From 5545685d7d6fbc4e4f9c1928eecbaad3c225f59f Mon Sep 17 00:00:00 2001
From: Impact <pascal.mouquet@ird.fr>
Date: Tue, 28 Jan 2020 16:53:37 +0400
Subject: [PATCH] updated Tile.archive_l1c, updated l1c QL, updated monthly
summaries
---
sen2chain/__init__.py | 4 +--
sen2chain/colormap.py | 61 ++++++++++++++++++++++++++++++++++++
sen2chain/config.py | 2 +-
sen2chain/monthly_summary.py | 11 +++----
sen2chain/products.py | 34 +++++++++++++++++++-
sen2chain/tiles.py | 7 +++--
6 files changed, 107 insertions(+), 12 deletions(-)
diff --git a/sen2chain/__init__.py b/sen2chain/__init__.py
index b314874..29474a7 100644
--- a/sen2chain/__init__.py
+++ b/sen2chain/__init__.py
@@ -31,7 +31,7 @@ from .automatization import Automatization
from .utils import format_word, grouper, datetime_to_str, str_to_datetime
from .geo_utils import serialise_tiles_index, get_processed_indices_vect
from .multi_processing import l2a_multiprocessing, cldidx_multiprocessing, cld_multiprocessing, idx_multiprocessing
-#~ from .monthly_summary import MonthlySummary
+from .monthly_summary import MonthlySummary
__version__ = "0.1.0"
-__author__ = "Jérémy Commins <jebins@openmailbox.org>"
+__author__ = "Jérémy Commins <jebins@openmailbox.org> & Impact <pascal.mouquet@ird.fr>"
diff --git a/sen2chain/colormap.py b/sen2chain/colormap.py
index 6caeb2b..1e06888 100644
--- a/sen2chain/colormap.py
+++ b/sen2chain/colormap.py
@@ -356,3 +356,64 @@ def create_l2a_ql(b02: Union[str, pathlib.PosixPath],
raster_band = raster_band.astype(np.uint8)
dst.write_band(id, raster_band)
return str(Path(str(out_path)).absolute)
+
+def create_l1c_ql(tci: Union[str, pathlib.PosixPath],
+ out_path: Union[str, pathlib.PosixPath] = "./L1C_QL.tif",
+ out_resolution: Tuple[int, int] = (100, 100),
+ jpg = False,
+ ) -> str:
+ """
+ Creating a color RVB quicklook from tci 3 bands file passed as argument
+ :param tci: path to tci raster
+ :param out_path: path to the output.
+ :param out_resolution: output resolution, default 100mx100m .
+ """
+
+ logger.info("creating L1C QL")
+
+ with rasterio.open(str(tci)) as src:
+ profile = src.profile
+
+ fact = int(1000 // out_resolution[0])
+
+ dst_transform, dst_width, dst_height = calculate_default_transform(
+ src.crs,
+ src.crs,
+ src.width,
+ src.height,
+ *src.bounds,
+ resolution=out_resolution)
+
+ if out_path.suffix == ".jpg" or jpg:
+ profile.update(nodata=0,
+ driver="JPEG",
+ dtype=np.uint8,
+ transform=dst_transform,
+ width=dst_width,
+ height=dst_height,
+ tiled=False,
+ count=3)
+ profile.pop('tiled', None)
+ profile.pop('blockxsize', None)
+ profile.pop('blockysize', None)
+ profile.pop('interleave', None)
+ else:
+ profile.update(nodata=0,
+ driver="Gtiff",
+ dtype=np.uint8,
+ transform=dst_transform,
+ width=dst_width,
+ height=dst_height,
+ tiled=False,
+ count=3)
+
+ with rasterio.open(str(out_path), 'w', **profile) as dst:
+ #~ with rasterio.open(str(tci)) as src1:
+ for band_id in range(1,4):
+ logger.info(band_id)
+ raster_band = src.read(band_id, out_shape=(1, int(src.height // fact), int(src.height // fact))).astype(np.uint8)
+ #~ raster_band = np.where(raster_band > 2000, 2000, raster_band)
+ #~ raster_band = np.where(raster_band > 1, (raster_band/2000)*255, raster_band)
+ #~ raster_band = raster_band.astype(np.uint8)
+ dst.write_band(band_id, raster_band)
+ return str(Path(str(out_path)).absolute)
diff --git a/sen2chain/config.py b/sen2chain/config.py
index b6ca55c..5047fb5 100644
--- a/sen2chain/config.py
+++ b/sen2chain/config.py
@@ -47,7 +47,7 @@ class Config:
"l2a_archive_path": "/ARCHIVE_SENTINEL-PROD/S2_L2A_ARCHIVE",
"indices_path": "",
"time_series_path": "",
- "monthly_summaries_path": ""}
+ "temporal_summaries_path": ""}
self._config_params["SEN2COR PATH"] = {"sen2cor_bashrc_path": ""}
self._config_params["HUBS LOGINS"] = {"scihub_id": "",
"scihub_pwd": "",
diff --git a/sen2chain/monthly_summary.py b/sen2chain/monthly_summary.py
index 06bfa65..ea87f62 100644
--- a/sen2chain/monthly_summary.py
+++ b/sen2chain/monthly_summary.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python3
