Module eoreader.products.optical.s2_product
Sentinel-2 products
Expand source code
# -*- coding: utf-8 -*-
# Copyright 2021, SERTIT-ICube - France, https://sertit.unistra.fr/
# This file is part of eoreader project
# https://github.com/sertit/eoreader
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
""" Sentinel-2 products """
import glob
import logging
import os
import re
import zipfile
from datetime import datetime
from enum import unique
from typing import Union
import geopandas as gpd
import numpy as np
import xarray as xr
from lxml import etree
from rasterio import features
from rasterio.enums import Resampling
from eoreader.bands.alias import ALL_CLOUDS, CIRRUS, CLOUDS, RAW_CLOUDS, SHADOWS
from eoreader.bands.bands import BandNames
from eoreader.bands.bands import OpticalBandNames as obn
from eoreader.exceptions import InvalidProductError, InvalidTypeError
from eoreader.products.optical.optical_product import OpticalProduct
from eoreader.utils import DATETIME_FMT, EOREADER_NAME
from sertit import files, rasters
from sertit.misc import ListEnum
from sertit.rasters import ORIGIN_DTYPE, XDS_TYPE
LOGGER = logging.getLogger(EOREADER_NAME)
@unique
class S2ProductType(ListEnum):
"""Sentinel-2 products types (L1C or L2A)"""
L1C = "L1C"
L2A = "L2A"
BAND_DIR_NAMES = {
S2ProductType.L1C: "IMG_DATA",
S2ProductType.L2A: {
"01": ["R60m"],
"02": ["R10m", "R20m", "R60m"],
"03": ["R10m", "R20m", "R60m"],
"04": ["R10m", "R20m", "R60m"],
"05": ["R20m", "R60m"],
"06": ["R20m", "R60m"],
"07": ["R20m", "R60m"],
"08": ["R10m"],
"8A": ["R20m", "R60m"],
"09": ["R60m"],
"11": ["R20m", "R60m"],
"12": ["R20m", "R60m"],
},
}
class S2Product(OpticalProduct):
"""
Class of Sentinel-2 Products
You can use directly the .zip file
"""
def _post_init(self) -> None:
"""
Function used to post_init the products
(setting sensor type, band names and so on)
"""
self.tile_name = self._get_tile_name()
self.needs_extraction = False
# Post init done by the super class
super()._post_init()
def _set_resolution(self) -> float:
"""
Set product default resolution (in meters)
"""
# S2: use 20m resolution, even if we have 60m and 10m resolution
# In the future maybe set one resolution per band ?
return 20.0
def _get_tile_name(self) -> str:
"""
Retrieve tile name
Returns:
str: Tile name
"""
return self.split_name[-2]
def _set_product_type(self) -> None:
"""Get products type"""
if "MSIL2A" in self.name:
self.product_type = S2ProductType.L2A
self.band_names.map_bands(
{
obn.CA: "01",
obn.BLUE: "02",
obn.GREEN: "03",
obn.RED: "04",
obn.VRE_1: "05",
obn.VRE_2: "06",
obn.VRE_3: "07",
obn.NIR: "08",
obn.NARROW_NIR: "8A",
obn.WV: "09",
obn.SWIR_1: "11",
obn.SWIR_2: "12",
}
)
elif "MSIL1C" in self.name:
self.product_type = S2ProductType.L1C
self.band_names.map_bands(
{
obn.CA: "01",
obn.BLUE: "02",
obn.GREEN: "03",
obn.RED: "04",
obn.VRE_1: "05",
obn.VRE_2: "06",
obn.VRE_3: "07",
obn.NIR: "08",
obn.NARROW_NIR: "8A",
obn.WV: "09",
obn.SWIR_CIRRUS: "10",
obn.SWIR_1: "11",
obn.SWIR_2: "12",
}
)
else:
raise InvalidProductError(f"Invalid Sentinel-2 name: {self.name}")
def get_datetime(self, as_datetime: bool = False) -> Union[str, datetime]:
"""
Get the product's acquisition datetime, with format `YYYYMMDDTHHMMSS` <-> `%Y%m%dT%H%M%S`
```python
>>> from eoreader.reader import Reader
>>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip"
>>> prod = Reader().open(path)
>>> prod.get_datetime(as_datetime=True)
datetime.datetime(2020, 8, 24, 11, 6, 31)
>>> prod.get_datetime(as_datetime=False)
'20200824T110631'
```
Args:
as_datetime (bool): Return the date as a datetime.datetime. If false, returns a string.
Returns:
Union[str, datetime.datetime]: Its acquisition datetime
"""
date = self.split_name[2]
if as_datetime:
date = datetime.strptime(date, DATETIME_FMT)
return date
def _get_res_band_folder(self, band_list: list, resolution: float = None) -> dict:
"""
Return the folder containing the bands of a proper S2 products.
(IMG_DATA for L1C, IMG_DATA/Rx0m for L2A)
Args:
band_list (list): Wanted bands (listed as 01, 02...)
resolution (float): Band resolution for Sentinel-2 products {R10m, R20m, R60m}.
The wanted bands will be chosen in this proper folder.
Returns:
dict: Dictionary containing the folder path for each queried band
"""
# Open the band directory names
s2_bands_folder = {}
# Manage L2A
band_dir = BAND_DIR_NAMES[self.product_type]
for band in band_list:
assert band in obn
band_nb = self.band_names[band]
if band_nb is None:
raise InvalidProductError(
f"Non existing band ({band.name}) for S2-{self.product_type.name} products"
)
# If L2A products, we care about the resolution
if self.product_type == S2ProductType.L2A:
# If we got a true S2 resolution, open the corresponding band
if resolution and f"R{int(resolution)}m" in band_dir[band_nb]:
dir_name = f"R{int(resolution)}m"
# Else open the first one, it will be resampled when the ban will be read
else:
dir_name = band_dir[band_nb][0]
# If L1C, we do not
else:
dir_name = band_dir
if self.is_archived:
# Open the zip file
with zipfile.ZipFile(self.path, "r") as zip_ds:
# Get the band folder (use dirname is the first of the list is a band)
s2_bands_folder[band] = [
os.path.dirname(f.filename)
for f in zip_ds.filelist
if dir_name in f.filename
][0]
else:
# Search for the name of the folder into the S2 products
for root, folders, _ in os.walk(os.path.abspath(self.path)):
for folder in folders:
if folder == dir_name:
s2_bands_folder[band] = os.path.join(root, folder)
for band in band_list:
if band not in s2_bands_folder:
raise InvalidProductError(
f"Band folder for band {band.value} not found in {self.path}"
)
return s2_bands_folder
def get_band_paths(self, band_list: list, resolution: float = None) -> dict:
"""
Return the paths of required bands.
