def test_copyDEM(self):
files = ["small25", "jebja30", "tunez"]
for file in files:
dem = DEM("{}/{}.tif".format(infolder, file))
dem2 = dem.copy()
computed = np.array_equal(dem._array, dem2._array)
self.assertEqual(computed, True)
def test_fill_01(self):
arr = np.array([[49, 36, 29, 29], [32, 19, 17, 20], [19, 18, 31, 39],
[19, 29, 42, 51]])
dem = DEM()
dem.set_array(arr)
fill = dem.fill_sinks()
computed = fill.read_array().tolist()
arr = np.array([[49, 36, 29, 29], [32, 19, 19, 20], [19, 19, 31, 39],
[19, 29, 42, 51]])
expected = arr.tolist()
self.assertEqual(computed, expected)
def test_fill_05(self):
dem = DEM(infolder + "/tunez.tif")
fill = dem.fill_sinks().read_array().astype("int16")
mfill = sio.loadmat(infolder + '/mlab_files/fill_tunez.mat')['fill']
mfill = mfill.astype("int16")
# Matlab files contain "nan" in the nodata positions
nodatapos = dem.get_nodata_pos()
mfill[nodatapos] = dem.get_nodata()
computed = np.array_equal(fill, mfill)
self.assertEqual(computed, True)
def test_BasinClass01(self):
files = ["small25", "jebja30", "tunez"]
for file in files:
# Cargamos flow
flw_path = "{}/{}_fd.tif".format(infolder, file)
dem_path = "{}/{}.tif".format(infolder, file)
dem = DEM(dem_path)
fd = Flow(flw_path)
# Obtenemos cuencas
cuencas = fd.get_drainage_basins(min_area=0.0025)
# Mayor, menor, y random
bids, counts = np.unique(cuencas.read_array(), return_counts=True)
if 0 in bids:
bids = bids[1:]
counts = counts[1:]
idmax = bids[np.argmax(counts)]
idmin = bids[np.argmin(counts)]
idrdn = np.random.choice(bids)
idxs = [idmax, idmin, idrdn]
lbls = ["max", "min", "rdn"]
for n in range(3):
basin = Basin(dem, cuencas, idxs[n])
basin_path = "{}/{}_basin{}.tif".format(
outfolder, file, lbls[n])
basin.save(basin_path)
basin2 = Basin(basin_path)
computed = np.array_equal(basin.read_array(),
basin2.read_array())
self.assertEqual(computed, True)
def test_BNetwork_class01(self):
"""
Test00 Crea BNetwork para cuencas de prueba a partir de un objeto Basin
Sin utilizar cabeceras
"""
files = ["small25", "jebja30", "tunez"]
for file in files:
# Cargamos DEM, Flow, Network
fd = Flow("{}/{}_fd.tif".format(infolder, file))
dem = DEM("{}/{}.tif".format(infolder, file))
net = Network("{}/{}_net.dat".format(infolder, file))
# Cargamos outlets y generamos cuencas
outlets = np.loadtxt("{}/{}_bnet_outlets.txt".format(
infolder, file),
delimiter=";")
outlets = net.snap_points(outlets)
cuencas = fd.get_drainage_basins(outlets)
for bid in np.unique(cuencas.read_array()):
if bid == 0:
continue
basin = Basin(dem, cuencas, bid)
bnet = BNetwork(net, basin)
# Este test solo verifica que se realice sin fallos y que
# el objeto bnet tiene una única cabecera
bnet = BNetwork(net, cuencas, None, bid)
self.assertEqual(int(bnet._heads[0]), self.results[file][bid])
def test_create_Flow_03(self):
# Create Flow object with previously filled DEM (auxtopo is ignored)
files = ["small", "small25", "morocco", "tunez", "jebja30"]
for file in files:
dem_path = infolder + "/{0}_fil.tif".format(file)
flw_path = infolder + "/{0}_fd.tif".format(file)
dem = DEM(dem_path)
fd = Flow(dem, auxtopo=False, filled=True, verbose=False) # Flow obj with filled dem and without auxiliar topography
fd2 = Flow(flw_path)
computed = np.array_equal(fd2._ix, fd._ix)
self.assertEqual(computed, True)
def test_identify_flats_02(self):
# Create a DEM object and make fill
dem = DEM(infolder + "/small25.tif")
fill = dem.fill_sinks()
# Identify flats and sills and load arrays
flats, sills = fill.identify_flats(nodata=False)
flats = flats.read_array()
sills = sills.read_array()
# Load matlab flats and sills
m_flats = sio.loadmat(infolder +
"/mlab_files/flats_small25.mat")['flats']
m_sills = sio.loadmat(infolder +
"/mlab_files/sills_small25.mat")['sills']
# Compare
computed = (np.array_equal(m_flats,
flats), np.array_equal(m_sills, sills))
