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Commit 9749ac2b authored by pascal.mouquet_ird.fr's avatar pascal.mouquet_ird.fr
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New NDR function more generic to compute indices, new IRECI

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Stage: test
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sen2chain/indices.py
+ 95
− 139
View file @ 9749ac2b
......@@ -13,9 +13,9 @@ import os
# type annotations
from typing import Union, List
from .indices_functions import (create_raw_ndvi, create_raw_ndre, create_raw_ndwigao, create_raw_ndwimcf,
from .indices_functions import (create_raw_ndr, create_raw_ireci,
#~ create_raw_ndvi, create_raw_ndre, create_raw_ndwigao, create_raw_ndwimcf, create_raw_mndwi
create_raw_bigr, create_raw_birnir, create_raw_bibg,
create_raw_mndwi, create_raw_ndr,
create_masked_indice, index_tiff_2_jp2)
from .colormap import matplotlib_colormap_to_rgb, create_colormap, create_rvb
......@@ -66,7 +66,6 @@ class Ndvi(Indice):
ext = ".jp2"
ext_raw = ".tif"
colormap = cm.RdYlGn
# _colors_table_path = functions_data_path = Path("../share/data/RdYlGn.lut")
def __init__(self, l2a_product_object, cm_product_object):
if (l2a_product_object or cm_product_object) is None:
......@@ -75,10 +74,8 @@ class Ndvi(Indice):
self.l2a_product = l2a_product_object
self.cm_product = cm_product_object
# output path
self.out_path = None
# filenames
self.indice_stem = self.filename_template.format(product_identifier=self.l2a_product.identifier, ext="")
self.indice_filename = self.indice_stem + self.ext
self.indice_raw = self.indice_stem + self.ext_raw
......@@ -100,11 +97,12 @@ class Ndvi(Indice):
if (out_path / self.indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(self.indice_filename))
else:
create_raw_ndvi(nir_path=self.l2a_product.b08_10m,
vir_path=self.l2a_product.b04_10m,
out_path=(out_path / self.indice_raw))
create_raw_ndr(b1_path=self.l2a_product.b08_10m,
b2_path=self.l2a_product.b04_10m,
out_path=(out_path / self.indice_raw))
index_tiff_2_jp2(img_path=(out_path / self.indice_raw),
out_path=(out_path / self.indice_filename))
out_path=(out_path / self.indice_filename),
quality = 20)
if nodata_clouds:
if not self.cm_product.path.exists():
......@@ -112,11 +110,6 @@ class Ndvi(Indice):
masked_indice_filename = self.indice_stem + "_" + self.cm_product.suffix + self.ext
masked_indice_raw = self.indice_stem + "_" + self.cm_product.suffix + self.ext_raw
#~ if self.l2a_product.user_cloud_mask is None:
#~ raise ValueError("Cloud mask does not exist")
#~ masked_indice_filename = self.indice_stem + "_MASKED" + self.ext
#~ masked_indice_raw = self.indice_stem + "_MASKED" + self.ext_raw
if (out_path / masked_indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(masked_indice_filename))
else:
......@@ -128,7 +121,8 @@ class Ndvi(Indice):
cloud_mask_path=self.cm_product.path,
out_path=(out_path / masked_indice_raw))
index_tiff_2_jp2(img_path=(out_path / masked_indice_raw),
out_path=(out_path / masked_indice_filename))
out_path=(out_path / masked_indice_filename),
quality = 20)
os.remove(str(out_path / masked_indice_raw))
try:
......@@ -146,24 +140,11 @@ class Ndvi(Indice):
logger.info("{} already exists".format(quicklook_filename))
else:
logger.info("creating quicklook")
# create_colormap(raster=(self.out_path / self.indice_filename),
# cloud_mask=self.l2a_product.user_cloud_mask,
# # lut_dict=get_colormap(self._colors_table_path.absolute()),
# lut_dict=cmap, clouds_color="white",
# out_path=(self.out_path / quicklook_filename))
#~ create_colormap2(raster=(self.out_path / self.indice_filename),
