def main(args):
config = load_config(args.config)
check_channels(config)
check_classes(config)
assert torch.cuda.is_available(
), "No GPU support found. Check CUDA and NVidia Driver install."
assert torch.distributed.is_nccl_available(
), "No NCCL support found. Check your PyTorch install."
world_size = torch.cuda.device_count()
args.bs = args.bs if args.bs is not None else math.floor(os.cpu_count() /
world_size)
args.workers = args.workers if args.workers is not None else args.bs
palette, transparency = make_palette(
[classe["color"] for classe in config["classes"]])
args.cover = [
tile for tile in tiles_from_csv(os.path.expanduser(args.cover))
] if args.cover else None
args.out = os.path.expanduser(args.out)
log = Logs(os.path.join(args.out, "log"))
chkpt = torch.load(args.checkpoint, map_location=torch.device("cpu"))
chkpt["loader"] = "SemSeg"
log.log("neo predict on {} GPUs, with {} workers/GPU and {} tiles/batch".
format(world_size, args.workers, args.bs))
log.log("Model {} - UUID: {}".format(chkpt["nn"], chkpt["uuid"]))
log.log("---")
loader = load_module("neat_eo.loaders.{}".format(chkpt["loader"].lower()))
lock_file = os.path.abspath(os.path.join(args.out, str(uuid.uuid1())))
dataset = getattr(loader, chkpt["loader"])(
config,
chkpt["shape_in"][1:3],
args.dataset,
args.cover,
mode="predict",
metatiles=args.metatiles,
keep_borders=args.keep_borders,
)
mp.spawn(gpu_worker,
nprocs=world_size,
args=(world_size, lock_file, args, config, dataset, palette,
transparency))
if os.path.exists(lock_file):
os.remove(lock_file)
if not args.no_web_ui and dataset.cover:
template = "leaflet.html" if not args.web_ui_template else args.web_ui_template
base_url = args.web_ui_base_url if args.web_ui_base_url else "."
web_ui(args.out, base_url, dataset.cover, dataset.cover, "png",
template)
def main(args):
assert args.out or args.delete, "out parameter is required"
args.out = os.path.expanduser(args.out)
print("neo subset {} with cover {}, on CPU".format(args.dir, args.cover),
file=sys.stderr,
flush=True)
ext = set()
tiles = set(tiles_from_csv(os.path.expanduser(args.cover)))
assert len(tiles), "Empty Cover: {}".format(args.cover)
for tile in tqdm(tiles, ascii=True, unit="tiles"):
if isinstance(tile, mercantile.Tile):
src_tile = tile_from_xyz(args.dir, tile.x, tile.y, tile.z)
if not src_tile:
if not args.quiet:
print("WARNING: skipping tile {}".format(tile),
file=sys.stderr,
flush=True)
continue
_, src = src_tile
dst_dir = os.path.join(args.out, str(tile.z), str(tile.x))
else:
src = tile
dst_dir = os.path.join(args.out, os.path.dirname(tile))
assert os.path.isfile(src)
dst = os.path.join(dst_dir, os.path.basename(src))
ext.add(os.path.splitext(src)[1][1:])
if not os.path.isdir(dst_dir):
os.makedirs(dst_dir, exist_ok=True)
if args.delete:
os.remove(src)
assert not os.path.lexists(src)
elif args.copy:
shutil.copyfile(src, dst)
assert os.path.exists(dst)
else:
if os.path.islink(dst):
os.remove(dst)
os.symlink(os.path.relpath(src, os.path.dirname(dst)), dst)
assert os.path.islink(dst)
if tiles and not args.no_web_ui and not args.delete:
assert len(ext) == 1, "ERROR: Mixed extensions, can't generate Web UI"
template = "leaflet.html" if not args.web_ui_template else args.web_ui_template
base_url = args.web_ui_base_url if args.web_ui_base_url else "."
