def Krige_Interpolate(
X, Y, new_X, variogram_parameters={"slope": 1e-4, "nugget": 1e-5}
):
# X, Y, new_X, variogram_parameters={"sill": 1e3, "range": 1e2, "nugget": 0.0001}
uk = OrdinaryKriging(
X,
np.zeros(X.shape),
Y,
pseudo_inv=True,
# weight=True,
# nlags=2,
# variogram_model="gaussian",
# exact_values = False,
variogram_model="linear",
variogram_parameters=variogram_parameters
# variogram_model="gaussian",
# variogram_parameters=variogram_parameters,
)
y_pred, y_std = uk.execute("grid", new_X, np.array([0.0]))
y_pred = np.squeeze(y_pred)
y_std = np.squeeze(y_std)
return new_X, y_pred, y_std
def do_krigin_for_one_sigma(sig):
T = get_T_from_metric_and_sigma(Metric, sig)
x = np.arange(min, max, T)
y = np.copy(x)
for i in range(len(x)):
y[i] = np.random.normal(fonction_to_follow(x[i]), sig)
uk = OrdinaryKriging(x, np.zeros(x.shape), y, variogram_model="gaussian", variogram_parameters={'nugget': sig, 'psill': 0.1, 'range' : 3})
y_pred, y_std = uk.execute("grid", inputs, np.array([0.0]))
y_pred = np.squeeze(y_pred)
y_std = np.squeeze(y_std)
fig, ax = plt.subplots(1, 1, figsize=(10, 4))
ax.scatter(x, y, s=40, label="Input data")
ax.plot(inputs, y_pred, label="Predicted values")
ax.fill_between(
inputs,
y_pred - 3 * y_std,
y_pred + 3 * y_std,
alpha=0.3,
label="Confidence interval",
)
ax.legend(loc=9)
ax.set_xlabel("x")
ax.set_ylabel("y")
plt.show()
return y_pred, y_std
def krige_greenery(green_res, lat_grid, long_grid, init_kwargs={}, **kwargs):
coor, green = _stack_green_res(green_res)
OK = OrdinaryKriging(coor[:, 0], coor[:, 1], green,
**init_kwargs)
lat_grid, long_grid = _lat_long_to_metric(lat_grid, long_grid)
z, _ = OK.execute('grid', long_grid, lat_grid, backend='loop',
**kwargs)
return z
def create_kriged_overlay(green_res, grid=[200, 200], cmap="gist_rainbow",
overlay_fp="krige_map.json", name=None,
n_closest_points=None):
"""
Create an overlay for openstreetmap using kriging as interpolation.
Arguments
---------
green_res: dict
Contains greenery values with coordinates.
n_grid: int
Number of grid points.
cmap: str
Matplotlib color map.
overlay_fp: str
Filepath to store kriged map. Use as cache if available.
name: str
Name to give to the overlay.
n_closest_points: int
Used in kriging procedure to limit memory/compute time.
"""
# Load overlay from file if available.
# try:
# overlay = MapImageOverlay(overlay_fp)
# return overlay
# except FileNotFoundError:
# pass
if name is None:
name = overlay_fp
lat = np.array(green_res['lat'])
long = np.array(green_res['long'])
lat_grid = np.linspace(lat.min(), lat.max(), num=grid[1])
long_grid = np.linspace(long.min(), long.max(), num=grid[0])
green = np.zeros((len(green_res["green"]), 3))
for i in range(len(green_res["green"])):
green[i][0] = green_res["long"][i]
green[i][1] = green_res["lat"][i]
green[i][2] = green_res["green"][i]
OK = OrdinaryKriging(green[:, 0], green[:, 1], green[:, 2],
variogram_model='spherical')
z, _ = OK.execute('grid', long_grid, lat_grid, backend='loop',
n_closest_points=n_closest_points)
alpha_map = _alpha_from_coordinates(lat, long, grid)
overlay = MapImageOverlay(z, lat_grid=lat_grid, long_grid=long_grid,
alpha_map=alpha_map,
cmap=cmap, name=name)
overlay.save(overlay_fp)
return overlay
def krige_greenery(greenery_dict, krige_tiles, tile, init_kwargs={},
dots_per_tile=10):
coor, green = _compile_greenery(greenery_dict, krige_tiles)
OK = OrdinaryKriging(coor[:, 0], coor[:, 1], green,
**init_kwargs)
bbox = tile["bbox"]
lat_grid_degree = np.linspace(bbox[0][0], bbox[1][0], dots_per_tile, endpoint=False)
