CoastSat_WRL/SDS_download.py

"""This module contains all the functions needed to download the satellite images from the Google
Earth Engine Server
    
   Author: Kilian Vos, Water Research Laboratory, University of New South Wales
"""

# load modules
import os
import numpy as np
import matplotlib.pyplot as plt
import pdb

# earth engine modules
import ee
from urllib.request import urlretrieve
import zipfile
import copy
import gdal_merge

# additional modules
from datetime import datetime
import pytz
import pickle
import skimage.morphology as morphology

# own modules
import SDS_preprocess, SDS_tools

np.seterr(all='ignore') # raise/ignore divisions by 0 and nans


# initialise connection with GEE server
ee.Initialize()

def download_tif(image, polygon, bandsId, filepath):
    """
    Downloads a .TIF image from the ee server and stores it in a temp file
        
    Arguments:
    -----------
        image: ee.Image
            Image object to be downloaded
        polygon: list
            polygon containing the lon/lat coordinates to be extracted
            longitudes in the first column and latitudes in the second column
        bandsId: list of dict
            list of bands to be downloaded
        filepath: location where the temporary file should be saved
            
    """
    
    url = ee.data.makeDownloadUrl(ee.data.getDownloadId({
        'image': image.serialize(),
        'region': polygon,
        'bands': bandsId,
        'filePerBand': 'false',
        'name': 'data',
        }))
    local_zip, headers = urlretrieve(url)
    with zipfile.ZipFile(local_zip) as local_zipfile:
        return local_zipfile.extract('data.tif', filepath)


def retrieve_images(inputs):
    """
    Downloads all images from Landsat 5, Landsat 7, Landsat 8 and Sentinel-2 covering the area of 
    interest and acquired between the specified dates. 
    The downloaded images are in .TIF format and organised in subfolders, divided by satellite 
    mission and pixel resolution.
    
    KV WRL 2018
        
    Arguments:
    -----------
        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
            contains all the information about the satellite images that were downloaded
           
    """
    
    # read inputs dictionnary
    sitename = inputs['sitename']
    polygon = inputs['polygon']
    dates = inputs['dates']
    sat_list= inputs['sat_list']
    
    # format in which the images are downloaded
    suffix = '.tif'
 
    # initialize metadata dictionnary (stores timestamps and georefencing accuracy of each image)       
    metadata = dict([])
    
    # create directories
    try:
        os.makedirs(os.path.join(os.getcwd(), 'data',sitename))
    except:
        print('')
        
    #=============================================================================================#
    # download L5 images
    #=============================================================================================#
    
    if 'L5' in sat_list or 'Landsat5' in sat_list:
        
        satname = 'L5'
        # create a subfolder to store L5 images
        filepath = os.path.join(os.getcwd(), 'data', sitename, satname, '30m')
        try:
            os.makedirs(filepath)
        except:
            print('')
        
        # Landsat 5 collection
        input_col = ee.ImageCollection('LANDSAT/LT05/C01/T1_TOA')
        # filter by location and dates
        flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
        # get all images in the filtered collection
        im_all = flt_col.getInfo().get('features')
        # remove very cloudy images (>95% cloud)
        cloud_cover = [_['properties']['CLOUD_COVER'] for _ in im_all]
        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) if k not in idx_delete]
        else:
            im_all_cloud = im_all
        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)
            timestamps.append(im_timestamp)
            im_date = im_timestamp.strftime('%Y-%m-%d-%H-%M-%S')
            # get EPSG code of reference system
            im_epsg.append(int(im_dic['bands'][0]['crs'][5:]))
            # get geometric accuracy
            try:
                acc_georef.append(im_dic['properties']['GEOMETRIC_RMSE_MODEL'])
            except:
                # default value of accuracy (RMSE = 12m)
                acc_georef.append(12)   
            # 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 L5
            ms_bands = [im_bands[0], im_bands[1], im_bands[2], im_bands[3], im_bands[4], im_bands[7]]
            # filenames for the images
            filename = im_date + '_' + satname + '_' + sitename + suffix
            # if two images taken at the same date add 'dup' in the name (duplicate)
            if any(filename in _ for _ in all_names):
                filename = im_date + '_' + satname + '_' + sitename + '_dup' + suffix 
            all_names.append(filename)
            filenames.append(filename)
            # download .TIF image
            local_data = download_tif(im, polygon, ms_bands, filepath)
            # update filename
            try:
                os.rename(local_data, os.path.join(filepath, filename))
            except:
                os.remove(os.path.join(filepath, filename))
                os.rename(local_data, os.path.join(filepath, filename))
                    
            print(i+1, end='..')
        
        # sort timestamps and georef accuracy (downloaded 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]
        # save into dict
        metadata[satname] = {'dates':timestamps_sorted, 'acc_georef':acc_georef_sorted,
                'epsg':im_epsg_sorted, 'filenames':filenames_sorted}   
        print('\nFinished with ' + satname)
    
    
    
    #=============================================================================================#
    # download L7 images
    #=============================================================================================#
    
    if 'L7' in sat_list or 'Landsat7' in sat_list:
        
        satname = 'L7'
        # create subfolders (one for 30m multispectral bands and one for 15m pan bands)
        filepath = os.path.join(os.getcwd(), 'data', sitename, 'L7')
        filepath_pan = os.path.join(filepath, 'pan')
        filepath_ms = os.path.join(filepath, 'ms')
        try:
            os.makedirs(filepath_pan)
            os.makedirs(filepath_ms)
        except:
            print('')
         