web_ui(args.out, base_url, tiles, tiles, list(ext)[0], template)
def main(args):
assert not (args.label and args.format), "Format option not supported for label, output must be kept as png"
try:
args.bands = list(map(int, args.bands.split(","))) if args.bands else None
except:
raise ValueError("invalid --args.bands value")
if not args.workers:
args.workers = min(os.cpu_count(), len(args.rasters))
if args.label:
config = load_config(args.config)
check_classes(config)
colors = [classe["color"] for classe in config["classes"]]
palette = make_palette(colors)
assert len(args.ts.split(",")) == 2, "--ts expect width,height value (e.g 512,512)"
width, height = list(map(int, args.ts.split(",")))
cover = [tile for tile in tiles_from_csv(os.path.expanduser(args.cover))] if args.cover else None
splits_path = os.path.join(os.path.expanduser(args.out), ".splits")
args.out = os.path.expanduser(args.out)
if os.path.dirname(os.path.expanduser(args.out)):
os.makedirs(args.out, exist_ok=True)
log = Logs(os.path.join(args.out, "log"), out=sys.stderr)
raster = rasterio_open(os.path.expanduser(args.rasters[0]))
args.bands = args.bands if args.bands else raster.indexes
raster.close()
print(
"neo tile {} rasters on bands {}, on CPU with {} workers".format(len(args.rasters), args.bands, args.workers),
file=sys.stderr,
flush=True,
)
skip = []
tiles_map = {}
total = 0
for path in args.rasters:
raster = rasterio_open(os.path.expanduser(path))
assert set(args.bands).issubset(set(raster.indexes)), "Missing bands in raster {}".format(path)
try:
w, s, e, n = transform_bounds(raster.crs, "EPSG:4326", *raster.bounds)
except:
log.log("WARNING: missing or invalid raster projection, SKIPPING: {}".format(path))
skip.append(path)
continue
tiles = [mercantile.Tile(x=x, y=y, z=z) for x, y, z in mercantile.tiles(w, s, e, n, args.zoom)]
tiles = list(set(tiles) & set(cover)) if cover else tiles
total += len(tiles)
for tile in tiles:
tile_key = (str(tile.x), str(tile.y), str(tile.z))
if tile_key not in tiles_map.keys():
tiles_map[tile_key] = []
tiles_map[tile_key].append(path)
raster.close()
assert total, "Nothing left to tile"
if len(args.bands) == 1 or args.label:
ext = "png" if args.format is None else args.format
if len(args.bands) == 3:
ext = "webp" if args.format is None else args.format
if len(args.bands) > 3:
ext = "tiff" if args.format is None else args.format
tiles = []
progress = tqdm(desc="Coverage tiling", total=total, ascii=True, unit="tile")
with futures.ThreadPoolExecutor(args.workers) as executor:
def worker(path):
if path in skip:
return None
raster = rasterio_open(path)
w, s, e, n = transform_bounds(raster.crs, "EPSG:4326", *raster.bounds)
tiles = [mercantile.Tile(x=x, y=y, z=z) for x, y, z in mercantile.tiles(w, s, e, n, args.zoom)]
tiled = []
for tile in tiles:
if cover and tile not in cover:
continue
w, s, e, n = mercantile.xy_bounds(tile)
warp_vrt = WarpedVRT(
raster,
crs="epsg:3857",
resampling=Resampling.bilinear,
add_alpha=False,
transform=from_bounds(w, s, e, n, width, height),
width=width,
height=height,
)
data = warp_vrt.read(
out_shape=(len(args.bands), width, height), indexes=args.bands, window=warp_vrt.window(w, s, e, n)
)
if data.dtype == "uint16": # GeoTiff could be 16 bits
data = np.uint8(data / 256)
elif data.dtype == "uint32": # or 32 bits
data = np.uint8(data / (256 * 256))
image = np.moveaxis(data, 0, 2) # C,H,W -> H,W,C
tile_key = (str(tile.x), str(tile.y), str(tile.z))
if (
not args.label
and len(tiles_map[tile_key]) == 1
and is_nodata(image, args.nodata, args.nodata_threshold, args.keep_borders)
):
progress.update()
continue
if len(tiles_map[tile_key]) > 1:
out = os.path.join(splits_path, str(tiles_map[tile_key].index(path)))
else:
out = args.out
x, y, z = map(int, tile)
if not args.label:
tile_image_to_file(out, mercantile.Tile(x=x, y=y, z=z), image, ext=ext)
if args.label:
tile_label_to_file(out, mercantile.Tile(x=x, y=y, z=z), palette, args.nodata, image)
if len(tiles_map[tile_key]) == 1:
tiled.append(mercantile.Tile(x=x, y=y, z=z))