self.assertEqual(computed, (True, True))
def test_create_Flow_02(self):
# Create Flow object with auxiliar topography
files = ["small", "small25", "tunez", "jebja30"]
for file in files:
dem_path = infolder + "/{0}.tif".format(file)
flw_path = infolder + "/{0}_fd_auxtp.tif".format(file)
dem = DEM(dem_path)
fd = Flow(dem, auxtopo=True, filled=False, verbose=False) # Flow obj with auxiliar topography
fd2 = Flow(flw_path)
computed = np.array_equal(fd2._ix, fd._ix)
self.assertEqual(computed, True)
def test_flow_properties_02(self):
# Testing an empty Flow object
dem = DEM()
fd = Flow()
computed = (fd.get_size(), fd.get_dims(), fd.get_ncells(), fd.get_projection(), fd.get_cellsize(), fd.get_geotransform())
expected = (dem.get_size(), dem.get_dims(), dem.get_ncells(), dem.get_projection(), dem.get_cellsize(), dem.get_geotransform())
self.assertEqual(computed, expected)
def test_flow_properties_01(self):
files = ["small", "small25", "morocco", "tunez", "jebja30"]
for file in files:
dem = DEM(infolder + "/{0}.tif".format(file))
fd = Flow(infolder + "/{0}_fd.tif".format(file))
computed = (fd.get_size(), fd.get_dims(), fd.get_ncells(), fd.get_projection(), fd.get_cellsize(), fd.get_geotransform())
expected = (dem.get_size(), dem.get_dims(), dem.get_ncells(), dem.get_projection(), dem.get_cellsize(), dem.get_geotransform())
self.assertEqual(computed, expected)
def test_stream_poi_02(self):
dem_files = ['tunez.tif', 'small25.tif', "jebja30.tif"]
for file in dem_files:
dem = DEM(infolder + "/" + file)
fd = Flow(dem)
thr = int(fd.get_ncells() * 0.01)
net = Network(fd, dem, thr)
out01 = fd.get_stream_poi(thr, "confluences", "CELL")
out02 = net.get_stream_poi("confluences", "CELL")
computed = np.array_equal(out01, out02)
print(file)
self.assertEqual(computed, True)
def test_fill_03(self):
arr = np.array([[49, 36, 29, 29], [32, 17, 12, 20], [19, 17, 19, 39],
[19, 29, 42, -99]])
dem = DEM()
dem.set_nodata(-99)
dem.set_array(arr)
fill = dem.fill_sinks()
computed = fill.read_array(False).tolist()
arr = np.array([[49, 36, 29, 29], [32, 19, 19, 20], [19, 19, 19, 39],
[19, 29, 42, -99]])
expected = arr.tolist()
self.assertEqual(computed, expected)
def test_BNetwork_class05(self):
"""
Test de creado masivo de cuencas con cabeceras aleatorias
"""
files = ["small25", "jebja30", "tunez"]
for file in files:
# Cargamos DEM, Flow, Network
fd = Flow("{}/{}_fd.tif".format(infolder, file))
net = Network("{}/{}_net.dat".format(infolder, file))
dem = DEM("{}/{}.tif".format(infolder, file))
# Generamos todas las cuencas
cuencas = fd.get_drainage_basins(min_area=0.0025)
# Generamos 50 puntos aleatorios dentro de la extensión del objeto Network
# Estos 50 puntos se usaran como cabeceras
xmin, xmax, ymin, ymax = net.get_extent()
xi = np.random.randint(xmin, xmax, 50)
yi = np.random.randint(ymin, ymax, 50)
heads = np.array((xi, yi)).T
# Cogemos 5 cuencas aleatorias
bids = np.random.choice(np.unique(cuencas.read_array())[1:], 5)
for bid in bids:
try:
if np.random.randint(100) < 70:
bnet = BNetwork(net, cuencas, heads, bid)
else:
basin = Basin(dem, cuencas, bid)
bnet = BNetwork(net, basin, heads)
except NetworkError:
print(
"Network of {} file inside the basin {} has not enough pixels"
.format(file, bid))
continue
# Salvamos BNetwork y volvemos a cargar para comprobar que se cargan-guardan bien
bnet_path = "{}/{}_{}_bnet.dat".format(outfolder, file, bid)
bnet.save(bnet_path)
bnet2 = BNetwork(bnet_path)
computed = np.array_equal(bnet._ix, bnet2._ix)
self.assertEqual(computed, True)
# borramos archivo
os.remove(bnet_path)
def test_stream_poi_01(self):
files = ["small25", "morocco", "tunez", "jebja30"]
for file in files:
flw_path = infolder + "/{0}_fd.tif".format(file)
dem_path = infolder + "/{0}.tif".format(file)
net_path = infolder + "/{0}_network.net".format(file)
dem = DEM(dem_path)
fd = Flow(flw_path)
