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805 lines
35 KiB
Python
805 lines
35 KiB
Python
"""This module contains all the functions needed to download the satellite images from the Google
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Earth Engine Server
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Author: Kilian Vos, Water Research Laboratory, University of New South Wales
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"""
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# load modules
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import os
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import numpy as np
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import matplotlib.pyplot as plt
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import pdb
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# earth engine modules
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import ee
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from urllib.request import urlretrieve
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import zipfile
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import copy
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import gdal_merge
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# additional modules
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from datetime import datetime
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import pytz
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import pickle
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import skimage.morphology as morphology
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# own modules
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import SDS_preprocess, SDS_tools
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np.seterr(all='ignore') # raise/ignore divisions by 0 and nans
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# initialise connection with GEE server
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ee.Initialize()
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def download_tif(image, polygon, bandsId, filepath):
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"""
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Downloads a .TIF image from the ee server and stores it in a temp file
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Arguments:
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-----------
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image: ee.Image
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Image object to be downloaded
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polygon: list
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polygon containing the lon/lat coordinates to be extracted
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longitudes in the first column and latitudes in the second column
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bandsId: list of dict
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list of bands to be downloaded
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filepath: location where the temporary file should be saved
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"""
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url = ee.data.makeDownloadUrl(ee.data.getDownloadId({
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'image': image.serialize(),
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'region': polygon,
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'bands': bandsId,
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'filePerBand': 'false',
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'name': 'data',
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}))
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local_zip, headers = urlretrieve(url)
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with zipfile.ZipFile(local_zip) as local_zipfile:
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return local_zipfile.extract('data.tif', filepath)
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def retrieve_images(inputs):
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"""
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Downloads all images from Landsat 5, Landsat 7, Landsat 8 and Sentinel-2 covering the area of
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interest and acquired between the specified dates.
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The downloaded images are in .TIF format and organised in subfolders, divided by satellite
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mission and pixel resolution.
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KV WRL 2018
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Arguments:
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-----------
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inputs: dict
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dictionnary that contains the following fields:
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'sitename': str
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String containig the name of the site
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'polygon': list
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polygon containing the lon/lat coordinates to be extracted
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longitudes in the first column and latitudes in the second column
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'dates': list of str
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list that contains 2 strings with the initial and final dates in format 'yyyy-mm-dd'
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e.g. ['1987-01-01', '2018-01-01']
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'sat_list': list of str
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list that contains the names of the satellite missions to include
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e.g. ['L5', 'L7', 'L8', 'S2']
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Returns:
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-----------
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metadata: dict
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contains all the information about the satellite images that were downloaded
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"""
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# read inputs dictionnary
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sitename = inputs['sitename']
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polygon = inputs['polygon']
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dates = inputs['dates']
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sat_list= inputs['sat_list']
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# format in which the images are downloaded
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suffix = '.tif'
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# initialize metadata dictionnary (stores timestamps and georefencing accuracy of each image)
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metadata = dict([])
