sds interpolation on 3d quadbike surface

functions/utils.py

@@ -9,7 +9,6 @@ Contains all the utilities, convenience functions and small functions that do si
 
 import matplotlib.pyplot as plt
 import numpy as np
-import datetime
 import pdb
 
 

time_coverage.py

@@ -17,15 +17,9 @@ from datetime import datetime, timedelta
 import pickle
 import pytz
 import scipy.io as sio
+import scipy.interpolate as interpolate
+import statsmodels.api as sm
 
-# image processing modules
-import skimage.filters as filters 
-import skimage.exposure as exposure
-import skimage.transform as transform
-import skimage.morphology as morphology
-import skimage.measure as measure
-import sklearn.decomposition as decomposition
-from scipy import spatial
 # my functions
 import functions.utils as utils
 import functions.sds as sds
@@ -65,6 +59,8 @@ dates_wave = [datetime(wave_data['dates'][i,0], wave_data['dates'][i,1],
                        wave_data['dates'][i,4], wave_data['dates'][i,5],
                        tzinfo=au_tz) for i in idx]
 #%% make a plot of all the dates
+orange = [255/255,140/255,0]
+blue = [0,191/255,255/255]
 f = plt.figure()
 months = mdates.MonthLocator()
 month_fmt = mdates.DateFormatter('%b %Y')
@@ -80,18 +76,18 @@ for k in range(len(years)):
     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=[255/255,140/255,0], label='survey')
+                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=[255/255,140/255,0])
+                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=[0,191/255,255/255], label='landsat8')
+                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=[0,191/255,255/255])
+                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)))
@@ -101,9 +97,7 @@ for k in range(len(years)):
     ax.xaxis.set_major_formatter(month_fmt)
 f.subplots_adjust(hspace=0.2)
 plt.draw()
-#%%
+#%% calculate days difference
-
-# calculate days difference
 diff_days = [ [(x - _).days for _ in dates_quad] for x in dates_l8]
 max_diff = 5
 idx_closest = [utils.find_indices(_, lambda e: abs(e) <= max_diff) for _ in diff_days]
@@ -126,7 +120,11 @@ for i in range(len(idx_closest)):
 
 np.mean([ np.abs(_['days diff']) for _ in dates_diff])
 
-#%%
+#%% compare shorelines
+
+dist_thresh = 200 # maximum distance between an sds point and a narrabeen point
+frac_smooth = 1./12 # fraction of the data used for smoothing (the bigger the smoother)
+dist_buffer = 50 # buffer of points selected for interpolation
 
 # load quadbike .mat files 
 foldername = 'data\quadbike\surveys3D'
@@ -136,43 +134,88 @@ filenames = os.listdir(folderpath)
 # load the satellite shorelines
 sl = output['shorelines']
 
+# load narrabeen beach points (manually digitized)
+with open(os.path.join(os.getcwd(), 'olddata', 'narra_beach' + '.pkl'), 'rb') as f:
+    narrabeach = pickle.load(f)
+    
 dates_quad = [datetime(int(_[6:10]), int(_[11:13]), int(_[14:16]), tzinfo= au_tz) for _ in filenames]
-# for each satellite shoreline, load the corresponding 3D survey
+zav = []
 for i in range(len(dates_diff)):
+    # select closest 3D survey
     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]))
-    
+    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])
+    idx_nan = np.isnan(zs)
+    xs = xs[~idx_nan]
+    ys = ys[~idx_nan]
+    zs = zs[~idx_nan]
+    # smooth (LOWESS) satellite shoreline
+    idx_beach = [np.min(np.linalg.norm(sl[i][k,:] - narrabeach, axis=1)) < dist_thresh for k in range(sl[i].shape[0])]
+    sl_smooth = sm.nonparametric.lowess(sl[i][idx_beach,0],sl[i][idx_beach,1], frac=frac_smooth, it = 6)
+    sl_smooth = sl_smooth[:,[1,0]]
+    # make plot
     plt.figure()
     plt.axis('equal')
-    plt.scatter(survey3d['x'], survey3d['y'], s=10, c=survey3d['z'], marker='o', cmap=cm.get_cmap('jet'),
+    plt.scatter(xs, ys, s=10, c=zs, marker='o', cmap=cm.get_cmap('jet'),
             label='quad data')
-    plt.plot(sl[i][:,0], sl[i][:,1], 'ko')
+    plt.plot(sl[i][idx_beach,0], sl[i][idx_beach,1], 'ko-', markersize=3)
+    plt.plot(sl_smooth[:,0], sl_smooth[:,1], 'ro-', markersize=3)
+    plt.xlabel('Eastings [m]')
+    plt.ylabel('Northings [m]')
+    plt.title('Local weighted scatterplot smoothing (LOWESS)')
     plt.draw()
     
-import statsmodels.api as sm
+    zq = np.zeros((sl_smooth.shape[0], 1))
-lowess = sm.nonparametric.lowess
+    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
+        
+        
+#        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()
+        
+        tck = interpolate.bisplrep(xs[idx_buffer], ys[idx_buffer], zs[idx_buffer])
+        zq[j] = interpolate.bisplev(xq, yq, tck)
+
+    zav.append(np.median(zq))
+    plt.figure()
+    plt.plot(sl_smooth[:,1], zq, 'ko-', markersize=5)
+    plt.plot([sl_smooth[0,1], sl_smooth[-1,1]], [zav[i], zav[i]], 'r--')
+    plt.xlabel('Northings [m]')
+    plt.ylabel('Elevation [mAHD]')
+    plt.title('Interpolated SDS elevation')
+    plt.draw()
 
 
 
-# For the 1D case:
+
-x = sl[i][:,0]
+
-y = sl[i][:,1]
+#%%
-x0 = x
+i = 0
-f_hat = lo.lowess(x, y, x)
+lowess = sm.nonparametric.lowess
-fig,ax = plt.subplots(1)
+x = sl[i][idx_beach,0]
-ax.scatter(x,y)
+y = sl[i][idx_beach,1]
-ax.plot(x0,f_hat,'ro')
+sl_smooth = lowess(x,y, frac=1./15, it = 6)
-plt.show()
+
-
+plt.figure()
-# 2D case (and more...)
+plt.axis('equal')
-x = np.random.randn(2, 100)
+plt.scatter
-f = -1 * np.sin(x[0]) + 0.5 * np.cos(x[1]) + 0.2*np.random.randn(100)
+plt.plot(x,y,'bo-', linewidth=2, marker='o',
-x0 = np.mgrid[-1:1:.1, -1:1:.1]
+         color='b', label='original')
-x0 = np.vstack([x0[0].ravel(), x0[1].ravel()])
+plt.plot(sl_smooth[:,1], sl_smooth[:,0], linewidth=2, marker='o',
-f_hat = lo.lowess(x, f, x0, kernel=lo.tri_cube)
+         color='r', label='smooth')
-from mpl_toolkits.mplot3d import Axes3D
+plt.legend()
-fig = plt.figure()
+plt.xlabel('Eastings [m]')
-ax = fig.add_subplot(111, projection='3d')
+plt.ylabel('Northings [m]')
-ax.scatter(x[0], x[1], f)
+plt.title('Local weighted scatterplot smoothing (LOWESS)')
-ax.scatter(x0[0], x0[1], f_hat, color='r')
+plt.draw()
-    
+