```python
>>> from eoreader.reader import Reader
>>> from eoreader.bands.alias import *
>>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip"
>>> prod = Reader().open(path)
>>> prod.get_band_paths([GREEN, RED])
{
<OpticalBandNames.GREEN: 'GREEN'>: 'zip+file://S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip!/S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE/GRANULE/L1C_T30TTK_A027018_20200824T111345/IMG_DATA/T30TTK_20200824T110631_B03.jp2',
<OpticalBandNames.RED: 'RED'>: 'zip+file://S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip!/S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE/GRANULE/L1C_T30TTK_A027018_20200824T111345/IMG_DATA/T30TTK_20200824T110631_B04.jp2'
}
```
Args:
band_list (list): List of the wanted bands
resolution (float): Band resolution
Returns:
dict: Dictionary containing the path of each queried band
"""
band_folders = self._get_res_band_folder(band_list, resolution)
band_paths = {}
for band in band_list:
try:
if self.is_archived:
band_paths[band] = files.get_archived_rio_path(
self.path,
f".*{band_folders[band]}.*_B{self.band_names[band]}.*.jp2",
)
else:
band_paths[band] = files.get_file_in_dir(
band_folders[band],
"_B" + self.band_names[band],
extension="jp2",
)
except (FileNotFoundError, IndexError) as ex:
raise InvalidProductError(
f"Non existing {band} ({self.band_names[band]}) band for {self.path}"
) from ex
return band_paths
def _read_band(
self,
path: str,
resolution: Union[tuple, list, float] = None,
size: Union[list, tuple] = None,
) -> XDS_TYPE:
"""
Read band from a dataset.
.. WARNING::
Invalid pixels are not managed here !
Args:
path (str): Band path
resolution (Union[tuple, list, float]): Resolution of the wanted band, in dataset resolution unit (X, Y)
size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided.
Returns:
XDS_TYPE: Radiometrically coherent band, saved as float 32
"""
# Read band
band = rasters.read(
path, resolution=resolution, size=size, resampling=Resampling.bilinear
)
# Compute the correct radiometry of the band
if band.attrs[ORIGIN_DTYPE] == "uint16":
band /= 10000.0
return band
def open_mask(self, mask_str: str, band: Union[obn, str]) -> gpd.GeoDataFrame:
"""
Open S2 mask (GML files stored in QI_DATA) as `gpd.GeoDataFrame`.
Masks than can be called that way are:
- `TECQUA`: Technical quality mask
- `SATURA`: Saturated Pixels
- `NODATA`: Pixel nodata (inside the detectors)
- `DETFOO`: Detectors footprint -> used to process nodata outside the detectors
- `DEFECT`: Defective pixels
- `CLOUDS`, **only with `00` as a band !**
```python
>>> from eoreader.reader import Reader
>>> from eoreader.bands.alias import *
>>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip"
>>> prod.open_mask("NODATA", GREEN)
Empty GeoDataFrame
Columns: [geometry]
Index: []
>>> prod.open_mask("SATURA", GREEN)
Empty GeoDataFrame
Columns: [geometry]
Index: []
>>> prod.open_mask("DETFOO", GREEN)
gml_id ... geometry
0 detector_footprint-B03-02-0 ... POLYGON Z ((199980.000 4500000.000 0.000, 1999...
1 detector_footprint-B03-03-1 ... POLYGON Z ((222570.000 4500000.000 0.000, 2225...
2 detector_footprint-B03-05-2 ... POLYGON Z ((273050.000 4500000.000 0.000, 2730...
3 detector_footprint-B03-07-3 ... POLYGON Z ((309770.000 4453710.000 0.000, 3097...
4 detector_footprint-B03-04-4 ... POLYGON Z ((248080.000 4500000.000 0.000, 2480...
5 detector_footprint-B03-06-5 ... POLYGON Z ((297980.000 4500000.000 0.000, 2979...
[6 rows x 3 columns]
```
Args:
mask_str (str): Mask name, such as DEFECT, NODATA, SATURA...
band (Union[obn, str]): Band number as an OpticalBandNames or str (for clouds: 00)
Returns:
gpd.GeoDataFrame: Mask as a vector
"""
# Check inputs
assert mask_str in ["DEFECT", "DETFOO", "NODATA", "SATURA", "TECQUA", "CLOUDS"]
if mask_str == "CLOUDS":
band = "00"
def _open_mask(fct, *args, **kwargs):
# Read the GML file
try:
# Discard some weird error concerning a NULL pointer that outputs a ValueError (as we already except it)
fiona_logger = logging.getLogger("fiona._env")
fiona_logger.setLevel(logging.CRITICAL)
# Read mask
mask = fct(*args, **kwargs)
# Set fiona logger back to what it was
fiona_logger.setLevel(logging.INFO)
except ValueError:
mask = gpd.GeoDataFrame(geometry=[], crs=self.crs())
return mask
# Get QI_DATA path
if isinstance(band, obn):
band_name = self.band_names[band]
else:
band_name = band
if self.is_archived:
# Open the zip file
# WE DON'T KNOW WHY BUT DO NOT USE files.read_archived_vector HERE !!!
with zipfile.ZipFile(self.path, "r") as zip_ds:
filenames = [f.filename for f in zip_ds.filelist]
regex = re.compile(
f".*GRANULE.*QI_DATA.*MSK_{mask_str}_B{band_name}.gml"
)
with zip_ds.open(list(filter(regex.match, filenames))[0]) as mask_path:
mask = _open_mask(gpd.read_file, mask_path)
# mask = _open_mask(files.read_archived_vector,
# self.path,
# f".*GRANULE.*QI_DATA.*MSK_{mask_str}_B{band_name}\.gml")
else:
qi_data_path = os.path.join(self.path, "GRANULE", "*", "QI_DATA")
# Get mask path
mask_path = files.get_file_in_dir(
qi_data_path, f"MSK_{mask_str}_B{band_name}.gml", exact_name=True
)
mask = _open_mask(gpd.read_file, mask_path)
return mask
# pylint: disable=R0913
# R0913: Too many arguments (6/5) (too-many-arguments)
def _manage_invalid_pixels(
self,
band_arr: XDS_TYPE,
band: obn,
resolution: float = None,
size: Union[list, tuple] = None,
) -> XDS_TYPE:
"""
Manage invalid pixels (Nodata, saturated, defective...)
See there: https://sentinel.esa.int/documents/247904/349490/S2_MSI_Product_Specification.pdf
Args:
band_arr (XDS_TYPE): Band array
band (obn): Band name as an OpticalBandNames
resolution (float): Band resolution in meters
size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided.
