'inputs': inputs,
# [ONLY FOR ADVANCED USERS] shoreline detection parameters:
'min_beach_area':
4500, # minimum area (in metres^2) for an object to be labelled as a beach
'buffer_size':
150, # radius (in metres) of the buffer around sandy pixels considered in the shoreline detection
'min_length_sl':
200, # minimum length (in metres) of shoreline perimeter to be valid
'cloud_mask_issue':
False, # switch this parameter to True if sand pixels are masked (in black) on many images
'sand_color':
'default', # 'default', 'dark' (for grey/black sand beaches) or 'bright' (for white sand beaches)
}
# [OPTIONAL] preprocess images (cloud masking, pansharpening/down-sampling)
SDS_preprocess.save_jpg(metadata, settings)
# [OPTIONAL] create a reference shoreline (helps to identify outliers and false detections)
settings['reference_shoreline'] = SDS_preprocess.get_reference_sl(
metadata, settings)
# set the max distance (in meters) allowed from the reference shoreline for a detected shoreline to be valid
settings['max_dist_ref'] = 100
# extract shorelines from all images (also saves output.pkl and shorelines.kml)
output = SDS_shoreline.extract_shorelines(metadata, settings)
# plot the mapped shorelines
fig = plt.figure()
plt.axis('equal')
plt.xlabel('Eastings')
plt.ylabel('Northings')
def extract_shorelines(metadata, settings):
"""
Main function to extract shorelines from satellite images
KV WRL 2018
Arguments:
-----------
metadata: dict
contains all the information about the satellite images that were downloaded
settings: dict with the following keys
'inputs': dict
input parameters (sitename, filepath, polygon, dates, sat_list)
'cloud_thresh': float
value between 0 and 1 indicating the maximum cloud fraction in
the cropped image that is accepted
'cloud_mask_issue': boolean
True if there is an issue with the cloud mask and sand pixels
are erroneously being masked on the images
'buffer_size': int
size of the buffer (m) around the sandy pixels over which the pixels
are considered in the thresholding algorithm
'min_beach_area': int
minimum allowable object area (in metres^2) for the class 'sand',
the area is converted to number of connected pixels
'min_length_sl': int
minimum length (in metres) of shoreline contour to be valid
'sand_color': str
default', 'dark' (for grey/black sand beaches) or 'bright' (for white sand beaches)
'output_epsg': int
output spatial reference system as EPSG code
'check_detection': bool
if True, lets user manually accept/reject the mapped shorelines
'save_figure': bool
if True, saves a -jpg file for each mapped shoreline
Returns:
-----------
output: dict
contains the extracted shorelines and corresponding dates + metadata
"""
sitename = settings['inputs']['sitename']
filepath_data = settings['inputs']['filepath']
filepath_models = os.path.join(os.getcwd(), 'classification', 'models')
# initialise output structure
output = dict([])
# create a subfolder to store the .jpg images showing the detection
filepath_jpg = os.path.join(filepath_data, sitename, 'jpg_files', 'detection')
if not os.path.exists(filepath_jpg):
os.makedirs(filepath_jpg)
# close all open figures
plt.close('all')
print('Mapping shorelines:')
# loop through satellite list
for satname in metadata.keys():
# get images
filepath = SDS_tools.get_filepath(settings['inputs'],satname)
filenames = metadata[satname]['filenames']
# initialise the output variables
output_timestamp = [] # datetime at which the image was acquired (UTC time)
output_shoreline = [] # vector of shoreline points
output_filename = [] # filename of the images from which the shorelines where derived
output_cloudcover = [] # cloud cover of the images
output_geoaccuracy = []# georeferencing accuracy of the images
output_idxkeep = [] # index that were kept during the analysis (cloudy images are skipped)
# load classifiers and
if satname in ['L5','L7','L8']:
pixel_size = 15
if settings['sand_color'] == 'dark':
clf = joblib.load(os.path.join(filepath_models, 'NN_4classes_Landsat_dark.pkl'))
elif settings['sand_color'] == 'bright':
clf = joblib.load(os.path.join(filepath_models, 'NN_4classes_Landsat_bright.pkl'))
else:
clf = joblib.load(os.path.join(filepath_models, 'NN_4classes_Landsat.pkl'))
elif satname == 'S2':
pixel_size = 10
clf = joblib.load(os.path.join(filepath_models, 'NN_4classes_S2.pkl'))