long_grid_degree = np.linspace(bbox[0][1], bbox[1][1], dots_per_tile, endpoint=False)
lat_grid, long_grid = _lat_long_to_metric(lat_grid_degree, long_grid_degree)
z, _ = OK.execute('grid', long_grid, lat_grid, backend='loop')
return z
def fit(self, X, y):
if self.interpolation_type == 'kriging':
# pykrige doesn't support 1D data for now, only 2D or 3D
# adapting the 1D input to 2D
self.model = OrdinaryKriging(X,
np.zeros(X.shape),
y,
variogram_model='gaussian')
if self.interpolation_type == 'linear':
self.model = scipy.interpolate.interp1d(X,
y,
fill_value="extrapolate")
if self.interpolation_type == 'gmm':
self.model = cluster_utils.gmr(X, y)
def _interpol_func(self, x, y, z, xi, yi):
ok = OrdinaryKriging(x,
y,
z,
nlags=self.nlags,
variogram_model=self.variogram_model,
weight=self.weight)
# coordinates_type=self.coordinates_type)
zi, sigma = ok.execute(style='points',
xpoints=xi,
ypoints=yi,
n_closest_points=self.n_closest_points,
backend=self.backend)
self.sigma = sigma
return zi
def Krige_Interpolate(
X, Y, new_X, variogram_parameters={"slope": 1e-4, "nugget": 1e-5}
):
uk = OrdinaryKriging(
X,
np.zeros(X.shape),
Y,
pseudo_inv=True,
variogram_model="linear",
variogram_parameters=variogram_parameters
)
y_pred, y_std = uk.execute("grid", new_X, np.array([0.0]))
y_pred = np.squeeze(y_pred)
y_std = np.squeeze(y_std)
return new_X, y_pred, y_std
class Interpolator1D(BaseEstimator):
def __init__(self, interpolation_type):
self.interpolation_type = interpolation_type
def fit_density(self, X):
if frequency_interpolation_type == 'linear_density':
self.model = scipy.interpolate.interp1d(list(Counter(X).keys()),
list(Counter(X).values()),
fill_value="extrapolate")
if self.interpolation_type == 'kde':
self.model = mlab.GaussianKDE(X, 'scott')
def fit(self, X, y):
if self.interpolation_type == 'kriging':
# pykrige doesn't support 1D data for now, only 2D or 3D
# adapting the 1D input to 2D
self.model = OrdinaryKriging(X,
np.zeros(X.shape),
y,
variogram_model='gaussian')
if self.interpolation_type == 'linear':
self.model = scipy.interpolate.interp1d(X,
y,
fill_value="extrapolate")
if self.interpolation_type == 'gmm':
self.model = cluster_utils.gmr(X, y)
def predict(self, X_pred):
if self.interpolation_type == 'kriging':
y_pred, y_std = self.model.execute('grid', X_pred, np.array([0.]))
return np.squeeze(y_pred)
if self.interpolation_type in ['linear', 'linear_density']:
return self.model(X_pred)
if self.interpolation_type == 'kde':
return self.model.evaluate(X_pred)
if self.interpolation_type == 'gmm':
return self.model.predict(np.array([0]),
X_pred[:, np.newaxis]).ravel()
def Krige_Interpolate(X, Y, new_X):
uk = OrdinaryKriging(
X,
np.zeros(X.shape),
Y,
pseudo_inv=True,
weight=True,
# nlags=3,
# exact_values=False,
variogram_model="linear",
variogram_parameters={"slope": 3e-5, "nugget": 0.0002}
# variogram_model="gaussian",
# variogram_parameters={"sill": 1e2, "range": 1e2, "nugget": 0.0006},
)
y_pred, y_std = uk.execute("grid", new_X, np.array([0.0]), backend="loop")
y_pred = np.squeeze(y_pred)
y_std = np.squeeze(y_std)
return new_X, y_pred, y_std
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from mpl_toolkits.basemap import Basemap
import fiona
from pykrige import OrdinaryKriging
from shapely.geometry import Polygon, Point
workbook = pd.read_excel("pmdata.xlsx")
lon, lat, pm = workbook['lon'], workbook['lat'], workbook['PM2.5']
#116.362 30.7578 121.9752 35.1245
un_lon = np.linspace(116.362, 121.9752, 400)
un_lat = np.linspace(30.7578, 35.1245, 400)
OK = OrdinaryKriging(lon, lat, pm, variogram_model='gaussian', nlags=6)
