forked from kilianv/CoastSat_WRL
finalised new shoreline detection method
kvos
7 years ago
parent
b99c2acaf3
commit
c1c1e6aacb
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@ -0,0 +1,228 @@
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# -*- coding: utf-8 -*-
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#==========================================================#
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# Run Neural Network on image to extract sandy pixels
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#==========================================================#
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# Initial settings
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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 matplotlib.patches as mpatches
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import matplotlib.lines as mlines
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from matplotlib import gridspec
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from datetime import datetime, timedelta
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import pytz
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import ee
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import pdb
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import time
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import pandas as pd
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# other modules
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from osgeo import gdal, ogr, osr
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import pickle
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import matplotlib.cm as cm
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from pylab import ginput
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# image processing modules
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import skimage.filters as filters
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import skimage.exposure as exposure
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import skimage.transform as transform
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import sklearn.decomposition as decomposition
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import skimage.measure as measure
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import skimage.morphology as morphology
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from scipy import ndimage
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import imageio
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# machine learning modules
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from sklearn.model_selection import train_test_split
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from sklearn.neural_network import MLPClassifier
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from sklearn.preprocessing import StandardScaler, Normalizer
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from sklearn.externals import joblib
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# import own modules
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import functions.utils as utils
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import functions.sds as sds
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# some settings
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np.seterr(all='ignore') # raise/ignore divisions by 0 and nans
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plt.rcParams['axes.grid'] = True
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plt.rcParams['figure.max_open_warning'] = 100
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ee.Initialize()
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# parameters
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cloud_thresh = 0.2 # threshold for cloud cover
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plot_bool = False # if you want the plots
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prob_high = 100 # upper probability to clip and rescale pixel intensity
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min_contour_points = 100# minimum number of points contained in each water line
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output_epsg = 28356 # GDA94 / MGA Zone 56
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buffer_size = 10 # radius (in pixels) of disk for buffer (pixel classification)
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min_beach_size = 10 # number of pixels in a beach (pixel classification)
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# load metadata (timestamps and epsg code) for the collection
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satname = 'L8'
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#sitename = 'NARRA_all'
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#sitename = 'NARRA'
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#sitename = 'OLDBAR'
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#sitename = 'OLDBAR_inlet'
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#sitename = 'SANDMOTOR'
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#sitename = 'TAIRUA'
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#sitename = 'DUCK'
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#sitename = 'BROULEE'
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sitename = 'MURI'
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# Load metadata
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filepath = os.path.join(os.getcwd(), 'data', satname, sitename)
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with open(os.path.join(filepath, sitename + '_timestamps' + '.pkl'), 'rb') as f:
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timestamps = pickle.load(f)
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timestamps_sorted = sorted(timestamps)
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daysall = (datetime(2019,1,1,tzinfo=pytz.utc) - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
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# path to images
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file_path_pan = os.path.join(os.getcwd(), 'data', satname, sitename, 'pan')
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file_path_ms = os.path.join(os.getcwd(), 'data', satname, sitename, 'ms')
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file_names_pan = os.listdir(file_path_pan)
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file_names_ms = os.listdir(file_path_ms)
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N = len(file_names_pan)
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# initialise some variables
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idx_skipped = []
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idx_nocloud = []
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n_features = 10
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train_pos = np.nan*np.ones((1,n_features))
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train_neg = np.nan*np.ones((1,n_features))
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columns = ('B','G','R','NIR','SWIR','Pan','WI','VI','BR', 'mWI', 'class')
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#%%
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for i in range(N):
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# read pan image
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fn_pan = os.path.join(file_path_pan, file_names_pan[i])
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data = gdal.Open(fn_pan, gdal.GA_ReadOnly)
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georef = np.array(data.GetGeoTransform())
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bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
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im_pan = np.stack(bands, 2)[:,:,0]
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nrow = im_pan.shape[0]
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ncol = im_pan.shape[1]
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# read ms image
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fn_ms = os.path.join(file_path_ms, file_names_ms[i])
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data = gdal.Open(fn_ms, gdal.GA_ReadOnly)
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bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
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im_ms = np.stack(bands, 2)
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# cloud mask
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im_qa = im_ms[:,:,5]
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cloud_mask = sds.create_cloud_mask(im_qa, satname, plot_bool)
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cloud_mask = transform.resize(cloud_mask, (im_pan.shape[0], im_pan.shape[1]),
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order=0, preserve_range=True,
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mode='constant').astype('bool_')
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# resize the image using bilinear interpolation (order 1)
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im_ms = transform.resize(im_ms,(im_pan.shape[0], im_pan.shape[1]),
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order=1, preserve_range=True, mode='constant')
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# check if -inf or nan values and add to cloud mask
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im_inf = np.isin(im_ms[:,:,0], -np.inf)
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im_nan = np.isnan(im_ms[:,:,0])
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cloud_mask = np.logical_or(np.logical_or(cloud_mask, im_inf), im_nan)
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# skip if cloud cover is more than the threshold
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cloud_cover = sum(sum(cloud_mask.astype(int)))/(cloud_mask.shape[0]*cloud_mask.shape[1])
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if cloud_cover > cloud_thresh:
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print('skip ' + str(i) + ' - cloudy (' + str(np.round(cloud_cover*100).astype(int)) + '%)')
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idx_skipped.append(i)
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continue
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idx_nocloud.append(i)
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# pansharpen rgb image
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im_ms_ps = sds.pansharpen(im_ms[:,:,[0,1,2]], im_pan, cloud_mask, plot_bool)
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# add down-sized bands for NIR and SWIR (since pansharpening is not possible)
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im_ms_ps = np.append(im_ms_ps, im_ms[:,:,[3,4]], axis=2)
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im_classif, im_labels = sds.classify_image_NN(im_ms_ps, im_pan, cloud_mask, min_beach_size, plot_bool)
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# if there are no sand pixels, skip the image (maybe later change the detection method with old method)
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if sum(sum(im_labels[:,:,0])) == 0 :
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print('skip ' + str(i) + ' - no sand')
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idx_skipped.append(i)
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continue
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contours_wi, contours_mwi = sds.find_wl_contours2(im_ms_ps, im_labels, cloud_mask, buffer_size, False)
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im_display = sds.rescale_image_intensity(im_ms_ps[:,:,[2,1,0]], cloud_mask, 100, False)
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im = np.copy(im_display)
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# define colours for plot
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colours = np.array([[1,128/255,0/255],[204/255,1,1],[0,0,204/255]])
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for k in range(0,im_labels.shape[2]):
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im[im_labels[:,:,k],0] = colours[k,0]
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im[im_labels[:,:,k],1] = colours[k,1]
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im[im_labels[:,:,k],2] = colours[k,2]
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# fig = plt.figure()
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# plt.suptitle(date_im, fontsize=17, fontweight='bold')
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# ax1 = plt.subplot(121)