# convert settings['min_beach_area'] and settings['buffer_size'] from metres to pixels
buffer_size_pixels = np.ceil(settings['buffer_size']/pixel_size)
min_beach_area_pixels = np.ceil(settings['min_beach_area']/pixel_size**2)
# loop through the images
for i in range(len(filenames)):
print('\r%s: %d%%' % (satname,int(((i+1)/len(filenames))*100)), end='')
# get image filename
fn = SDS_tools.get_filenames(filenames[i],filepath, satname)
# preprocess image (cloud mask + pansharpening/downsampling)
im_ms, georef, cloud_mask, im_extra, im_QA, im_nodata = SDS_preprocess.preprocess_single(fn, satname, settings['cloud_mask_issue'])
# get image spatial reference system (epsg code) from metadata dict
image_epsg = metadata[satname]['epsg'][i]
# define an advanced cloud mask (for L7 it takes into account the fact that diagonal
# bands of no data are not clouds)
if not satname == 'L7' or sum(sum(im_nodata)) == 0 or sum(sum(im_nodata)) > 0.5*im_nodata.size:
cloud_mask_adv = cloud_mask
else:
cloud_mask_adv = np.logical_xor(cloud_mask, im_nodata)
# calculate cloud cover
cloud_cover = np.divide(sum(sum(cloud_mask_adv.astype(int))),
(cloud_mask.shape[0]*cloud_mask.shape[1]))
# skip image if cloud cover is above threshold
if cloud_cover > settings['cloud_thresh']:
continue
# calculate a buffer around the reference shoreline (if any has been digitised)
im_ref_buffer = create_shoreline_buffer(cloud_mask.shape, georef, image_epsg,
pixel_size, settings)
# classify image in 4 classes (sand, whitewater, water, other) with NN classifier
im_classif, im_labels = classify_image_NN(im_ms, im_extra, cloud_mask,
min_beach_area_pixels, clf)
# there are two options to map the contours:
# if there are pixels in the 'sand' class --> use find_wl_contours2 (enhanced)
# otherwise use find_wl_contours2 (traditional)
try: # use try/except structure for long runs
if sum(sum(im_labels[:,:,0])) < 10 :
# compute MNDWI image (SWIR-G)
im_mndwi = SDS_tools.nd_index(im_ms[:,:,4], im_ms[:,:,1], cloud_mask)
# find water contours on MNDWI grayscale image
contours_mwi = find_wl_contours1(im_mndwi, cloud_mask, im_ref_buffer)
else:
# use classification to refine threshold and extract the sand/water interface
contours_wi, contours_mwi = find_wl_contours2(im_ms, im_labels,
cloud_mask, buffer_size_pixels, im_ref_buffer)
except:
print('Could not map shoreline for this image: ' + filenames[i])
continue
# process the water contours into a shoreline
shoreline = process_shoreline(contours_mwi, cloud_mask, georef, image_epsg, settings)
# visualise the mapped shorelines, there are two options:
# if settings['check_detection'] = True, shows the detection to the user for accept/reject
# if settings['save_figure'] = True, saves a figure for each mapped shoreline
if settings['check_detection'] or settings['save_figure']:
date = filenames[i][:19]
if not settings['check_detection']:
plt.ioff() # turning interactive plotting off
skip_image = show_detection(im_ms, cloud_mask, im_labels, shoreline,
image_epsg, georef, settings, date, satname)
# if the user decides to skip the image, continue and do not save the mapped shoreline
if skip_image:
continue
# append to output variables
output_timestamp.append(metadata[satname]['dates'][i])
output_shoreline.append(shoreline)
output_filename.append(filenames[i])
output_cloudcover.append(cloud_cover)
output_geoaccuracy.append(metadata[satname]['acc_georef'][i])
output_idxkeep.append(i)
# create dictionnary of output
output[satname] = {
'dates': output_timestamp,
'shorelines': output_shoreline,
'filename': output_filename,
'cloud_cover': output_cloudcover,
'geoaccuracy': output_geoaccuracy,
'idx': output_idxkeep
}
print('')
# Close figure window if still open
if plt.get_fignums():
plt.close()
# change the format to have one list sorted by date with all the shorelines (easier to use)
output = SDS_tools.merge_output(output)
# save outputput structure as output.pkl
filepath = os.path.join(filepath_data, sitename)
with open(os.path.join(filepath, sitename + '_output.pkl'), 'wb') as f:
pickle.dump(output, f)
# save output into a gdb.GeoDataFrame
gdf = SDS_tools.output_to_gdf(output)
# set projection
gdf.crs = {'init':'epsg:'+str(settings['output_epsg'])}
# save as geojson
gdf.to_file(os.path.join(filepath, sitename + '_output.geojson'), driver='GeoJSON', encoding='utf-8')
return output
def merge_overlapping_images(metadata, inputs):
"""
Merge simultaneous overlapping images that cover the area of interest.
