def visualise_results(results, tile_size, out_path):
"""Given the predictions, false positves and the labels of our model visualise them on the satellite
image they belong to."""
# The tiles of the predictions, false positives and labels are all in "results".
# We need ways to get extract them individually to pass them to overlay_bitmap.
get_predictions = lambda (tiles, pos, path): (tiles[0], pos, path)
get_labels = lambda (tiles, pos, path): (tiles[1], pos, path)
get_false_positives = lambda (tiles, pos, path): (tiles[2], pos, path)
get_path = lambda (tiles,pos , path): path
sorted_by_path = sorted(results, key=get_path)
for path, result_tiles in itertools.groupby(sorted_by_path, get_path):
raster_dataset = rasterio.open(path)
dataset_shape = (raster_dataset.shape[0], raster_dataset.shape[1])
result_tiles = list(result_tiles)
predictions = map(get_predictions, result_tiles)
labels = map(get_labels, result_tiles)
false_positives = map(get_false_positives, result_tiles)
satellite_img_name = get_file_name(path)
out_file_name = "{}_results.tif".format(satellite_img_name)
out = os.path.join(out_path, out_file_name)
# We first write the labels in blue, then predictions in green and then false positives in red.
# This way the true positives will be green, false positives red, false negatives blue and everything
# else in the image will be true negatives.
for tiles, color in [(labels, 'blue'), (predictions, 'green'), (false_positives, 'red')]:
bitmap = image_from_tiles(tiles, tile_size, dataset_shape)
raster_dataset = overlay_bitmap(bitmap, raster_dataset, out, color=color)
def reproject_dataset(geotiff_path):
"""Project a GeoTIFF to the WGS84 coordinate reference system.
See https://mapbox.github.io/rasterio/topics/reproject.html"""
# We want to project the GeoTIFF coordinate reference system (crs)
# to WGS84 (e.g. into the familiar Lat/Lon pairs). WGS84 is analogous
# to EPSG:4326
dst_crs = 'EPSG:4326'
with rasterio.open(geotiff_path) as src:
transform, width, height = rasterio.warp.calculate_default_transform(
src.crs, dst_crs, src.width, src.height, *src.bounds)
kwargs = src.meta.copy()
kwargs.update({
'crs': dst_crs,
'transform': transform,
'width': width,
'height': height
})
satellite_img_name = get_file_name(geotiff_path)
out_file_name = "{}_wgs84.tif".format(satellite_img_name)
out_path = os.path.join(WGS84_DIR, out_file_name)
with rasterio.open(out_path, 'w', **kwargs) as dst:
for i in range(1, src.count + 1):
rasterio.warp.reproject(
source=rasterio.band(src, i),
destination=rasterio.band(dst, i),
src_transform=src.transform,
src_crs=src.crs,
dst_transform=transform,
dst_crs=dst_crs,
resampling=rasterio.warp.Resampling.nearest)
return rasterio.open(out_path), out_path
def reproject_dataset(geotiff_path):
"""Project a GeoTIFF to the WGS84 coordinate reference system.
See https://mapbox.github.io/rasterio/topics/reproject.html"""
# We want to project the GeoTIFF coordinate reference system (crs)
# to WGS84 (e.g. into the familiar Lat/Lon pairs). WGS84 is analogous
# to EPSG:4326
dst_crs = 'EPSG:4326'
with rasterio.open(geotiff_path) as src:
transform, width, height = rasterio.warp.calculate_default_transform(
src.crs, dst_crs, src.width, src.height, *src.bounds)
kwargs = src.meta.copy()
kwargs.update({
'crs': dst_crs,
'transform': transform,
'width': width,
'height': height
})
satellite_img_name = get_file_name(geotiff_path)
out_file_name = "{}_wgs84.tif".format(satellite_img_name)
out_path = os.path.join(WGS84_DIR, out_file_name)
with rasterio.open(out_path, 'w', **kwargs) as dst:
for i in range(1, src.count + 1):
rasterio.warp.reproject(
source=rasterio.band(src, i),
destination=rasterio.band(dst, i),
src_transform=src.transform,
src_crs=src.crs,
dst_transform=transform,
dst_crs=dst_crs,
resampling=rasterio.warp.Resampling.nearest)
return rasterio.open(out_path), out_path
def create_patched_features_and_labels(geotiff_path,
geotiff_bitmap_path,
patch_size,
dist,
only_cache=False):
""" Create the features and labels for a given satellite image and its shapefiles. """
# Try to load patch from cache.
satellite_img_name = get_file_name(geotiff_path)
cache_file_name = "{}_{}.pickle".format(satellite_img_name, patch_size)
cache_path = os.path.join(PATCHES_DIR, cache_file_name)
try:
print('Load patches from {}.'.format(cache_path))
with open(cache_path, 'rb') as f:
patches = pickle.load(f)
return patches["features"], patches["labels"]
except IOError as e:
if only_cache:
raise
print("Cache not available. Compute patches.")
