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ESPACE-DEV
Sen2Chain
Commits
087e39be
Commit
087e39be
authored
5 years ago
by
pascal.mouquet_ird.fr
Browse files
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Plain Diff
OTB removed from cloud masks processing
parent
5b988340
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2 changed files
requirements.txt
+1
-0
1 addition, 0 deletions
requirements.txt
sen2chain/cloud_mask.py
+165
-87
165 additions, 87 deletions
sen2chain/cloud_mask.py
with
166 additions
and
87 deletions
requirements.txt
+
1
−
0
View file @
087e39be
...
...
@@ -11,4 +11,5 @@ typing>=3.6.6
pandas
>=0.23.4
urllib3
>=1.22
geopandas
>=0.5.0
scipy
This diff is collapsed.
Click to expand it.
sen2chain/cloud_mask.py
+
165
−
87
View file @
087e39be
...
...
@@ -8,13 +8,14 @@ import logging
import
pathlib
from
pathlib
import
Path
import
pyproj
import
otbApplication
#~
import otbApplication
import
shapely.geometry
from
shapely.geometry
import
box
,
Polygon
,
MultiPolygon
,
GeometryCollection
,
mapping
,
shape
from
shapely.ops
import
transform
import
rasterio
from
rasterio.features
import
shapes
,
rasterize
import
numpy
as
np
from
scipy
import
ndimage
from
typing
import
Sequence
,
List
,
Dict
,
Union
import
gdal
import
os
...
...
@@ -264,44 +265,79 @@ def create_cloud_mask_v2(
logger
.
info
(
"
Creating cloud-mask_v2
"
)
out_temp_path
=
Path
(
Config
().
get
(
"
temp_path
"
))
out_bin
=
str
(
out_temp_path
/
(
out_path
.
stem
+
"
tmp_bin.tif
"
))
out_erode
=
str
(
out_temp_path
/
(
out_path
.
stem
+
"
tmp_erode.tif
"
))
out_dilate
=
str
(
out_temp_path
/
(
out_path
.
stem
+
"
tmp_dilate.tif
"
))
# Seuillage du masque nuage Sen2Cor
#~
out_bin = str(out_temp_path / (out_path.stem + "
_
tmp_bin.tif"))
#~
out_erode = str(out_temp_path / (out_path.stem + "
_
tmp_erode.tif"))
out_dilate
=
str
(
out_temp_path
/
(
out_path
.
stem
+
"
_
tmp_dilate.tif
"
))
logger
.
info
(
'
Loading cloud_prb...
'
)
CLD_seuil
=
25
BandMath
=
otbApplication
.
Registry
.
CreateApplication
(
"
BandMath
"
)
BandMath
.
SetParameterStringList
(
"
il
"
,
[
str
(
cloud_mask
)])
BandMath
.
SetParameterString
(
"
out
"
,
out_bin
)
BandMath
.
SetParameterOutputImagePixelType
(
"
out
"
,
0
)
BandMath
.
SetParameterString
(
"
exp
"
,
"
im1b1 >
"
+
str
(
CLD_seuil
))
BandMath
.
ExecuteAndWriteOutput
()
# Erosion
BinaryMorphologicalOperation
=
otbApplication
.
Registry
.
CreateApplication
(
"
BinaryMorphologicalOperation
"
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
in
"
,
out_bin
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
out
"
,
out_erode
)
BinaryMorphologicalOperation
.
SetParameterOutputImagePixelType
(
"
out
"
,
0
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
channel
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.xradius
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.yradius
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterFloat
(
"
filter.erode.foreval
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
filter
"
,
"
erode
"
)
BinaryMorphologicalOperation
.
ExecuteAndWriteOutput
()
# Dilatation
BinaryMorphologicalOperation
=
otbApplication
.
Registry
.
CreateApplication
(
"
BinaryMorphologicalOperation
"
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
in
"
,
out_erode
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
out
"
,
out_dilate
)
BinaryMorphologicalOperation
.
SetParameterOutputImagePixelType
(
"
out
"
,
0
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
channel
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.xradius
"
,
dilatation
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.yradius
"
,
dilatation
)
BinaryMorphologicalOperation
.
SetParameterFloat
(
"
filter.dilate.foreval
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
filter
"
,
"
dilate
"
)
BinaryMorphologicalOperation
.