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 with the following keys
'sitename': str
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,
there are 5 pairs of lat/lon with the fifth point equal to the first point:
```
polygon = [[[151.3, -33.7],[151.4, -33.7],[151.4, -33.8],[151.3, -33.8],
[151.3, -33.7]]]
```
'dates': list of str
list that contains 2 strings with the initial and final dates in
format 'yyyy-mm-dd':
```
dates = ['1987-01-01', '2018-01-01']
```
'sat_list': list of str
list that contains the names of the satellite missions to include:
```
sat_list = ['L5', 'L7', 'L8', 'S2']
```
'filepath_data': str
filepath to the directory where the images are downloaded
Returns:
-----------
metadata_updated: dict
updated metadata
"""
# only for Sentinel-2 at this stage (not sure if this is needed for Landsat images)
sat = 'S2'
filepath = os.path.join(inputs['filepath'], inputs['sitename'])
filenames = metadata[sat]['filenames']
total_images = len(filenames)
# nested function
def duplicates_dict(lst):
"return duplicates and indices"
def duplicates(lst, item):
return [i for i, x in enumerate(lst) if x == item]
return dict(
(x, duplicates(lst, x)) for x in set(lst) if lst.count(x) > 1)
# first pass on images that have the exact same timestamp
duplicates = duplicates_dict([_.split('_')[0] for _ in filenames])
if len(duplicates) > 0:
total_removed_step1 = 0
# loop through each pair of duplicates and merge them
for key in duplicates.keys():
idx_dup = duplicates[key]
# get full filenames (3 images and .txtt) for each index and bounding polygons
fn_im, polygons, im_epsg = [], [], []
for index in range(len(idx_dup)):
# image names
fn_im.append([
os.path.join(filepath, 'S2', '10m',
filenames[idx_dup[index]]),
os.path.join(
filepath, 'S2', '20m',
filenames[idx_dup[index]].replace('10m', '20m')),
os.path.join(
filepath, 'S2', '60m',
filenames[idx_dup[index]].replace('10m', '60m')),
os.path.join(
filepath, 'S2', 'meta',
filenames[idx_dup[index]].replace('_10m', '').replace(
'.tif', '.txt'))
])
# bounding polygons
polygons.append(SDS_tools.get_image_bounds(fn_im[index][0]))
im_epsg.append(metadata[sat]['epsg'][idx_dup[index]])
# check if epsg are the same, print a warning message
if len(np.unique(im_epsg)) > 1:
print(
'WARNING: there was an error as two S2 images do not have the same epsg,'
+
' please open an issue on Github at https://github.com/kvos/CoastSat/issues'
+
' and include your script so I can find out what happened.'
)
# find which images contain other images
contain_bools_list = []
for i, poly1 in enumerate(polygons):
contain_bools = []
for k, poly2 in enumerate(polygons):
if k == i:
contain_bools.append(True)
# print('%d*: '%k+str(poly1.contains(poly2)))
else:
# print('%d: '%k+str(poly1.contains(poly2)))
contain_bools.append(poly1.contains(poly2))
contain_bools_list.append(contain_bools)
# look if one image contains all the others
contain_all = [np.all(_) for _ in contain_bools_list]
# if one image contains all the others, keep that one and delete the rest
if np.any(contain_all):
idx_keep = np.where(contain_all)[0][0]
for i in [_ for _ in range(len(idx_dup)) if not _ == idx_keep]:
# print('removed %s'%(fn_im[i][-1]))
# remove the 3 .tif files + the .txt file
for k in range(4):
os.chmod(fn_im[i][k], 0o777)
os.remove(fn_im[i][k])
total_removed_step1 += 1
# load metadata again and update filenames
metadata = get_metadata(inputs)
filenames = metadata[sat]['filenames']
# find the pairs of images that are within 5 minutes of each other and merge them
time_delta = 5 * 60 # 5 minutes in seconds