#~ cloud_mask=self.l2a_product.user_cloud_mask,
#~ # lut_dict=get_colormap(self._colors_table_path.absolute()),
#~ lut_dict=cmap, clouds_color="white",
#~ out_path=(self.out_path / quicklook_filename))
create_rvb(raster=(self.out_path / self.indice_filename),
cloud_mask=self.cm_product.path,
# lut_dict=get_colormap(self._colors_table_path.absolute()),
lut_dict=cmap, clouds_color="white",
out_path=(self.out_path / quicklook_filename))
#~ IndiceProduct(identifier = self.indice_filename).init_md()
#~ IndiceProduct(identifier = masked_indice_filename).init_md()
#~ IndiceProduct(identifier = quicklook_filename).init_md()
class NdwiMcf(Indice):
"""
......@@ -176,7 +157,6 @@ class NdwiMcf(Indice):
filename_template = "{product_identifier}_NDWIMCF{ext}"
ext = ".jp2"
ext_raw = ".tif"
#~ colormap = cm.RdYlBu
colormap = cm.colors.LinearSegmentedColormap.from_list("", ["green", "white", "blue"])
......@@ -187,10 +167,8 @@ class NdwiMcf(Indice):
self.l2a_product = l2a_product_object
self.cm_product = cm_product_object
# output path
self.out_path = None
# filenames
self.indice_stem = self.filename_template.format(product_identifier=self.l2a_product.identifier, ext="")
self.indice_filename = self.indice_stem + self.ext
self.indice_raw = self.indice_stem + self.ext_raw
......@@ -207,11 +185,12 @@ class NdwiMcf(Indice):
if (out_path / self.indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(self.indice_filename))
else:
create_raw_ndwimcf(nir_path=self.l2a_product.b08_10m,
green_path=self.l2a_product.b03_10m,
out_path=(out_path / self.indice_raw))
create_raw_ndr(b1_path=self.l2a_product.b03_10m,
b2_path=self.l2a_product.b08_10m,
out_path=(out_path / self.indice_raw))
index_tiff_2_jp2(img_path=(out_path / self.indice_raw),
out_path=(out_path / self.indice_filename))
out_path=(out_path / self.indice_filename),
quality = 20)
if nodata_clouds:
if not self.cm_product.path.exists():
......@@ -230,7 +209,8 @@ class NdwiMcf(Indice):
cloud_mask_path=self.cm_product.path,
out_path=(out_path / masked_indice_raw))
index_tiff_2_jp2(img_path=(out_path / masked_indice_raw),
out_path=(out_path / masked_indice_filename))
out_path=(out_path / masked_indice_filename),
quality = 20)
os.remove(str(out_path / masked_indice_raw))
try:
......@@ -254,21 +234,18 @@ class NdwiMcf(Indice):
out_path=(self.out_path / quicklook_filename))
class GenericNDR(Indice):
class NdwiGao(Indice):
"""
NDR = (B1-B2) / (B1+B2)
NDWI(Gao) = (NIR-SWIR) / (NIR+SWIR)
B1: band
B2: band
NIR: band 08
SWIR: band 11
"""
name = "GENERICNDR"
filename_template = "{product_identifier}_GENERICNDR{ext}"
name = "NDWIGAO"
filename_template = "{product_identifier}_NDWIGAO{ext}"
ext = ".jp2"
ext_raw = ".tif"
#~ colormap = cm.RdYlBu
colormap = cm.colors.LinearSegmentedColormap.from_list("", ["red", "white", "blue"])
colormap = cm.RdYlBu
def __init__(self, l2a_product_object, cm_product_object):
if (l2a_product_object or cm_product_object) is None:
......@@ -277,10 +254,8 @@ class GenericNDR(Indice):
self.l2a_product = l2a_product_object
self.cm_product = cm_product_object
# output path
self.out_path = None
# filenames
self.indice_stem = self.filename_template.format(product_identifier=self.l2a_product.identifier, ext="")
self.indice_filename = self.indice_stem + self.ext
self.indice_raw = self.indice_stem + self.ext_raw
......@@ -294,6 +269,7 @@ class GenericNDR(Indice):
) -> None:
""" process """
self.out_path = out_path
if (out_path / self.indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(self.indice_filename))