progress.update()
raster.close()
return tiled
for tiled in executor.map(worker, args.rasters):
if tiled is not None:
tiles.extend(tiled)
total = sum([1 for tile_key in tiles_map.keys() if len(tiles_map[tile_key]) > 1])
progress = tqdm(desc="Aggregate splits", total=total, ascii=True, unit="tile")
with futures.ThreadPoolExecutor(args.workers) as executor:
def worker(tile_key):
if len(tiles_map[tile_key]) == 1:
return
image = np.zeros((width, height, len(args.bands)), np.uint8)
x, y, z = map(int, tile_key)
for i in range(len(tiles_map[tile_key])):
root = os.path.join(splits_path, str(i))
_, path = tile_from_xyz(root, x, y, z)
if not args.label:
split = tile_image_from_file(path)
if args.label:
split = tile_label_from_file(path)
if len(split.shape) == 2:
split = split.reshape((width, height, 1)) # H,W -> H,W,C
assert image.shape == split.shape, "{}, {}".format(image.shape, split.shape)
image[np.where(image == 0)] += split[np.where(image == 0)]
if not args.label and is_nodata(image, args.nodata, args.nodata_threshold, args.keep_borders):
progress.update()
return
tile = mercantile.Tile(x=x, y=y, z=z)
if not args.label:
tile_image_to_file(args.out, tile, image)
if args.label:
tile_label_to_file(args.out, tile, palette, image)
progress.update()
return tile
for tiled in executor.map(worker, tiles_map.keys()):
if tiled is not None:
tiles.append(tiled)
if splits_path and os.path.isdir(splits_path):
shutil.rmtree(splits_path) # Delete suffixes dir if any
if tiles and not args.no_web_ui:
template = "leaflet.html" if not args.web_ui_template else args.web_ui_template
base_url = args.web_ui_base_url if args.web_ui_base_url else "."
web_ui(args.out, base_url, tiles, tiles, ext, template)
def main(args):
assert not (args.geojson is not None and args.pg is not None), "You have to choose between --pg or --geojson"
assert len(args.ts.split(",")) == 2, "--ts expect width,height value (e.g 512,512)"
config = load_config(args.config)
check_classes(config)
args.pg = config["auth"]["pg"] if not args.pg and "pg" in config["auth"].keys() else args.pg
assert not (args.sql and not args.pg), "With --sql option, --pg dsn setting must also be provided"
palette, transparency = make_palette([classe["color"] for classe in config["classes"]], complementary=True)
index = [config["classes"].index(classe) for classe in config["classes"] if classe["title"] == args.type]
assert index, "Requested type is not contains in your config file classes."
burn_value = index[0]
assert 0 < burn_value <= 255
if args.sql:
assert "limit" not in args.sql.lower(), "LIMIT is not supported"
assert "TILE_GEOM" in args.sql, "TILE_GEOM filter not found in your SQL"
sql = re.sub(r"ST_Intersects( )*\((.*)?TILE_GEOM(.*)?\)", "1=1", args.sql, re.I)
assert sql and sql != args.sql, "Incorrect TILE_GEOM filter in your SQL"
if os.path.dirname(os.path.expanduser(args.out)):
os.makedirs(os.path.expanduser(args.out), exist_ok=True)
args.out = os.path.expanduser(args.out)
log = Logs(os.path.join(args.out, "log"), out=sys.stderr)
tiles = [tile for tile in tiles_from_csv(os.path.expanduser(args.cover))]
assert len(tiles), "Empty Cover: {}".format(args.cover)
if args.geojson:
zoom = tiles[0].z
assert not [tile for tile in tiles if tile.z != zoom], "Unsupported zoom mixed cover. Use PostGIS instead"
feature_map = collections.defaultdict(list)
log.log("neo rasterize - Compute spatial index")
for geojson_file in args.geojson:
with open(os.path.expanduser(geojson_file)) as geojson:
feature_collection = json.load(geojson)
srid = geojson_srid(feature_collection)
for i, feature in enumerate(tqdm(feature_collection["features"], ascii=True, unit="feature")):
feature_map = geojson_parse_feature(zoom, srid, feature_map, feature, args.buffer)
features = args.geojson
if args.sql:
conn = psycopg2.connect(args.pg)
db = conn.cursor()
db.execute("""SELECT ST_Srid("1") AS srid FROM ({} LIMIT 1) AS t("1")""".format(sql))
srid = db.fetchone()[0]
assert srid and int(srid) > 0, "Unable to retrieve geometry SRID."