dates = metadata[sat]['dates'].copy()
pairs = []
for i, date in enumerate(metadata[sat]['dates']):
# dummy value so it does not match it again
dates[i] = pytz.utc.localize(datetime(1, 1, 1) + timedelta(days=i + 1))
# calculate time difference
time_diff = np.array(
[np.abs((date - _).total_seconds()) for _ in dates])
# find the matching times and add to pairs list
boolvec = time_diff <= time_delta
if np.sum(boolvec) == 0:
continue
else:
idx_dup = np.where(boolvec)[0][0]
pairs.append([i, idx_dup])
total_merged_step2 = len(pairs)
# because they could be triplicates in S2 images, adjust the pairs for consecutive merges
for i in range(1, len(pairs)):
if pairs[i - 1][1] == pairs[i][0]:
pairs[i][0] = pairs[i - 1][0]
# check also for quadruplicates and remove them
pair_first = [_[0] for _ in pairs]
idx_remove_pair = []
for idx in np.unique(pair_first):
# quadruplicate if trying to merge 3 times the same image with a successive image
if sum(pair_first == idx) == 3:
# remove the last image: 3 .tif files + the .txt file
idx_last = [pairs[_]
for _ in np.where(pair_first == idx)[0]][-1][-1]
fn_im = [
os.path.join(filepath, 'S2', '10m', filenames[idx_last]),
os.path.join(filepath, 'S2', '20m',
filenames[idx_last].replace('10m', '20m')),
os.path.join(filepath, 'S2', '60m',
filenames[idx_last].replace('10m', '60m')),
os.path.join(
filepath, 'S2', 'meta',
filenames[idx_last].replace('_10m',
'').replace('.tif', '.txt'))
]
for k in range(4):
os.chmod(fn_im[k], 0o777)
os.remove(fn_im[k])
# store the index of the pair to remove it outside the loop
idx_remove_pair.append(np.where(pair_first == idx)[0][-1])
# remove quadruplicates from list of pairs
pairs = [i for j, i in enumerate(pairs) if j not in idx_remove_pair]
# for each pair of image, first check if one image completely contains the other
# in that case keep the larger image. Otherwise merge the two images.
for i, pair in enumerate(pairs):
# get filenames of all the files corresponding to the each image in the pair
fn_im = []
for index in range(len(pair)):
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')),
os.path.join(
filepath, 'S2', 'meta',
filenames[pair[index]].replace('_10m',
'').replace('.tif', '.txt'))
])
# get polygon for first image
polygon0 = SDS_tools.get_image_bounds(fn_im[0][0])
im_epsg0 = metadata[sat]['epsg'][pair[0]]
# get polygon for second image
polygon1 = SDS_tools.get_image_bounds(fn_im[1][0])
im_epsg1 = metadata[sat]['epsg'][pair[1]]
# check if epsg are the same
if not im_epsg0 == im_epsg1:
print(
'WARNING: there was an error as two S2 images do not have the same epsg,'
+
' please open an issue on Github at https://github.com/kvos/CoastSat/issues'
+ ' and include your script so we can find out what happened.')
break
# check if one image contains the other one
if polygon0.contains(polygon1):
# if polygon0 contains polygon1, remove files for polygon1
for k in range(4): # remove the 3 .tif files + the .txt file
os.chmod(fn_im[1][k], 0o777)
os.remove(fn_im[1][k])
# print('removed 1')
continue
elif polygon1.contains(polygon0):
# if polygon1 contains polygon0, remove image0
for k in range(4): # remove the 3 .tif files + the .txt file
os.chmod(fn_im[0][k], 0o777)
os.remove(fn_im[0][k])
# print('removed 0')
# adjust the order in case of triplicates
if i + 1 < len(pairs):
if pairs[i + 1][0] == pair[0]: pairs[i + 1][0] = pairs[i][1]
continue
# otherwise merge the two images after masking the nodata values
else:
for index in range(len(pair)):
# read image
im_ms, georef, cloud_mask, im_extra, im_QA, im_nodata, im_proj = 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.