Returns:
XDS_TYPE: Cleaned band array
"""
nodata_true = 1
nodata_false = 0
# Get detector footprint to deduce the outside nodata
nodata_det = self.open_mask(
"DETFOO", band
) # Detector nodata, -> pixels that are outside of the detectors
# Rasterize nodata
mask = features.rasterize(
nodata_det.geometry,
out_shape=(band_arr.rio.width, band_arr.rio.height),
fill=nodata_true, # Outside detector = nodata
default_value=nodata_false, # Inside detector = acceptable value
transform=band_arr.rio.transform(),
dtype=np.uint8,
)
# Load masks and merge them into the nodata
nodata_pix = self.open_mask(
"NODATA", band
) # Pixel nodata, not pixels that are outside of the detectors !!!
if len(nodata_pix) > 0:
# Discard pixels corrected during crosstalk
nodata_pix = nodata_pix[nodata_pix.gml_id == "QT_NODATA_PIXELS"]
nodata_pix.append(self.open_mask("DEFECT", band))
nodata_pix.append(self.open_mask("SATURA", band))
# Technical quality mask
tecqua = self.open_mask("TECQUA", band)
if len(tecqua) > 0:
# Do not take into account ancillary data
tecqua = tecqua[tecqua.gml_id.isin(["MSI_LOST", "MSI_DEG"])]
nodata_pix.append(tecqua)
if len(nodata_pix) > 0:
# Rasterize mask
mask_pix = features.rasterize(
nodata_pix.geometry,
out_shape=(band_arr.rio.width, band_arr.rio.height),
fill=nodata_false, # OK pixels = OK value
default_value=nodata_true, # Discarded pixels = nodata
transform=band_arr.rio.transform(),
dtype=np.uint8,
)
mask[mask_pix] = nodata_true
return self._set_nodata_mask(band_arr, mask)
def _load_bands(
self, bands: list, resolution: float = None, size: Union[list, tuple] = None
) -> dict:
"""
Load bands as numpy arrays with the same resolution (and same metadata).
Args:
bands (list): List of the wanted bands
resolution (float): Band resolution in meters
size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided.
Returns:
dict: Dictionary {band_name, band_xarray}
"""
# Return empty if no band are specified
if not bands:
return {}
band_paths = self.get_band_paths(bands, resolution)
# Open bands and get array (resampled if needed)
band_arrays = self._open_bands(band_paths, resolution=resolution, size=size)
return band_arrays
def _get_condensed_name(self) -> str:
"""
Get S2 products condensed name ({date}_S2_{tile}_{product_type}_{processed_hours}).
Returns:
str: Condensed S2 name
"""
# Used to make the difference between 2 products acquired on the same tile at the same date but cut differently
proc_time = self.split_name[-1].split("T")[-1]
return f"{self.get_datetime()}_S2_{self.tile_name}_{self.product_type.value}_{proc_time}"
def get_mean_sun_angles(self) -> (float, float):
"""
Get Mean Sun angles (Azimuth and Zenith angles)
```python
>>> from eoreader.reader import Reader
>>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip"
>>> prod = Reader().open(path)
>>> prod.get_mean_sun_angles()
(149.148155074489, 32.6627897525474)
```
Returns:
(float, float): Mean Azimuth and Zenith angle
"""
# Init angles
zenith_angle = None
azimuth_angle = None
# Read metadata
root, namespace = self.read_mtd()
# Open zenith and azimuth angle
for element in root:
if element.tag == namespace + "Geometric_Info":
for node in element:
if node.tag == "Tile_Angles":
mean_sun_angles = node.find("Mean_Sun_Angle")
zenith_angle = float(mean_sun_angles.findtext("ZENITH_ANGLE"))
azimuth_angle = float(mean_sun_angles.findtext("AZIMUTH_ANGLE"))
break # Only one Mean_Sun_Angle
break # Only one Geometric_Info
if not zenith_angle or not azimuth_angle:
raise InvalidProductError("Azimuth or Zenith angles not found")
return azimuth_angle, zenith_angle
def read_mtd(self) -> (etree._Element, str):
"""
Read metadata and outputs the metadata XML root and its namespace
```python
>>> from eoreader.reader import Reader
>>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip"
>>> prod = Reader().open(path)
>>> prod.read_mtd()
(<Element {https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}Level-2A_Tile_ID at ...>,
'{https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}')
```
Returns:
(etree._Element, str): Metadata XML root and its namespace
"""
# Get MTD XML file
if self.is_archived:
root = files.read_archived_xml(self.path, ".*GRANULE.*\.xml")
else:
# Open metadata file
try:
mtd_file = glob.glob(os.path.join(self.path, "GRANULE", "*", "*.xml"))[
0
]
# pylint: disable=I1101:
# Module 'lxml.etree' has no 'parse' member, but source is unavailable.
xml_tree = etree.parse(mtd_file)
root = xml_tree.getroot()
except IndexError as ex:
raise InvalidProductError(
f"Metadata file not found in {self.path}"
) from ex
# Get namespace
idx = root.tag.rindex("}")
namespace = root.tag[: idx + 1]
return root, namespace
def _has_cloud_band(self, band: BandNames) -> bool:
"""
Does this products has the specified cloud band ?
https://sentinels.copernicus.eu/web/sentinel/technical-guides/sentinel-2-msi/level-1c/cloud-masks
"""
if band == SHADOWS:
has_band = False
else:
has_band = True
return has_band
def _load_clouds(
self, bands: list, resolution: float = None, size: Union[list, tuple] = None
) -> dict:
"""
Load cloud files as numpy arrays with the same resolution (and same metadata).
Read S2 cloud mask .GML files (both valid for L2A and L1C products).
https://sentinels.copernicus.eu/web/sentinel/technical-guides/sentinel-2-msi/level-1c/cloud-masks
Args:
bands (list): List of the wanted bands
resolution (int): Band resolution in meters
size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided.
Returns:
dict: Dictionary {band_name, band_xarray}
"""
band_dict = {}
if bands:
def_band = self.get_default_band()
cloud_vec = self.open_mask("CLOUDS", "00")
# Open a bands to mask it
def_band = self.load(def_band, resolution=resolution)[def_band]
nodata = np.where(np.isnan(def_band), 1, 0)
for band in bands:
if band == ALL_CLOUDS:
band_dict[band] = self._rasterize(def_band, cloud_vec, nodata)
elif band == CIRRUS:
try:
cirrus = cloud_vec[cloud_vec.maskType == "CIRRUS"]
except AttributeError:
# No masktype -> empty
cirrus = gpd.GeoDataFrame(geometry=[], crs=cloud_vec.crs)
band_dict[band] = self._rasterize(def_band, cirrus, nodata)
elif band == CLOUDS:
try:
clouds = cloud_vec[cloud_vec.maskType == "OPAQUE"]
except AttributeError:
# No masktype -> empty
clouds = gpd.GeoDataFrame(geometry=[], crs=cloud_vec.crs)
band_dict[band] = self._rasterize(def_band, clouds, nodata)
elif band == RAW_CLOUDS:
band_dict[band] = self._rasterize(def_band, cloud_vec, nodata)
else:
raise InvalidTypeError(
f"Non existing cloud band for Sentinel-2: {band}"
)
return band_dict
def _rasterize(
self, xds: XDS_TYPE, geometry: gpd.GeoDataFrame, nodata: np.ndarray
) -> xr.DataArray:
"""
Rasterize a vector on a memory dataset
Args:
xds: xarray
geometry (gpd.GeoDataFrame): Geometry to rasterize
nodata (np.ndarray): Nodata mask
Returns:
xr.DataArray: Rasterized vector
"""
if not geometry.empty:
# Just in case
if geometry.crs != xds.rio.crs:
geometry = geometry.to_crs(xds.rio.crs)