features = args.sql
if not len(feature_map):
log.log("-----------------------------------------------")
log.log("NOTICE: no feature to rasterize, seems peculiar")
log.log("-----------------------------------------------")
log.log("neo rasterize - rasterizing {} from {} on cover {}".format(args.type, features, args.cover))
with open(os.path.join(os.path.expanduser(args.out), args.type.lower() + "_cover.csv"), mode="w") as cover:
for tile in tqdm(tiles, ascii=True, unit="tile"):
geojson = None
if args.sql:
w, s, e, n = tile_bbox(tile)
tile_geom = "ST_Transform(ST_MakeEnvelope({},{},{},{}, 4326), {})".format(w, s, e, n, srid)
query = """
WITH
sql AS ({}),
geom AS (SELECT "1" AS geom FROM sql AS t("1")),
json AS (SELECT '{{"type": "Feature", "geometry": '
|| ST_AsGeoJSON((ST_Dump(ST_Transform(ST_Force2D(geom.geom), 4326))).geom, 6)
|| '}}' AS features
FROM geom)
SELECT '{{"type": "FeatureCollection", "features": [' || Array_To_String(array_agg(features), ',') || ']}}'
FROM json
""".format(
args.sql.replace("TILE_GEOM", tile_geom)
)
db.execute(query)
row = db.fetchone()
try:
geojson = json.loads(row[0])["features"] if row and row[0] else None
except Exception:
log.log("Warning: Invalid geometries, skipping {}".format(tile))
conn = psycopg2.connect(args.pg)
db = conn.cursor()
if args.geojson:
geojson = feature_map[tile] if tile in feature_map else None
if geojson:
num = len(geojson)
out = geojson_tile_burn(tile, geojson, 4326, list(map(int, args.ts.split(","))), burn_value)
if not geojson or out is None:
num = 0
out = np.zeros(shape=list(map(int, args.ts.split(","))), dtype=np.uint8)
tile_label_to_file(args.out, tile, palette, transparency, out, append=args.append)
cover.write("{},{},{} {}{}".format(tile.x, tile.y, tile.z, num, os.linesep))
if not args.no_web_ui:
template = "leaflet.html" if not args.web_ui_template else args.web_ui_template
base_url = args.web_ui_base_url if args.web_ui_base_url else "."
tiles = [tile for tile in tiles_from_csv(args.cover)]
web_ui(args.out, base_url, tiles, tiles, "png", template)
def main(args):
if not args.masks or not args.labels:
assert args.mode != "list", "Parameters masks and labels are mandatories in list mode."
assert not (args.min or args.max), "Both --masks and --labels mandatory, for metric filtering."