if len(im_ms) > 0:
# calculate image std for the first 10m band
im_std = SDS_tools.image_std(im_ms[:, :, 0], 1)
# convert to binary
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
# dilate to fill the edges (which have high std)
mask10 = morphology.dilation(im_binary,
morphology.square(3))
# mask the 10m .tif file (add no_data where mask is True)
SDS_tools.mask_raster(fn_im[index][0], mask10)
# now calculate the mask for the 20m band (SWIR1)
# for the older version of the ee api calculate the image std again
if int(ee.__version__[-3:]) <= 201:
# calculate std to create another mask for the 20m band (SWIR1)
im_std = SDS_tools.image_std(im_extra, 1)
im_binary = np.logical_or(im_std < 1e-6,
np.isnan(im_std))
mask20 = morphology.dilation(im_binary,
morphology.square(3))
# for the newer versions just resample the mask for the 10m bands
else:
# create mask for the 20m band (SWIR1) by resampling the 10m one
mask20 = ndimage.zoom(mask10, zoom=1 / 2, order=0)
mask20 = transform.resize(mask20,
im_extra.shape,
mode='constant',
order=0,
preserve_range=True)
mask20 = mask20.astype(bool)
# mask the 20m .tif file (im_extra)
SDS_tools.mask_raster(fn_im[index][1], mask20)
# create a mask for the 60m QA band by resampling the 20m one
mask60 = ndimage.zoom(mask20, zoom=1 / 3, order=0)
mask60 = transform.resize(mask60,
im_QA.shape,
mode='constant',
order=0,
preserve_range=True)
mask60 = mask60.astype(bool)
# mask the 60m .tif file (im_QA)
SDS_tools.mask_raster(fn_im[index][2], mask60)
# make a figure for quality control/debugging
# im_RGB = SDS_preprocess.rescale_image_intensity(im_ms[:,:,[2,1,0]], cloud_mask, 99.9)
# fig,ax= plt.subplots(2,3,tight_layout=True)
# ax[0,0].imshow(im_RGB)
# ax[0,0].set_title('RGB original')
# ax[1,0].imshow(mask10)
# ax[1,0].set_title('Mask 10m')
# ax[0,1].imshow(mask20)
# ax[0,1].set_title('Mask 20m')
# ax[1,1].imshow(mask60)
# ax[1,1].set_title('Mask 60 m')
# ax[0,2].imshow(im_QA)
# ax[0,2].set_title('Im QA')
# ax[1,2].imshow(im_nodata)
# ax[1,2].set_title('Im nodata')
else:
continue
# once all the pairs of .tif files have been masked with no_data, merge the using gdal_merge
fn_merged = os.path.join(filepath, 'merged.tif')
for k in range(3):
# merge masked bands
gdal_merge.main(
['', '-o', fn_merged, '-n', '0', fn_im[0][k], fn_im[1][k]])
# remove old files
os.chmod(fn_im[0][k], 0o777)
os.remove(fn_im[0][k])
os.chmod(fn_im[1][k], 0o777)
os.remove(fn_im[1][k])
# rename new file
fn_new = fn_im[0][k].split('.')[0] + '_merged.tif'
os.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_new)
# open both metadata files
metadict0 = dict([])
with open(fn_im[0][3], 'r') as f:
metadict0['filename'] = f.readline().split('\t')[1].replace(
'\n', '')
metadict0['acc_georef'] = float(
f.readline().split('\t')[1].replace('\n', ''))
metadict0['epsg'] = int(f.readline().split('\t')[1].replace(
'\n', ''))
metadict1 = dict([])
with open(fn_im[1][3], 'r') as f:
metadict1['filename'] = f.readline().split('\t')[1].replace(
'\n', '')
metadict1['acc_georef'] = float(
f.readline().split('\t')[1].replace('\n', ''))
metadict1['epsg'] = int(f.readline().split('\t')[1].replace(
'\n', ''))
# check if both images have the same georef accuracy
if np.any(
np.array([
metadict0['acc_georef'], metadict1['acc_georef']
]) == -1):
metadict0['georef'] = -1
# add new name
metadict0['filename'] = metadict0['filename'].split(
'.')[0] + '_merged.tif'
# remove the old metadata.txt files
os.chmod(fn_im[0][3], 0o777)
os.remove(fn_im[0][3])
os.chmod(fn_im[1][3], 0o777)
os.remove(fn_im[1][3])
# rewrite the .txt file with a new metadata file
fn_new = fn_im[0][3].split('.')[0] + '_merged.txt'
with open(fn_new, 'w') as f:
for key in metadict0.keys():
f.write('%s\t%s\n' % (key, metadict0[key]))
# update filenames list (in case there are triplicates)
filenames[pair[0]] = metadict0['filename']
print(
'%d out of %d Sentinel-2 images were merged (overlapping or duplicate)'
% (total_removed_step1 + total_merged_step2, total_images))
# update the metadata dict
metadata_updated = get_metadata(inputs)
return metadata_updated
def show_detection(im_ms, cloud_mask, im_labels, shoreline,image_epsg, georef,
settings, date, satname):
"""
Shows the detected shoreline to the user for visual quality control.
The user can accept/reject the detected shorelines by using keep/skip
buttons.