else:
......@@ -301,9 +277,8 @@ class GenericNDR(Indice):
b2_path=self.l2a_product.b11_20m,
out_path=(out_path / self.indice_raw))
index_tiff_2_jp2(img_path=(out_path / self.indice_raw),
out_path=(out_path / self.indice_filename),
quality = 20
)
out_path=(out_path / self.indice_filename),
quality = 20)
if nodata_clouds:
if not self.cm_product.path.exists():
......@@ -315,18 +290,19 @@ class GenericNDR(Indice):
logger.info("{} already exists".format(masked_indice_filename))
else:
if (out_path / self.indice_raw).exists():
ndwimcf_path = (out_path / self.indice_raw)
ndwigao_name = (out_path / self.indice_raw)
else:
ndwimcf_path = (out_path / self.indice_filename)
create_masked_indice(indice_path=ndwimcf_path,
ndwigao_name = (out_path / self.indice_filename)
create_masked_indice(indice_path=ndwigao_name,
cloud_mask_path=self.cm_product.path,
out_path=(out_path / masked_indice_raw))
index_tiff_2_jp2(img_path=(out_path / masked_indice_raw),
out_path=(out_path / masked_indice_filename))
#~ os.remove(str(out_path / masked_indice_raw))
out_path=(out_path / masked_indice_filename),
quality = 20)
os.remove(str(out_path / masked_indice_raw))
try:
#~ os.remove(str(out_path / self.indice_raw))
os.remove(str(out_path / self.indice_raw))
logger.info("Removing {}".format(self.indice_raw))
except:
pass
......@@ -334,8 +310,7 @@ class GenericNDR(Indice):
if quicklook:
cmap = matplotlib_colormap_to_rgb(self.colormap, revers=False)
quicklook_filename = self.indice_stem + "_" + self.cm_product.suffix + "_QL.tif"
quicklook_filename = self.indice_stem + "_QUICKLOOK.tif"
if (self.out_path / quicklook_filename).exists() and not reprocess:
logger.info("{} already exists".format(quicklook_filename))
else:
......@@ -346,18 +321,18 @@ class GenericNDR(Indice):
out_path=(self.out_path / quicklook_filename))
class NdwiGao(Indice):
class Mndwi(Indice):
"""
NDWI(Gao) = (NIR-SWIR) / (NIR+SWIR)
MNDWI = (GREEN-SWIR) / (GREEN+SWIR)
NIR: band 08
GREEN: band 03
SWIR: band 11
"""
name = "NDWIGAO"
filename_template = "{product_identifier}_NDWIGAO{ext}"
name = "MNDWI"
filename_template = "{product_identifier}_MNDWI{ext}"
ext = ".jp2"
ext_raw = ".tif"
colormap = cm.RdYlBu
colormap = cm.BrBG
def __init__(self, l2a_product_object, cm_product_object):
if (l2a_product_object or cm_product_object) is None:
......@@ -366,11 +341,8 @@ class NdwiGao(Indice):
self.l2a_product = l2a_product_object
self.cm_product = cm_product_object
# output path
self.out_path = None
# filenames
self.indice_stem = self.filename_template.format(product_identifier=self.l2a_product.identifier, ext="")
self.indice_filename = self.indice_stem + self.ext
self.indice_raw = self.indice_stem + self.ext_raw
......@@ -388,30 +360,32 @@ class NdwiGao(Indice):
if (out_path / self.indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(self.indice_filename))
else:
create_raw_ndwigao(nir_path=self.l2a_product.b08_10m,
swir_path=self.l2a_product.b11_20m,
out_path=(out_path / self.indice_raw))
create_raw_ndr(b1_path=self.l2a_product.b03_10m,
b2_path=self.l2a_product.b11_20m,
out_path=(out_path / self.indice_raw))
index_tiff_2_jp2(img_path=(out_path / self.indice_raw),
out_path=(out_path / self.indice_filename))
out_path=(out_path / self.indice_filename),
quality = 20)
if nodata_clouds:
if not self.cm_product.path.exists():
raise ValueError("Cloud mask does not exist")
masked_indice_filename = self.indice_stem + "_" + self.cm_product.suffix + self.ext
masked_indice_raw = self.indice_stem + "_" + self.cm_product.suffix + self.ext_raw