thr = int(fd.get_ncells() * 0.01)
# Creamos objeto network
net = Network(dem, fd, thr)
net.save(net_path)
# Cargamos objeto network guardado
net2 = Network(net_path)
# Comparamos propiedades,
prop_net = [
net._size, net._dims, net._geot, net._cellsize, net._ncells,
net._proj
]
prop_net2 = [
net2._size, net2._dims, net2._geot, net2._cellsize,
net2._ncells, net2._proj
]
self.assertEqual(prop_net, prop_net2)
# Comparamos los datos
arr1 = np.array(
(net._ix, net._ixc, net._ax, net._dx, net._zx, net._chi,
net._slp, net._ksn, net._r2slp, net._r2ksn, net._dd))
arr2 = np.array(
(net2._ix, net2._ixc, net2._ax, net2._dx, net2._zx, net2._chi,
net2._slp, net2._ksn, net2._r2slp, net2._r2ksn, net2._dd))
res = np.array_equal(arr1, arr2)
self.assertEqual(res, True)
def processAlgorithm(self, parameters, context, feedback):
dem_raster = self.parameterAsRasterLayer(parameters, self.INPUT_DEM,
context)
fac_raster = self.parameterAsOutputLayer(parameters, self.OUTPUT_FAC,
context)
fd_raster = self.parameterAsOutputLayer(parameters, self.OUTPUT_FD,
context)
verbose = self.parameterAsBool(parameters, self.VERBOSE, context)
filled = self.parameterAsBool(parameters, self.FILLED, context)
auxtopo = self.parameterAsBool(parameters, self.AUXTOPO, context)
dem = DEM(dem_raster.source())
fd = Flow(dem,
auxtopo=auxtopo,
filled=filled,
verbose=verbose,
verb_func=feedback.setProgressText)
fac = fd.get_flow_accumulation()
fd.save_gtiff(fd_raster)
fac.save(fac_raster)
results = {}
results[self.OUTPUT_FD] = fd_raster
results[self.OUTPUT_FAC] = fac_raster
return results
# -*- coding: utf-8 -*-
"""
Editor de Spyder
Este es un archivo temporal
"""
import numpy as np
from topopy import DEM, Flow, Network
import matplotlib.pyplot as plt
import gdal, ogr, osr
dem = DEM("../data/in/jebja30.tif")
fd = Flow("../data/in/jebja30_fd.tif")
net = Network(dem, fd, 2000)
path = "../data/out/jebja_streams.shp"
# Prepare auxiliar arrays
seg_array = net.get_stream_segments(False).ravel()
seg_array = seg_array[net._ix]
ord_array = net.get_stream_order('strahler', False).ravel()
ord_array = ord_array[net._ix]
ixcix = np.zeros(net._ncells, np.int)
ixcix[net._ix] = np.arange(net._ix.size)
# Create output shapefile
driver = ogr.GetDriverByName("ESRI Shapefile")
dataset = driver.CreateDataSource(path)
sp = osr.SpatialReference()
sp.ImportFromWkt(net._proj)
layer = dataset.CreateLayer("rios", sp, ogr.wkbLineString)
layer.CreateField(ogr.FieldDefn("sid", ogr.OFTInteger))
# -*- coding: utf-8 -*- """ Created on 08 October, 2018 Testing suite for Network export_to_shp function @author: J. Vicente Perez @email: [email protected] @date: 23 October, 2018 """ from topopy import Network, DEM, Flow, Grid import matplotlib.pyplot as plt import numpy as np infolder = "../data/in" outfolder = "../data/out" dem = DEM(infolder + "/morocco.tif") fd = Flow(dem) net = Network(dem, fd, 1500) streams = net.get_streams() streams.save(outfolder + "/canales_orig.tif") outlet = np.array([579213, 504282]).reshape(1, 2) basin = fd.get_drainage_basins(net.snap_points(outlet), asgrid=False) c1 = basin.max(axis=0).argmax() r1 = basin.max(axis=1).argmax() c2 = basin.shape[1] - np.fliplr(basin).max(axis=0).argmax() r2 = basin.shape[0] - np.flipud(basin).max(axis=1).argmax() basin_cl = basin[r1:r2, c1:c2]
@author: vicen
"""
import sys
import numpy as np
from scipy import ndimage
import time
# Add to the path code folder and data folder
sys.path.append("../../")
from topopy import DEM
from skimage import graph
start = time.time()
# Get DEM and fill sinks
dem = DEM("../data/tunez2.tif")
dims = dem._array.shape
ncells = dem._array.size
time_lap = time.time()
# 01 Fill sinks
fill = dem.fill_sinks()
topodiff = fill.read_array() - dem.read_array()
topodiff = topodiff.astype(np.float32)
dem = fill
print("Sinks filled -- {0:.3f} seconds".format(time.time() - time_lap))