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# create directories
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try:
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os.makedirs(os.path.join(os.getcwd(), 'data',sitename))
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except:
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print('')
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#=============================================================================================#
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# download L5 images
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#=============================================================================================#
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if 'L5' in sat_list or 'Landsat5' in sat_list:
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satname = 'L5'
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# create a subfolder to store L5 images
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filepath = os.path.join(os.getcwd(), 'data', sitename, satname, '30m')
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try:
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os.makedirs(filepath)
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except:
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print('')
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# Landsat 5 collection
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input_col = ee.ImageCollection('LANDSAT/LT05/C01/T1_TOA')
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# filter by location and dates
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flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
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# get all images in the filtered collection
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im_all = flt_col.getInfo().get('features')
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# remove very cloudy images (>95% cloud)
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cloud_cover = [_['properties']['CLOUD_COVER'] for _ in im_all]
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if np.any([_ > 95 for _ in cloud_cover]):
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idx_delete = np.where([_ > 95 for _ in cloud_cover])[0]
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im_all_cloud = [x for k,x in enumerate(im_all) if k not in idx_delete]
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else:
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im_all_cloud = im_all
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n_img = len(im_all_cloud)
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# print how many images there are
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print('Number of ' + satname + ' images covering ' + sitename + ':', n_img)
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# loop trough images
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timestamps = []
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acc_georef = []
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filenames = []
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all_names = []
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im_epsg = []
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for i in range(n_img):
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# find each image in ee database
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im = ee.Image(im_all_cloud[i].get('id'))
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# read metadata
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im_dic = im.getInfo()
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# get bands
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im_bands = im_dic.get('bands')
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# get time of acquisition (UNIX time)
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t = im_dic['properties']['system:time_start']
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# convert to datetime
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im_timestamp = datetime.fromtimestamp(t/1000, tz=pytz.utc)
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timestamps.append(im_timestamp)
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im_date = im_timestamp.strftime('%Y-%m-%d-%H-%M-%S')
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# get EPSG code of reference system
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im_epsg.append(int(im_dic['bands'][0]['crs'][5:]))
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# get geometric accuracy
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try:
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acc_georef.append(im_dic['properties']['GEOMETRIC_RMSE_MODEL'])
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except:
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# default value of accuracy (RMSE = 12m)
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acc_georef.append(12)
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# delete dimensions key from dictionnary, otherwise the entire image is extracted
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for j in range(len(im_bands)): del im_bands[j]['dimensions']
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# bands for L5
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ms_bands = [im_bands[0], im_bands[1], im_bands[2], im_bands[3], im_bands[4], im_bands[7]]
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# filenames for the images
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filename = im_date + '_' + satname + '_' + sitename + suffix
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# if two images taken at the same date add 'dup' in the name (duplicate)
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if any(filename in _ for _ in all_names):
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filename = im_date + '_' + satname + '_' + sitename + '_dup' + suffix
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all_names.append(filename)
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filenames.append(filename)
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# download .TIF image
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local_data = download_tif(im, polygon, ms_bands, filepath)
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# update filename
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try:
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os.rename(local_data, os.path.join(filepath, filename))
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except:
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os.remove(os.path.join(filepath, filename))
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os.rename(local_data, os.path.join(filepath, filename))
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print(i+1, end='..')
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# sort timestamps and georef accuracy (downloaded images are sorted by date in directory)
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timestamps_sorted = sorted(timestamps)