if (out_path / masked_indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(masked_indice_filename))
else:
if (out_path / self.indice_raw).exists():
ndwigao_name = (out_path / self.indice_raw)
mndwi_name = (out_path / self.indice_raw)
else:
ndwigao_name = (out_path / self.indice_filename)
create_masked_indice(indice_path=ndwigao_name,
mndwi_name = (out_path / self.indice_filename)
create_masked_indice(indice_path=mndwi_name,
cloud_mask_path=self.cm_product.path,
out_path=(out_path / masked_indice_raw))
index_tiff_2_jp2(img_path=(out_path / masked_indice_raw),
out_path=(out_path / masked_indice_filename))
out_path=(out_path / masked_indice_filename),
quality = 20)
os.remove(str(out_path / masked_indice_raw))
try:
......@@ -423,33 +397,29 @@ class NdwiGao(Indice):
if quicklook:
cmap = matplotlib_colormap_to_rgb(self.colormap, revers=False)
quicklook_filename = self.indice_stem + "_QUICKLOOK.tif"
quicklook_filename = self.indice_stem + "_" + self.cm_product.suffix + "_QL.tif"
if (self.out_path / quicklook_filename).exists() and not reprocess:
logger.info("{} already exists".format(quicklook_filename))
else:
logger.info("creating quicklook")
# create_colormap(raster=(self.out_path / self.indice_filename),
# cloud_mask=self.l2a_product.user_cloud_mask,
# lut_dict=cmap, clouds_color="white",
# out_path=(self.out_path / quicklook_filename))
create_rvb(raster=(self.out_path / self.indice_filename),
cloud_mask=self.cm_product.path,
lut_dict=cmap, clouds_color="white",
out_path=(self.out_path / quicklook_filename))
class Mndwi(Indice):
class Ndre(Indice):
"""
MNDWI = (GREEN-SWIR) / (GREEN+SWIR)
NDRE = (NIR - REDEDGE) / (NIR + REDEDGE)
GREEN: band 03
SWIR: band 11
NIR: band 08
REDEDGE: band 05
"""
name = "MNDWI"
filename_template = "{product_identifier}_MNDWI{ext}"
name = "NDRE"
filename_template = "{product_identifier}_NDRE{ext}"
ext = ".jp2"
ext_raw = ".tif"
colormap = cm.BrBG
colormap = cm.Spectral
def __init__(self, l2a_product_object, cm_product_object):
if (l2a_product_object or cm_product_object) is None:
......@@ -457,33 +427,31 @@ class Mndwi(Indice):
else:
self.l2a_product = l2a_product_object
self.cm_product = cm_product_object
# output path
self.out_path = None
# filenames
self.indice_stem = self.filename_template.format(product_identifier=self.l2a_product.identifier, ext="")
self.indice_filename = self.indice_stem + self.ext
self.indice_raw = self.indice_stem + self.ext_raw
def process_indice(
self,
out_path: pathlib.PosixPath,
reprocess: bool = False,
nodata_clouds: bool = False,
quicklook: bool = False
) -> None:
def process_indice(self,
out_path: pathlib.PosixPath,
reprocess: bool = False,
nodata_clouds: bool = False,
quicklook: bool = False
) -> None:
""" process """
self.out_path = out_path
if (out_path / self.indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(self.indice_filename))
else:
create_raw_mndwi(green_path=self.l2a_product.b03_10m,
swir_path=self.l2a_product.b11_20m,
out_path=(out_path / self.indice_raw))
create_raw_ndr(b1_path=self.l2a_product.b08_10m,
b2_path=self.l2a_product.b05_20m,
out_path=(out_path / self.indice_raw))
index_tiff_2_jp2(img_path=(out_path / self.indice_raw),
out_path=(out_path / self.indice_filename))
out_path=(out_path / self.indice_filename),
quality = 20)
if nodata_clouds:
if not self.cm_product.path.exists():
......@@ -495,14 +463,15 @@ class Mndwi(Indice):
logger.info("{} already exists".format(masked_indice_filename))
else:
if (out_path / self.indice_raw).exists():
mndwi_name = (out_path / self.indice_raw)
