetParameterInputImage('in', msk_pipe[-2].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('filter', 'erode')
msk_pipe[-1].SetParameterString('structype', 'ball')
msk_pipe[-1].SetParameterString('xradius', '5')
msk_pipe[-1].SetParameterString('yradius', '5')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('BinaryMorphologicalOperation'))
msk_pipe[-1].SetParameterInputImage('in', msk_pipe[-2].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('filter', 'dilate')
msk_pipe[-1].SetParameterString('structype', 'ball')
msk_pipe[-1].SetParameterString('xradius', '20')
msk_pipe[-1].SetParameterString('yradius', '20')
msk_pipe[-1].Execute()
return msk_pipe
"""
def _process_mask(self, msks):
msk_pipe = [otb.Registry.CreateApplication('BandMath')]
msk_pipe[-1].AddImageToParameterInputImageList('il', msks[0].GetParameterOutputImage('out'))
# excluding thin cirrus from masking : no im1b1 == 10 below
# excluding cloud shadows here (for opening) : no im1b1 == 3 below
msk_pipe[-1].SetParameterString('exp', 'im1b1==0 || im1b1==1 || im1b1==8 || im1b1==9')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('BandMath'))
msk_pipe[-1].AddImageToParameterInputImageList('il', msks[0].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('exp', 'im1b1==2 || im1b1 == 3 || im1b1==7')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('BinaryMorphologicalOperation'))
msk_pipe[-1].SetParameterInputImage('in', msk_pipe[-2].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('filter', 'opening')
msk_pipe[-1].SetParameterString('structype', 'ball')
msk_pipe[-1].SetParameterString('xradius', '5')
msk_pipe[-1].SetParameterString('yradius', '5')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('BandMath'))
msk_pipe[-1].AddImageToParameterInputImageList('il', msk_pipe[-4].GetParameterOutputImage('out'))
msk_pipe[-1].AddImageToParameterInputImageList('il', msk_pipe[-2].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('exp', 'im1b1 || im2b1')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('BinaryMorphologicalOperation'))
msk_pipe[-1].SetParameterInputImage('in', msk_pipe[-2].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('filter', 'dilate')
msk_pipe[-1].SetParameterString('structype', 'ball')
msk_pipe[-1].SetParameterString('xradius', '20')
msk_pipe[-1].SetParameterString('yradius', '20')
msk_pipe[-1].Execute()
msk_pipe.append(otb.Registry.CreateApplication('Superimpose'))
msk_pipe[-1].SetParameterInputImage('inr', self.pipe[-1].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterInputImage('inm', msk_pipe[-2].GetParameterOutputImage('out'))
msk_pipe[-1].SetParameterString('interpolator', 'nn')
msk_pipe[-1].Execute()
return msk_pipe
# ---- END SENSOR PROTOTYPE ----
class S2Sen2CorPipeline(S2TheiaPipeline):
S2TilePipeline = S2Sen2CorTilePipeline
_check = S2TilePipeline._check
_tile_id = S2TilePipeline._tile_id