# Mask the file -> do not use rasterize to get a correct nodata mask !
rstrzd = rasters.mask(xds, geometry.geometry, nodata=xds.rio.encoded_nodata)
# Get cloud raster
cond = np.where(rstrzd.data > 0, self._mask_true, self._mask_false)
else:
# If empty geometry, just
cond = np.full(
shape=(xds.rio.count, xds.rio.height, xds.rio.width),
fill_value=self._mask_false,
dtype=np.uint8,
)
return self._create_mask(xds, cond, nodata)
Classes
class S2ProductType (value, names=None, *, module=None, qualname=None, type=None, start=1)
-
Sentinel-2 products types (L1C or L2A)
Expand source code
class S2ProductType(ListEnum): """Sentinel-2 products types (L1C or L2A)""" L1C = "L1C" L2A = "L2A"
Ancestors
- sertit.misc.ListEnum
- enum.Enum
Class variables
var L1C
var L2A
class S2Product (product_path, archive_path=None, output_path=None)
-
Class of Sentinel-2 Products
You can use directly the .zip file
Expand source code
class S2Product(OpticalProduct): """ Class of Sentinel-2 Products You can use directly the .zip file """ def _post_init(self) -> None: """ Function used to post_init the products (setting sensor type, band names and so on) """ self.tile_name = self._get_tile_name() self.needs_extraction = False # Post init done by the super class super()._post_init() def _set_resolution(self) -> float: """ Set product default resolution (in meters) """ # S2: use 20m resolution, even if we have 60m and 10m resolution # In the future maybe set one resolution per band ? return 20.0 def _get_tile_name(self) -> str: """ Retrieve tile name Returns: str: Tile name """ return self.split_name[-2] def _set_product_type(self) -> None: """Get products type""" if "MSIL2A" in self.name: self.product_type = S2ProductType.L2A self.band_names.map_bands( { obn.CA: "01", obn.BLUE: "02", obn.GREEN: "03", obn.RED: "04", obn.VRE_1: "05", obn.VRE_2: "06", obn.VRE_3: "07", obn.NIR: "08", obn.NARROW_NIR: "8A", obn.WV: "09", obn.SWIR_1: "11", obn.SWIR_2: "12", } ) elif "MSIL1C" in self.name: self.product_type = S2ProductType.L1C self.band_names.map_bands( { obn.CA: "01", obn.BLUE: "02", obn.GREEN: "03", obn.RED: "04", obn.VRE_1: "05", obn.VRE_2: "06", obn.VRE_3: "07", obn.NIR: "08", obn.NARROW_NIR: "8A", obn.WV: "09", obn.SWIR_CIRRUS: "10", obn.SWIR_1: "11", obn.SWIR_2: "12", } ) else: raise InvalidProductError(f"Invalid Sentinel-2 name: {self.name}") def get_datetime(self, as_datetime: bool = False) -> Union[str, datetime]: """ Get the product's acquisition datetime, with format `YYYYMMDDTHHMMSS` <-> `%Y%m%dT%H%M%S` ```python >>> from eoreader.reader import Reader >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.get_datetime(as_datetime=True) datetime.datetime(2020, 8, 24, 11, 6, 31) >>> prod.get_datetime(as_datetime=False) '20200824T110631' ``` Args: as_datetime (bool): Return the date as a datetime.datetime. If false, returns a string. Returns: Union[str, datetime.datetime]: Its acquisition datetime """ date = self.split_name[2] if as_datetime: date = datetime.strptime(date, DATETIME_FMT) return date def _get_res_band_folder(self, band_list: list, resolution: float = None) -> dict: """ Return the folder containing the bands of a proper S2 products. (IMG_DATA for L1C, IMG_DATA/Rx0m for L2A) Args: band_list (list): Wanted bands (listed as 01, 02...) resolution (float): Band resolution for Sentinel-2 products {R10m, R20m, R60m}. The wanted bands will be chosen in this proper folder. Returns: dict: Dictionary containing the folder path for each queried band """ # Open the band directory names s2_bands_folder = {} # Manage L2A band_dir = BAND_DIR_NAMES[self.product_type] for band in band_list: assert band in obn band_nb = self.band_names[band] if band_nb is None: raise InvalidProductError( f"Non existing band ({band.name}) for S2-{self.product_type.name} products" ) # If L2A products, we care about the resolution if self.product_type == S2ProductType.L2A: # If we got a true S2 resolution, open the corresponding band if resolution and f"R{int(resolution)}m" in band_dir[band_nb]: dir_name = f"R{int(resolution)}m" # Else open the first one, it will be resampled when the ban will be read else: dir_name = band_dir[band_nb][0] # If L1C, we do not else: dir_name = band_dir if self.is_archived: # Open the zip file with zipfile.ZipFile(self.path, "r") as zip_ds: # Get the band folder (use dirname is the first of the list is a band) s2_bands_folder[band] = [ os.path.dirname(f.filename) for f in zip_ds.filelist if dir_name in f.filename ][0] else: # Search for the name of the folder into the S2 products for root, folders, _ in os.walk(os.path.abspath(self.path)): for folder in folders: if folder == dir_name: s2_bands_folder[band] = os.path.join(root, folder) for band in band_list: if band not in s2_bands_folder: raise InvalidProductError( f"Band folder for band {band.value} not found in {self.path}" ) return s2_bands_folder def get_band_paths(self, band_list: list, resolution: float = None) -> dict: """ Return the paths of required bands. ```python >>> from eoreader.reader import Reader >>> from eoreader.bands.alias import * >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.get_band_paths([GREEN, RED]) { <OpticalBandNames.GREEN: 'GREEN'>: 'zip+file://S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip!/S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE/GRANULE/L1C_T30TTK_A027018_20200824T111345/IMG_DATA/T30TTK_20200824T110631_B03.jp2', <OpticalBandNames.RED: 'RED'>: 'zip+file://S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip!/S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE/GRANULE/L1C_T30TTK_A027018_20200824T111345/IMG_DATA/T30TTK_20200824T110631_B04.jp2' } ``` Args: band_list (list): List of the wanted bands resolution (float): Band resolution Returns: dict: Dictionary containing the path of each queried band """ band_folders = self._get_res_band_folder(band_list, resolution) band_paths = {} for band in band_list: try: if self.is_archived: band_paths[band] = files.get_archived_rio_path( self.path, f".*{band_folders[band]}.*_B{self.band_names[band]}.