time_lap = time.time()
# 02 Get flats and sills
flats, sills = dem.identify_flats(False)
print("Flats identified -- {0:.3f} seconds".format(time.time() - time_lap))
import sys
sys.path.append("../../")
from topopy import Flow, Grid, DEM
import numpy as np
from scipy.sparse import csc_matrix
import matplotlib.pyplot as plt
arr = np.array([[49, 50, 50, 50],
[49, 47, 47, 46],
[49, 48, 45, 45],
[49, 47, 46, 43],
[46, 47, 47, 47]], dtype=np.int16)
dem = DEM()
dem.set_array(arr)
flow = Flow(dem)
ixcix = np.zeros(flow._ncells, np.int)
ixcix[flow._ix] = np.arange(len(flow._ix))
new_ind = 0
channel_points = [new_ind]
while ixcix[new_ind] != 0:
new_ind = flow._ixc[ixcix[new_ind]]
channel_points.append(new_ind)
print(flow._ix)
print(flow._ixc)
print(ixcix)
def test_empty_dem02(self):
dem = DEM()
computed = np.array([[0]], dtype=np.float)
expected = dem._array
self.assertEqual(np.array_equal(computed, expected), True)
sum_arr = np.asarray(np.sum(sp_arr, 0)).ravel()
out_pos = (sum_arr == 0) & w
elif kind == 'confluences':
sum_arr = np.asarray(np.sum(sp_arr, 0)).ravel()
out_pos = sum_arr > 1
elif kind == 'outlets':
sum_arr = np.asarray(np.sum(sp_arr, 1)).ravel()
out_pos = (sum_arr == 0) & w
out_pos = out_pos.reshape(fd._dims)
row, col = np.where(out_pos)
return row, col
dem = DEM("../data/tunez.tif")
fd = Flow()
fd.load_gtiff("../data/tunez_fd.tif")
fig, ax = plt.subplots()
dem.plot(ax)
streams = fd.get_network(1000)
streams.plot(ax)
# Heads
row, col = get_stream_poi(fd, 1000, 'heads')
ax.plot(col, row, "ro")
#
# Confluences
row, col = get_stream_poi(fd, 1000, 'confluences')
ax.plot(col, row, "bs")
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 23 17:14:39 2018
Temp testing script for Network
@author: vicen
"""
import sys
sys.path.append("../../")
from topopy import DEM, Network
from scipy.sparse import csc_matrix
import numpy as np
dem = DEM("../data/small25.tif")
fd = Network()
fd.load_gtiff("sample_fd.tif")
fac = fd.flow_accumulation()
fac.save("small25_fac.tif")
nodata = fac.get_nodata_pos()
fac = fac.read_array()
fac[nodata] = 0
# Get pixels larger than threshold
w = fac > 1000
siz = fd._dims
nrc = fd._ncells
w = w.ravel()
I = w[fd._ix]
ix = fd._ix[I]
ixc = fd._ixc[I]
@author: vicen
"""
import warnings
warnings.filterwarnings('ignore')
import sys
import numpy as np
from scipy import ndimage
# Add to the path code folder and data folder
sys.path.append("../")
from topopy import DEM
from topopy.ext.distance import cost
from mcompare import compare_indexes, compare_row_cols, compare_arrays, load_array
from skimage import graph
import scipy.io as sio
dem = DEM("../data/tunez.tif")
# USED TO DEBUG
dims = dem._array.shape
ncells = dem._array.size
def _get_aux_topography(dem):
"""
This function calculate the auxiliary topography by using the topography in
depressions to derive the most realistic flow paths. It uses as weight sweights the
differences between the filled and the raw DEM.
References:
-----------
This algoritm is adapted to Python from TopoToolbox matlab codes by Wolfgang Schwanghart
# -*- coding: utf-8 -*-
"""
Editor de Spyder
Este es un archivo temporal
"""
from topopy import DEM, Flow, Network
infolder = "data/in"
outfolder = "data/out"
files = ["small25", "morocco", "tunez", "jebja30"]
for file in files:
flw_path = infolder + "/{0}_fd.tif".format(file)
dem_path = infolder + "/{0}.tif".format(file)
dem = DEM(dem_path)
fd = Flow(flw_path)
thr = int(fd.get_ncells() * 0.001)
# Simplemente probamos que no hay fallos al crear el objeto net
net = Network(dem, fd, thr)
net.save(infolder + "/{0}_network.net".format(file))
def test_empty_dem(self):
# test an empty DEM
dem = DEM()
computed = (dem._size, dem._geot, dem._proj, dem._nodata)
expected = ((1, 1), (0.0, 1.0, 0.0, 1.0, 0.0, -1.0), "", -9999.0)
self.assertEqual(computed, expected)