KV WRL 2018
Arguments:
-----------
im_ms: np.array
RGB + downsampled NIR and SWIR
cloud_mask: np.array
2D cloud mask with True where cloud pixels are
im_labels: np.array
3D image containing a boolean image for each class in the order (sand, swash, water)
shoreline: np.array
array of points with the X and Y coordinates of the shoreline
image_epsg: int
spatial reference system of the image from which the contours were extracted
georef: np.array
vector of 6 elements [Xtr, Xscale, Xshear, Ytr, Yshear, Yscale]
date: string
date at which the image was taken
satname: string
indicates the satname (L5,L7,L8 or S2)
settings: dict with the following keys
'inputs': dict
input parameters (sitename, filepath, polygon, dates, sat_list)
'output_epsg': int
output spatial reference system as EPSG code
'check_detection': bool
if True, lets user manually accept/reject the mapped shorelines
'save_figure': bool
if True, saves a -jpg file for each mapped shoreline
Returns:
-----------
skip_image: boolean
True if the user wants to skip the image, False otherwise
"""
sitename = settings['inputs']['sitename']
filepath_data = settings['inputs']['filepath']
# subfolder where the .jpg file is stored if the user accepts the shoreline detection
filepath = os.path.join(filepath_data, sitename, 'jpg_files', 'detection')
im_RGB = SDS_preprocess.rescale_image_intensity(im_ms[:,:,[2,1,0]], cloud_mask, 99.9)
# compute classified image
im_class = np.copy(im_RGB)
cmap = cm.get_cmap('tab20c')
colorpalette = cmap(np.arange(0,13,1))
colours = np.zeros((3,4))
colours[0,:] = colorpalette[5]
colours[1,:] = np.array([204/255,1,1,1])
colours[2,:] = np.array([0,91/255,1,1])
for k in range(0,im_labels.shape[2]):
im_class[im_labels[:,:,k],0] = colours[k,0]
im_class[im_labels[:,:,k],1] = colours[k,1]
im_class[im_labels[:,:,k],2] = colours[k,2]
# compute MNDWI grayscale image
im_mwi = SDS_tools.nd_index(im_ms[:,:,4], im_ms[:,:,1], cloud_mask)
# transform world coordinates of shoreline into pixel coordinates
# use try/except in case there are no coordinates to be transformed (shoreline = [])
try:
sl_pix = SDS_tools.convert_world2pix(SDS_tools.convert_epsg(shoreline,
settings['output_epsg'],
image_epsg)[:,[0,1]], georef)
except:
# if try fails, just add nan into the shoreline vector so the next parts can still run
sl_pix = np.array([[np.nan, np.nan],[np.nan, np.nan]])
if plt.get_fignums():
# get open figure if it exists
fig = plt.gcf()
ax1 = fig.axes[0]
ax2 = fig.axes[1]
ax3 = fig.axes[2]
else:
# else create a new figure
fig = plt.figure()
fig.set_size_inches([18, 9])
mng = plt.get_current_fig_manager()
mng.window.showMaximized()
# according to the image shape, decide whether it is better to have the images
# in vertical subplots or horizontal subplots
if im_RGB.shape[1] > 2.5*im_RGB.shape[0]:
# vertical subplots
gs = gridspec.GridSpec(3, 1)
gs.update(bottom=0.03, top=0.97, left=0.03, right=0.97)
ax1 = fig.add_subplot(gs[0,0])
ax2 = fig.add_subplot(gs[1,0], sharex=ax1, sharey=ax1)
ax3 = fig.add_subplot(gs[2,0], sharex=ax1, sharey=ax1)
else:
# horizontal subplots
gs = gridspec.GridSpec(1, 3)
gs.update(bottom=0.05, top=0.95, left=0.05, right=0.95)
ax1 = fig.add_subplot(gs[0,0])
ax2 = fig.add_subplot(gs[0,1], sharex=ax1, sharey=ax1)
ax3 = fig.add_subplot(gs[0,2], sharex=ax1, sharey=ax1)