*.jp2", ) else: band_paths[band] = files.get_file_in_dir( band_folders[band], "_B" + self.band_names[band], extension="jp2", ) except (FileNotFoundError, IndexError) as ex: raise InvalidProductError( f"Non existing {band} ({self.band_names[band]}) band for {self.path}" ) from ex return band_paths def _read_band( self, path: str, resolution: Union[tuple, list, float] = None, size: Union[list, tuple] = None, ) -> XDS_TYPE: """ Read band from a dataset. .. WARNING:: Invalid pixels are not managed here ! Args: path (str): Band path resolution (Union[tuple, list, float]): Resolution of the wanted band, in dataset resolution unit (X, Y) size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided. Returns: XDS_TYPE: Radiometrically coherent band, saved as float 32 """ # Read band band = rasters.read( path, resolution=resolution, size=size, resampling=Resampling.bilinear ) # Compute the correct radiometry of the band if band.attrs[ORIGIN_DTYPE] == "uint16": band /= 10000.0 return band def open_mask(self, mask_str: str, band: Union[obn, str]) -> gpd.GeoDataFrame: """ Open S2 mask (GML files stored in QI_DATA) as `gpd.GeoDataFrame`. Masks than can be called that way are: - `TECQUA`: Technical quality mask - `SATURA`: Saturated Pixels - `NODATA`: Pixel nodata (inside the detectors) - `DETFOO`: Detectors footprint -> used to process nodata outside the detectors - `DEFECT`: Defective pixels - `CLOUDS`, **only with `00` as a band !** ```python >>> from eoreader.reader import Reader >>> from eoreader.bands.alias import * >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod.open_mask("NODATA", GREEN) Empty GeoDataFrame Columns: [geometry] Index: [] >>> prod.open_mask("SATURA", GREEN) Empty GeoDataFrame Columns: [geometry] Index: [] >>> prod.open_mask("DETFOO", GREEN) gml_id ... geometry 0 detector_footprint-B03-02-0 ... POLYGON Z ((199980.000 4500000.000 0.000, 1999... 1 detector_footprint-B03-03-1 ... POLYGON Z ((222570.000 4500000.000 0.000, 2225... 2 detector_footprint-B03-05-2 ... POLYGON Z ((273050.000 4500000.000 0.000, 2730... 3 detector_footprint-B03-07-3 ... POLYGON Z ((309770.000 4453710.000 0.000, 3097... 4 detector_footprint-B03-04-4 ... POLYGON Z ((248080.000 4500000.000 0.000, 2480... 5 detector_footprint-B03-06-5 ... POLYGON Z ((297980.000 4500000.000 0.000, 2979... [6 rows x 3 columns] ``` Args: mask_str (str): Mask name, such as DEFECT, NODATA, SATURA... band (Union[obn, str]): Band number as an OpticalBandNames or str (for clouds: 00) Returns: gpd.GeoDataFrame: Mask as a vector """ # Check inputs assert mask_str in ["DEFECT", "DETFOO", "NODATA", "SATURA", "TECQUA", "CLOUDS"] if mask_str == "CLOUDS": band = "00" def _open_mask(fct, *args, **kwargs): # Read the GML file try: # Discard some weird error concerning a NULL pointer that outputs a ValueError (as we already except it) fiona_logger = logging.getLogger("fiona._env") fiona_logger.setLevel(logging.CRITICAL) # Read mask mask = fct(*args, **kwargs) # Set fiona logger back to what it was fiona_logger.setLevel(logging.INFO) except ValueError: mask = gpd.GeoDataFrame(geometry=[], crs=self.crs()) return mask # Get QI_DATA path if isinstance(band, obn): band_name = self.band_names[band] else: band_name = band if self.is_archived: # Open the zip file # WE DON'T KNOW WHY BUT DO NOT USE files.read_archived_vector HERE !!! with zipfile.ZipFile(self.path, "r") as zip_ds: filenames = [f.filename for f in zip_ds.filelist] regex = re.compile( f".*GRANULE.*QI_DATA.*MSK_{mask_str}_B{band_name}.gml" ) with zip_ds.open(list(filter(regex.match, filenames))[0]) as mask_path: mask = _open_mask(gpd.read_file, mask_path) # mask = _open_mask(files.read_archived_vector, # self.path, # f".*GRANULE.*QI_DATA.*MSK_{mask_str}_B{band_name}\.gml") else: qi_data_path = os.path.join(self.path, "GRANULE", "*", "QI_DATA") # Get mask path mask_path = files.get_file_in_dir( qi_data_path, f"MSK_{mask_str}_B{band_name}.gml", exact_name=True ) mask = _open_mask(gpd.read_file, mask_path) return mask # pylint: disable=R0913 # R0913: Too many arguments (6/5) (too-many-arguments) def _manage_invalid_pixels( self, band_arr: XDS_TYPE, band: obn, resolution: float = None, size: Union[list, tuple] = None, ) -> XDS_TYPE: """ Manage invalid pixels (Nodata, saturated, defective...) See there: https://sentinel.esa.int/documents/247904/349490/S2_MSI_Product_Specification.pdf Args: band_arr (XDS_TYPE): Band array band (obn): Band name as an OpticalBandNames resolution (float): Band resolution in meters size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided. Returns: XDS_TYPE: Cleaned band array """ nodata_true = 1 nodata_false = 0 # Get detector footprint to deduce the outside nodata nodata_det = self.open_mask( "DETFOO", band ) # Detector nodata, -> pixels that are outside of the detectors # Rasterize nodata mask = features.rasterize( nodata_det.geometry, out_shape=(band_arr.rio.width, band_arr.rio.height), fill=nodata_true, # Outside detector = nodata default_value=nodata_false, # Inside detector = acceptable value transform=band_arr.rio.transform(), dtype=np.uint8, ) # Load masks and merge them into the nodata nodata_pix = self.open_mask( "NODATA", band ) # Pixel nodata, not pixels that are outside of the detectors !!! if len(nodata_pix) > 0: # Discard pixels corrected during crosstalk nodata_pix = nodata_pix[nodata_pix.gml_id == "QT_NODATA_PIXELS"] nodata_pix.append(self.open_mask("DEFECT", band)) nodata_pix.append(self.open_mask("SATURA", band)) # Technical quality mask tecqua = self.open_mask("TECQUA", band) if len(tecqua) > 0: # Do not take into account ancillary data tecqua = tecqua[tecqua.gml_id.isin(["MSI_LOST", "MSI_DEG"])] nodata_pix.append(tecqua) if len(nodata_pix) > 0: # Rasterize mask mask_pix = features.rasterize( nodata_pix.geometry, out_shape=(band_arr.rio.width, band_arr.rio.height), fill=nodata_false, # OK pixels = OK value default_value=nodata_true, # Discarded pixels = nodata transform=band_arr.rio.transform(), dtype=np.uint8, ) mask[mask_pix] = nodata_true return self._set_nodata_mask(band_arr, mask) def _load_bands( self, bands: list, resolution: float = None, size: Union[list, tuple] = None ) -> dict: """ Load bands as numpy arrays with the same resolution (and same metadata). Args: bands (list): List of the wanted bands resolution (float): Band resolution in meters size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided. Returns: dict: Dictionary {band_name, band_xarray} """ # Return empty if no band are specified if not bands: return {} band_paths = self.get_band_paths(bands, resolution) # Open bands and get array (resampled if needed) band_arrays = self._open_bands(band_paths, resolution=resolution, size=size) return