diff --git a/functions/sds.py b/functions/sds.py index ec62f0e..e9b73fe 100644 --- a/functions/sds.py +++ b/functions/sds.py @@ -26,6 +26,7 @@ import skimage.transform as transform import sklearn.decomposition as decomposition import skimage.measure as measure import skimage.morphology as morphology +from sklearn.cluster import KMeans # import own modules @@ -605,3 +606,75 @@ def convert_epsg(points, epsg_in, epsg_out): raise return points_converted + +def classify_sand_unsupervised(im_ms_ps, im_pan, cloud_mask, wl_pix, buffer_size, min_beach_size, plot_bool): + """ + Classifies sand pixels using an unsupervised algorithm (Kmeans) + + KV WRL 2018 + + Arguments: + ----------- + im_ms_ps: np.ndarray + Pansharpened RGB + downsampled NIR and SWIR + im_pan: + Panchromatic band + cloud_mask: np.ndarray + 2D cloud mask with True where cloud pixels are + wl_pix: list of np.ndarray + list of arrays containig the pixel coordinates of the water line + buffer_size: int + radius of the disk used to create a buffer around the water line + min_beach_size: int + minimum number of connected pixels belonging to a single beach + plot_bool: boolean + True if plot is wanted + + Returns: ----------- + im_sand: np.ndarray + 2D binary image containing True where sand pixels are located + + """ + # reshape the 2D images into vectors + vec_ms_ps = im_ms_ps.reshape(im_ms_ps.shape[0] * im_ms_ps.shape[1], im_ms_ps.shape[2]) + vec_pan = im_pan.reshape(im_pan.shape[0]*im_pan.shape[1]) + vec_mask = cloud_mask.reshape(im_ms_ps.shape[0] * im_ms_ps.shape[1]) + # add B,G,R,NIR and pan bands to the vector of features + vec_features = np.zeros((vec_ms_ps.shape[0], 5)) + vec_features[:,[0,1,2,3]] = vec_ms_ps[:,[0,1,2,3]] + vec_features[:,4] = vec_pan + + # create binary image with ones where the detected water lines is + im_buffer = np.zeros((im_ms_ps.shape[0], im_ms_ps.shape[1])) + for i, contour in enumerate(wl_pix): + indices = [(int(_[0]), int(_[1])) for _ in list(np.round(contour))] + for j, idx in enumerate(indices): + im_buffer[idx] = 1 + # perform a dilation on the binary image + se = morphology.disk(buffer_size) + im_buffer = morphology.binary_dilation(im_buffer, se) + vec_buffer = (im_buffer == 1).reshape(im_ms_ps.shape[0] * im_ms_ps.shape[1]) + # add cloud mask to buffer + vec_buffer= np.logical_and(vec_buffer, ~vec_mask) + # perform kmeans (6 clusters) + kmeans = KMeans(n_clusters=6, random_state=0).fit(vec_features[vec_buffer,:]) + labels = np.ones((len(vec_mask))) * np.nan + labels[vec_buffer] = kmeans.labels_ + im_labels = labels.reshape(im_ms_ps.shape[0], im_ms_ps.shape[1]) + # find the class with maximum reflection in the B,G,R,Pan + im_sand = im_labels == np.argmax(np.mean(kmeans.cluster_centers_[:,[0,1,2,4]], axis=1)) + im_sand = morphology.remove_small_objects(im_sand, min_size=min_beach_size, connectivity=2) +# im_sand = morphology.binary_dilation(im_sand, morphology.disk(1)) + + if plot_bool: + im = np.copy(im_ms_ps) + im[im_sand,0] = 0 + im[im_sand,1] = 0 + im[im_sand,2] = 1 + plt.figure() + plt.imshow(im[:,:,[2,1,0]]) + plt.axis('image') + plt.title('Sand classification') + plt.show() + + return im_sand diff --git a/sds_extract.py b/sds_extract.py index 8de4f40..a6f4126 100644 --- a/sds_extract.py +++ b/sds_extract.py @@ -40,6 +40,8 @@ plot_bool = True # if you want the plots prob_high = 99.9 # 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 of disk for buffer (sand classif parameter) +min_beach_size = 50 # number of pixels in a beach (sand classif parameter) # select collection satname = 'L8' @@ -99,3 +101,6 @@ wl_coords = sds.convert_pix2world(wl_pix, crs['crs_15m']) # convert to output epsg spatial reference wl = sds.convert_epsg(wl_coords, crs['epsg_code'], output_epsg) + +# classify sand pixels +im_sand = sds.classify_sand_unsupervised(im_ms_ps, im_pan, im_cloud, wl_pix, buffer_size, min_beach_size, plot_bool)