if args.min or args.max:
config = load_config(args.config)
args.out = os.path.expanduser(args.out)
cover = [tile for tile in tiles_from_csv(os.path.expanduser(args.cover))] if args.cover else None
args_minmax = set()
args.min = {(m[0], m[1]): m[2] for m in args.min} if args.min else dict()
args.max = {(m[0], m[1]): m[2] for m in args.max} if args.max else dict()
args_minmax.update(args.min.keys())
args_minmax.update(args.max.keys())
minmax = dict()
for mm in args_minmax:
mm_min = float(args.min[mm]) if mm in args.min else 0.0
mm_max = float(args.max[mm]) if mm in args.max else 1.0
assert mm_min < mm_max, "--min must be lower than --max, on {}".format(mm)
minmax[mm] = {
"min": mm_min,
"max": mm_max,
"class_id": [c for c, classe in enumerate(config["classes"]) if classe["title"] == mm[0]][0],
"module": load_module("neat_eo.metrics." + mm[1]),
}
if not args.workers:
args.workers = os.cpu_count()
print("neo compare {} on CPU, with {} workers".format(args.mode, args.workers), file=sys.stderr, flush=True)
if args.images:
tiles = [tile for tile in tiles_from_dir(args.images[0], cover=cover)]
assert len(tiles), "Empty images dir: {}".format(args.images[0])
for image in args.images[1:]:
assert sorted(tiles) == sorted([tile for tile in tiles_from_dir(image, cover=cover)]), "Unconsistent images dirs"
if args.labels and args.masks:
tiles_masks = [tile for tile in tiles_from_dir(args.masks, cover=cover)]
tiles_labels = [tile for tile in tiles_from_dir(args.labels, cover=cover)]
if args.images:
assert sorted(tiles) == sorted(tiles_masks) == sorted(tiles_labels), "Unconsistent images/label/mask directories"
else:
assert len(tiles_masks), "Empty masks dir: {}".format(args.masks)
assert len(tiles_labels), "Empty labels dir: {}".format(args.labels)
assert sorted(tiles_masks) == sorted(tiles_labels), "Label and Mask directories are not consistent"
tiles = tiles_masks
tiles_list = []
tiles_compare = []
progress = tqdm(total=len(tiles), ascii=True, unit="tile")
log = False if args.mode == "list" else Logs(os.path.join(args.out, "log"))
with futures.ThreadPoolExecutor(args.workers) as executor:
def worker(tile):
x, y, z = list(map(str, tile))
if args.masks and args.labels:
label = np.array(Image.open(os.path.join(args.labels, z, x, "{}.png".format(y))))
mask = np.array(Image.open(os.path.join(args.masks, z, x, "{}.png".format(y))))
assert label.shape == mask.shape, "Inconsistent tiles (size or dimensions)"
metrics = dict()
for mm in minmax:
try:
metrics[mm] = getattr(minmax[mm]["module"], "get")(
torch.as_tensor(label, device="cpu"),
torch.as_tensor(mask, device="cpu"),
minmax[mm]["class_id"],
)
except:
progress.update()
return False, tile
if not (minmax[mm]["min"] <= metrics[mm] <= minmax[mm]["max"]):
progress.update()
return True, tile
tiles_compare.append(tile)
if args.mode == "side":
for i, root in enumerate(args.images):
img = tile_image_from_file(tile_from_xyz(root, x, y, z)[1], force_rgb=True)
if i == 0:
side = np.zeros((img.shape[0], img.shape[1] * len(args.images), 3))
side = np.swapaxes(side, 0, 1) if args.vertical else side
image_shape = img.shape
else:
assert image_shape[0:2] == img.shape[0:2], "Unconsistent image size to compare"
if args.vertical:
side[i * image_shape[0] : (i + 1) * image_shape[0], :, :] = img
else:
side[:, i * image_shape[0] : (i + 1) * image_shape[0], :] = img
tile_image_to_file(args.out, tile, np.uint8(side))
elif args.mode == "stack":
for i, root in enumerate(args.images):
tile_image = tile_image_from_file(tile_from_xyz(root, x, y, z)[1], force_rgb=True)
if i == 0:
image_shape = tile_image.shape[0:2]
stack = tile_image / len(args.images)
else:
assert image_shape == tile_image.shape[0:2], "Unconsistent image size to compare"
stack = stack + (tile_image / len(args.images))
tile_image_to_file(args.out, tile, np.uint8(stack))
elif args.mode == "list":
tiles_list.append([tile, metrics])
progress.update()
return True, tile
for ok, tile in executor.map(worker, tiles):
if not ok and log:
log.log("Warning: skipping. {}".format(str(tile)))
if args.mode == "list":
with open(args.out, mode="w") as out:
if args.geojson:
out.write('{"type":"FeatureCollection","features":[')
first = True
for tile_list in tiles_list:
tile, metrics = tile_list
x, y, z = list(map(str, tile))
if args.geojson:
prop = '"properties":{{"x":{},"y":{},"z":{}'.format(x, y, z)
for metric in metrics:
prop += ',"{}":{:.3f}'.format(metric, metrics[metric])
geom = '"geometry":{}'.format(json.dumps(feature(tile, precision=6)["geometry"]))
out.write('{}{{"type":"Feature",{},{}}}}}'.format("," if not first else "", geom, prop))
first = False
if not args.geojson:
out.write("{},{},{}".format(x, y, z))
for metric in metrics:
out.write("\t{:.3f}".format(metrics[metric]))
out.write(os.linesep)
if args.geojson:
out.write("]}")
out.close()
base_url = args.web_ui_base_url if args.web_ui_base_url else "."