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idx_sorted = sorted(range(len(timestamps)), key=timestamps.__getitem__)
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acc_georef_sorted = [acc_georef[j] for j in idx_sorted]
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filenames_sorted = [filenames[j] for j in idx_sorted]
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im_epsg_sorted = [im_epsg[j] for j in idx_sorted]
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# save into dict
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metadata[satname] = {'dates':timestamps_sorted, 'acc_georef':acc_georef_sorted,
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'epsg':im_epsg_sorted, 'filenames':filenames_sorted}
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print('\nFinished with ' + satname)
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#=============================================================================================#
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# download L7 images
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#=============================================================================================#
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if 'L7' in sat_list or 'Landsat7' in sat_list:
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satname = 'L7'
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# create subfolders (one for 30m multispectral bands and one for 15m pan bands)
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filepath = os.path.join(os.getcwd(), 'data', sitename, 'L7')
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filepath_pan = os.path.join(filepath, 'pan')
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filepath_ms = os.path.join(filepath, 'ms')
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try:
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os.makedirs(filepath_pan)
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os.makedirs(filepath_ms)
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except:
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print('')
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# landsat 7 collection
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input_col = ee.ImageCollection('LANDSAT/LE07/C01/T1_RT_TOA')
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# filter by location and dates
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flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
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# get all images in the filtered collection
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im_all = flt_col.getInfo().get('features')
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# remove very cloudy images (>95% cloud)
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cloud_cover = [_['properties']['CLOUD_COVER'] for _ in im_all]
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if np.any([_ > 95 for _ in cloud_cover]):
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idx_delete = np.where([_ > 95 for _ in cloud_cover])[0]
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im_all_cloud = [x for k,x in enumerate(im_all) if k not in idx_delete]
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else:
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im_all_cloud = im_all
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n_img = len(im_all_cloud)
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# print how many images there are
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print('Number of ' + satname + ' images covering ' + sitename + ':', n_img)
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# loop trough images
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timestamps = []
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acc_georef = []
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filenames = []
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all_names = []
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im_epsg = []
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for i in range(n_img):
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# find each image in ee database
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im = ee.Image(im_all_cloud[i].get('id'))
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# read metadata
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im_dic = im.getInfo()
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# get bands
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im_bands = im_dic.get('bands')
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# get time of acquisition (UNIX time)
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t = im_dic['properties']['system:time_start']
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# convert to datetime
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im_timestamp = datetime.fromtimestamp(t/1000, tz=pytz.utc)
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timestamps.append(im_timestamp)
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im_date = im_timestamp.strftime('%Y-%m-%d-%H-%M-%S')
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# get EPSG code of reference system
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im_epsg.append(int(im_dic['bands'][0]['crs'][5:]))
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# get geometric accuracy
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try:
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acc_georef.append(im_dic['properties']['GEOMETRIC_RMSE_MODEL'])
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except:
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# default value of accuracy (RMSE = 12m)
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acc_georef.append(12)
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# delete dimensions key from dictionnary, otherwise the entire image is extracted
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for j in range(len(im_bands)): del im_bands[j]['dimensions']
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# bands for L7
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pan_band = [im_bands[8]]
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ms_bands = [im_bands[0], im_bands[1], im_bands[2], im_bands[3], im_bands[4], im_bands[9]]
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# filenames for the images
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filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + suffix
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filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + suffix
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# if two images taken at the same date add 'dup' in the name
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if any(filename_pan in _ for _ in all_names):
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filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + '_dup' + suffix
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filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + '_dup' + suffix
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all_names.append(filename_pan)