# change the color of nans to either black (0.0) or white (1.0) or somewhere in between
nan_color = 1.0
im_RGB = np.where(np.isnan(im_RGB), nan_color, im_RGB)
im_class = np.where(np.isnan(im_class), 1.0, im_class)
# create image 1 (RGB)
ax1.imshow(im_RGB)
ax1.plot(sl_pix[:,0], sl_pix[:,1], 'k.', markersize=3)
ax1.axis('off')
ax1.set_title(sitename, fontweight='bold', fontsize=16)
# create image 2 (classification)
ax2.imshow(im_class)
ax2.plot(sl_pix[:,0], sl_pix[:,1], 'k.', markersize=3)
ax2.axis('off')
orange_patch = mpatches.Patch(color=colours[0,:], label='sand')
white_patch = mpatches.Patch(color=colours[1,:], label='whitewater')
blue_patch = mpatches.Patch(color=colours[2,:], label='water')
black_line = mlines.Line2D([],[],color='k',linestyle='-', label='shoreline')
ax2.legend(handles=[orange_patch,white_patch,blue_patch, black_line],
bbox_to_anchor=(1, 0.5), fontsize=10)
ax2.set_title(date, fontweight='bold', fontsize=16)
# create image 3 (MNDWI)
ax3.imshow(im_mwi, cmap='bwr')
ax3.plot(sl_pix[:,0], sl_pix[:,1], 'k.', markersize=3)
ax3.axis('off')
ax3.set_title(satname, fontweight='bold', fontsize=16)
# additional options
# ax1.set_anchor('W')
# ax2.set_anchor('W')
# cb = plt.colorbar()
# cb.ax.tick_params(labelsize=10)
# cb.set_label('MNDWI values')
# ax3.set_anchor('W')
# if check_detection is True, let user manually accept/reject the images
skip_image = False
if settings['check_detection']:
# set a key event to accept/reject the detections (see https://stackoverflow.com/a/15033071)
# this variable needs to be immuatable so we can access it after the keypress event
key_event = {}
def press(event):
# store what key was pressed in the dictionary
key_event['pressed'] = event.key
# let the user press a key, right arrow to keep the image, left arrow to skip it
# to break the loop the user can press 'escape'
while True:
btn_keep = plt.text(1.1, 0.9, 'keep ⇨', size=12, ha="right", va="top",
transform=ax1.transAxes,
bbox=dict(boxstyle="square", ec='k',fc='w'))
btn_skip = plt.text(-0.1, 0.9, '⇦ skip', size=12, ha="left", va="top",
transform=ax1.transAxes,
bbox=dict(boxstyle="square", ec='k',fc='w'))
btn_esc = plt.text(0.5, 0, '<esc> to quit', size=12, ha="center", va="top",
transform=ax1.transAxes,
bbox=dict(boxstyle="square", ec='k',fc='w'))
plt.draw()
fig.canvas.mpl_connect('key_press_event', press)
plt.waitforbuttonpress()
# after button is pressed, remove the buttons
btn_skip.remove()
btn_keep.remove()
btn_esc.remove()
# keep/skip image according to the pressed key, 'escape' to break the loop
if key_event.get('pressed') == 'right':
skip_image = False
break
elif key_event.get('pressed') == 'left':
skip_image = True
break
elif key_event.get('pressed') == 'escape':
plt.close()
raise StopIteration('User cancelled checking shoreline detection')
else:
plt.waitforbuttonpress()
# if save_figure is True, save a .jpg under /jpg_files/detection
if settings['save_figure'] and not skip_image:
fig.savefig(os.path.join(filepath, date + '_' + satname + '.jpg'), dpi=150)
# Don't close the figure window, but remove all axes and settings, ready for next plot
for ax in fig.axes:
ax.clear()
return skip_image
def merge_overlapping_images(metadata, inputs):
"""
Merge simultaneous overlapping images that cover the area of interest.