if args.mode == "side" and not args.no_web_ui:
template = "compare.html" if not args.web_ui_template else args.web_ui_template
web_ui(args.out, base_url, tiles, tiles_compare, args.format, template, union_tiles=False)
if args.mode == "stack" and not args.no_web_ui:
template = "leaflet.html" if not args.web_ui_template else args.web_ui_template
tiles = [tile for tile in tiles_from_dir(args.images[0])]
web_ui(args.out, base_url, tiles, tiles_compare, args.format, template)
def main(args):
tiles = list(tiles_from_csv(args.cover))
assert len(tiles), "Empty cover: {}".format(args.cover)
args.workers = min(os.cpu_count(),
args.rate) if not args.workers else args.workers
if os.path.dirname(os.path.expanduser(args.out)):
os.makedirs(os.path.expanduser(args.out), exist_ok=True)
log = Logs(os.path.join(args.out, "log"), out=sys.stderr)
log.log("neo download with {} workers, at max {} req/s, from: {}".format(
args.workers, args.rate, args.url))
already_dl = 0
dl = 0
with requests.Session() as session:
progress = tqdm(total=len(tiles), ascii=True, unit="image")
with futures.ThreadPoolExecutor(args.workers) as executor:
def worker(tile):
tick = time.monotonic()
progress.update()
try:
x, y, z = map(str, [tile.x, tile.y, tile.z])
os.makedirs(os.path.join(args.out, z, x), exist_ok=True)
except:
return tile, None, False
path = os.path.join(args.out, z, x,
"{}.{}".format(y, args.format))
if os.path.isfile(path): # already downloaded
return tile, None, True
if args.type == "XYZ":
url = args.url.format(x=tile.x, y=tile.y, z=tile.z)
elif args.type == "WMS":
xmin, ymin, xmax, ymax = xy_bounds(tile)
url = args.url.format(xmin=xmin,
ymin=ymin,
xmax=xmax,
ymax=ymax)
res = tile_image_from_url(session, url, args.timeout)
if res is None: # let's retry once
res = tile_image_from_url(session, url, args.timeout)
if res is None:
return tile, url, False
try:
tile_image_to_file(args.out, tile, res)
except OSError:
return tile, url, False
tock = time.monotonic()
time_for_req = tock - tick
time_per_worker = args.workers / args.rate
if time_for_req < time_per_worker:
time.sleep(time_per_worker - time_for_req)
return tile, url, True
for tile, url, ok in executor.map(worker, tiles):
if url and ok:
dl += 1
elif not url and ok:
already_dl += 1
else:
log.log("Warning:\n {} failed, skipping.\n {}\n".format(
tile, url))
if already_dl:
log.log(
"Notice: {} tiles were already downloaded previously, and so skipped now."
.format(already_dl))
if already_dl + dl == len(tiles):
log.log("Notice: Coverage is fully downloaded.")
if not args.no_web_ui:
template = "leaflet.html" if not args.web_ui_template else args.web_ui_template
base_url = args.web_ui_base_url if args.web_ui_base_url else "."
web_ui(args.out, base_url, tiles, tiles, args.format, template)