diff --git a/TimeSeries/planet_mosaics.py b/TimeSeries/planet_mosaics.py
index ce8cb236b5915a60e9ad7a92c5dd9be06214ef95..8d0563f6685a7c23b58d53068485691af7c7f843 100644
--- a/TimeSeries/planet_mosaics.py
+++ b/TimeSeries/planet_mosaics.py
@@ -8,6 +8,8 @@ from tqdm import tqdm
import urllib.request
from datetime import datetime
from dateutil.relativedelta import *
+import uuid
+import glob
def fetch(shp, dt, out_fld, api_key):
ds = ogr.Open(shp)
@@ -80,21 +82,12 @@ def fetch(shp, dt, out_fld, api_key):
return
-
-
-
-
-
-
-
-'''
-class PlanetMosaicQuadPipeline:
+class PlanetMosaicPipeline:
# --- BEGIN SENSOR PROTOTYPE ---
NAME = 'PLANET-MOSAICS'
REF_TYPE = otb.ImagePixelType_uint16
- PTRN_dir = '*'
- PTRN_ref = '*'
+ PTRN_name = 'PlanetMosaic_*.tif'
FEAT_exp = {
'B': 'im1b1',
'G': 'im1b2',
@@ -104,119 +97,83 @@ class PlanetMosaicQuadPipeline:
}
NDT = 0
+ # ---- END SENSOR PROTOTYPE ----
+
@classmethod
def _check(cls,x):
- return cls.PTRN_dir.split('_')[-1].replace('*', '') in os.path.basename(x)
+ return (cls.PTRN_name.split('*')[0] in os.path.basename(x) and
+ cls.PTRN_name.split('*')[1] 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
+ return os.path.splitext(os.path.basename(x))
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
+ return os.path.splitext(os.path.basename(x))[0].split('_')[-1]
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 ----
-'''
\ No newline at end of file
+ def __init__(self, fld, input_date_interval=None):
+ self.pipe = []
+ self.files = []
+ self.types = []
+ self.out_p = []
+ self.out_idx = []
+
+ self.id = str(uuid.uuid4())
+ self.folder = os.path.abspath(fld)
+ self.image_list = self.parse_folder(self.folder)
+ self.input_dates = [self._img_date(x) for x in self.image_list]
+
+ if input_date_interval is not None:
+ idx = [i for i in range(len(self.input_dates)) if
+ input_date_interval[0] <= self.input_dates[i] <= input_date_interval[1]]
+ self.image_list = [self.image_list[i] for i in idx]
+ self.input_dates = [self.input_dates[i] for i in idx]
+
+ for img in self.image_list:
+ self.append(to_otb_pipeline(img), os.path.basename(img), self.REF_TYPE, 'out', is_output=True)
+
+ def __del__(self):
+ return
+
+ def parse_folder(self, fld):
+ img_list = [os.path.abspath(x) for x in glob.glob(os.path.join(fld, self.PTRN_dir))]
+ return sorted(img_list, key=lambda x: self._img_id(x))
+
+ def compute_features(self, feat_list=['B', 'G', 'R', 'NIR', 'NDVI']):
+ proc_idx = self.out_idx.copy()
+ self.out_idx = []
+ for k in range(len(proc_idx)):
+ bm = otb.Registry.CreateApplication('BandMathX')
+ expr = []
+ for f in feat_list:
+ expr.append(self.FEAT_exp[f])
+ expr = '{' + ';'.join(expr) + '}'
+ bm.SetParameterString('exp', expr)
+ bm.Execute()
+ fn = self.files[proc_idx[k]].replace('.tif', '_FEAT.tif')
+ self.append(bm, fn, self.REF_TYPE, 'out', is_output=True)
+
+ def write_outputs(self, fld, update_pipe=False, compress=False):
+ out = []
+ proc_idx = self.out_idx.copy()
+ if update_pipe:
+ self.out_idx = []
+ for t in proc_idx:
+ out_file = os.path.join(fld, self.files[t])
+ if compress:
+ out_file += '?gdal:co:compress=deflate'
+ if not os.path.exists(os.path.dirname(out_file)):
+ os.makedirs(os.path.dirname(out_file))
+ self.pipe[t].SetParameterString(self.out_p[t], out_file)
+ self.pipe[t].SetParameterOutputImagePixelType(self.out_p[t], self.types[t])
+ self.pipe[t].ExecuteAndWriteOutput()
+ out.append(out_file)
+ if update_pipe:
+ self.append(to_otb_pipeline(out_file), self.files[t], self.types[t], 'out', is_output=True)
+ return out
diff --git a/TimeSeries/s1base.py b/TimeSeries/s1base.py
index 22f897513d94957e565d28f8030575a267dd464d..3a53d80936f37c59660546bb6e045536a4abf95e 100644
--- a/TimeSeries/s1base.py
+++ b/TimeSeries/s1base.py
@@ -113,7 +113,6 @@ class S1GRDPipeline:
shutil.rmtree(self.temp_fld)
def parse_folder(self, fld, roi_min_surf=0.0):
- print(glob.glob(os.path.join(fld, self.PTRN_dir)))
img_list = [os.path.abspath(x) for x in glob.glob(os.path.join(fld, self.PTRN_dir))
if os.path.isdir(x) and self._check_roi(x, self.roi, roi_min_surf)]