+#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@@ -47,8 +47,8 @@ class MonthlySummary:
logger.info("Usage: MonthlySummary('40KCB', 'ndvi', '2019-01-01', '2019-05-20')")
return
- _monthly_summary_path = Path(Config().get("monthly_summaries_path"))
- logger.info(_monthly_summary_path)
+ _temporal_summary_path = Path(Config().get("temporal_summaries_path"))
+ logger.info(_temporal_summary_path)
self.start_list = sorted(set([self.datetime_start.strftime("%Y-%m-%d")] + pd.date_range(self.datetime_start, self.datetime_stop, freq='MS').strftime("%Y-%m-%d").to_list()))
self.stop_list = sorted(set(pd.date_range(self.datetime_start, self.datetime_stop, freq='M').strftime("%Y-%m-%d").to_list() + [self.datetime_stop.strftime("%Y-%m-%d")]))
@@ -75,7 +75,6 @@ class MonthlySummary:
prod_profile = prod_src.profile
prod = prod_src.read(1).astype(np.int16)
try:
-
summary_count += np.where(prod != 16383, prod * (1-ccover/100), 0).astype(np.int32)
#~ summary_count += prod * (1-ccover/100)
#~ coef_count += (1-ccover/100)
@@ -99,10 +98,10 @@ class MonthlySummary:
prod_profile.pop('tiled', None)
#~ prod_profile.pop('nodata', None)
- outpath_tif = _monthly_summary_path / \
+ outpath_tif = _temporal_summary_path / \
self.indice.upper() / \
self.tile.name / \
- (self.tile.name + "_" + self.indice.upper() + "_" + start[:-3] + '.tif')
+ (self.tile.name + "_" + self.indice.upper() + "_MONTHLY_" + start[:-3] + '.tif')
outpath_tif.parent.mkdir(parents = True, exist_ok = True)
with rasterio.Env(GDAL_CACHEMAX=512) as env:
diff --git a/sen2chain/products.py b/sen2chain/products.py
index 40e8f35..3cf6f34 100755
--- a/sen2chain/products.py
+++ b/sen2chain/products.py
@@ -19,7 +19,7 @@ from .xmlparser import MetadataParser
from .sen2cor import process_sen2cor
from .cloud_mask import create_cloud_mask, create_cloud_mask_v2, create_cloud_mask_b11
from .indices import IndicesCollection
-from .colormap import create_l2a_ql
+from .colormap import create_l2a_ql, create_l1c_ql
s2_tiles_index = SHARED_DATA.get("tiles_index")
@@ -209,6 +209,38 @@ class L1cProduct(Product):
L2aProduct(l2a_identifier).setPermissions()
return self
+ def process_ql(self,
+ reprocess: bool = False,
+ out_path: pathlib.PosixPath = None,
+ out_resolution: Tuple[int, int] = (100, 100),
+ jpg = False,
+ ) -> "L1cProduct":
+ """
+ """
+ logger.info("{}: processing L1C Quicklook".format(self.identifier))
+
+ if jpg:
+ ql_filename = self.identifier + "_QL.jpg"
+ else:
+ ql_filename = self.identifier + "_QL.tif"
+
+ if out_path is None:
+ ql_folder = self.library_path.parent / "QL"
+ ql_folder.mkdir(parents=True, exist_ok=True)
+ ql_path = ql_folder / ql_filename
+ else:
+ ql_path = Path(out_path)
+
+ if ql_path.exists() and not reprocess:
+ logger.info("{} Quicklook already exists".format(self.identifier))
+ else:
+ create_l1c_ql(tci = self.tci,
+ out_path = ql_path,
+ out_resolution = out_resolution,
+ jpg = jpg)
+ self.user_ql = ql_path
+
+ return ql_path
# METADATA
@property
diff --git a/sen2chain/tiles.py b/sen2chain/tiles.py
index 0faf504..9f59b29 100644
--- a/sen2chain/tiles.py
+++ b/sen2chain/tiles.py
@@ -9,6 +9,7 @@ import re
import fiona
import shutil
from PIL import Image
+import distutils
from pathlib import Path
from collections import namedtuple
@@ -518,7 +519,9 @@ class Tile:
move_path = l1c_archive_path / l1c.tile / l1c.path.name
logger.info("archiving {}".format(l1c.identifier))
move_path.parent.mkdir(exist_ok=True)
- shutil.move(str(l1c.path), str(move_path.parent))
+ #~ shutil.move(str(l1c.path), str(move_path.parent))
+ distutils.dir_util.copy_tree(str(l1c.path), str(move_path))
+ distutils.dir_util.remove_tree(str(l1c.path))
l1c.path.symlink_to(move_path, target_is_directory = True)
logger.info("{} products archived".format(count))
if not count:
@@ -556,7 +559,7 @@ class Tile:
def update_latest_ql(self):
"""
- Produce or update the latest quicklook for the tile
+ Produce or update the latest l2a quicklook for the tile
"""
p = self.l2a.last.identifier
l2a = L2aProduct(p)
--
GitLab