ExecuteAndWriteOutput
()
with
rasterio
.
open
(
str
(
cloud_mask
))
as
cld_src
:
cld
=
cld_src
.
read
(
1
).
astype
(
np
.
int16
)
cld_profile
=
cld_src
.
profile
cld_bin
=
np
.
where
(
cld
>
CLD_seuil
,
1
,
0
).
astype
(
np
.
uint8
)
cld_erode
=
ndimage
.
binary_erosion
(
cld_bin
).
astype
(
cld_bin
.
dtype
)
kernel
=
np
.
array
([[
0
,
0
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
0
,
0
],
[
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
],
[
0
,
0
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
0
,
0
]])
cld_dilate
=
ndimage
.
binary_dilation
(
cld_erode
,
kernel
).
astype
(
cld_erode
.
dtype
)
logger
.
info
(
"
saving TIFF file...
"
)
cld_profile
.
update
(
driver
=
"
Gtiff
"
,
compress
=
"
NONE
"
,
tiled
=
False
,
dtype
=
np
.
int8
,
transform
=
cld_src
.
transform
,
count
=
1
)
cld_profile
.
pop
(
'
tiled
'
,
None
)
cld_profile
.
pop
(
'
nodata
'
,
None
)
with
rasterio
.
Env
(
GDAL_CACHEMAX
=
512
)
as
env
:
with
rasterio
.
open
(
out_dilate
,
"
w
"
,
**
cld_profile
)
as
dst
:
dst
.
write
(
cld_dilate
.
astype
(
np
.
int8
),
1
)
#~ # Seuillage du masque nuage Sen2Cor
#~ CLD_seuil = 25
#~ BandMath = otbApplication.Registry.CreateApplication("BandMath")
#~ BandMath.SetParameterStringList("il", [str(cloud_mask)])
#~ BandMath.SetParameterString("out", out_bin)
#~ BandMath.SetParameterOutputImagePixelType("out", 0)
#~ BandMath.SetParameterString("exp", "im1b1 > " + str(CLD_seuil))
#~ BandMath.ExecuteAndWriteOutput()
#~ # Erosion
#~ BinaryMorphologicalOperation = otbApplication.Registry.CreateApplication("BinaryMorphologicalOperation")
#~ BinaryMorphologicalOperation.SetParameterString("in", out_bin)
#~ BinaryMorphologicalOperation.SetParameterString("out", out_erode)
#~ BinaryMorphologicalOperation.SetParameterOutputImagePixelType("out", 0)
#~ BinaryMorphologicalOperation.SetParameterInt("channel", 1)
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.xradius", 1)
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.yradius", 1)
#~ BinaryMorphologicalOperation.SetParameterFloat("filter.erode.foreval", 1)
#~ BinaryMorphologicalOperation.SetParameterString("filter", "erode")
#~ BinaryMorphologicalOperation.ExecuteAndWriteOutput()
#~ # Dilatation
#~ BinaryMorphologicalOperation = otbApplication.Registry.CreateApplication("BinaryMorphologicalOperation")
#~ BinaryMorphologicalOperation.SetParameterString("in", out_erode)
#~ BinaryMorphologicalOperation.SetParameterString("out", out_dilate)
#~ BinaryMorphologicalOperation.SetParameterOutputImagePixelType("out", 0)
#~ BinaryMorphologicalOperation.SetParameterInt("channel", 1)
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.xradius", dilatation)
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.yradius", dilatation)
#~ BinaryMorphologicalOperation.SetParameterFloat("filter.dilate.foreval", 1)
#~ BinaryMorphologicalOperation.SetParameterString("filter", "dilate")
#~ BinaryMorphologicalOperation.ExecuteAndWriteOutput()
# Save to JP2000
logger
.
info
(
"
converting to JP2000 file...
"
)
src_ds
=
gdal
.
Open
(
out_dilate
)
driver
=
gdal
.
GetDriverByName
(
"
JP2OpenJPEG
"
)
dst_ds
=
driver
.
CreateCopy
(
str
(
out_path
),
src_ds
,
...
...
@@ -309,8 +345,8 @@ def create_cloud_mask_v2(
dst_ds
=
None
src_ds
=
None
os
.
remove
(
out_bin
)
os
.
remove
(
out_erode
)
#~
os.remove(out_bin)
#~
os.remove(out_erode)
os
.
remove
(
out_dilate
)
...
...
@@ -332,72 +368,114 @@ def create_cloud_mask_b11(
logger
.
info
(
"
Masking cloud-mask_v2 with B11
"
)
out_temp_path
=
Path
(
Config
().
get
(
"
temp_path
"
))
out_bin
=
str
(
out_temp_path
/
(
out_path
.
stem
+
"
_tmp_bin.tif
"
))
out_dilate
=
str
(
out_temp_path
/
(
out_path
.
stem
+
"
_tmp_dilate.tif
"
))
#~
out_bin = str(out_temp_path / (out_path.stem + "_tmp_bin.tif"))
#~
out_dilate = str(out_temp_path / (out_path.stem + "_tmp_dilate.tif"))
out_mask
=
str
(
out_temp_path
/
(
out_path
.
stem
+
"
_tmp_mask.tif
"
))
# Seuillage du masque B1
logger
.
info
(
'
Loading B11...