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 with the following keys
'sitename': str
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,
there are 5 pairs of lat/lon with the fifth point equal to the first point:
```
polygon = [[[151.3, -33.7],[151.4, -33.7],[151.4, -33.8],[151.3, -33.8],
[151.3, -33.7]]]
```
'dates': list of str
list that contains 2 strings with the initial and final dates in
format 'yyyy-mm-dd':
```
dates = ['1987-01-01', '2018-01-01']
```
'sat_list': list of str
list that contains the names of the satellite missions to include:
```
sat_list = ['L5', 'L7', 'L8', 'S2']
```
'filepath_data': str
filepath to the directory where the images are downloaded
Returns:
-----------
metadata_updated: dict
updated metadata
"""
# only for Sentinel-2 at this stage (not sure if this is needed for Landsat images)
sat = 'S2'
filepath = os.path.join(inputs['filepath'], inputs['sitename'])
filenames = metadata[sat]['filenames']
# find the pairs of images that are within 5 minutes of each other
time_delta = 5 * 60 # 5 minutes in seconds
dates = metadata[sat]['dates'].copy()
pairs = []
for i, date in enumerate(metadata[sat]['dates']):
# dummy value so it does not match it again
dates[i] = pytz.utc.localize(datetime(1, 1, 1) + timedelta(days=i + 1))
# calculate time difference
time_diff = np.array(
[np.abs((date - _).total_seconds()) for _ in dates])
# find the matching times and add to pairs list
boolvec = time_diff <= time_delta
if np.sum(boolvec) == 0:
continue
else:
idx_dup = np.where(boolvec)[0][0]
pairs.append([i, idx_dup])
# because they could be triplicates in S2 images, adjust the for consecutive merges
for i in range(1, len(pairs)):
if pairs[i - 1][1] == pairs[i][0]:
pairs[i][0] = pairs[i - 1][0]
# for each pair of image, create a mask and add no_data into the .tif file (this is needed before merging .tif files)
for i, pair in enumerate(pairs):
fn_im = []
for index in range(len(pair)):
# get filenames of all the files corresponding to the each image in the pair
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')),
os.path.join(
filepath, 'S2', 'meta',
filenames[pair[index]].replace('_10m',
'').replace('.tif', '.txt'))
])
# read that image
im_ms, georef, cloud_mask, im_extra, im_QA, im_nodata = SDS_preprocess.preprocess_single(
fn_im[index], sat, False)
# im_RGB = SDS_preprocess.rescale_image_intensity(im_ms[:,:,[2,1,0]], cloud_mask, 99.9)
# 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.
if len(im_ms) > 0:
# calculate image std for the first 10m band
im_std = SDS_tools.image_std(im_ms[:, :, 0], 1)
# convert to binary
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
# dilate to fill the edges (which have high std)
mask10 = morphology.dilation(im_binary, morphology.square(3))
# mask all 10m bands
for k in range(im_ms.shape[2]):
im_ms[mask10, k] = np.nan
# mask the 10m .tif file (add no_data where mask is True)
SDS_tools.mask_raster(fn_im[index][0], mask10)
# create another mask for the 20m band (SWIR1)
im_std = SDS_tools.image_std(im_extra, 1)
im_binary = np.logical_or(im_std < 1e-6, np.isnan(im_std))
mask20 = morphology.dilation(im_binary, morphology.square(3))
im_extra[mask20] = np.nan
# mask the 20m .tif file (im_extra)
SDS_tools.mask_raster(fn_im[index][1], mask20)
# use the 20m mask to create a mask for the 60m QA band (by resampling)
mask60 = ndimage.zoom(mask20, zoom=1 / 3, order=0)
mask60 = transform.resize(mask60,
im_QA.shape,
mode='constant',
order=0,
preserve_range=True)
mask60 = mask60.astype(bool)
# mask the 60m .tif file (im_QA)
SDS_tools.mask_raster(fn_im[index][2], mask60)
else:
continue
# make a figure for quality control
# fig,ax= plt.subplots(2,2,tight_layout=True)
# ax[0,0].imshow(im_RGB)
# ax[0,0].set_title('RGB original')
# ax[1,0].imshow(mask10)
# ax[1,0].set_title('Mask 10m')
# ax[0,1].imshow(mask20)
# ax[0,1].set_title('Mask 20m')
# ax[1,1].imshow(mask60)
# ax[1,1].set_title('Mask 60 m')
# once all the pairs of .tif files have been masked with no_data, merge the using gdal_merge
fn_merged = os.path.join(filepath, 'merged.tif')
# merge masked 10m bands and remove duplicate file
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.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_im[0][0])
# merge masked 20m band (SWIR band)
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.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_im[0][1])
# merge QA band (60m band)
gdal_merge.main(
['', '-o', fn_merged, '-n', '0', 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.chmod(fn_merged, 0o777)
os.rename(fn_merged, fn_im[0][2])
# remove the metadata .txt file of the duplicate image
os.chmod(fn_im[1][3], 0o777)
os.remove(fn_im[1][3])
print('%d Sentinel-2 images were merged (overlapping or duplicate)' %
len(pairs))
# update the metadata dict
metadata_updated = copy.deepcopy(metadata)
idx_removed = []
idx_kept = []
for pair in pairs:
idx_removed.append(pair[1])
for idx in np.arange(0, len(metadata[sat]['dates'])):
if not idx in idx_removed: idx_kept.append(idx)
for key in metadata_updated[sat].keys():
metadata_updated[sat][key] = [
metadata_updated[sat][key][_] for _ in idx_kept
]
return metadata_updated