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filenames.append(filename_pan)
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# download .TIF image
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local_data_pan = download_tif(im, polygon, pan_band, filepath_pan)
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local_data_ms = download_tif(im, polygon, ms_bands, filepath_ms)
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# update filename
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try:
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os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
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except:
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os.remove(os.path.join(filepath_pan, filename_pan))
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os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
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try:
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os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
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except:
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os.remove(os.path.join(filepath_ms, filename_ms))
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os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
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print(i+1, end='..')
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# sort timestamps and georef accuracy (dowloaded images are sorted by date in directory)
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timestamps_sorted = sorted(timestamps)
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idx_sorted = sorted(range(len(timestamps)), key=timestamps.__getitem__)
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acc_georef_sorted = [acc_georef[j] for j in idx_sorted]
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filenames_sorted = [filenames[j] for j in idx_sorted]
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im_epsg_sorted = [im_epsg[j] for j in idx_sorted]
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# save into dict
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metadata[satname] = {'dates':timestamps_sorted, 'acc_georef':acc_georef_sorted,
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'epsg':im_epsg_sorted, 'filenames':filenames_sorted}
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print('\nFinished with ' + satname)
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#=============================================================================================#
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# download L8 images
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#=============================================================================================#
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if 'L8' in sat_list or 'Landsat8' in sat_list:
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satname = 'L8'
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# create subfolders (one for 30m multispectral bands and one for 15m pan bands)
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filepath = os.path.join(os.getcwd(), 'data', sitename, 'L8')
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filepath_pan = os.path.join(filepath, 'pan')
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filepath_ms = os.path.join(filepath, 'ms')
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try:
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os.makedirs(filepath_pan)
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os.makedirs(filepath_ms)
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except:
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print('')
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# landsat 8 collection
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input_col = ee.ImageCollection('LANDSAT/LC08/C01/T1_RT_TOA')
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# filter by location and dates
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flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
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# get all images in the filtered collection
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im_all = flt_col.getInfo().get('features')
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# remove very cloudy images (>95% cloud)
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cloud_cover = [_['properties']['CLOUD_COVER'] for _ in im_all]
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if np.any([_ > 95 for _ in cloud_cover]):
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idx_delete = np.where([_ > 95 for _ in cloud_cover])[0]
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im_all_cloud = [x for k,x in enumerate(im_all) if k not in idx_delete]
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else:
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im_all_cloud = im_all
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n_img = len(im_all_cloud)
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# print how many images there are
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print('Number of ' + satname + ' images covering ' + sitename + ':', n_img)
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# loop trough images
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timestamps = []
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acc_georef = []
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filenames = []
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all_names = []
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im_epsg = []
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for i in range(n_img):
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# find each image in ee database
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im = ee.Image(im_all_cloud[i].get('id'))
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# read metadata
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im_dic = im.getInfo()
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# get bands
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im_bands = im_dic.get('bands')
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# get time of acquisition (UNIX time)
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t = im_dic['properties']['system:time_start']
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# convert to datetime
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im_timestamp = datetime.fromtimestamp(t/1000, tz=pytz.utc)
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timestamps.append(im_timestamp)
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im_date = im_timestamp.strftime('%Y-%m-%d-%H-%M-%S')
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# get EPSG code of reference system
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im_epsg.append(int(im_dic['bands'][0]['crs'][5:]))
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# get geometric accuracy
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try:
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acc_georef.append(im_dic['properties']['GEOMETRIC_RMSE_MODEL'])
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except:
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# default value of accuracy (RMSE = 12m)
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acc_georef.append(12)
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# delete dimensions key from dictionnary, otherwise the entire image is extracted
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for j in range(len(im_bands)): del im_bands[j]['dimensions']
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# bands for L8
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pan_band = [im_bands[7]]
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ms_bands = [im_bands[1], im_bands[2], im_bands[3], im_bands[4], im_bands[5], im_bands[11]]
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# filenames for the images
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filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + suffix
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filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + suffix
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# if two images taken at the same date add 'dup' in the name
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if any(filename_pan in _ for _ in all_names):
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filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + '_dup' + suffix
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filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + '_dup' + suffix
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all_names.append(filename_pan)
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filenames.append(filename_pan)
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# download .TIF image
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local_data_pan = download_tif(im, polygon, pan_band, filepath_pan)
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local_data_ms = download_tif(im, polygon, ms_bands, filepath_ms)
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# update filename
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try:
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os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
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except:
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os.remove(os.path.join(filepath_pan, filename_pan))
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os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
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try:
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os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
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except:
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os.remove(os.path.join(filepath_ms, filename_ms))
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os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
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print(i+1, end='..')
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# sort timestamps and georef accuracy (dowloaded images are sorted by date in directory)
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timestamps_sorted = sorted(timestamps)
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idx_sorted = sorted(range(len(timestamps)), key=timestamps.__getitem__)
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acc_georef_sorted = [acc_georef[j] for j in idx_sorted]
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filenames_sorted = [filenames[j] for j in idx_sorted]
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im_epsg_sorted = [im_epsg[j] for j in idx_sorted]
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metadata[satname] = {'dates':timestamps_sorted, 'acc_georef':acc_georef_sorted,
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'epsg':im_epsg_sorted, 'filenames':filenames_sorted}
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print('\nFinished with ' + satname)
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#=============================================================================================#
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# download S2 images
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#=============================================================================================#
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if 'S2' in sat_list or 'Sentinel2' in sat_list:
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satname = 'S2'
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# create subfolders for the 10m, 20m and 60m multipectral bands
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filepath = os.path.join(os.getcwd(), 'data', sitename, 'S2')
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try:
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os.makedirs(os.path.join(filepath, '10m'))
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os.makedirs(os.path.join(filepath, '20m'))
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os.makedirs(os.path.join(filepath, '60m'))
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except:
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print('')
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# Sentinel2 collection
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input_col = ee.ImageCollection('COPERNICUS/S2')
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# filter by location and dates
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flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
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# get all images in the filtered collection
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im_all = flt_col.getInfo().get('features')
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# remove duplicates in the collection (there are many in S2 collection)
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|
timestamps = [datetime.fromtimestamp(_['properties']['system:time_start']/1000,
|
|
tz=pytz.utc) for _ in im_all]
|
|
# utm zone projection
|
|
utm_zones = np.array([int(_['bands'][0]['crs'][5:]) for _ in im_all])
|
|
utm_zone_selected = np.max(np.unique(utm_zones))
|
|
# find the images that were acquired at the same time but have different utm zones
|
|
idx_all = np.arange(0,len(im_all),1)
|
|
idx_covered = np.ones(len(im_all)).astype(bool)
|
|
idx_delete = []
|
|
i = 0
|
|
while 1:
|
|
same_time = np.abs([(timestamps[i]-_).total_seconds() for _ in timestamps]) < 60*60*24
|
|
idx_same_time = np.where(same_time)[0]
|
|
same_utm = utm_zones == utm_zone_selected
|
|
idx_temp = np.where([same_time[j] == True and same_utm[j] == False for j in idx_all])[0]
|
|
idx_keep = idx_same_time[[_ not in idx_temp for _ in idx_same_time ]]
|
|
# if more than 2 images with same date and same utm, drop the last ones
|
|
if len(idx_keep) > 2:
|
|
idx_temp = np.append(idx_temp,idx_keep[-(len(idx_keep)-2):])
|
|
for j in idx_temp:
|
|
idx_delete.append(j)
|
|
idx_covered[idx_same_time] = False
|
|
if np.any(idx_covered):
|
|
i = np.where(idx_covered)[0][0]
|
|
else:
|
|
break
|
|
# update the collection by deleting all those images that have same timestamp and different
|
|
# utm projection
|
|
im_all_updated = [x for k,x in enumerate(im_all) if k not in idx_delete]
|
|
|
|
# remove very cloudy images (>95% cloud)
|
|
cloud_cover = [_['properties']['CLOUDY_PIXEL_PERCENTAGE'] for _ in im_all_updated]
|
|
if np.any([_ > 95 for _ in cloud_cover]):
|
|
idx_delete = np.where([_ > 95 for _ in cloud_cover])[0]
|
|
im_all_cloud = [x for k,x in enumerate(im_all_updated) if k not in idx_delete]
|
|
else:
|
|
im_all_cloud = im_all_updated
|
|
|
|
n_img = len(im_all_cloud)
|
|
# print how many images there are
|
|
print('Number of ' + satname + ' images covering ' + sitename + ':', n_img)
|
|
|
|
# loop trough images
|
|
timestamps = []
|
|
acc_georef = []
|
|
filenames = []
|
|
all_names = []
|
|
im_epsg = []
|
|
for i in range(n_img):
|
|
|
|
# find each image in ee database
|
|
im = ee.Image(im_all_cloud[i].get('id'))
|
|
# read metadata
|
|
im_dic = im.getInfo()
|
|
# get bands
|
|
im_bands = im_dic.get('bands')
|
|
# get time of acquisition (UNIX time)
|
|
t = im_dic['properties']['system:time_start']
|
|
# convert to datetime
|
|
im_timestamp = datetime.fromtimestamp(t/1000, tz=pytz.utc)
|
|
im_date = im_timestamp.strftime('%Y-%m-%d-%H-%M-%S')
|
|
# delete dimensions key from dictionnary, otherwise the entire image is extracted
|
|
for j in range(len(im_bands)): del im_bands[j]['dimensions']
|
|
# bands for S2
|
|
bands10 = [im_bands[1], im_bands[2], im_bands[3], im_bands[7]]
|
|
bands20 = [im_bands[11]]
|
|
bands60 = [im_bands[15]]
|
|
# filenames for images
|
|
filename10 = im_date + '_' + satname + '_' + sitename + '_' + '10m' + suffix
|
|
filename20 = im_date + '_' + satname + '_' + sitename + '_' + '20m' + suffix
|
|
filename60 = im_date + '_' + satname + '_' + sitename + '_' + '60m' + suffix
|
|
# if two images taken at the same date skip the second image (they are the same)
|
|
if any(filename10 in _ for _ in all_names):
|
|
filename10 = filename10[:filename10.find('.')] + '_dup' + suffix
|
|
filename20 = filename20[:filename20.find('.')] + '_dup' + suffix
|
|
filename60 = filename60[:filename60.find('.')] + '_dup' + suffix
|
|
all_names.append(filename10)
|
|
filenames.append(filename10)
|
|
|
|
# download .TIF image and update filename
|
|
local_data = download_tif(im, polygon, bands10, os.path.join(filepath, '10m'))
|
|
try:
|
|
os.rename(local_data, os.path.join(filepath, '10m', filename10))
|
|
except:
|
|
os.remove(os.path.join(filepath, '10m', filename10))
|
|
os.rename(local_data, os.path.join(filepath, '10m', filename10))
|
|
|
|
local_data = download_tif(im, polygon, bands20, os.path.join(filepath, '20m'))
|
|
try:
|
|
os.rename(local_data, os.path.join(filepath, '20m', filename20))
|
|
except:
|
|
os.remove(os.path.join(filepath, '20m', filename20))
|
|
os.rename(local_data, os.path.join(filepath, '20m', filename20))
|
|
|
|
local_data = download_tif(im, polygon, bands60, os.path.join(filepath, '60m'))
|
|
try:
|
|
os.rename(local_data, os.path.join(filepath, '60m', filename60))
|
|
except:
|
|
os.remove(os.path.join(filepath, '60m', filename60))
|
|
os.rename(local_data, os.path.join(filepath, '60m', filename60))
|
|
|
|
# save timestamp, epsg code and georeferencing accuracy (1 if passed 0 if not passed)
|
|
timestamps.append(im_timestamp)
|
|
im_epsg.append(int(im_dic['bands'][0]['crs'][5:]))
|
|
# Sentinel-2 products don't provide a georeferencing accuracy (RMSE as in Landsat)
|
|
# but they have a flag indicating if the geometric quality control was passed or failed
|
|
# if passed a value of 1 is stored if failed a value of -1 is stored in the metadata
|
|
if 'GEOMETRIC_QUALITY_FLAG' in im_dic['properties'].keys():
|
|
if im_dic['properties']['GEOMETRIC_QUALITY_FLAG'] == 'PASSED':
|
|
acc_georef.append(1)
|
|
else:
|
|
acc_georef.append(-1)
|
|
elif 'quality_check' in im_dic['properties'].keys():
|
|
if im_dic['properties']['quality_check'] == 'PASSED':
|
|
acc_georef.append(1)
|
|
else:
|
|
acc_georef.append(-1)
|
|
else:
|
|
acc_georef.append(-1)
|
|
|
|
print(i+1, end='..')
|
|
|
|
# sort timestamps and georef accuracy (dowloaded images are sorted by date in directory)
|
|
timestamps_sorted = sorted(timestamps)
|
|
idx_sorted = sorted(range(len(timestamps)), key=timestamps.__getitem__)
|
|
acc_georef_sorted = [acc_georef[j] for j in idx_sorted]
|
|
filenames_sorted = [filenames[j] for j in idx_sorted]
|
|
im_epsg_sorted = [im_epsg[j] for j in idx_sorted]
|
|
|
|
metadata[satname] = {'dates':timestamps_sorted, 'acc_georef':acc_georef_sorted,
|
|
'epsg':im_epsg_sorted, 'filenames':filenames_sorted}
|
|
print('\nFinished with ' + satname)
|
|
|
|
# merge overlapping images (necessary only if the polygon is at the boundary of an image)
|
|
if 'S2' in metadata.keys():
|
|
metadata = merge_overlapping_images(metadata,inputs)
|
|
|
|
# save metadata dict
|
|
filepath = os.path.join(os.getcwd(), 'data', sitename)
|
|
with open(os.path.join(filepath, sitename + '_metadata' + '.pkl'), 'wb') as f:
|
|
pickle.dump(metadata, f)
|
|
|
|
return metadata
|
|
|
|
|
|
def merge_overlapping_images(metadata,inputs):
|
|
"""
|
|
When the area of interest is located at the boundary between 2 images, there will be overlap
|
|
between the 2 images and both will be downloaded from Google Earth Engine. This function
|
|
merges the 2 images, so that the area of interest is covered by only 1 image.
|
|
|
|
KV WRL 2018
|
|
|
|
Arguments:
|
|
-----------
|
|
metadata: dict
|
|
contains all the information about the satellite images that were downloaded
|
|
inputs: dict
|
|
dictionnary that contains the following fields:
|
|
'sitename': str
|
|
String containig the name of the site
|
|
'polygon': list
|
|
polygon containing the lon/lat coordinates to be extracted
|
|
longitudes in the first column and latitudes in the second column
|
|
'dates': list of str
|
|
list that contains 2 strings with the initial and final dates in format 'yyyy-mm-dd'
|
|
e.g. ['1987-01-01', '2018-01-01']
|
|
'sat_list': list of str
|
|
list that contains the names of the satellite missions to include
|
|
e.g. ['L5', 'L7', 'L8', 'S2']
|
|
|
|
Returns:
|
|
-----------
|
|
metadata: dict
|
|
updated metadata with the information of the merged images
|
|
|
|
"""
|
|
|
|
# only for Sentinel-2 at this stage (could be implemented for Landsat as well)
|
|
sat = 'S2'
|
|
filepath = os.path.join(os.getcwd(), 'data', inputs['sitename'])
|
|
|
|
# find the images that are overlapping (same date in S2 filenames)
|
|
filenames = metadata[sat]['filenames']
|
|
filenames_copy = filenames.copy()
|
|
|
|
# loop through all the filenames and find the pairs of overlapping images (same date and time of acquisition)
|
|
pairs = []
|
|
for i,fn in enumerate(filenames):
|
|
filenames_copy[i] = []
|
|
# find duplicate
|
|
boolvec = [fn[:22] == _[:22] for _ in filenames_copy]
|
|
if np.any(boolvec):
|
|
idx_dup = np.where(boolvec)[0][0]
|
|
if len(filenames[i]) > len(filenames[idx_dup]):
|
|
pairs.append([idx_dup,i])
|
|
else:
|
|
pairs.append([i,idx_dup])
|
|
|
|
msg = 'Merging %d pairs of overlapping images...' % len(pairs)
|
|
print(msg)
|
|
|
|
# for each pair of images, merge them into one complete image
|
|
for i,pair in enumerate(pairs):
|
|
print(i+1, end='..')