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# plt.imshow(im_display)
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# plt.axis('off')
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# ax2 = plt.subplot(122, sharex=ax1, sharey=ax1)
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# plt.imshow(im)
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# plt.axis('off')
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# plt.gcf().set_size_inches(17.99,7.55)
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# plt.tight_layout()
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# orange_patch = mpatches.Patch(color=[1,128/255,0/255], label='sand')
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# white_patch = mpatches.Patch(color=[204/255,1,1], label='swash/whitewater')
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# blue_patch = mpatches.Patch(color=[0,0,204/255], label='water')
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# plt.legend(handles=[orange_patch,white_patch,blue_patch], bbox_to_anchor=(0.95, 0.2))
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# plt.draw()
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date_im = timestamps_sorted[i].strftime('%d %b %Y')
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daysnow = (timestamps_sorted[i] - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
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fig = plt.figure()
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gs = gridspec.GridSpec(2, 2, height_ratios=[1, 20])
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ax1 = fig.add_subplot(gs[0,:])
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plt.plot(0,0,'ko',daysall,0,'ko')
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plt.plot([0,daysall],[0,0],'k-')
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plt.plot(daysnow,0,'ro')
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plt.text(0,0.05,'2013')
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plt.text(daysall,0.05,'2019')
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plt.plot((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
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plt.plot((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
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plt.plot((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
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plt.plot((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
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plt.plot((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
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plt.text((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2014')
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plt.text((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2015')
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plt.text((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2016')
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plt.text((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2017')
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plt.text((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2018')
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plt.axis('off')
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ax2 = fig.add_subplot(gs[1,0])
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plt.imshow(im_display)
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plt.axis('off')
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plt.title(date_im, fontsize=17, fontweight='bold')
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ax3 = fig.add_subplot(gs[1,1])
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plt.imshow(im)
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for l,contour in enumerate(contours_mwi): plt.plot(contour[:, 1], contour[:, 0], linewidth=2, color='k', linestyle='--')
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plt.axis('off')
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orange_patch = mpatches.Patch(color=[1,128/255,0/255], label='sand')
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white_patch = mpatches.Patch(color=[204/255,1,1], label='swash/whitewater')
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blue_patch = mpatches.Patch(color=[0,0,204/255], label='water')
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black_line = mlines.Line2D([],[],color='k',linestyle='-', label='shoreline')
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plt.legend(handles=[orange_patch,white_patch,blue_patch, black_line], bbox_to_anchor=(0.95, 0.2))
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plt.gcf().set_size_inches(17.99,7.55)
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plt.gcf().set_tight_layout(True)
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plt.draw()
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plt.savefig(os.path.join(filepath,'plots_classif', file_names_pan[i][len(satname)+1+len(sitename)+1:len(satname)+1+len(sitename)+1+10] + '.jpg'), dpi = 300)
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plt.close()
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# create gif
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images = []
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filenames = os.listdir(os.path.join(filepath, 'plots_classif'))
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with imageio.get_writer(sitename + '.gif', mode='I', duration=0.4) as writer:
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for filename in filenames:
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image = imageio.imread(os.path.join(filepath,'plots_classif',filename))
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writer.append_data(image)
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@ -0,0 +1,193 @@
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# -*- coding: utf-8 -*-
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#==========================================================#
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# Run Neural Network on image to extract sandy pixels
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#==========================================================#
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# Initial settings
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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 matplotlib.patches as mpatches
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import matplotlib.lines as mlines
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from matplotlib import gridspec
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from datetime import datetime, timedelta
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import pytz
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import ee
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import pdb
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import time
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import pandas as pd
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# other modules
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from osgeo import gdal, ogr, osr
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import pickle
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import matplotlib.cm as cm
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from pylab import ginput
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# image processing modules
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import skimage.filters as filters
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import skimage.exposure as exposure
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import skimage.transform as transform
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import sklearn.decomposition as decomposition
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import skimage.measure as measure
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import skimage.morphology as morphology
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from scipy import ndimage
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import imageio
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# machine learning modules
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from sklearn.model_selection import train_test_split
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from sklearn.neural_network import MLPClassifier
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from sklearn.preprocessing import StandardScaler, Normalizer
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from sklearn.externals import joblib
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# import own modules
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import functions.utils as utils
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import functions.sds as sds
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# some settings
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np.seterr(all='ignore') # raise/ignore divisions by 0 and nans
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plt.rcParams['axes.grid'] = True
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plt.rcParams['figure.max_open_warning'] = 100
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ee.Initialize()
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# parameters
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cloud_thresh = 0.5 # threshold for cloud cover
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plot_bool = False # if you want the plots
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prob_high = 100 # upper probability to clip and rescale pixel intensity
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min_contour_points = 30# minimum number of points contained in each water line
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output_epsg = 28356 # GDA94 / MGA Zone 56
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buffer_size = 10 # radius (in pixels) of disk for buffer (pixel classification)
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min_beach_size = 10 # number of pixels in a beach (pixel classification)
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# load metadata (timestamps and epsg code) for the collection
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satname = 'L8'
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#sitename = 'NARRA_all'
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#sitename = 'NARRA'
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#sitename = 'OLDBAR'
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#sitename = 'OLDBAR_inlet'
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#sitename = 'SANDMOTOR'
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#sitename = 'TAIRUA'
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#sitename = 'DUCK'
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#sitename = 'BROULEE'
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sitename = 'MURI2'
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# Load metadata
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filepath = os.path.join(os.getcwd(), 'data', satname, sitename)
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with open(os.path.join(filepath, sitename + '_timestamps' + '.pkl'), 'rb') as f:
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timestamps = pickle.load(f)
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timestamps_sorted = sorted(timestamps)
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daysall = (datetime(2019,1,1,tzinfo=pytz.utc) - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
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# path to images
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file_path_pan = os.path.join(os.getcwd(), 'data', satname, sitename, 'pan')
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file_path_ms = os.path.join(os.getcwd(), 'data', satname, sitename, 'ms')
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file_names_pan = os.listdir(file_path_pan)
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file_names_ms = os.listdir(file_path_ms)
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N = len(file_names_pan)
|
||||||
|
|
||||||
|
# initialise some variables
|
||||||
|
idx_skipped = []
|
||||||
|
idx_nocloud = []
|
||||||
|
n_features = 10
|
||||||
|
train_pos = np.nan*np.ones((1,n_features))
|
||||||
|
train_neg = np.nan*np.ones((1,n_features))
|
||||||
|
columns = ('B','G','R','NIR','SWIR','Pan','WI','VI','BR', 'mWI', 'class')
|
||||||
|
|
||||||
|
#%%
|
||||||
|
for i in range(N):
|
||||||
|
# read pan image
|
||||||
|