# The provided satellite images have a different coordinate reference system as
# the familiar WGS84 which uses Latitude and Longitude. SO we need to reproject
# the satellite image to the WGS84 coordinate reference system
#print('geotiff_path: ',geotiff_path)
dataset, wgs84_path = reproject_dataset(geotiff_path)
bands = np.dstack(dataset.read())
#print('bands,dataset,wgs84_path : ',bands,dataset,wgs84_path)
# For the given satellite image, create a bitmap which has 1 at every pixel corresponding
# to building in the satellite image. In order to do this we use building polygons from OSM.
#The building polygons are stored in forms of shapefiles and are given by "shapefiles_paths".
building_bitmap = create_bitmap(geotiff_path, geotiff_bitmap_path, dataset)
#patched_bands = create_patches(bands, patch_size, wgs84_path)
#patched_bitmap = create_patches(building_bitmap, patch_size, wgs84_path)
#patched_bitmap = create_patches(building_bitmap, patch_size, geotiff_bitmap_path)
patched_bands, patched_bitmap = create_patches(bands, building_bitmap,
patch_size, wgs84_path,
geotiff_bitmap_path, dist)
# Due to the projection, the satellite image in the GeoTIFF is not a perfect rectangle and the
# remaining space on the edges is blacked out. When we overlay the GeoTIFF with the
# shapefile it also overlays features for the blacked out parts which means that if we don't
# remove these patches the classifier will be fed with non-empty labels for empty features.
#patched_bands, patched_bitmap = remove_edge_patches(patched_bands,
# patched_bitmap, patch_size, dataset.shape)
save_patches(cache_path, patched_bands, patched_bitmap)
return patched_bands, patched_bitmap
def create_bitmap(raster_dataset, shapefile_paths, satellite_path):
"""Create the bitmap for a given satellite image."""
satellite_img_name = get_file_name(satellite_path)
cache_file_name = "{}_water.tif".format(satellite_img_name)
cache_path = os.path.join(WATER_BITMAPS_DIR, cache_file_name)
try:
# Try loading the water bitmap from cache.
print("Load water bitmap from {}".format(cache_path))
bitmap = load_bitmap(cache_path)
bitmap[bitmap == 255] = 1
return bitmap
except IOError as e:
print("No cache file found.")
water_features = np.empty((0, ))
print("Create bitmap for water features.")
for shapefile_path in shapefile_paths:
try:
print("Load shapefile {}.".format(shapefile_path))
with fiona.open(shapefile_path) as shapefile:
# Each feature in the shapefile also contains meta information such as
# wether the features is a lake or a river. We only care about the geometry
# of the feature i.e. where it is located and what shape it has.
geometries = [feature['geometry'] for feature in shapefile]
water_features = np.concatenate(
(water_features, geometries), axis=0)
except IOError as e:
print("No shapefile found.")
sys.exit(1)
# Now that we have the vector data of all water features in our satellite image
# we "burn it" into a new raster so that we get a B/W image with water features
# in white and the rest in black. We choose the value 255 so that there is a stark
# contrast between water and non-water pixels. This is only for visualisation
# purposes. For the classifier we use 0s and 1s.
bitmap_image = rasterio.features.rasterize(
((g, 255) for g in water_features),
out_shape=raster_dataset.shape,
transform=raster_dataset.transform)
save_bitmap(cache_path, bitmap_image, raster_dataset)
bitmap_image[bitmap_image == 255] = 1
return bitmap_image
def create_tiled_features_and_labels(geotiff_path,
shapefile_paths,
tile_size,
only_cache=False):
"""Create the features and labels for a given satellite image and its shapefiles."""
# Try to load tiles from cache.
satellite_img_name = get_file_name(geotiff_path)
cache_file_name = "{}_{}.pickle".format(satellite_img_name, tile_size)
cache_path = os.path.join(TILES_DIR, cache_file_name)
try:
print("Load tiles from {}.".format(cache_path))
with open(cache_path) as f:
tiles = pickle.load(f)
return tiles["features"], tiles["labels"]
except IOError as e:
if only_cache:
raise
print("Cache not available. Compute tiles.")
# The provided satellite images have a different coordinate reference system as
# the familiar WGS 84 which uses Latitude and Longitude. So we need to reproject
# the satellite image to the WGS 84 coordinate reference system.
dataset, wgs84_path = reproject_dataset(geotiff_path)
bands = np.dstack(dataset.read())
# For the given satellite image create a bitmap which has 1 at every pixel which corresponds
# to water in the satellite image. In order to do this we use water polygons from OpenStreetMap.
# The water polygons are stored in forms of shapefiles and are given by "shapefile_paths".
water_bitmap = create_bitmap(dataset, shapefile_paths, geotiff_path)
# Tile the RGB bands of the satellite image and the bitmap.
tiled_bands = create_tiles(bands, tile_size, wgs84_path)
tiled_bitmap = create_tiles(water_bitmap, tile_size, wgs84_path)
# Due to the projection the satellite image in the GeoTIFF is not a perfect rectangle and the
# remaining space on the edges is blacked out. When we overlay the GeoTIFF with the
# shapefile it also overlays features for the blacked out parts which means that if we don't
# remove these tiles the classifier will be fed with non-empty labels for empty features.
tiled_bands, tiled_bitmap = remove_edge_tiles(tiled_bands, tiled_bitmap,
tile_size, dataset.shape)
save_tiles(cache_path, tiled_bands, tiled_bitmap)
return tiled_bands, tiled_bitmap
def visualise_labels(labels, tile_size, out_path):
"""Given the labels of a satellite image as tiles. Overlay the source image with the labels
to check if labels are roughly correct."""