'
)
b11_seuil
=
1500
BandMath
=
otbApplication
.
Registry
.
CreateApplication
(
"
BandMath
"
)
BandMath
.
SetParameterStringList
(
"
il
"
,
[
str
(
b11_path
)])
BandMath
.
SetParameterString
(
"
out
"
,
out_bin
)
BandMath
.
SetParameterOutputImagePixelType
(
"
out
"
,
0
)
BandMath
.
SetParameterString
(
"
exp
"
,
"
im1b1 <
"
+
str
(
b11_seuil
))
BandMath
.
ExecuteAndWriteOutput
()
#~ # Erosion
with
rasterio
.
open
(
str
(
b11_path
))
as
b11_src
:
b11
=
b11_src
.
read
(
1
).
astype
(
np
.
int16
)
b11_bin
=
np
.
where
(
b11
<
b11_seuil
,
1
,
0
).
astype
(
np
.
uint8
)
kernel
=
np
.
array
([[
0
,
0
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
0
,
0
],
[
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
],
[
0
,
0
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
0
,
0
]])
b11_dilate
=
ndimage
.
binary_dilation
(
b11_bin
,
kernel
).
astype
(
b11_bin
.
dtype
)
with
rasterio
.
open
(
str
(
cloud_mask
))
as
cld_src
:
cld
=
cld_src
.
read
(
1
).
astype
(
np
.
int16
)
cld_profile
=
cld_src
.
profile
cld_mskd
=
((
cld
==
1
)
*
(
b11_dilate
==
0
)).
astype
(
np
.
uint8
)
kernel
=
np
.
array
([[
0
,
0
,
0
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
0
,
0
,
0
],
[
0
,
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
,
0
],
[
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
],
[
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
],
[
0
,
0
,
0
,
1
,
1
,
1
,
1
,
1
,
1
,
1
,
0
,
0
,
0
],
[
0
,
0
,
0
,
0
,
0
,
1
,
1
,
1
,
0
,
0
,
0
,
0
,
0
]])
cld_mskd_dilate
=
ndimage
.
binary_dilation
(
cld_mskd
,
kernel
).
astype
(
cld_mskd
.
dtype
)
logger
.
info
(
"
saving TIFF file...
"
)
cld_profile
.
update
(
driver
=
"
Gtiff
"
,
compress
=
"
NONE
"
,
tiled
=
False
,
dtype
=
np
.
int8
,
transform
=
cld_src
.
transform
,
count
=
1
)
cld_profile
.
pop
(
'
tiled
'
,
None
)
cld_profile
.
pop
(
'
nodata
'
,
None
)
with
rasterio
.
Env
(
GDAL_CACHEMAX
=
512
)
as
env
:
with
rasterio
.
open
(
out_mask
,
"
w
"
,
**
cld_profile
)
as
dst
:
dst
.
write
(
cld_mskd_dilate
.
astype
(
np
.
int8
),
1
)
#~ # Seuillage du masque B11
#~ b11_seuil = 1500
#~ BandMath = otbApplication.Registry.CreateApplication("BandMath")
#~ BandMath.SetParameterStringList("il", [str(b11_path)])
#~ BandMath.SetParameterString("out", out_bin)
#~ BandMath.SetParameterOutputImagePixelType("out", 0)
#~ BandMath.SetParameterString("exp", "im1b1 < " + str(b11_seuil))
#~ BandMath.ExecuteAndWriteOutput()
#~ # Dilatation
#~ BinaryMorphologicalOperation = otbApplication.Registry.CreateApplication("BinaryMorphologicalOperation")
#~ BinaryMorphologicalOperation.SetParameterString("in", out_bin)
#~ BinaryMorphologicalOperation.SetParameterString("out", out_
erod
e)
#~ BinaryMorphologicalOperation.SetParameterString("out", out_
dilat
e)
#~ BinaryMorphologicalOperation.SetParameterOutputImagePixelType("out", 0)
#~ BinaryMorphologicalOperation.SetParameterInt("channel", 1)
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.xradius",
1
)
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.yradius",
1
)
#~ BinaryMorphologicalOperation.SetParameterFloat("filter.
erod
e.foreval", 1)
#~ BinaryMorphologicalOperation.SetParameterString("filter", "
erod
e")
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.xradius",
dilatation
)
#~ BinaryMorphologicalOperation.SetParameterInt("structype.ball.yradius",
dilatation
)
#~ BinaryMorphologicalOperation.SetParameterFloat("filter.
dilat
e.foreval", 1)
#~ BinaryMorphologicalOperation.SetParameterString("filter", "
dilat
e")
#~ BinaryMorphologicalOperation.ExecuteAndWriteOutput()
# Dilatation
BinaryMorphologicalOperation
=
otbApplication
.