fn_pan = os.path.join(file_path_pan, file_names_pan[i])
|
||||||
|
data = gdal.Open(fn_pan, gdal.GA_ReadOnly)
|
||||||
|
georef = np.array(data.GetGeoTransform())
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_pan = np.stack(bands, 2)[:,:,0]
|
||||||
|
nrow = im_pan.shape[0]
|
||||||
|
ncol = im_pan.shape[1]
|
||||||
|
# read ms image
|
||||||
|
fn_ms = os.path.join(file_path_ms, file_names_ms[i])
|
||||||
|
data = gdal.Open(fn_ms, gdal.GA_ReadOnly)
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_ms = np.stack(bands, 2)
|
||||||
|
# cloud mask
|
||||||
|
im_qa = im_ms[:,:,5]
|
||||||
|
cloud_mask = sds.create_cloud_mask(im_qa, satname, plot_bool)
|
||||||
|
cloud_mask = transform.resize(cloud_mask, (im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=0, preserve_range=True,
|
||||||
|
mode='constant').astype('bool_')
|
||||||
|
# resize the image using bilinear interpolation (order 1)
|
||||||
|
im_ms = transform.resize(im_ms,(im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=1, preserve_range=True, mode='constant')
|
||||||
|
# check if -inf or nan values and add to cloud mask
|
||||||
|
im_inf = np.isin(im_ms[:,:,0], -np.inf)
|
||||||
|
im_nan = np.isnan(im_ms[:,:,0])
|
||||||
|
cloud_mask = np.logical_or(np.logical_or(cloud_mask, im_inf), im_nan)
|
||||||
|
# skip if cloud cover is more than the threshold
|
||||||
|
cloud_cover = sum(sum(cloud_mask.astype(int)))/(cloud_mask.shape[0]*cloud_mask.shape[1])
|
||||||
|
if cloud_cover > cloud_thresh:
|
||||||
|
print('skip ' + str(i) + ' - cloudy (' + str(np.round(cloud_cover*100).astype(int)) + '%)')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
idx_nocloud.append(i)
|
||||||
|
|
||||||
|
# pansharpen rgb image
|
||||||
|
im_ms_ps = sds.pansharpen(im_ms[:,:,[0,1,2]], im_pan, cloud_mask, plot_bool)
|
||||||
|
# add down-sized bands for NIR and SWIR (since pansharpening is not possible)
|
||||||
|
im_ms_ps = np.append(im_ms_ps, im_ms[:,:,[3,4]], axis=2)
|
||||||
|
|
||||||
|
# extract shorelines (old method)
|
||||||
|
im_ndwi = sds.nd_index(im_ms_ps[:,:,3], im_ms_ps[:,:,1], cloud_mask, plot_bool)
|
||||||
|
wl_pix = sds.find_wl_contours(im_ndwi, cloud_mask, min_contour_points, plot_bool)
|
||||||
|
|
||||||
|
im_display = sds.rescale_image_intensity(im_ms_ps[:,:,[2,1,0]], cloud_mask, 100, False)
|
||||||
|
|
||||||
|
date_im = timestamps_sorted[i].strftime('%d %b %Y')
|
||||||
|
daysnow = (timestamps_sorted[i] - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
|
||||||
|
|
||||||
|
fig = plt.figure()
|
||||||
|
gs = gridspec.GridSpec(2, 2, height_ratios=[1, 20])
|
||||||
|
|
||||||
|
ax1 = fig.add_subplot(gs[0,:])
|
||||||
|
plt.plot(0,0,'ko',daysall,0,'ko')
|
||||||
|
plt.plot([0,daysall],[0,0],'k-')
|
||||||
|
plt.plot(daysnow,0,'ro')
|
||||||
|
plt.text(0,0.05,'2013')
|
||||||
|
plt.text(daysall,0.05,'2019')
|
||||||
|
plt.plot((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.text((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2014')
|
||||||
|
plt.text((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2015')
|
||||||
|
plt.text((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2016')
|
||||||
|
plt.text((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2017')
|
||||||
|
plt.text((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2018')
|
||||||
|
plt.axis('off')
|
||||||
|
|
||||||
|
# ax2 = fig.add_subplot(gs[1,0])
|
||||||
|
# plt.imshow(im_display)
|
||||||
|
# plt.axis('off')
|
||||||
|
# plt.title(date_im, fontsize=17, fontweight='bold')
|
||||||
|
|
||||||
|
ax3 = fig.add_subplot(gs[1,:])
|
||||||
|
plt.imshow(im_display)
|
||||||
|
for l,contour in enumerate(wl_pix): plt.plot(contour[:, 1], contour[:, 0], linewidth=2, color='k', linestyle='--')
|
||||||
|
plt.title(date_im, fontsize=17, fontweight='bold')
|
||||||
|
plt.axis('off')
|
||||||
|
|
||||||
|
plt.gcf().set_size_inches(5.34,9.18)
|
||||||
|
plt.gcf().set_tight_layout(True)
|
||||||
|
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
plt.savefig(os.path.join(filepath,'plots_classif', file_names_pan[i][len(satname)+1+len(sitename)+1:len(satname)+1+len(sitename)+1+10] + '.jpg'), dpi = 300)
|
||||||
|
plt.close()
|
||||||
|
|
||||||
|
# create gif
|
||||||
|
images = []
|
||||||
|
filenames = os.listdir(os.path.join(filepath, 'plots_classif'))
|
||||||
|
with imageio.get_writer(sitename + '_final.gif', mode='I', duration=0.6) as writer:
|
||||||
|
for filename in filenames:
|
||||||
|
image = imageio.imread(os.path.join(filepath,'plots_classif',filename))
|
||||||
|
writer.append_data(image)
|
||||||
|
|
||||||
@ -0,0 +1,227 @@
|
|||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
|
||||||
|
#==========================================================#
|
||||||
|
# Run Neural Network on image to extract sandy pixels
|
||||||
|
#==========================================================#
|
||||||
|
|
||||||
|
# Initial settings
|
||||||
|
import os
|
||||||
|
import numpy as np
|
||||||
|
import matplotlib.pyplot as plt
|
||||||
|
import matplotlib.patches as mpatches
|
||||||
|
import matplotlib.lines as mlines
|
||||||
|
from matplotlib import gridspec
|
||||||
|
from datetime import datetime, timedelta
|
||||||
|
import pytz
|
||||||
|
import ee
|
||||||
|
import pdb
|
||||||
|
import time
|
||||||
|
import pandas as pd
|
||||||
|
# other modules
|
||||||
|
from osgeo import gdal, ogr, osr
|
||||||
|
import pickle
|
||||||
|
import matplotlib.cm as cm
|
||||||
|
from pylab import ginput
|
||||||
|
|
||||||
|
# image processing modules
|
||||||
|
import skimage.filters as filters
|
||||||
|
import skimage.exposure as exposure
|
||||||
|
import skimage.transform as transform
|
||||||
|
import sklearn.decomposition as decomposition
|
||||||
|
import skimage.measure as measure
|
||||||
|
import skimage.morphology as morphology
|
||||||
|
from scipy import ndimage
|
||||||
|
import imageio
|
||||||
|
|
||||||
|
|
||||||
|
# machine learning modules
|
||||||
|
from sklearn.model_selection import train_test_split
|
||||||
|
from sklearn.neural_network import MLPClassifier
|
||||||
|
from sklearn.preprocessing import StandardScaler, Normalizer
|
||||||
|
from sklearn.externals import joblib
|
||||||
|
|
||||||
|
# import own modules
|
||||||
|
import functions.utils as utils
|
||||||
|
import functions.sds as sds
|
||||||
|
|
||||||
|
# some settings
|
||||||
|
np.seterr(all='ignore') # raise/ignore divisions by 0 and nans
|
||||||
|
plt.rcParams['axes.grid'] = True
|
||||||
|
plt.rcParams['figure.max_open_warning'] = 100
|
||||||
|
ee.Initialize()
|
||||||
|
|
||||||
|
# parameters
|
||||||
|
cloud_thresh = 0.2 # threshold for cloud cover
|
||||||
|
plot_bool = False # if you want the plots
|
||||||
|
prob_high = 100 # upper probability to clip and rescale pixel intensity
|
||||||
|
min_contour_points = 100# minimum number of points contained in each water line
|
||||||
|
output_epsg = 28356 # GDA94 / MGA Zone 56
|
||||||
|
buffer_size = 10 # radius (in pixels) of disk for buffer (pixel classification)
|
||||||
|
min_beach_size = 20 # number of pixels in a beach (pixel classification)
|
||||||
|
|
||||||
|
# load metadata (timestamps and epsg code) for the collection
|
||||||
|
satname = 'L8'
|
||||||
|
#sitename = 'NARRA_all'
|
||||||
|
sitename = 'NARRA'
|
||||||
|
#sitename = 'OLDBAR'
|
||||||
|
#sitename = 'OLDBAR_inlet'
|
||||||
|
#sitename = 'SANDMOTOR'
|
||||||
|
#sitename = 'TAIRUA'
|
||||||
|
#sitename = 'DUCK'
|
||||||
|
#sitename = 'BROULEE'
|
||||||
|
|
||||||
|
# Load metadata
|
||||||
|
filepath = os.path.join(os.getcwd(), 'data', satname, sitename)
|
||||||
|
with open(os.path.join(filepath, sitename + '_timestamps' + '.pkl'), 'rb') as f:
|
||||||
|
timestamps = pickle.load(f)
|
||||||
|
timestamps_sorted = sorted(timestamps)
|
||||||
|
daysall = (datetime(2019,1,1,tzinfo=pytz.utc) - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
|
||||||
|
# path to images
|
||||||
|
file_path_pan = os.path.join(os.getcwd(), 'data', satname, sitename, 'pan')
|
||||||
|
file_path_ms = os.path.join(os.getcwd(), 'data', satname, sitename, 'ms')
|
||||||
|
file_names_pan = os.listdir(file_path_pan)
|
||||||
|
file_names_ms = os.listdir(file_path_ms)
|
||||||
|
N = len(file_names_pan)
|
||||||
|
|
||||||
|
# initialise some variables
|
||||||
|
idx_skipped = []
|
||||||
|
idx_nocloud = []
|
||||||
|
n_features = 10
|
||||||
|
train_pos = np.nan*np.ones((1,n_features))
|
||||||
|
train_neg = np.nan*np.ones((1,n_features))
|
||||||
|
columns = ('B','G','R','NIR','SWIR','Pan','WI','VI','BR', 'mWI', 'class')
|
||||||
|
|
||||||
|
#%%
|
||||||
|
for i in range(N):
|
||||||
|
# read pan image
|
||||||
|
fn_pan = os.path.join(file_path_pan, file_names_pan[i])
|
||||||
|
data = gdal.Open(fn_pan, gdal.GA_ReadOnly)
|
||||||
|
georef = np.array(data.GetGeoTransform())
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_pan = np.stack(bands, 2)[:,:,0]
|
||||||
|
nrow = im_pan.shape[0]
|
||||||
|
ncol = im_pan.shape[1]
|
||||||
|
# read ms image
|
||||||
|
fn_ms = os.path.join(file_path_ms, file_names_ms[i])
|
||||||
|
data = gdal.Open(fn_ms, gdal.GA_ReadOnly)
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_ms = np.stack(bands, 2)
|
||||||
|
# cloud mask
|
||||||
|
im_qa = im_ms[:,:,5]
|
||||||
|
cloud_mask = sds.create_cloud_mask(im_qa, satname, plot_bool)
|
||||||
|
cloud_mask = transform.resize(cloud_mask, (im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=0, preserve_range=True,
|
||||||
|
mode='constant').astype('bool_')
|
||||||
|
# resize the image using bilinear interpolation (order 1)
|
||||||
|
im_ms = transform.resize(im_ms,(im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=1, preserve_range=True, mode='constant')
|
||||||
|
# check if -inf or nan values and add to cloud mask
|
||||||
|
im_inf = np.isin(im_ms[:,:,0], -np.inf)
|
||||||
|
im_nan = np.isnan(im_ms[:,:,0])
|
||||||
|
cloud_mask = np.logical_or(np.logical_or(cloud_mask, im_inf), im_nan)
|
||||||
|
# skip if cloud cover is more than the threshold
|
||||||
|
cloud_cover = sum(sum(cloud_mask.astype(int)))/(cloud_mask.shape[0]*cloud_mask.shape[1])
|
||||||
|
if cloud_cover > cloud_thresh:
|
||||||
|
print('skip ' + str(i) + ' - cloudy (' + str(np.round(cloud_cover*100).astype(int)) + '%)')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
idx_nocloud.append(i)
|
||||||
|
|
||||||
|
# pansharpen rgb image
|
||||||
|
im_ms_ps = sds.pansharpen(im_ms[:,:,[0,1,2]], im_pan, cloud_mask, plot_bool)
|
||||||
|
# add down-sized bands for NIR and SWIR (since pansharpening is not possible)
|
||||||
|
im_ms_ps = np.append(im_ms_ps, im_ms[:,:,[3,4]], axis=2)
|
||||||
|
|
||||||
|
im_classif, im_labels = sds.classify_image_NN(im_ms_ps, im_pan, cloud_mask, min_beach_size, plot_bool)
|
||||||
|
|
||||||
|
# if there are no sand pixels, skip the image (maybe later change the detection method with old method)
|
||||||
|
if sum(sum(im_labels[:,:,0])) == 0 :
|
||||||
|
print('skip ' + str(i) + ' - no sand')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
|
||||||
|
contours_wi, contours_mwi = sds.find_wl_contours2(im_ms_ps, im_labels, cloud_mask, buffer_size, False)
|
||||||
|
|
||||||
|
|
||||||
|
im_display = sds.rescale_image_intensity(im_ms_ps[:,:,[2,1,0]], cloud_mask, 100, False)
|
||||||
|
im = np.copy(im_display)
|
||||||
|
# define colours for plot
|
||||||
|
colours = np.array([[1,128/255,0/255],[204/255,1,1],[0,0,204/255]])
|
||||||
|
for k in range(0,im_labels.shape[2]):
|
||||||
|
im[im_labels[:,:,k],0] = colours[k,0]
|
||||||
|
im[im_labels[:,:,k],1] = colours[k,1]
|
||||||
|
im[im_labels[:,:,k],2] = colours[k,2]
|
||||||
|
|
||||||
|
|
||||||
|
# fig = plt.figure()
|
||||||
|
# plt.suptitle(date_im, fontsize=17, fontweight='bold')
|
||||||
|
# ax1 = plt.subplot(121)
|
||||||
|
# plt.imshow(im_display)
|
||||||
|
# plt.axis('off')
|
||||||
|
# ax2 = plt.subplot(122, sharex=ax1, sharey=ax1)
|
||||||
|
# plt.imshow(im)
|
||||||
|
# plt.axis('off')
|
||||||
|
# plt.gcf().set_size_inches(17.99,7.55)
|
||||||
|
# plt.tight_layout()
|
||||||
|
# orange_patch = mpatches.Patch(color=[1,128/255,0/255], label='sand')
|
||||||
|
# white_patch = mpatches.Patch(color=[204/255,1,1], label='swash/whitewater')
|
||||||
|
# blue_patch = mpatches.Patch(color=[0,0,204/255], label='water')
|
||||||
|
# plt.legend(handles=[orange_patch,white_patch,blue_patch], bbox_to_anchor=(0.95, 0.2))
|
||||||
|
# plt.draw()
|
||||||
|
|
||||||
|
date_im = timestamps_sorted[i].strftime('%d %b %Y')
|
||||||
|
daysnow = (timestamps_sorted[i] - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
|
||||||
|
|
||||||
|
fig = plt.figure()
|
||||||
|
gs = gridspec.GridSpec(2, 2, height_ratios=[1, 20])
|
||||||
|
|
||||||
|
ax1 = fig.add_subplot(gs[0,:])
|
||||||
|
plt.plot(0,0,'ko',daysall,0,'ko')
|
||||||
|
plt.plot([0,daysall],[0,0],'k-')
|
||||||
|
plt.plot(daysnow,0,'ro')
|
||||||
|
plt.text(0,0.05,'2013')
|
||||||
|