ndre_name = (out_path / self.indice_raw)
else:
mndwi_name = (out_path / self.indice_filename)
create_masked_indice(indice_path=mndwi_name,
ndre_name = (out_path / self.indice_filename)
create_masked_indice(indice_path=ndre_name,
cloud_mask_path=self.cm_product.path,
out_path=(out_path / masked_indice_raw))
index_tiff_2_jp2(img_path=(out_path / masked_indice_raw),
out_path=(out_path / masked_indice_filename))
out_path=(out_path / masked_indice_filename),
quality = 20)
os.remove(str(out_path / masked_indice_raw))
try:
......@@ -510,10 +479,8 @@ class Mndwi(Indice):
logger.info("Removing {}".format(self.indice_raw))
except:
pass
if quicklook:
cmap = matplotlib_colormap_to_rgb(self.colormap, revers=False)
quicklook_filename = self.indice_stem + "_" + self.cm_product.suffix + "_QL.tif"
if (self.out_path / quicklook_filename).exists() and not reprocess:
logger.info("{} already exists".format(quicklook_filename))
......@@ -525,19 +492,20 @@ class Mndwi(Indice):
out_path=(self.out_path / quicklook_filename))
class Ndre(Indice):
class IRECI(Indice):
"""
NDRE = (NIR - REDEDGE) / (NIR + REDEDGE)
NIR: band 08
REDEDGE: band 05
IRECI = (NIR-R)/(RE1/RE2)
NIR: band 783nm (B7 - 20m)
R: band 665nm (B4 - 10m)
RE1: band 705nm (B5 - 20m)
RE2: band 740nm (B6 - 20m)
"""
name = "NDRE"
filename_template = "{product_identifier}_NDRE{ext}"
name = "IRECI"
filename_template = "{product_identifier}_IRECI{ext}"
ext = ".jp2"
ext_raw = ".tif"
colormap = cm.Spectral
def __init__(self, l2a_product_object, cm_product_object):
if (l2a_product_object or cm_product_object) is None:
raise ValueError("A L2aProduct and NewCloudMask objects must be provided")
......@@ -545,10 +513,8 @@ class Ndre(Indice):
self.l2a_product = l2a_product_object
self.cm_product = cm_product_object
# output path
self.out_path = None
# filenames
self.indice_stem = self.filename_template.format(product_identifier=self.l2a_product.identifier, ext="")
self.indice_filename = self.indice_stem + self.ext
self.indice_raw = self.indice_stem + self.ext_raw
......@@ -565,11 +531,14 @@ class Ndre(Indice):
if (out_path / self.indice_filename).exists() and not reprocess:
logger.info("{} already exists".format(self.indice_filename))
else:
create_raw_ndre(nir_path=self.l2a_product.b08_10m,
redge_path=self.l2a_product.b05_20m,
out_path=(out_path / self.indice_raw))
create_raw_ireci(b1_path = self.l2a_product.b07_20m,
b2_path = self.l2a_product.b04_10m,
b3_path = self.l2a_product.b05_20m,
b4_path = self.l2a_product.b06_20m,
out_path=(out_path / self.indice_raw))
index_tiff_2_jp2(img_path=(out_path / self.indice_raw),
out_path=(out_path / self.indice_filename))
out_path=(out_path / self.indice_filename),
quality = 30)
if nodata_clouds:
if not self.cm_product.path.exists():
......@@ -588,7 +557,8 @@ class Ndre(Indice):
cloud_mask_path=self.cm_product.path,
out_path=(out_path / masked_indice_raw))
index_tiff_2_jp2(img_path=(out_path / masked_indice_raw),
out_path=(out_path / masked_indice_filename))
out_path=(out_path / masked_indice_filename),
quality = 30)
os.remove(str(out_path / masked_indice_raw))
try:
......@@ -609,20 +579,6 @@ class Ndre(Indice):
out_path=(self.out_path / quicklook_filename))
# A faire
class IRECI(Indice):
"""
IRECI =
"""
name = "IRECI"
filename_template = "{product_identifier}_IRECI{ext}"
ext = ".jp2"
ext_raw = ".tif"
colormap = cm.Spectral
class BIGR(Indice):
"""
Brightness Index Green Red = ( (GREEN² + RED²)/2 ) ^ 0.5
......
sen2chain/indices_functions.py
+ 259
− 297
View file @ 9749ac2b
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