|
|
|
|
fn_im = []
|
|
for index in range(len(pair)):
|
|
# read image
|
|
fn_im.append([os.path.join(filepath, 'S2', '10m', filenames[pair[index]]),
|
|
os.path.join(filepath, 'S2', '20m', filenames[pair[index]].replace('10m','20m')),
|
|
os.path.join(filepath, 'S2', '60m', filenames[pair[index]].replace('10m','60m'))])
|
|
im_ms, georef, cloud_mask, im_extra, imQA = SDS_preprocess.preprocess_single(fn_im[index], sat, False)
|
|
|
|
# in Sentinel2 images close to the edge of the image there are some artefacts,
|
|
# that are squares with constant pixel intensities. They need to be masked in the
|
|
# raster (GEOTIFF). It can be done using the image standard deviation, which
|
|
# indicates values close to 0 for the artefacts.
|
|
|
|
# First mask the 10m bands
|
|
if len(im_ms) > 0:
|
|
im_std = SDS_tools.image_std(im_ms[:,:,0],1)
|
|
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
|
|
mask = morphology.dilation(im_binary, morphology.square(3))
|
|
for k in range(im_ms.shape[2]):
|
|
im_ms[mask,k] = np.nan
|
|
|
|
SDS_tools.mask_raster(fn_im[index][0], mask)
|
|
|
|
# Then mask the 20m band
|
|
im_std = SDS_tools.image_std(im_extra,1)
|
|
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
|
|
mask = morphology.dilation(im_binary, morphology.square(3))
|
|
im_extra[mask] = np.nan
|
|
|
|
SDS_tools.mask_raster(fn_im[index][1], mask)
|
|
else:
|
|
continue
|
|
|
|
# make a figure for quality control
|
|
# plt.figure()
|
|
# plt.subplot(221)
|
|
# plt.imshow(im_ms[:,:,[2,1,0]])
|
|
# plt.title('imRGB')
|
|
# plt.subplot(222)
|
|
# plt.imshow(im20, cmap='gray')
|
|
# plt.title('im20')
|
|
# plt.subplot(223)
|
|
# plt.imshow(imQA, cmap='gray')
|
|
# plt.title('imQA')
|
|
# plt.subplot(224)
|
|
# plt.title(fn_im[index][0][-30:])
|
|
|
|
# merge masked 10m bands
|
|
fn_merged = os.path.join(os.getcwd(), 'merged.tif')
|
|
gdal_merge.main(['', '-o', fn_merged, '-n', '0', fn_im[0][0], fn_im[1][0]])
|
|
os.chmod(fn_im[0][0], 0o777)
|
|
os.remove(fn_im[0][0])
|
|
os.chmod(fn_im[1][0], 0o777)
|
|
os.remove(fn_im[1][0])
|
|
os.rename(fn_merged, fn_im[0][0])
|
|
|
|
# merge masked 20m band (SWIR band)
|
|
fn_merged = os.path.join(os.getcwd(), 'merged.tif')
|
|
gdal_merge.main(['', '-o', fn_merged, '-n', '0', fn_im[0][1], fn_im[1][1]])
|
|
os.chmod(fn_im[0][1], 0o777)
|
|
os.remove(fn_im[0][1])
|
|
os.chmod(fn_im[1][1], 0o777)
|
|
os.remove(fn_im[1][1])
|
|
os.rename(fn_merged, fn_im[0][1])
|
|
|
|
# merge QA band (60m band)
|
|
fn_merged = os.path.join(os.getcwd(), 'merged.tif')
|
|
gdal_merge.main(['', '-o', fn_merged, '-n', 'nan', fn_im[0][2], fn_im[1][2]])
|
|
os.chmod(fn_im[0][2], 0o777)
|
|
os.remove(fn_im[0][2])
|
|
os.chmod(fn_im[1][2], 0o777)
|
|
os.remove(fn_im[1][2])
|
|
os.rename(fn_merged, fn_im[0][2])
|
|
|
|
# update the metadata dict (delete all the duplicates)
|
|