plt.text(daysall,0.05,'2019')
|
||||||
|
plt.plot((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.text((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2014')
|
||||||
|
plt.text((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2015')
|
||||||
|
plt.text((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2016')
|
||||||
|
plt.text((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2017')
|
||||||
|
plt.text((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2018')
|
||||||
|
|
||||||
|
plt.axis('off')
|
||||||
|
|
||||||
|
# ax2 = fig.add_subplot(gs[1,0])
|
||||||
|
# plt.imshow(im_display)
|
||||||
|
# plt.axis('off')
|
||||||
|
# plt.title(date_im, fontsize=17, fontweight='bold')
|
||||||
|
|
||||||
|
ax3 = fig.add_subplot(gs[1,:])
|
||||||
|
plt.imshow(im)
|
||||||
|
for l,contour in enumerate(contours_mwi): plt.plot(contour[:, 1], contour[:, 0], linewidth=2, color='k', linestyle='--')
|
||||||
|
plt.axis('off')
|
||||||
|
orange_patch = mpatches.Patch(color=[1,128/255,0/255], label='sand')
|
||||||
|
white_patch = mpatches.Patch(color=[204/255,1,1], label='swash/whitewater')
|
||||||
|
blue_patch = mpatches.Patch(color=[0,0,204/255], label='water')
|
||||||
|
black_line = mlines.Line2D([],[],color='k',linestyle='--', label='shoreline')
|
||||||
|
plt.legend(handles=[orange_patch,white_patch,blue_patch, black_line], bbox_to_anchor=(0.6, 0.6))
|
||||||
|
plt.title(date_im, fontsize=17, fontweight='bold')
|
||||||
|
|
||||||
|
plt.gcf().set_size_inches(5.34,9.18)
|
||||||
|
plt.gcf().set_tight_layout(True)
|
||||||
|
|
||||||
|
plt.draw()
|
||||||
|
plt.savefig(os.path.join(filepath,'plots_classif', file_names_pan[i][len(satname)+1+len(sitename)+1:len(satname)+1+len(sitename)+1+10] + '.jpg'), dpi = 300)
|
||||||
|
plt.close()
|
||||||
|
|
||||||
|
# create gif
|
||||||
|
images = []
|
||||||
|
filenames = os.listdir(os.path.join(filepath, 'plots_classif'))
|
||||||
|
with imageio.get_writer(sitename + '.gif', mode='I', duration=0.4) as writer:
|
||||||
|
for filename in filenames:
|
||||||
|
image = imageio.imread(os.path.join(filepath,'plots_classif',filename))
|
||||||
|
writer.append_data(image)
|
||||||
|
|
||||||
@ -0,0 +1,229 @@
|
|||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
|
||||||
|
#==========================================================#
|
||||||
|
# Run Neural Network on image to extract sandy pixels
|
||||||
|
#==========================================================#
|
||||||
|
|
||||||
|
# Initial settings
|
||||||
|
import os
|
||||||
|
import numpy as np
|
||||||
|
import matplotlib.pyplot as plt
|
||||||
|
import matplotlib.patches as mpatches
|
||||||
|
import matplotlib.lines as mlines
|
||||||
|
from matplotlib import gridspec
|
||||||
|
from datetime import datetime, timedelta
|
||||||
|
import pytz
|
||||||
|
import ee
|
||||||
|
import pdb
|
||||||
|
import time
|
||||||
|
import pandas as pd
|
||||||
|
# other modules
|
||||||
|
from osgeo import gdal, ogr, osr
|
||||||
|
import pickle
|
||||||
|
import matplotlib.cm as cm
|
||||||
|
from pylab import ginput
|
||||||
|
|
||||||
|
# image processing modules
|
||||||
|
import skimage.filters as filters
|
||||||
|
import skimage.exposure as exposure
|
||||||
|
import skimage.transform as transform
|
||||||
|
import sklearn.decomposition as decomposition
|
||||||
|
import skimage.measure as measure
|
||||||
|
import skimage.morphology as morphology
|
||||||
|
from scipy import ndimage
|
||||||
|
import imageio
|
||||||
|
|
||||||
|
|
||||||
|
# machine learning modules
|
||||||
|
from sklearn.model_selection import train_test_split
|
||||||
|
from sklearn.neural_network import MLPClassifier
|
||||||
|
from sklearn.preprocessing import StandardScaler, Normalizer
|
||||||
|
from sklearn.externals import joblib
|
||||||
|
|
||||||
|
# import own modules
|
||||||
|
import functions.utils as utils
|
||||||
|
import functions.sds as sds
|
||||||
|
|
||||||
|
# some settings
|
||||||
|
np.seterr(all='ignore') # raise/ignore divisions by 0 and nans
|
||||||
|
plt.rcParams['axes.grid'] = True
|
||||||
|
plt.rcParams['figure.max_open_warning'] = 100
|
||||||
|
ee.Initialize()
|
||||||
|
|
||||||
|
# parameters
|
||||||
|
cloud_thresh = 0.2 # threshold for cloud cover
|
||||||
|
plot_bool = False # if you want the plots
|
||||||
|
prob_high = 100 # upper probability to clip and rescale pixel intensity
|
||||||
|
min_contour_points = 100# minimum number of points contained in each water line
|
||||||
|
output_epsg = 28356 # GDA94 / MGA Zone 56
|
||||||
|
buffer_size = 10 # radius (in pixels) of disk for buffer (pixel classification)
|
||||||
|
min_beach_size = 50 # number of pixels in a beach (pixel classification)
|
||||||
|
|
||||||
|
# load metadata (timestamps and epsg code) for the collection
|
||||||
|
satname = 'L8'
|
||||||
|
sitename = 'NARRA_all'
|
||||||
|
#sitename = 'NARRA'
|
||||||
|
#sitename = 'OLDBAR'
|
||||||
|
#sitename = 'OLDBAR_inlet'
|
||||||
|
#sitename = 'SANDMOTOR'
|
||||||
|
#sitename = 'TAIRUA'
|
||||||
|
#sitename = 'DUCK'
|
||||||
|
#sitename = 'BROULEE'
|
||||||
|
|
||||||
|
# Load metadata
|
||||||
|
filepath = os.path.join(os.getcwd(), 'data', satname, sitename)
|
||||||
|
with open(os.path.join(filepath, sitename + '_timestamps' + '.pkl'), 'rb') as f:
|
||||||
|
timestamps = pickle.load(f)
|
||||||
|
timestamps_sorted = sorted(timestamps)
|
||||||
|
daysall = (datetime(2019,1,1,tzinfo=pytz.utc) - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
|
||||||
|
# path to images
|
||||||
|
file_path_pan = os.path.join(os.getcwd(), 'data', satname, sitename, 'pan')
|
||||||
|
file_path_ms = os.path.join(os.getcwd(), 'data', satname, sitename, 'ms')
|
||||||
|
file_names_pan = os.listdir(file_path_pan)
|
||||||
|
file_names_ms = os.listdir(file_path_ms)
|
||||||
|
N = len(file_names_pan)
|
||||||
|
|
||||||
|
# initialise some variables
|
||||||
|
idx_skipped = []
|
||||||
|
idx_nocloud = []
|
||||||
|
n_features = 10
|
||||||
|
train_pos = np.nan*np.ones((1,n_features))
|
||||||
|
train_neg = np.nan*np.ones((1,n_features))
|
||||||
|
columns = ('B','G','R','NIR','SWIR','Pan','WI','VI','BR', 'mWI', 'class')
|
||||||
|
|
||||||
|
#%%
|
||||||
|
for i in range(1):
|
||||||
|
i = 156 # open (96 close)
|
||||||
|
# read pan image
|
||||||
|
fn_pan = os.path.join(file_path_pan, file_names_pan[i])
|
||||||
|
data = gdal.Open(fn_pan, gdal.GA_ReadOnly)
|
||||||
|
georef = np.array(data.GetGeoTransform())
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_pan = np.stack(bands, 2)[:,:,0]
|
||||||
|
nrow = im_pan.shape[0]
|
||||||
|
ncol = im_pan.shape[1]
|
||||||
|
# read ms image
|
||||||
|
fn_ms = os.path.join(file_path_ms, file_names_ms[i])
|
||||||
|
data = gdal.Open(fn_ms, gdal.GA_ReadOnly)
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_ms = np.stack(bands, 2)
|
||||||
|
# cloud mask
|
||||||
|
im_qa = im_ms[:,:,5]
|
||||||
|
cloud_mask = sds.create_cloud_mask(im_qa, satname, plot_bool)
|
||||||
|
cloud_mask = transform.resize(cloud_mask, (im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=0, preserve_range=True,
|
||||||
|
mode='constant').astype('bool_')
|
||||||
|
# resize the image using bilinear interpolation (order 1)
|
||||||
|
im_ms = transform.resize(im_ms,(im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=1, preserve_range=True, mode='constant')
|
||||||
|
# check if -inf or nan values and add to cloud mask
|
||||||
|
im_inf = np.isin(im_ms[:,:,0], -np.inf)
|
||||||
|
im_nan = np.isnan(im_ms[:,:,0])
|
||||||
|
cloud_mask = np.logical_or(np.logical_or(cloud_mask, im_inf), im_nan)
|
||||||
|
# skip if cloud cover is more than the threshold
|
||||||
|
cloud_cover = sum(sum(cloud_mask.astype(int)))/(cloud_mask.shape[0]*cloud_mask.shape[1])
|
||||||
|
if cloud_cover > cloud_thresh:
|
||||||
|
print('skip ' + str(i) + ' - cloudy (' + str(np.round(cloud_cover*100).astype(int)) + '%)')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
idx_nocloud.append(i)
|
||||||
|
|
||||||
|
# pansharpen rgb image
|
||||||
|
im_ms_ps = sds.pansharpen(im_ms[:,:,[0,1,2]], im_pan, cloud_mask, plot_bool)
|
||||||
|
# add down-sized bands for NIR and SWIR (since pansharpening is not possible)
|
||||||
|
im_ms_ps = np.append(im_ms_ps, im_ms[:,:,[3,4]], axis=2)
|
||||||
|
|
||||||
|
im_classif, im_labels = sds.classify_image_NN(im_ms_ps, im_pan, cloud_mask, min_beach_size, plot_bool)
|
||||||
|
|
||||||
|
# if there are no sand pixels, skip the image (maybe later change the detection method with old method)
|
||||||
|
if sum(sum(im_labels[:,:,0])) == 0 :
|
||||||
|
print('skip ' + str(i) + ' - no sand')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
|
||||||
|
contours_wi, contours_mwi = sds.find_wl_contours2(im_ms_ps, im_labels, cloud_mask, buffer_size, False)
|
||||||
|
|
||||||
|
|
||||||
|
im_display = sds.rescale_image_intensity(im_ms_ps[:,:,[2,1,0]], cloud_mask, 100, False)
|
||||||
|
im = np.copy(im_display)
|
||||||
|
# define colours for plot
|
||||||
|
colours = np.array([[1,128/255,0/255],[0,0,204/255],[0,0,204/255]])
|
||||||
|
|
||||||
|
for k in range(0,im_labels.shape[2]):
|
||||||
|
im[im_labels[:,:,k],0] = colours[k,0]
|
||||||
|
im[im_labels[:,:,k],1] = colours[k,1]
|
||||||
|
im[im_labels[:,:,k],2] = colours[k,2]
|
||||||
|
|
||||||
|
|
||||||
|
# fig = plt.figure()
|
||||||
|
# plt.suptitle(date_im, fontsize=17, fontweight='bold')
|
||||||
|
# ax1 = plt.subplot(121)
|
||||||
|
# plt.imshow(im_display)
|
||||||
|
# plt.axis('off')
|
||||||
|
# ax2 = plt.subplot(122, sharex=ax1, sharey=ax1)
|
||||||
|
# plt.imshow(im)
|
||||||
|
# plt.axis('off')
|
||||||
|
# plt.gcf().set_size_inches(17.99,7.55)
|
||||||
|
# plt.tight_layout()
|
||||||
|
# orange_patch = mpatches.Patch(color=[1,128/255,0/255], label='sand')
|
||||||
|
# white_patch = mpatches.Patch(color=[204/255,1,1], label='swash/whitewater')
|
||||||
|
# blue_patch = mpatches.Patch(color=[0,0,204/255], label='water')
|
||||||
|
# plt.legend(handles=[orange_patch,white_patch,blue_patch], bbox_to_anchor=(0.95, 0.2))
|
||||||
|
# plt.draw()
|
||||||
|
|
||||||
|
date_im = timestamps_sorted[i].strftime('%d %b %Y')
|
||||||
|
daysnow = (timestamps_sorted[i] - datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds()
|
||||||
|
|
||||||
|
fig = plt.figure()
|
||||||
|
gs = gridspec.GridSpec(2, 2, height_ratios=[1, 20])
|
||||||
|
|
||||||
|
ax1 = fig.add_subplot(gs[0,:])
|
||||||
|
plt.plot(0,0,'ko',daysall,0,'ko')
|
||||||
|
plt.plot([0,daysall],[0,0],'k-')
|
||||||
|
plt.plot(daysnow,0,'ro')
|
||||||
|
plt.text(0,0.05,'2013')
|
||||||
|
plt.text(daysall,0.05,'2019')
|
||||||
|
plt.plot((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.plot((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0,'ko',markersize=3)
|
||||||
|
plt.text((datetime(2014,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2014')
|
||||||
|
plt.text((datetime(2015,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2015')
|
||||||
|
plt.text((datetime(2016,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2016')
|
||||||
|
plt.text((datetime(2017,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2017')
|
||||||
|
plt.text((datetime(2018,1,1,tzinfo=pytz.utc)- datetime(2013,1,1,tzinfo=pytz.utc)).total_seconds(),0.05,'2018')
|
||||||
|
|
||||||
|
plt.axis('off')
|
||||||
|
|
||||||
|
ax2 = fig.add_subplot(gs[1,0])
|
||||||
|
plt.imshow(im_display)
|
||||||
|
plt.axis('off')
|
||||||
|
plt.title(date_im, fontsize=17, fontweight='bold')
|
||||||
|
|
||||||
|
ax3 = fig.add_subplot(gs[1,1], sharex=ax2, sharey=ax2)
|
||||||
|
plt.imshow(im)
|
||||||
|
for l,contour in enumerate(contours_mwi): plt.plot(contour[:, 1], contour[:, 0], linewidth=2, color='k', linestyle='--')
|
||||||
|
plt.axis('off')
|
||||||
|
orange_patch = mpatches.Patch(color=[1,128/255,0/255], label='sand')
|
||||||
|
blue_patch = mpatches.Patch(color=[0,0,204/255], label='water')
|
||||||
|
black_line = mlines.Line2D([],[],color='k',linestyle='--', label='water line')
|
||||||
|
plt.legend(handles=[orange_patch,blue_patch, black_line], bbox_to_anchor=(0.6, 0.6))
|
||||||
|
# plt.title(date_im, fontsize=17, fontweight='bold')
|
||||||
|
|
||||||
|
plt.gcf().set_size_inches(11.38, 7.51)
|
||||||
|
plt.gcf().set_tight_layout(True)
|
||||||
|
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
# plt.savefig(os.path.join(filepath,'plots_classif', file_names_pan[i][len(satname)+1+len(sitename)+1:len(satname)+1+len(sitename)+1+10] + '.jpg'), dpi = 300)
|
||||||
|
# plt.close()
|
||||||
|
|
||||||
|
# create gif
|
||||||
|
#images = []
|
||||||
|
#filenames = os.listdir(os.path.join(filepath, 'plots_classif'))
|
||||||
|
#with imageio.get_writer(sitename + '.gif', mode='I', duration=0.4) as writer:
|
||||||
|
# for filename in filenames:
|
||||||
|
# image = imageio.imread(os.path.join(filepath,'plots_classif',filename))
|
||||||
|
# writer.append_data(image)
|
||||||
|
|
||||||
Binary file not shown.