band_arrays def _get_condensed_name(self) -> str: """ Get S2 products condensed name ({date}_S2_{tile}_{product_type}_{processed_hours}). Returns: str: Condensed S2 name """ # Used to make the difference between 2 products acquired on the same tile at the same date but cut differently proc_time = self.split_name[-1].split("T")[-1] return f"{self.get_datetime()}_S2_{self.tile_name}_{self.product_type.value}_{proc_time}" def get_mean_sun_angles(self) -> (float, float): """ Get Mean Sun angles (Azimuth and Zenith angles) ```python >>> from eoreader.reader import Reader >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.get_mean_sun_angles() (149.148155074489, 32.6627897525474) ``` Returns: (float, float): Mean Azimuth and Zenith angle """ # Init angles zenith_angle = None azimuth_angle = None # Read metadata root, namespace = self.read_mtd() # Open zenith and azimuth angle for element in root: if element.tag == namespace + "Geometric_Info": for node in element: if node.tag == "Tile_Angles": mean_sun_angles = node.find("Mean_Sun_Angle") zenith_angle = float(mean_sun_angles.findtext("ZENITH_ANGLE")) azimuth_angle = float(mean_sun_angles.findtext("AZIMUTH_ANGLE")) break # Only one Mean_Sun_Angle break # Only one Geometric_Info if not zenith_angle or not azimuth_angle: raise InvalidProductError("Azimuth or Zenith angles not found") return azimuth_angle, zenith_angle def read_mtd(self) -> (etree._Element, str): """ Read metadata and outputs the metadata XML root and its namespace ```python >>> from eoreader.reader import Reader >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.read_mtd() (<Element {https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}Level-2A_Tile_ID at ...>, '{https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}') ``` Returns: (etree._Element, str): Metadata XML root and its namespace """ # Get MTD XML file if self.is_archived: root = files.read_archived_xml(self.path, ".*GRANULE.*\.xml") else: # Open metadata file try: mtd_file = glob.glob(os.path.join(self.path, "GRANULE", "*", "*.xml"))[ 0 ] # pylint: disable=I1101: # Module 'lxml.etree' has no 'parse' member, but source is unavailable. xml_tree = etree.parse(mtd_file) root = xml_tree.getroot() except IndexError as ex: raise InvalidProductError( f"Metadata file not found in {self.path}" ) from ex # Get namespace idx = root.tag.rindex("}") namespace = root.tag[: idx + 1] return root, namespace def _has_cloud_band(self, band: BandNames) -> bool: """ Does this products has the specified cloud band ? https://sentinels.copernicus.eu/web/sentinel/technical-guides/sentinel-2-msi/level-1c/cloud-masks """ if band == SHADOWS: has_band = False else: has_band = True return has_band def _load_clouds( self, bands: list, resolution: float = None, size: Union[list, tuple] = None ) -> dict: """ Load cloud files as numpy arrays with the same resolution (and same metadata). Read S2 cloud mask .GML files (both valid for L2A and L1C products). https://sentinels.copernicus.eu/web/sentinel/technical-guides/sentinel-2-msi/level-1c/cloud-masks Args: bands (list): List of the wanted bands resolution (int): Band resolution in meters size (Union[tuple, list]): Size of the array (width, height). Not used if resolution is provided. Returns: dict: Dictionary {band_name, band_xarray} """ band_dict = {} if bands: def_band = self.get_default_band() cloud_vec = self.open_mask("CLOUDS", "00") # Open a bands to mask it def_band = self.load(def_band, resolution=resolution)[def_band] nodata = np.where(np.isnan(def_band), 1, 0) for band in bands: if band == ALL_CLOUDS: band_dict[band] = self._rasterize(def_band, cloud_vec, nodata) elif band == CIRRUS: try: cirrus = cloud_vec[cloud_vec.maskType == "CIRRUS"] except AttributeError: # No masktype -> empty cirrus = gpd.GeoDataFrame(geometry=[], crs=cloud_vec.crs) band_dict[band] = self._rasterize(def_band, cirrus, nodata) elif band == CLOUDS: try: clouds = cloud_vec[cloud_vec.maskType == "OPAQUE"] except AttributeError: # No masktype -> empty clouds = gpd.GeoDataFrame(geometry=[], crs=cloud_vec.crs) band_dict[band] = self._rasterize(def_band, clouds, nodata) elif band == RAW_CLOUDS: band_dict[band] = self._rasterize(def_band, cloud_vec, nodata) else: raise InvalidTypeError( f"Non existing cloud band for Sentinel-2: {band}" ) return band_dict def _rasterize( self, xds: XDS_TYPE, geometry: gpd.GeoDataFrame, nodata: np.ndarray ) -> xr.DataArray: """ Rasterize a vector on a memory dataset Args: xds: xarray geometry (gpd.GeoDataFrame): Geometry to rasterize nodata (np.ndarray): Nodata mask Returns: xr.DataArray: Rasterized vector """ if not geometry.empty: # Just in case if geometry.crs != xds.rio.crs: geometry = geometry.to_crs(xds.rio.crs) # Mask the file -> do not use rasterize to get a correct nodata mask ! rstrzd = rasters.mask(xds, geometry.geometry, nodata=xds.rio.encoded_nodata) # Get cloud raster cond = np.where(rstrzd.data > 0, self._mask_true, self._mask_false) else: # If empty geometry, just cond = np.full( shape=(xds.rio.count, xds.rio.height, xds.rio.width), fill_value=self._mask_false, dtype=np.uint8, ) return self._create_mask(xds, cond, nodata)
Ancestors
Instance variables
var output
-
Inherited from:
OpticalProduct
.output
Output directory of the product, to write orthorectified data for example.
var name
-
Inherited from:
OpticalProduct
.name
Product name (its filename without any extension).
var split_name
-
Inherited from:
OpticalProduct
.split_name
Split name, to retrieve every information from its filename (dates, tile, product type…).
var archive_path
-
Inherited from:
OpticalProduct
.archive_path
Archive path, same as the product path if not specified. Useful when you want to know where both the extracted and archived version of your product …
var path
-
Inherited from:
OpticalProduct
.path
Usable path to the product, either extracted or archived path, according to the satellite.
var is_archived
-
Inherited from:
OpticalProduct
.is_archived
Is the archived product is processed (a products is considered as archived if its products path is a directory).
var needs_extraction
-
Inherited from:
OpticalProduct
.needs_extraction
Does this products needs to be extracted to be processed ? (
True
by default). var date
-
Inherited from:
OpticalProduct
.date
Acquisition date.
var datetime
-
Inherited from:
OpticalProduct
.datetime
Acquisition datetime.