metadata2 = copy.deepcopy(metadata)
|
|
filenames_copy = metadata2[sat]['filenames']
|
|
index_list = []
|
|
for i in range(len(filenames_copy)):
|
|
if filenames_copy[i].find('dup') == -1:
|
|
index_list.append(i)
|
|
for key in metadata2[sat].keys():
|
|
metadata2[sat][key] = [metadata2[sat][key][_] for _ in index_list]
|
|
|
|
return metadata2
|
|
|
|
def remove_cloudy_images(metadata,inputs,cloud_thresh):
|
|
"""
|
|
Deletes the .TIF file of images that have a cloud cover percentage that is above the cloud
|
|
threshold.
|
|
|
|
KV WRL 2018
|
|
|
|
Arguments:
|
|
-----------
|
|
metadata: dict
|
|
contains all the information about the satellite images that were downloaded
|
|
inputs: dict
|
|
dictionnary that contains the following fields:
|
|
'sitename': str
|
|
String containig the name of the site
|
|
'polygon': list
|
|
polygon containing the lon/lat coordinates to be extracted
|
|
longitudes in the first column and latitudes in the second column
|
|
'dates': list of str
|
|
list that contains 2 strings with the initial and final dates in format 'yyyy-mm-dd'
|
|
e.g. ['1987-01-01', '2018-01-01']
|
|
'sat_list': list of str
|
|
list that contains the names of the satellite missions to include
|
|
e.g. ['L5', 'L7', 'L8', 'S2']
|
|
cloud_thresh: float
|
|
value between 0 and 1 indicating the maximum cloud fraction in the image that is accepted
|
|
|
|
Returns:
|
|
-----------
|
|
metadata: dict
|
|
updated metadata with the information of the merged images
|
|
|
|
"""
|
|
|
|
# create a deep copy
|
|
metadata2 = copy.deepcopy(metadata)
|
|
|
|
for satname in metadata.keys():
|
|
|
|
# get the image filenames
|
|
filepath = SDS_tools.get_filepath(inputs,satname)
|
|
filenames = metadata[satname]['filenames']
|
|
|
|
# loop through images
|
|
idx_good = []
|
|
for i in range(len(filenames)):
|
|
# image filename
|
|
fn = SDS_tools.get_filenames(filenames[i],filepath, satname)
|
|
# preprocess image (cloud mask + pansharpening/downsampling)
|
|
im_ms, georef, cloud_mask, im_extra, imQA = SDS_preprocess.preprocess_single(fn, satname, False)
|
|
# calculate cloud cover
|
|
cloud_cover = np.divide(sum(sum(cloud_mask.astype(int))),
|
|
(cloud_mask.shape[0]*cloud_mask.shape[1]))
|
|
# skip image if cloud cover is above threshold
|
|
if cloud_cover > cloud_thresh or cloud_cover == 1:
|
|
# remove image files
|
|
if satname == 'L5':
|
|
os.chmod(fn, 0o777)
|
|
os.remove(fn)
|
|
else:
|
|
for j in range(len(fn)):
|
|
os.chmod(fn[j], 0o777)
|
|
os.remove(fn[j])
|
|
else:
|
|
idx_good.append(i)
|
|
|
|
msg = '\n%d cloudy images were removed for %s.' % (len(filenames)-len(idx_good), satname)
|
|
print(msg)
|
|
|
|
# update the metadata dict (delete all cloudy images)
|
|
for key in metadata2[satname].keys():
|
|
metadata2[satname][key] = [metadata2[satname][key][_] for _ in idx_good]
|
|
|
|
return metadata2 |