@ -0,0 +1,284 @@
|
|||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
|
||||||
|
#==========================================================#
|
||||||
|
# Extract shorelines from Landsat images
|
||||||
|
#==========================================================#
|
||||||
|
|
||||||
|
# Initial settings
|
||||||
|
import os
|
||||||
|
import numpy as np
|
||||||
|
import matplotlib.pyplot as plt
|
||||||
|
import ee
|
||||||
|
import pdb
|
||||||
|
|
||||||
|
# other modules
|
||||||
|
from osgeo import gdal, ogr, osr
|
||||||
|
import pickle
|
||||||
|
import matplotlib.cm as cm
|
||||||
|
from pylab import ginput
|
||||||
|
from shapely.geometry import LineString
|
||||||
|
|
||||||
|
# image processing modules
|
||||||
|
import skimage.filters as filters
|
||||||
|
import skimage.exposure as exposure
|
||||||
|
import skimage.transform as transform
|
||||||
|
import sklearn.decomposition as decomposition
|
||||||
|
import skimage.measure as measure
|
||||||
|
import skimage.morphology as morphology
|
||||||
|
|
||||||
|
# machine learning modules
|
||||||
|
from sklearn.model_selection import train_test_split
|
||||||
|
from sklearn.neural_network import MLPClassifier
|
||||||
|
from sklearn.preprocessing import StandardScaler, Normalizer
|
||||||
|
from sklearn.externals import joblib
|
||||||
|
|
||||||
|
# import own modules
|
||||||
|
import functions.utils as utils
|
||||||
|
import functions.sds as sds
|
||||||
|
|
||||||
|
# some settings
|
||||||
|
np.seterr(all='ignore') # raise/ignore divisions by 0 and nans
|
||||||
|
plt.rcParams['axes.grid'] = True
|
||||||
|
plt.rcParams['figure.max_open_warning'] = 100
|
||||||
|
ee.Initialize()
|
||||||
|
|
||||||
|
# parameters
|
||||||
|
cloud_thresh = 0.5 # threshold for cloud cover
|
||||||
|
plot_bool = False # if you want the plots
|
||||||
|
min_contour_points = 100# minimum number of points contained in each water line
|
||||||
|
output_epsg = 28356 # GDA94 / MGA Zone 56
|
||||||
|
buffer_size = 7 # radius (in pixels) of disk for buffer (pixel classification)
|
||||||
|
min_beach_size = 20 # number of pixels in a beach (pixel classification)
|
||||||
|
dist_ref = 100
|
||||||
|
min_length_wl = 300
|
||||||
|
|
||||||
|
# load metadata (timestamps and epsg code) for the collection
|
||||||
|
satname = 'L8'
|
||||||
|
sitename = 'NARRA'
|
||||||
|
#sitename = 'OLDBAR'
|
||||||
|
|
||||||
|
# Load metadata
|
||||||
|
filepath = os.path.join(os.getcwd(), 'data', satname, sitename)
|
||||||
|
with open(os.path.join(filepath, sitename + '_timestamps' + '.pkl'), 'rb') as f:
|
||||||
|
timestamps = pickle.load(f)
|
||||||
|
with open(os.path.join(filepath, sitename + '_accuracy_georef' + '.pkl'), 'rb') as f:
|
||||||
|
acc_georef = pickle.load(f)
|
||||||
|
with open(os.path.join(filepath, sitename + '_epsgcode' + '.pkl'), 'rb') as f:
|
||||||
|
input_epsg = pickle.load(f)
|
||||||
|
with open(os.path.join(filepath, sitename + '_refpoints2' + '.pkl'), 'rb') as f:
|
||||||
|
refpoints = pickle.load(f)
|
||||||
|
# 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]
|
||||||
|
|
||||||
|
# path to images
|
||||||
|
file_path_pan = os.path.join(os.getcwd(), 'data', satname, sitename, 'pan')
|
||||||
|
file_path_ms = os.path.join(os.getcwd(), 'data', satname, sitename, 'ms')
|
||||||
|
file_names_pan = os.listdir(file_path_pan)
|
||||||
|
file_names_ms = os.listdir(file_path_ms)
|
||||||
|
N = len(file_names_pan)
|
||||||
|
|
||||||
|
# initialise some variables
|
||||||
|
cloud_cover_ts = []
|
||||||
|
date_acquired_ts = []
|
||||||
|
acc_georef_ts = []
|
||||||
|
idx_skipped = []
|
||||||
|
idx_nocloud = []
|
||||||
|
t = []
|
||||||
|
shorelines = []
|
||||||
|
|
||||||
|
#%%
|
||||||
|
for i in range(N):
|
||||||
|
|
||||||
|
# read pan image
|
||||||
|
fn_pan = os.path.join(file_path_pan, file_names_pan[i])
|
||||||
|
data = gdal.Open(fn_pan, gdal.GA_ReadOnly)
|
||||||
|
georef = np.array(data.GetGeoTransform())
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_pan = np.stack(bands, 2)[:,:,0]
|
||||||
|
nrows = im_pan.shape[0]
|
||||||
|
ncols = im_pan.shape[1]
|
||||||
|
|
||||||
|
# read ms image
|
||||||
|
fn_ms = os.path.join(file_path_ms, file_names_ms[i])
|
||||||
|
data = gdal.Open(fn_ms, gdal.GA_ReadOnly)
|
||||||
|
bands = [data.GetRasterBand(i + 1).ReadAsArray() for k in range(data.RasterCount)]
|
||||||
|
im_ms = np.stack(bands, 2)
|
||||||
|
|
||||||
|
# cloud mask
|
||||||
|
im_qa = im_ms[:,:,5]
|
||||||
|
cloud_mask = sds.create_cloud_mask(im_qa, satname, plot_bool)
|
||||||
|
cloud_mask = transform.resize(cloud_mask, (im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=0, preserve_range=True,
|
||||||
|
mode='constant').astype('bool_')
|
||||||
|
# resize the image using bilinear interpolation (order 1)
|
||||||
|
im_ms = transform.resize(im_ms,(im_pan.shape[0], im_pan.shape[1]),
|
||||||
|
order=1, preserve_range=True, mode='constant')
|
||||||
|
|
||||||
|
# check if -inf or nan values and add to cloud mask
|
||||||
|
im_inf = np.isin(im_ms[:,:,0], -np.inf)
|
||||||
|
im_nan = np.isnan(im_ms[:,:,0])
|
||||||
|
cloud_mask = np.logical_or(np.logical_or(cloud_mask, im_inf), im_nan)
|
||||||
|
|
||||||
|
# calculate cloud cover and skip image if too high
|
||||||
|
cloud_cover = sum(sum(cloud_mask.astype(int)))/(cloud_mask.shape[0]*cloud_mask.shape[1])
|
||||||
|
if cloud_cover > cloud_thresh:
|
||||||
|
print('skip ' + str(i) + ' - cloudy (' + str(np.round(cloud_cover*100).astype(int)) + '%)')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
idx_nocloud.append(i)
|
||||||
|
|
||||||
|
# pansharpen rgb image
|
||||||
|
im_ms_ps = sds.pansharpen(im_ms[:,:,[0,1,2]], im_pan, cloud_mask, plot_bool)
|
||||||
|
# rescale pansharpened RGB for visualisation
|
||||||
|
im_display = sds.rescale_image_intensity(im_ms_ps[:,:,[2,1,0]], cloud_mask, 100, False)
|
||||||
|
# add down-sized bands for NIR and SWIR (since pansharpening is not possible)
|
||||||
|
im_ms_ps = np.append(im_ms_ps, im_ms[:,:,[3,4]], axis=2)
|
||||||
|
|
||||||
|
# classify image in 4 classes (sand, whitewater, water, other) with NN classifier
|
||||||
|
im_classif, im_labels = sds.classify_image_NN(im_ms_ps, im_pan, cloud_mask, min_beach_size, plot_bool)
|
||||||
|
|
||||||
|
# # manually validate classification
|
||||||
|
# pt_in = np.array(ginput(n=1, timeout=1000))
|
||||||
|
# if pt_in[0][1] > nrows/2:
|
||||||
|
# print('skip ' + str(i) + ' - wrong classification')
|
||||||
|
# idx_skipped.append(i)
|
||||||
|
# continue
|
||||||
|
|
||||||
|
# if there are no sand pixels, skip the image (maybe later change the detection method with old method)
|
||||||
|
if sum(sum(im_labels[:,:,0])) == 0 :
|
||||||
|
print('skip ' + str(i) + ' - no sand')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
|
||||||
|
# extract shorelines (new method)
|
||||||
|
contours_wi, contours_mwi = sds.find_wl_contours2(im_ms_ps, im_labels, cloud_mask, buffer_size, plot_bool)
|
||||||
|
|
||||||
|
plt.figure()
|
||||||
|
im = np.copy(im_display)
|
||||||
|
# define colours for plot
|
||||||
|
colours = np.array([[1,128/255,0/255],[204/255,1,1],[0,0,204/255]])
|
||||||
|
for k in range(0,im_labels.shape[2]):
|
||||||
|
im[im_labels[:,:,k],0] = colours[k,0]
|
||||||
|
im[im_labels[:,:,k],1] = colours[k,1]
|
||||||
|
im[im_labels[:,:,k],2] = colours[k,2]
|
||||||
|
plt.imshow(im)
|
||||||
|
for k,contour in enumerate(contours_mwi): plt.plot(contour[:, 1], contour[:, 0], linewidth=2, color='k', linestyle='--')