Registry
.
CreateApplication
(
"
BinaryMorphologicalOperation
"
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
in
"
,
out_bin
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
out
"
,
out_dilate
)
BinaryMorphologicalOperation
.
SetParameterOutputImagePixelType
(
"
out
"
,
0
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
channel
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.xradius
"
,
dilatation
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.yradius
"
,
dilatation
)
BinaryMorphologicalOperation
.
SetParameterFloat
(
"
filter.dilate.foreval
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
filter
"
,
"
dilate
"
)
BinaryMorphologicalOperation
.
ExecuteAndWriteOutput
()
# Masquage du masque
BandMath
=
otbApplication
.
Registry
.
CreateApplication
(
"
BandMath
"
)
BandMath
.
SetParameterStringList
(
"
il
"
,
[
str
(
cloud_mask
),
str
(
out_dilate
)])
BandMath
.
SetParameterString
(
"
out
"
,
out_mask
)
BandMath
.
SetParameterOutputImagePixelType
(
"
out
"
,
0
)
BandMath
.
SetParameterString
(
"
exp
"
,
"
(im1b1 == 1) * (im2b1 == 0)
"
)
BandMath
.
ExecuteAndWriteOutput
()
# Dilatation
BinaryMorphologicalOperation
=
otbApplication
.
Registry
.
CreateApplication
(
"
BinaryMorphologicalOperation
"
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
in
"
,
out_mask
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
out
"
,
out_dilate
)
BinaryMorphologicalOperation
.
SetParameterOutputImagePixelType
(
"
out
"
,
0
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
channel
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.xradius
"
,
dilatation
+
1
)
BinaryMorphologicalOperation
.
SetParameterInt
(
"
structype.ball.yradius
"
,
dilatation
+
1
)
BinaryMorphologicalOperation
.
SetParameterFloat
(
"
filter.dilate.foreval
"
,
1
)
BinaryMorphologicalOperation
.
SetParameterString
(
"
filter
"
,
"
dilate
"
)
BinaryMorphologicalOperation
.
ExecuteAndWriteOutput
()
#~
BandMath = otbApplication.Registry.CreateApplication("BandMath")
#~
BandMath.SetParameterStringList("il", [str(cloud_mask),str(out_dilate)])
#~
BandMath.SetParameterString("out", out_mask)
#~
BandMath.SetParameterOutputImagePixelType("out", 0)
#~
BandMath.SetParameterString("exp", "(im1b1 == 1) * (im2b1 == 0)")
#~
BandMath.ExecuteAndWriteOutput()
#~
# Dilatation
#~
BinaryMorphologicalOperation = otbApplication.Registry.CreateApplication("BinaryMorphologicalOperation")
#~
BinaryMorphologicalOperation.SetParameterString("in", out_mask)
#~
BinaryMorphologicalOperation.SetParameterString("out", out_dilate)
#~
BinaryMorphologicalOperation.SetParameterOutputImagePixelType("out", 0)
#~
BinaryMorphologicalOperation.SetParameterInt("channel", 1)
#~
BinaryMorphologicalOperation.SetParameterInt("structype.ball.xradius", dilatation+1)
#~
BinaryMorphologicalOperation.SetParameterInt("structype.ball.yradius", dilatation+1)
#~
BinaryMorphologicalOperation.SetParameterFloat("filter.dilate.foreval", 1)
#~
BinaryMorphologicalOperation.SetParameterString("filter", "dilate")
#~
BinaryMorphologicalOperation.ExecuteAndWriteOutput()
# Save to JP2000
src_ds
=
gdal
.
Open
(
out_dilate
)
logger
.
info
(
"
converting to JP2000 file...
"
)
src_ds
=
gdal
.
Open
(
out_mask
)
driver
=
gdal
.
GetDriverByName
(
"
JP2OpenJPEG
"
)
dst_ds
=
driver
.
CreateCopy
(
str
(
out_path
),
src_ds
,
options
=
[
"
CODEC=JP2
"
,
"
QUALITY=100
"
,
"
REVERSIBLE=YES
"
,
"
YCBCR420=NO
"
])
dst_ds
=
None
src_ds
=
None
os
.
remove
(
out_bin
)
os
.
remove
(
out_dilate
)
#~
os.remove(out_bin)
#~
os.remove(out_dilate)
os
.
remove
(
out_mask
)
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