var tile_name
-
Inherited from:
OpticalProduct
.tile_name
Tile if possible (for data that can be piled, for example S2 and Landsats).
var sensor_type
-
Inherited from:
OpticalProduct
.sensor_type
Sensor type, SAR or optical.
var product_type
-
Inherited from:
OpticalProduct
.product_type
Product type, satellite-related field, such as L1C or L2A for Sentinel-2 data.
var band_names
-
Inherited from:
OpticalProduct
.band_names
Band mapping between band wrapping names such as
GREEN
and band real number such as03
for Sentinel-2. var is_reference
-
Inherited from:
OpticalProduct
.is_reference
If the product is a reference, used for algorithms that need pre and post data, such as fire detection.
var corresponding_ref
-
Inherited from:
OpticalProduct
.corresponding_ref
The corresponding reference products to the current one (if the product is not a reference but has a reference data corresponding to it). A list …
var nodata
-
Inherited from:
OpticalProduct
.nodata
Product nodata, set to 0 by default. Please do not touch this or all index will fail.
var platform
-
Inherited from:
OpticalProduct
.platform
Product platform, such as Sentinel-2
var resolution
-
Inherited from:
OpticalProduct
.resolution
Default resolution in meters of the current product. For SAR product, we use Ground Range resolution as we will automatically orthorectify the tiles.
var condensed_name
-
Inherited from:
OpticalProduct
.condensed_name
Condensed name, the filename with only useful data to keep the name unique (ie.
20191215T110441_S2_30TXP_L2A_122756
). Used to shorten names and paths. var sat_id
-
Inherited from:
OpticalProduct
.sat_id
Satellite ID, i.e.
S2
for Sentinel-2
Methods
def get_datetime(
self,
as_datetime=False)-
Inherited from:
OpticalProduct
.get_datetime
Get the product's acquisition datetime, with format
YYYYMMDDTHHMMSS
<->%Y%m%dT%H%M%S
…Expand source code
def get_datetime(self, as_datetime: bool = False) -> Union[str, datetime]: """ Get the product's acquisition datetime, with format `YYYYMMDDTHHMMSS` <-> `%Y%m%dT%H%M%S` ```python >>> from eoreader.reader import Reader >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.get_datetime(as_datetime=True) datetime.datetime(2020, 8, 24, 11, 6, 31) >>> prod.get_datetime(as_datetime=False) '20200824T110631' ``` Args: as_datetime (bool): Return the date as a datetime.datetime. If false, returns a string. Returns: Union[str, datetime.datetime]: Its acquisition datetime """ date = self.split_name[2] if as_datetime: date = datetime.strptime(date, DATETIME_FMT) return date
def get_band_paths(
self,
band_list,
resolution=None)-
Inherited from:
OpticalProduct
.get_band_paths
Return the paths of required bands …
Expand source code
def get_band_paths(self, band_list: list, resolution: float = None) -> dict: """ Return the paths of required bands. ```python >>> from eoreader.reader import Reader >>> from eoreader.bands.alias import * >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.get_band_paths([GREEN, RED]) { <OpticalBandNames.GREEN: 'GREEN'>: 'zip+file://S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip!/S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE/GRANULE/L1C_T30TTK_A027018_20200824T111345/IMG_DATA/T30TTK_20200824T110631_B03.jp2', <OpticalBandNames.RED: 'RED'>: 'zip+file://S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip!/S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE/GRANULE/L1C_T30TTK_A027018_20200824T111345/IMG_DATA/T30TTK_20200824T110631_B04.jp2' } ``` Args: band_list (list): List of the wanted bands resolution (float): Band resolution Returns: dict: Dictionary containing the path of each queried band """ band_folders = self._get_res_band_folder(band_list, resolution) band_paths = {} for band in band_list: try: if self.is_archived: band_paths[band] = files.get_archived_rio_path( self.path, f".*{band_folders[band]}.*_B{self.band_names[band]}.*.jp2", ) else: band_paths[band] = files.get_file_in_dir( band_folders[band], "_B" + self.band_names[band], extension="jp2", ) except (FileNotFoundError, IndexError) as ex: raise InvalidProductError( f"Non existing {band} ({self.band_names[band]}) band for {self.path}" ) from ex return band_paths
def open_mask(
self,
mask_str,
band)-
Open S2 mask (GML files stored in QI_DATA) as
gpd.GeoDataFrame
.Masks than can be called that way are:
TECQUA
: Technical quality maskSATURA
: Saturated PixelsNODATA
: Pixel nodata (inside the detectors)DETFOO
: Detectors footprint -> used to process nodata outside the detectorsDEFECT
: Defective pixelsCLOUDS
, only with00
as a band !
>>> from eoreader.reader import Reader >>> from eoreader.bands.alias import * >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod.open_mask("NODATA", GREEN) Empty GeoDataFrame Columns: [geometry] Index: [] >>> prod.open_mask("SATURA", GREEN) Empty GeoDataFrame Columns: [geometry] Index: [] >>> prod.open_mask("DETFOO", GREEN) gml_id ... geometry 0 detector_footprint-B03-02-0 ... POLYGON Z ((199980.000 4500000.000 0.000, 1999... 1 detector_footprint-B03-03-1 ... POLYGON Z ((222570.000 4500000.000 0.000, 2225... 2 detector_footprint-B03-05-2 ... POLYGON Z ((273050.000 4500000.000 0.000, 2730... 3 detector_footprint-B03-07-3 ... POLYGON Z ((309770.000 4453710.000 0.000, 3097... 4 detector_footprint-B03-04-4 ... POLYGON Z ((248080.000 4500000.000 0.000, 2480... 5 detector_footprint-B03-06-5 ... POLYGON Z ((297980.000 4500000.000 0.000, 2979... [6 rows x 3 columns]
Args
mask_str
:str
- Mask name, such as DEFECT, NODATA, SATURA…
band
:Union[obn, str]
- Band number as an OpticalBandNames or str (for clouds: 00)
Returns
gpd.GeoDataFrame
- Mask as a vector
Expand source code