|
||||||
|
mng = plt.get_current_fig_manager()
|
||||||
|
mng.window.showMaximized()
|
||||||
|
plt.tight_layout()
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
|
||||||
|
# manually validate detection
|
||||||
|
pt_in = np.array(ginput(n=1, timeout=1000))
|
||||||
|
if pt_in[0][1] > nrows/2:
|
||||||
|
print('skip ' + str(i) + ' - wrong detection')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
|
||||||
|
# remove contour points that are around clouds (nan values)
|
||||||
|
for k, contour in enumerate(contours_mwi):
|
||||||
|
if np.any(np.isnan(contour)):
|
||||||
|
index_nan = np.where(np.isnan(contour))[0]
|
||||||
|
contour = np.delete(contour, index_nan, axis=0)
|
||||||
|
|
||||||
|
# convert from pixels to world coordinates
|
||||||
|
wl_coords = sds.convert_pix2world(contours_mwi, georef)
|
||||||
|
# convert to output epsg spatial reference
|
||||||
|
wl = sds.convert_epsg(wl_coords, input_epsg, output_epsg)
|
||||||
|
|
||||||
|
# remove contours that have a perimeter < min_length_wl as usually they are not shoreline
|
||||||
|
wl_good = []
|
||||||
|
for l, wls in enumerate(wl):
|
||||||
|
coords = [(wls[k,0], wls[k,1]) for k in range(len(wls))]
|
||||||
|
a = LineString(coords) # shapely LineString structure
|
||||||
|
if a.length >= min_length_wl:
|
||||||
|
wl_good.append(wls)
|
||||||
|
|
||||||
|
# pre-process points (list of arrays to single array of points)
|
||||||
|
x_points = np.array([])
|
||||||
|
y_points = np.array([])
|
||||||
|
for k in range(len(wl_good)):
|
||||||
|
x_points = np.append(x_points,wl_good[k][:,0])
|
||||||
|
y_points = np.append(y_points,wl_good[k][:,1])
|
||||||
|
wl_good = np.transpose(np.array([x_points,y_points]))
|
||||||
|
|
||||||
|
# only select points around Narrabeen beach (refpoints given)
|
||||||
|
temp = np.zeros((len(wl_good))).astype(bool)
|
||||||
|
for k in range(len(refpoints)):
|
||||||
|
temp = np.logical_or(np.linalg.norm(wl_good - refpoints[k,[0,1]], axis=1) < dist_ref, temp)
|
||||||
|
wl_final = wl_good[temp]
|
||||||
|
|
||||||
|
plt.figure()
|
||||||
|
plt.axis('equal')
|
||||||
|
plt.plot(wl_final[:,0],wl_final[:,1],'k.')
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
|
||||||
|
# check if image for that date already exists and choose the best in terms of cloud cover and georeferencing
|
||||||
|
if file_names_pan[i][len(satname)+1+len(sitename)+1:len(satname)+1+len(sitename)+1+10] in date_acquired_ts:
|
||||||
|
|
||||||
|
# find the index of the image that is repeated
|
||||||
|
idx_samedate = utils.find_indices(date_acquired_ts, lambda e : e == file_names_pan[i][9:19])
|
||||||
|
idx_samedate = idx_samedate[0]
|
||||||
|
# print('cloud cover ' + str(cloud_cover) + ' - ' + str(cloud_cover_ts[idx_samedate]))
|
||||||
|
# print('acc georef ' + str(acc_georef_sorted[i]) + ' - ' + str(acc_georef_ts[idx_samedate]))
|
||||||
|
|
||||||
|
# keep image with less cloud cover or best georeferencing accuracy
|
||||||
|
if cloud_cover < cloud_cover_ts[idx_samedate] - 0.01:
|
||||||
|
skip = False
|
||||||
|
elif acc_georef_sorted[i] < acc_georef_ts[idx_samedate]:
|
||||||
|
skip = False
|
||||||
|
else:
|
||||||
|
skip = True
|
||||||
|
|
||||||
|
if skip:
|
||||||
|
print('skip ' + str(i) + ' - repeated')
|
||||||
|
idx_skipped.append(i)
|
||||||
|
continue
|
||||||
|
else:
|
||||||
|
del shorelines[idx_samedate]
|
||||||
|
del t[idx_samedate]
|
||||||
|
del cloud_cover_ts[idx_samedate]
|
||||||
|
del date_acquired_ts[idx_samedate]
|
||||||
|
del acc_georef_ts[idx_samedate]
|
||||||
|
print('keep ' + str(i) + ' - deleted ' + str(idx_samedate))
|
||||||
|
|
||||||
|
|
||||||
|
# save data
|
||||||
|
shorelines.append(wl_final)
|
||||||
|
t.append(timestamps_sorted[i])
|
||||||
|
cloud_cover_ts.append(cloud_cover)
|
||||||
|
acc_georef_ts.append(acc_georef_sorted[i])
|
||||||
|
date_acquired_ts.append(file_names_pan[i][9:19])
|
||||||
|
|
||||||
|
output = {'t':t, 'shorelines':shorelines, 'cloud_cover':cloud_cover_ts, 'acc_georef':acc_georef_ts}
|
||||||
|
|
||||||
|
#with open(os.path.join(filepath, sitename + '_output2' + '.pkl'), 'wb') as f:
|
||||||
|
# pickle.dump(output, f)
|
||||||
|
#
|
||||||
|
#with open(os.path.join(filepath, sitename + '_skipped2' + '.pkl'), 'wb') as f:
|
||||||
|
# pickle.dump(idx_skipped, f)
|
||||||
|
#
|
||||||
|
#with open(os.path.join(filepath, sitename + '_idxnocloud2' + '.pkl'), 'wb') as f:
|
||||||
|
# pickle.dump(idx_nocloud, f)
|
||||||
|
|
||||||
|
# plt.figure()
|
||||||
|
# plt.axis('equal')
|
||||||
|
# plt.plot(refpoints[:,0], refpoints[:,1], 'ko')
|
||||||
|
# plt.plot(all_points[temp,0], all_points[temp,1], 'go')
|
||||||
|
# plt.plot(all_points[~temp,0], all_points[~temp,1], 'ro')
|
||||||
|
# plt.draw()
|
||||||
|
|
||||||
|
# extract shorelines (old method)
|
||||||
|
# im_ndwi = sds.nd_index(im_ms_ps[:,:,3], im_ms_ps[:,:,1], cloud_mask, plot_bool)
|
||||||
|
# wl_pix = sds.find_wl_contours(im_ndwi, cloud_mask, min_contour_points, plot_bool)
|
||||||
|
|
||||||
|
# plt.figure()
|
||||||
|
# plt.imshow(im_display)
|
||||||
|
# for i,contour in enumerate(contours_mwi): plt.plot(contour[:, 1], contour[:, 0], linewidth=3, color='k')
|
||||||
|
# for i,contour in enumerate(wl_pix): plt.plot(contour[:, 1], contour[:, 0], linestyle='--', linewidth=1, color='w')
|
||||||
|
# plt.draw()
|
||||||
|
|
||||||
@ -0,0 +1,382 @@
|
|||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
|
||||||
|
#==========================================================#
|
||||||
|
# Compare Narrabeen SDS with 3D quadbike surveys
|
||||||
|
#==========================================================#
|
||||||
|
|
||||||
|
# Initial settings
|
||||||
|
|
||||||
|
import os
|
||||||
|
import numpy as np
|
||||||
|
import matplotlib.pyplot as plt
|
||||||
|
import pdb
|
||||||
|
import ee
|
||||||
|
|
||||||
|
import matplotlib.dates as mdates
|
||||||
|
import matplotlib.cm as cm
|
||||||
|
from datetime import datetime, timedelta
|
||||||
|
import pickle
|
||||||
|
import pytz
|
||||||
|
import scipy.io as sio
|
||||||
|
import scipy.interpolate as interpolate
|
||||||
|
import statsmodels.api as sm
|
||||||
|
import skimage.measure as measure
|
||||||
|
|
||||||
|
# my functions
|
||||||
|
import functions.utils as utils
|
||||||
|
|
||||||
|
# some settings
|
||||||
|
np.seterr(all='ignore') # raise/ignore divisions by 0 and nans
|
||||||
|
plt.rcParams['axes.grid'] = True
|
||||||
|
plt.rcParams['figure.max_open_warning'] = 100
|
||||||
|
|
||||||
|
au_tz = pytz.timezone('Australia/Sydney')
|
||||||
|
|
||||||
|
# load quadbike dates and convert from datenum to datetime
|
||||||
|
filename = 'data\quadbike\survey_dates.mat'
|
||||||
|
filepath = os.path.join(os.getcwd(), filename)
|
||||||
|
dates_quad = sio.loadmat(filepath)['dates'] # matrix containing year, month, day
|
||||||
|
dates_quad = [datetime(dates_quad[i,0], dates_quad[i,1], dates_quad[i,2],
|
||||||
|
tzinfo=au_tz) for i in range(dates_quad.shape[0])]
|
||||||
|
|
||||||
|
# load timestamps from satellite images
|
||||||
|
satname = 'L8'
|
||||||
|
sitename = 'NARRA'
|
||||||
|
filepath = os.path.join(os.getcwd(), 'data', satname, sitename)
|
||||||
|
with open(os.path.join(filepath, sitename + '_output_new' + '.pkl'), 'rb') as f:
|
||||||
|
output = pickle.load(f)
|
||||||
|
|
||||||
|
dates_l8 = output['t']
|
||||||
|
# convert to AEST
|
||||||
|
dates_l8 = [_.astimezone(au_tz) for _ in dates_l8]
|
||||||
|
# remove duplicates
|
||||||
|