# The tiles might come from different satellite images so we have to
# group them according to their source image.
get_path = lambda (tiles, pos, path): path
sorted_by_path = sorted(labels, key=get_path)
for path, predictions in itertools.groupby(sorted_by_path, get_path):
raster_dataset = rasterio.open(path)
bitmap_shape = (raster_dataset.shape[0], raster_dataset.shape[1])
bitmap = image_from_tiles(predictions, tile_size, bitmap_shape)
satellite_img_name = get_file_name(path)
out_file_name = "{}.tif".format(satellite_img_name)
out = os.path.join(out_path, out_file_name)
overlay_bitmap(bitmap, raster_dataset, out)
def visualise_labels(labels, tile_size, out_path):
"""Given the labels of a satellite image as tiles. Overlay the source image with the labels
to check if labels are roughly correct."""
# The tiles might come from different satellite images so we have to
# group them according to their source image.
get_path = lambda (tiles, pos, path): path
sorted_by_path = sorted(labels, key=get_path)
for path, predictions in itertools.groupby(sorted_by_path, get_path):
raster_dataset = rasterio.open(path)
bitmap_shape = (raster_dataset.shape[0], raster_dataset.shape[1])
bitmap = image_from_tiles(predictions, tile_size, bitmap_shape)
satellite_img_name = get_file_name(path)
out_file_name = "{}.tif".format(satellite_img_name)
out = os.path.join(out_path, out_file_name)
overlay_bitmap(bitmap, raster_dataset, out)
def create_bitmap(satellite_path, satellite_bitmap_path, raster_dataset):
""" load the bitmap for a given satellite image. """
#print('satellite_path: {}, satellite_bitmap_path: {}'.format(satellite_path, satellite_bitmap_path))
satellite_img_name = get_file_name(satellite_path)
cache_file_name = "{}_building.tif".format(satellite_img_name)
cache_path = os.path.join(BUILDING_BITMAPS_DIR, cache_file_name)
try:
# Try loading the building bitmap from cache.
print("Load building bitmap {}".format(cache_path))
bitmap = load_bitmap(cache_path)
bitmap[bitmap == 255] = 1
return bitmap
except IOError as e:
print("No cache file found.")
print('Create bitmaps for building features')
print("Load shapefile {}.".format(satellite_bitmap_path))
bitmap_image = rasterio.open(satellite_bitmap_path).read(1)
save_bitmap(cache_path, bitmap_image, raster_dataset)
bitmap_image[bitmap_image == 255] = 1
return bitmap_image
def visualise_results(results, tile_size, out_path, out_format="GeoTIFF"):
"""Given the predictions, false positves and the labels of our model visualise them on the satellite
image they belong to."""
# The tiles of the predictions, false positives and labels are all in "results".
# We need ways to get extract them individually to pass them to overlay_bitmap.
get_predictions = lambda (tiles, pos, path): (tiles[0], pos, path)
get_labels = lambda (tiles, pos, path): (tiles[1], pos, path)
get_false_positives = lambda (tiles, pos, path): (tiles[2], pos, path)
get_path = lambda (tiles,pos , path): path
sorted_by_path = sorted(results, key=get_path)
for path, result_tiles in itertools.groupby(sorted_by_path, get_path):
raster_dataset = rasterio.open(path)
dataset_shape = (raster_dataset.shape[0], raster_dataset.shape[1])
result_tiles = list(result_tiles)
predictions = map(get_predictions, result_tiles)
labels = map(get_labels, result_tiles)
false_positives = map(get_false_positives, result_tiles)
satellite_img_name = get_file_name(path)
file_extension = "tif" if out_format == "GeoTIFF" else "shp"
out_file_name = "{}_results.{}".format(satellite_img_name, file_extension)
out = os.path.join(out_path, out_file_name)
if out_format == "GeoTIFF":
# We first write the labels in blue, then predictions in green and then false positives in red.
# This way the true positives will be green, false positives red, false negatives blue and everything
# else in the image will be true negatives.
for tiles, color in [(labels, 'blue'), (predictions, 'green'), (false_positives, 'red')]:
bitmap = image_from_tiles(tiles, tile_size, dataset_shape)
raster_dataset = overlay_bitmap(bitmap, raster_dataset, out, color=color)
elif out_format == "Shapefile":
bitmap = image_from_tiles(predictions, tile_size, dataset_shape)
create_shapefile(bitmap, raster_dataset, out)