def open_mask(self, mask_str: str, band: Union[obn, str]) -> gpd.GeoDataFrame: """ Open S2 mask (GML files stored in QI_DATA) as `gpd.GeoDataFrame`. Masks than can be called that way are: - `TECQUA`: Technical quality mask - `SATURA`: Saturated Pixels - `NODATA`: Pixel nodata (inside the detectors) - `DETFOO`: Detectors footprint -> used to process nodata outside the detectors - `DEFECT`: Defective pixels - `CLOUDS`, **only with `00` as a band !** ```python >>> from eoreader.reader import Reader >>> from eoreader.bands.alias import * >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod.open_mask("NODATA", GREEN) Empty GeoDataFrame Columns: [geometry] Index: [] >>> prod.open_mask("SATURA", GREEN) Empty GeoDataFrame Columns: [geometry] Index: [] >>> prod.open_mask("DETFOO", GREEN) gml_id ... geometry 0 detector_footprint-B03-02-0 ... POLYGON Z ((199980.000 4500000.000 0.000, 1999... 1 detector_footprint-B03-03-1 ... POLYGON Z ((222570.000 4500000.000 0.000, 2225... 2 detector_footprint-B03-05-2 ... POLYGON Z ((273050.000 4500000.000 0.000, 2730... 3 detector_footprint-B03-07-3 ... POLYGON Z ((309770.000 4453710.000 0.000, 3097... 4 detector_footprint-B03-04-4 ... POLYGON Z ((248080.000 4500000.000 0.000, 2480... 5 detector_footprint-B03-06-5 ... POLYGON Z ((297980.000 4500000.000 0.000, 2979... [6 rows x 3 columns] ``` Args: mask_str (str): Mask name, such as DEFECT, NODATA, SATURA... band (Union[obn, str]): Band number as an OpticalBandNames or str (for clouds: 00) Returns: gpd.GeoDataFrame: Mask as a vector """ # Check inputs assert mask_str in ["DEFECT", "DETFOO", "NODATA", "SATURA", "TECQUA", "CLOUDS"] if mask_str == "CLOUDS": band = "00" def _open_mask(fct, *args, **kwargs): # Read the GML file try: # Discard some weird error concerning a NULL pointer that outputs a ValueError (as we already except it) fiona_logger = logging.getLogger("fiona._env") fiona_logger.setLevel(logging.CRITICAL) # Read mask mask = fct(*args, **kwargs) # Set fiona logger back to what it was fiona_logger.setLevel(logging.INFO) except ValueError: mask = gpd.GeoDataFrame(geometry=[], crs=self.crs()) return mask # Get QI_DATA path if isinstance(band, obn): band_name = self.band_names[band] else: band_name = band if self.is_archived: # Open the zip file # WE DON'T KNOW WHY BUT DO NOT USE files.read_archived_vector HERE !!! with zipfile.ZipFile(self.path, "r") as zip_ds: filenames = [f.filename for f in zip_ds.filelist] regex = re.compile( f".*GRANULE.*QI_DATA.*MSK_{mask_str}_B{band_name}.gml" ) with zip_ds.open(list(filter(regex.match, filenames))[0]) as mask_path: mask = _open_mask(gpd.read_file, mask_path) # mask = _open_mask(files.read_archived_vector, # self.path, # f".*GRANULE.*QI_DATA.*MSK_{mask_str}_B{band_name}\.gml") else: qi_data_path = os.path.join(self.path, "GRANULE", "*", "QI_DATA") # Get mask path mask_path = files.get_file_in_dir( qi_data_path, f"MSK_{mask_str}_B{band_name}.gml", exact_name=True ) mask = _open_mask(gpd.read_file, mask_path) return mask
def get_mean_sun_angles(
self)
-
Inherited from:
OpticalProduct
.get_mean_sun_angles
Get Mean Sun angles (Azimuth and Zenith angles) …
Expand source code
def get_mean_sun_angles(self) -> (float, float): """ Get Mean Sun angles (Azimuth and Zenith angles) ```python >>> from eoreader.reader import Reader >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.get_mean_sun_angles() (149.148155074489, 32.6627897525474) ``` Returns: (float, float): Mean Azimuth and Zenith angle """ # Init angles zenith_angle = None azimuth_angle = None # Read metadata root, namespace = self.read_mtd() # Open zenith and azimuth angle for element in root: if element.tag == namespace + "Geometric_Info": for node in element: if node.tag == "Tile_Angles": mean_sun_angles = node.find("Mean_Sun_Angle") zenith_angle = float(mean_sun_angles.findtext("ZENITH_ANGLE")) azimuth_angle = float(mean_sun_angles.findtext("AZIMUTH_ANGLE")) break # Only one Mean_Sun_Angle break # Only one Geometric_Info if not zenith_angle or not azimuth_angle: raise InvalidProductError("Azimuth or Zenith angles not found") return azimuth_angle, zenith_angle
def read_mtd(
self)
-
Read metadata and outputs the metadata XML root and its namespace
>>> from eoreader.reader import Reader >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.read_mtd() (<Element {https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}Level-2A_Tile_ID at ...>, '{https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}')
Returns
(etree._Element, str): Metadata XML root and its namespace
Expand source code
def read_mtd(self) -> (etree._Element, str): """ Read metadata and outputs the metadata XML root and its namespace ```python >>> from eoreader.reader import Reader >>> path = r"S2A_MSIL1C_20200824T110631_N0209_R137_T30TTK_20200824T150432.SAFE.zip" >>> prod = Reader().open(path) >>> prod.read_mtd() (<Element {https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}Level-2A_Tile_ID at ...>, '{https://psd-14.sentinel2.eo.esa.int/PSD/S2_PDI_Level-2A_Tile_Metadata.xsd}') ``` Returns: (etree._Element, str): Metadata XML root and its namespace """ # Get MTD XML file if self.is_archived: root = files.read_archived_xml(self.path, ".*GRANULE.*\.xml") else: # Open metadata file try: mtd_file = glob.glob(os.path.join(self.path, "GRANULE", "*", "*.xml"))[ 0 ] # pylint: disable=I1101: # Module 'lxml.etree' has no 'parse' member, but source is unavailable. xml_tree = etree.parse(mtd_file) root = xml_tree.getroot() except IndexError as ex: raise InvalidProductError( f"Metadata file not found in {self.path}" ) from ex # Get namespace idx = root.tag.rindex("}") namespace = root.tag[: idx + 1] return root, namespace
def get_default_band(
self)
-
Inherited from:
OpticalProduct
.get_default_band
Get default band:
GREEN
for optical data as every optical satellite has a GREEN band … def get_default_band_path(
self)
-
Inherited from:
OpticalProduct
.get_default_band_path
Get default band (
GREEN
for optical data) path … def crs(
self)
-
Inherited from:
OpticalProduct
.crs
Get UTM projection of the tile …
def extent(
self)
-
Inherited from:
OpticalProduct
.extent
Get UTM extent of the tile …
def get_existing_bands(
self)
-
Inherited from:
OpticalProduct
.get_existing_bands
Return the existing band paths …
def get_existing_band_paths(
self)
-
Inherited from:
OpticalProduct
.get_existing_band_paths
Return the existing band paths …
def footprint(
self)
-
Inherited from:
OpticalProduct
.footprint
Get UTM footprint of the products (without nodata, in french == emprise utile) …
def get_date(
self,
as_date=False)-
Inherited from:
OpticalProduct
.get_date
Get the product's acquisition date …
def load(
self,
bands,
resolution=None,
size=None)-
Inherited from:
OpticalProduct
.load
Open the bands and compute the wanted index …
def has_band(
self,
band)-
Inherited from:
OpticalProduct
.has_band
Does this products has the specified band ? …
def stack(
self,
bands,
resolution=None,
stack_path=None,
save_as_int=False)-
Inherited from:
OpticalProduct
.stack
Stack bands and index of a products …