dates_l8_str = [_.strftime('%Y%m%d') for _ in dates_l8]
|
||||||
|
dupl = utils.duplicates_dict(dates_l8_str)
|
||||||
|
idx_remove = []
|
||||||
|
for k,v in dupl.items():
|
||||||
|
|
||||||
|
idx1 = v[0]
|
||||||
|
idx2 = v[1]
|
||||||
|
|
||||||
|
c1 = output['cloud_cover'][idx1]
|
||||||
|
c2 = output['cloud_cover'][idx2]
|
||||||
|
g1 = output['acc_georef'][idx1]
|
||||||
|
g2 = output['acc_georef'][idx2]
|
||||||
|
|
||||||
|
if c1 < c2 - 0.01:
|
||||||
|
idx_remove.append(idx2)
|
||||||
|
elif g1 < g2 - 0.1:
|
||||||
|
idx_remove.append(idx2)
|
||||||
|
else:
|
||||||
|
idx_remove.append(idx1)
|
||||||
|
idx_remove = sorted(idx_remove)
|
||||||
|
idx_all = np.linspace(0,70,71)
|
||||||
|
idx_keep = list(np.where(~np.isin(idx_all,idx_remove))[0])
|
||||||
|
output['t'] = [output['t'][k] for k in idx_keep]
|
||||||
|
output['shorelines'] = [output['shorelines'][k] for k in idx_keep]
|
||||||
|
output['cloud_cover'] = [output['cloud_cover'][k] for k in idx_keep]
|
||||||
|
output['acc_georef'] = [output['acc_georef'][k] for k in idx_keep]
|
||||||
|
# convert to AEST
|
||||||
|
dates_l8 = output['t']
|
||||||
|
dates_l8 = [_.astimezone(au_tz) for _ in dates_l8]
|
||||||
|
|
||||||
|
# load wave data (already AEST)
|
||||||
|
filename = 'data\wave\SydneyProcessed.mat'
|
||||||
|
filepath = os.path.join(os.getcwd(), filename)
|
||||||
|
wave_data = sio.loadmat(filepath)
|
||||||
|
idx = utils.find_indices(wave_data['dates'][:,0], lambda e: e >= dates_l8[0].year and e <= dates_l8[-1].year)
|
||||||
|
hsig = np.array([wave_data['Hsig'][i][0] for i in idx])
|
||||||
|
wdir = np.array([wave_data['Wdir'][i][0] for i in idx])
|
||||||
|
dates_wave = [datetime(wave_data['dates'][i,0], wave_data['dates'][i,1],
|
||||||
|
wave_data['dates'][i,2], wave_data['dates'][i,3],
|
||||||
|
wave_data['dates'][i,4], wave_data['dates'][i,5],
|
||||||
|
tzinfo=au_tz) for i in idx]
|
||||||
|
|
||||||
|
# load tide data (already AEST)
|
||||||
|
filename = 'SydTideData.mat'
|
||||||
|
filepath = os.path.join(os.getcwd(), 'data', 'tide', filename)
|
||||||
|
tide_data = sio.loadmat(filepath)
|
||||||
|
idx = utils.find_indices(tide_data['dates'][:,0], lambda e: e >= dates_l8[0].year and e <= dates_l8[-1].year)
|
||||||
|
tide = np.array([tide_data['tide'][i][0] for i in idx])
|
||||||
|
dates_tide = [datetime(tide_data['dates'][i,0], tide_data['dates'][i,1],
|
||||||
|
tide_data['dates'][i,2], tide_data['dates'][i,3],
|
||||||
|
tide_data['dates'][i,4], tide_data['dates'][i,5],
|
||||||
|
tzinfo=au_tz) for i in idx]
|
||||||
|
|
||||||
|
#%% make a plot of all the dates with wave data
|
||||||
|
orange = [255/255,140/255,0]
|
||||||
|
blue = [0,191/255,255/255]
|
||||||
|
f = plt.figure()
|
||||||
|
months = mdates.MonthLocator()
|
||||||
|
month_fmt = mdates.DateFormatter('%b %Y')
|
||||||
|
days = mdates.DayLocator()
|
||||||
|
years = [2013,2014,2015,2016]
|
||||||
|
for k in range(len(years)):
|
||||||
|
sel_year = years[k]
|
||||||
|
ax = plt.subplot(4,1,k+1)
|
||||||
|
idx_year = utils.find_indices(dates_wave, lambda e : e.year >= sel_year and e.year <= sel_year)
|
||||||
|
plt.plot([dates_wave[i] for i in idx_year], [hsig[i] for i in idx_year], 'k-', linewidth=0.5)
|
||||||
|
hsigmax = np.nanmax([hsig[i] for i in idx_year])
|
||||||
|
cbool = True
|
||||||
|
for j in range(len(dates_quad)):
|
||||||
|
if dates_quad[j].year == sel_year:
|
||||||
|
if cbool:
|
||||||
|
plt.plot([dates_quad[j], dates_quad[j]], [0, hsigmax], color=orange, label='survey')
|
||||||
|
cbool = False
|
||||||
|
else:
|
||||||
|
plt.plot([dates_quad[j], dates_quad[j]], [0, hsigmax], color=orange)
|
||||||
|
cbool = True
|
||||||
|
for j in range(len(dates_l8)):
|
||||||
|
if dates_l8[j].year == sel_year:
|
||||||
|
if cbool:
|
||||||
|
plt.plot([dates_l8[j], dates_l8[j]], [0, hsigmax], color=blue, label='landsat8')
|
||||||
|
cbool = False
|
||||||
|
else:
|
||||||
|
plt.plot([dates_l8[j], dates_l8[j]], [0, hsigmax], color=blue)
|
||||||
|
if k == 3:
|
||||||
|
plt.legend()
|
||||||
|
plt.xlim((datetime(sel_year,1,1), datetime(sel_year,12,31, tzinfo=au_tz)))
|
||||||
|
plt.ylim((0, hsigmax))
|
||||||
|
plt.ylabel('Hs [m]')
|
||||||
|
ax.xaxis.set_major_locator = months
|
||||||
|
ax.xaxis.set_major_formatter(month_fmt)
|
||||||
|
f.subplots_adjust(hspace=0.2)
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
#%% calculate difference between dates (quad and sat)
|
||||||
|
diff_days = [ [(x - _).days for _ in dates_quad] for x in dates_l8]
|
||||||
|
max_diff = 14
|
||||||
|
idx_closest = [utils.find_indices(_, lambda e: abs(e) <= max_diff) for _ in diff_days]
|
||||||
|
# store in dates_diff dictionnary
|
||||||
|
dates_diff = []
|
||||||
|
cloud_cover = []
|
||||||
|
for i in range(len(idx_closest)):
|
||||||
|
if not idx_closest[i]:
|
||||||
|
continue
|
||||||
|
elif len(idx_closest[i]) > 1:
|
||||||
|
idx_best = np.argmin(np.abs([diff_days[i][_] for _ in idx_closest[i]]))
|
||||||
|
dates_temp = [dates_quad[_] for _ in idx_closest[i]]
|
||||||
|
days_temp = [diff_days[i][_] for _ in idx_closest[i]]
|
||||||
|
dates_diff.append({"date sat": dates_l8[i],
|
||||||
|
"date quad": dates_temp[idx_best],
|
||||||
|
"days diff": days_temp[idx_best]})
|
||||||
|
else:
|
||||||
|
dates_diff.append({"date sat": dates_l8[i],
|
||||||
|
"date quad": dates_quad[idx_closest[i][0]],
|
||||||
|
"days diff": diff_days[i][idx_closest[i][0]]
|
||||||
|
})
|
||||||
|
# store cloud data
|
||||||
|
cloud_cover.append(output['cloud_cover'][i])
|
||||||
|
|
||||||
|
# store wave data
|
||||||
|
wave_hsig = []
|
||||||
|
for i in range(len(dates_diff)):
|
||||||
|
wave_hsig.append(hsig[np.argmin(np.abs(np.array([(dates_diff[i]['date sat'] - _).total_seconds() for _ in dates_wave])))])
|
||||||
|
|
||||||
|
# make a plot
|
||||||
|
plt.figure()
|
||||||
|
counter = 0
|
||||||
|
for i in range(len(dates_diff)):
|
||||||
|
counter = counter + 1
|
||||||
|
if dates_diff[i]['date quad'] > dates_diff[i]['date sat']:
|
||||||
|
date_min = dates_diff[i]['date sat']
|
||||||
|
date_max = dates_diff[i]['date quad']
|
||||||
|
color1 = orange
|
||||||
|
color2 = blue
|
||||||
|
else:
|
||||||
|
date_min = dates_diff[i]['date quad']
|
||||||
|
date_max = dates_diff[i]['date sat']
|
||||||
|
color1 = blue
|
||||||
|
color2 = orange
|
||||||
|
idx_t = utils.find_indices(dates_wave, lambda e : e >= date_min and e <= date_max)
|
||||||
|
hsigmax = np.nanmax([hsig[i] for i in idx_t])
|
||||||
|
hsigmin = np.nanmin([hsig[i] for i in idx_t])
|
||||||
|
if counter > 9:
|
||||||
|
counter = 1
|
||||||
|
plt.figure()
|
||||||
|
ax = plt.subplot(3,3,counter)
|
||||||
|
plt.plot([dates_wave[i] for i in idx_t], [hsig[i] for i in idx_t], 'k-', linewidth=1.5)
|
||||||
|
plt.plot([date_min, date_min], [0, 4.5], color=color2, label='survey')
|
||||||
|
plt.plot([date_max, date_max], [0, 4.5], color=color1, label='landsat8')
|
||||||
|
plt.ylabel('Hs [m]')
|
||||||
|
ax.xaxis.set_major_locator(mdates.DayLocator(tz=au_tz))
|
||||||
|
ax.xaxis.set_minor_locator(mdates.HourLocator(tz=au_tz))
|
||||||
|
ax.xaxis.set_major_formatter(mdates.DateFormatter('%d'))
|
||||||
|
ax.xaxis.set_minor_locator(months)
|
||||||
|
plt.title(dates_diff[i]['date sat'].strftime('%b %Y') + ' (' + str(abs(dates_diff[i]['days diff'])) + ' days)')
|
||||||
|
plt.draw()
|
||||||
|
plt.gcf().subplots_adjust(hspace=0.5)
|
||||||
|
|
||||||
|
# mean day difference
|
||||||
|
np.mean([ np.abs(_['days diff']) for _ in dates_diff])
|
||||||
|
|
||||||
|
#%% Compare shorelines in elevation