        # landsat 7 collection
        input_col = ee.ImageCollection('LANDSAT/LE07/C01/T1_RT_TOA')
        # filter by location and dates
        flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
        # get all images in the filtered collection
        im_all = flt_col.getInfo().get('features')
        # remove very cloudy images (>95% cloud)
        cloud_cover = [_['properties']['CLOUD_COVER'] for _ in im_all]
        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) if k not in idx_delete]
        else:
            im_all_cloud = im_all
        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)
            timestamps.append(im_timestamp)
            im_date = im_timestamp.strftime('%Y-%m-%d-%H-%M-%S')
            # get EPSG code of reference system
            im_epsg.append(int(im_dic['bands'][0]['crs'][5:]))
            # get geometric accuracy
            try:
                acc_georef.append(im_dic['properties']['GEOMETRIC_RMSE_MODEL'])
            except:
                # default value of accuracy (RMSE = 12m)
                acc_georef.append(12)   
            # 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 L7
            pan_band = [im_bands[8]]
            ms_bands = [im_bands[0], im_bands[1], im_bands[2], im_bands[3], im_bands[4], im_bands[9]] 
            # filenames for the images
            filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + suffix
            filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + suffix  
            # if two images taken at the same date add 'dup' in the name
            if any(filename_pan in _ for _ in all_names):
                filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + '_dup' + suffix
                filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + '_dup' + suffix 
            all_names.append(filename_pan)
            filenames.append(filename_pan)
            # download .TIF image
            local_data_pan = download_tif(im, polygon, pan_band, filepath_pan)
            local_data_ms = download_tif(im, polygon, ms_bands, filepath_ms)
            # update filename
            try:
                os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
            except:
                os.remove(os.path.join(filepath_pan, filename_pan))
                os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
            try:
                os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
            except:
                os.remove(os.path.join(filepath_ms, filename_ms))
                os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
            
            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]
        # save into dict
        metadata[satname] = {'dates':timestamps_sorted, 'acc_georef':acc_georef_sorted,
                'epsg':im_epsg_sorted, 'filenames':filenames_sorted}
        print('\nFinished with ' + satname)
        
        
    #=============================================================================================#
    # download L8 images
    #=============================================================================================#
    
    if 'L8' in sat_list or 'Landsat8' in sat_list:

        satname = 'L8'  
        # create subfolders (one for 30m multispectral bands and one for 15m pan bands)
        filepath = os.path.join(os.getcwd(), 'data', sitename, 'L8')
        filepath_pan = os.path.join(filepath, 'pan')
        filepath_ms = os.path.join(filepath, 'ms')
        try:
            os.makedirs(filepath_pan)
            os.makedirs(filepath_ms)
        except:
            print('')
            
        # landsat 8 collection
        input_col = ee.ImageCollection('LANDSAT/LC08/C01/T1_RT_TOA')
        # filter by location and dates
        flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
        # get all images in the filtered collection
        im_all = flt_col.getInfo().get('features')
        # remove very cloudy images (>95% cloud)
        cloud_cover = [_['properties']['CLOUD_COVER'] for _ in im_all]
        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) if k not in idx_delete]
        else:
            im_all_cloud = im_all
        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)
            timestamps.append(im_timestamp)
            im_date = im_timestamp.strftime('%Y-%m-%d-%H-%M-%S')
            # get EPSG code of reference system
            im_epsg.append(int(im_dic['bands'][0]['crs'][5:]))
            # get geometric accuracy
            try:
                acc_georef.append(im_dic['properties']['GEOMETRIC_RMSE_MODEL'])
            except:
                # default value of accuracy (RMSE = 12m)
                acc_georef.append(12)   
            # 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 L8    
            pan_band = [im_bands[7]]
            ms_bands = [im_bands[1], im_bands[2], im_bands[3], im_bands[4], im_bands[5], im_bands[11]]
            # filenames for the images
            filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + suffix
            filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + suffix  
            # if two images taken at the same date add 'dup' in the name
            if any(filename_pan in _ for _ in all_names):
                filename_pan = im_date + '_' + satname + '_' + sitename + '_pan' + '_dup' + suffix
                filename_ms = im_date + '_' + satname + '_' + sitename + '_ms' + '_dup' + suffix 
            all_names.append(filename_pan)  
            filenames.append(filename_pan)
            # download .TIF image
            local_data_pan = download_tif(im, polygon, pan_band, filepath_pan)
            local_data_ms = download_tif(im, polygon, ms_bands, filepath_ms)
            # update filename
            try:
                os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
            except:
                os.remove(os.path.join(filepath_pan, filename_pan))
                os.rename(local_data_pan, os.path.join(filepath_pan, filename_pan))
            try:
                os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
            except:
                os.remove(os.path.join(filepath_ms, filename_ms))
                os.rename(local_data_ms, os.path.join(filepath_ms, filename_ms))
                
            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)

    #=============================================================================================#
    # download S2 images
    #=============================================================================================#
    
    if 'S2' in sat_list or 'Sentinel2' in sat_list:

        satname = 'S2' 
        # create subfolders for the 10m, 20m and 60m multipectral bands
        filepath = os.path.join(os.getcwd(), 'data', sitename, 'S2')
        try:
            os.makedirs(os.path.join(filepath, '10m'))
            os.makedirs(os.path.join(filepath, '20m'))
            os.makedirs(os.path.join(filepath, '60m'))
        except:
            print('')
    
        # Sentinel2 collection
        input_col = ee.ImageCollection('COPERNICUS/S2')
        # filter by location and dates
        flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(dates[0],dates[1])
        # get all images in the filtered collection
        im_all = flt_col.getInfo().get('features')  
        # remove duplicates in the collection (there are many in S2 collection)
        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 faile a value of -1 is stored in the metadata
            try:
                if im_dic['properties']['GEOMETRIC_QUALITY_FLAG'] == 'PASSED':
                    acc_georef.append(1)
                else:
                    acc_georef.append(-1)
            except:
                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 (only if polygon is at the edge 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) 
        
            # 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)
            # 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