|
||||||
|
|
||||||
|
dist_buffer = 50 # buffer of points selected for interpolation
|
||||||
|
|
||||||
|
# load quadbike .mat files
|
||||||
|
foldername = 'data\quadbike\surveys3D'
|
||||||
|
folderpath = os.path.join(os.getcwd(), foldername)
|
||||||
|
filenames = os.listdir(folderpath)
|
||||||
|
|
||||||
|
# get the satellite shorelines
|
||||||
|
sl = output['shorelines']
|
||||||
|
|
||||||
|
# get dates from filenames
|
||||||
|
dates_quad = [datetime(int(_[6:10]), int(_[11:13]), int(_[14:16]), tzinfo= au_tz) for _ in filenames]
|
||||||
|
|
||||||
|
zav = []
|
||||||
|
ztide = []
|
||||||
|
sl_gt = []
|
||||||
|
for i in range(len(dates_diff)):
|
||||||
|
|
||||||
|
sl_smooth = sl[i]
|
||||||
|
|
||||||
|
# select closest 3D survey and load .mat file
|
||||||
|
idx_closest = np.argmin(np.abs(np.array([(dates_diff[i]['date sat'] - _).days for _ in dates_quad])))
|
||||||
|
survey3d = sio.loadmat(os.path.join(folderpath, filenames[idx_closest]))
|
||||||
|
# reshape to a vector
|
||||||
|
xs = survey3d['x'].reshape(survey3d['x'].shape[0] * survey3d['x'].shape[1])
|
||||||
|
ys = survey3d['y'].reshape(survey3d['y'].shape[0] * survey3d['y'].shape[1])
|
||||||
|
zs = survey3d['z'].reshape(survey3d['z'].shape[0] * survey3d['z'].shape[1])
|
||||||
|
# remove nan values
|
||||||
|
idx_nan = np.isnan(zs)
|
||||||
|
xs = xs[~idx_nan]
|
||||||
|
ys = ys[~idx_nan]
|
||||||
|
zs = zs[~idx_nan]
|
||||||
|
|
||||||
|
# find water level at the time the image was acquired
|
||||||
|
idx_closest = np.argmin(np.abs(np.array([(dates_diff[i]['date sat'] - _).total_seconds() for _ in dates_tide])))
|
||||||
|
tide_level = tide[idx_closest]
|
||||||
|
ztide.append(tide_level)
|
||||||
|
|
||||||
|
# find contour corresponding to the water level on 3D surface (if below minimum, add 0.05m increments)
|
||||||
|
if tide_level < np.nanmin(survey3d['z']):
|
||||||
|
tide_level = np.nanmin(survey3d['z'])
|
||||||
|
sl_tide = measure.find_contours(survey3d['z'], tide_level)
|
||||||
|
sl_tide = sl_tide[np.argmax(np.array([len(_) for _ in sl_tide]))]
|
||||||
|
count = 0
|
||||||
|
while len(sl_tide) < 900:
|
||||||
|
count = count + 1
|
||||||
|
tide_level = tide_level + 0.05*count
|
||||||
|
sl_tide = measure.find_contours(survey3d['z'], tide_level)
|
||||||
|
sl_tide = sl_tide[np.argmax(np.array([len(_) for _ in sl_tide]))]
|
||||||
|
print('added ' + str(0.05*count) + ' cm - contour with ' + str(len(sl_tide)) + ' points')
|
||||||
|
else:
|
||||||
|
sl_tide = measure.find_contours(survey3d['z'], tide_level)
|
||||||
|
sl_tide = sl_tide[np.argmax(np.array([len(_) for _ in sl_tide]))]
|
||||||
|
# remove nans
|
||||||
|
if np.any(np.isnan(sl_tide)):
|
||||||
|
index_nan = np.where(np.isnan(sl_tide))[0]
|
||||||
|
sl_tide = np.delete(sl_tide, index_nan, axis=0)
|
||||||
|
# get x,y coordinates
|
||||||
|
xtide = [survey3d['x'][int(np.round(sl_tide[m,0])), int(np.round(sl_tide[m,1]))] for m in range(sl_tide.shape[0])]
|
||||||
|
ytide = [survey3d['y'][int(np.round(sl_tide[m,0])), int(np.round(sl_tide[m,1]))] for m in range(sl_tide.shape[0])]
|
||||||
|
sl_gt.append(np.transpose(np.array([np.array(xtide), np.array(ytide)])))
|
||||||
|
# interpolate SDS on 3D surface to get elevation (point by point)
|
||||||
|
zq = []
|
||||||
|
for j in range(sl_smooth.shape[0]):
|
||||||
|
xq = sl_smooth[j,0]
|
||||||
|
yq = sl_smooth[j,1]
|
||||||
|
dist_q = np.linalg.norm(np.transpose(np.array([[xq - _ for _ in xs],[yq - _ for _ in ys]])), axis=1)
|
||||||
|
idx_buffer = dist_q <= dist_buffer
|
||||||
|
if sum(idx_buffer) > 0:
|
||||||
|
tck = interpolate.bisplrep(xs[idx_buffer], ys[idx_buffer], zs[idx_buffer])
|
||||||
|
zq.append(interpolate.bisplev(xq, yq, tck))
|
||||||
|
|
||||||
|
zq = np.array(zq)
|
||||||
|
plt.figure()
|
||||||
|
plt.hist(zq, bins=100)
|
||||||
|
plt.draw()
|
||||||
|
# plt.figure()
|
||||||
|
# plt.axis('equal')
|
||||||
|
# plt.scatter(xs, ys, s=10, c=zs, marker='o', cmap=cm.get_cmap('jet'),
|
||||||
|
# label='quad data')
|
||||||
|
# plt.plot(xs[idx_buffer], ys[idx_buffer], 'ko')
|
||||||
|
# plt.plot(xq,yq,'ro')
|
||||||
|
# plt.draw()
|
||||||
|
|
||||||
|
# store the alongshore median elevation
|
||||||
|
zav.append(np.median(utils.reject_outliers(zq, m=2)))
|
||||||
|
|
||||||
|
# make plot
|
||||||
|
red = [255/255, 0, 0]
|
||||||
|
gray = [0.75, 0.75, 0.75]
|
||||||
|
plt.figure()
|
||||||
|
plt.subplot(121)
|
||||||
|
plt.axis('equal')
|
||||||
|
plt.scatter(xs, ys, s=10, c=zs, marker='o', cmap=cm.get_cmap('jet'),
|
||||||
|
label='3D survey')
|
||||||
|
plt.plot(xtide, ytide, '--', color=gray, linewidth=2.5, label='tide level contour')
|
||||||
|
plt.plot(sl_smooth[:,0], sl_smooth[:,1], '-', color=red, linewidth=2.5, label='SDS')
|
||||||
|
# plt.plot(sl[i][idx_beach,0], sl[i][idx_beach,1], 'w-', linewidth=2)
|
||||||
|
plt.xlabel('Eastings [m]')
|
||||||
|
plt.ylabel('Northings [m]')
|
||||||
|
plt.title('Shoreline comparison')
|
||||||
|
plt.colorbar(label='mAHD')
|
||||||
|
plt.legend()
|
||||||
|
plt.ylim((6266100, 6267000))
|
||||||
|
plt.subplot(122)
|
||||||
|
plt.plot(np.linspace(0,1,len(zq)), zq, 'ko-', markersize=5)
|
||||||
|
plt.plot([0, 1], [zav[i], zav[i]], 'r-', label='median')
|
||||||
|
plt.plot([0, 1], [ztide[i], ztide[i]], 'g--', label = 'measured tide')
|
||||||
|
plt.xlabel('Northings [m]')
|
||||||
|
plt.ylabel('Elevation [mAHD]')
|
||||||
|
plt.title('Alongshore SDS elevation')
|
||||||
|
plt.legend()
|
||||||
|
mng = plt.get_current_fig_manager()
|
||||||
|
mng.window.showMaximized()
|
||||||
|
plt.tight_layout()
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
print(i)
|
||||||
|
|
||||||
|
#%% Calculate some error statistics
|
||||||
|
zav = np.array(zav)
|
||||||
|
ztide = np.array(ztide)
|
||||||
|
|
||||||
|
f = plt.figure()
|
||||||
|
plt.subplot(3,1,1)
|
||||||
|
plt.bar(np.linspace(1,len(zav),len(zav)), zav-ztide)
|
||||||
|
plt.ylabel('Error in z [m]')
|
||||||
|
plt.title('Elevation error')
|
||||||
|
plt.xticks([])
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
plt.subplot(3,1,2)
|
||||||
|
plt.bar(np.linspace(1,len(zav),len(zav)), wave_hsig, color=orange)
|
||||||
|
plt.ylabel('Hsig [m]')
|
||||||
|
plt.xticks([])
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
plt.subplot(3,1,3)
|
||||||
|
plt.bar(np.linspace(1,len(zav),len(zav)), np.array(cloud_cover)*100, color='g')
|
||||||
|
plt.ylabel('Cloud cover %')
|
||||||
|
plt.xlabel('comparison #')
|
||||||
|
plt.grid(False)
|
||||||
|
plt.grid(axis='y')
|
||||||
|
f.subplots_adjust(hspace=0)
|
||||||
|
plt.draw()
|
||||||
|
|
||||||
|
np.sqrt(np.mean((zav - ztide)**2))
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#%% plot to show LOWESS smoothing
|
||||||
|
#i = 0
|
||||||
|
#idx_beach = [np.min(np.linalg.norm(sl[i][k,:] - narrabeach, axis=1)) < dist_thresh for k in range(sl[i].shape[0])]
|
||||||
|
#x = sl[i][idx_beach,0]
|
||||||
|
#y = sl[i][idx_beach,1]
|
||||||
|
#sl_smooth = lowess(x,y, frac=1./10, it = 10)
|
||||||
|
#
|
||||||
|
#plt.figure()
|
||||||
|
#plt.axis('equal')
|
||||||
|
#plt.scatter
|
||||||
|
#plt.plot(x,y,'bo', linewidth=2, label='original SDS')
|
||||||
|
#plt.plot(sl_smooth[:,1], sl_smooth[:,0], 'ro', linewidth=2, label='smoothed SDS')
|
||||||
|
#plt.legend()
|
||||||
|
#plt.xlabel('Eastings [m]')
|
||||||
|
#plt.ylabel('Northings [m]')
|
||||||
|
#plt.title('Local weighted scatterplot smoothing (LOWESS)')
|
||||||
|
#plt.draw()
|
||||||
|
|
||||||
Loading…
Reference in New Issue