zgrid, ss = OK.execute('grid', un_lon, un_lat)
xgrid, ygrid = np.meshgrid(un_lon, un_lat)
shp = fiona.open('shp/江苏省_行政边界.shp')
pol = shp.next()
polygon = Polygon(pol['geometry']['coordinates'][0][0])
#np.nan
for i in range(xgrid.shape[0]):
for j in range(xgrid.shape[1]):
plon = xgrid[i][j]
plat = ygrid[i][j]
if not polygon.contains(Point(plon, plat)):
zgrid[i][j] = np.nan
def draw_function():
if markclick == 0: # mclick 如果不存在，则鼠标未点击色阶级数，则给mark1和mnum赋初始值
mark1 = 0
mnum = None
else:
mark1 = mark1_1
mnum = mnum_1
if btn_legendmin.get() == '默认':
mark2 = 0
mmin = None
else:
mark2 = 1
mmin = float(btn_legendmin.get())
if btn_legendmax.get() == '默认':
mark3 = 0
mmax = None
else:
mark3 = 1
mmax = float(btn_legendmax.get())
if mmax <= mmin:
tm.showwarning('警告', '图例最大值应大于最小值！')
# ------------警告提示框---------
if (mark1 == 0 or mark1 == 1) and mark2 == 0 and mark3 == 0:
pass
elif color_mark == 6:
pass
elif mark1 == 0 and (mark2 == 1 or mark3 == 1):
tm.showwarning('警告', '色阶级数默认情况下，图例最小值和图例最大值均应为“默认”。')
return
elif mark1 == 1 and mark2 == 1 and mark3 == 1:
pass
else:
tm.showinfo('提示', '色阶级数非默认情况下，需同时自定义设置图例最小值和图例最大值；否则图例最大值和最小值以默认值绘出。')
pass
path0 = 'DTool/dishi.shp'
file = shapefile.Reader(path0)
rec = file.shapeRecords()
polygon = list()
for r in rec:
polygon.append(Polygon(r.shape.points))
poly = cascaded_union(polygon) # 并集
ext = list(poly.exterior.coords) # 外部点
codes = [Path.MOVETO] + [Path.LINETO] * (len(ext) - 1) + [Path.CLOSEPOLY]
# codes += [Path.CLOSEPOLY]
ext.append(ext[0]) # 起始点
path = Path(np.array(ext), codes)
patch = PathPatch(path, facecolor='None')
x, y = df['经度'], df['纬度']
xi = np.arange(113, 118.5, 0.01)
yi = np.arange(24, 31, 0.01)
olon, olat = np.meshgrid(xi, yi)
# Rbf空间插值
# func = Rbf(x, y, z, function='linear')
# oz = func(olon, olat)
# 克里金插值
ok = OrdinaryKriging(x, y, z, variogram_model='linear')
oz, ss = ok.execute('grid', xi, yi)
ax = plt.axes(projection=ccrs.PlateCarree())
box = [113.4, 118.7, 24.1, 30.4]
ax.set_extent(box, crs=ccrs.PlateCarree())
ax.add_patch(patch)
shp = list(shpreader.Reader(path0).geometries())
ax.add_geometries(shp,
ccrs.PlateCarree(),
edgecolor='black',
facecolor='none',
alpha=0.3,
linewidth=0.5) # 加底图
if mark1 == 1 and mark2 == 1 and mark3 == 1 and btn_style.get(
) != 'CMA_Rain':
v = np.linspace(mmin, mmax, num=mnum, endpoint=True) # 设置显示数值范围和级数
if color_mark == 1:
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.jet)
elif color_mark == 2:
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.rainbow)
elif color_mark == 3:
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.gist_rainbow)
elif color_mark == 4:
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.OrRd)
elif btn_style.get() == 'CMA_Rain':
# 应加入超出levels的提示
try:
rain_levels = [0, 0.1, 10, 25, 50, 100, 250, 2500]
rain_colors = [
'#FFFFFF', '#A6F28F', '#38A800', '#61B8FF', '#0000FF',
'#FA00FA', '#730000', '#400000'
]
pic = plt.contourf(olon,
olat,
oz,
levels=rain_levels,
colors=rain_colors)
# cbar = plt.colorbar(pic, ticks=[0, 0.1, 10, 25, 50, 100, 250])
# position = fig.add_axes([0.65, 0.15, 0.03, 0.3]) # 位置
# plt.colorbar(pic, ticks=[0, 0.1, 10, 25, 50, 100, 250], cax=position, orientation='vertical')
# cbar.set_label(btn9.get(), fontproperties='SimHei') # 图例label在右边
except:
if np.min(z) < 0:
tm.showinfo(message='存在负数，超出降水图例范围！请换其他颜色样式。')
elif np.max(z) > 2500:
tm.showinfo(message='降水量过大，请何查数据！或请换其他颜色样式。')
# cbar.make_axes(locations='top')
# cbar.ax.set_xlabel(btn9.get(),fontproperties='SimHei')
else:
if color_mark == 1:
if mark1 == 0: # 未设置级数
pic = plt.contourf(olon, olat, oz, cmap=plt.cm.jet)
else:
v = np.linspace(np.min(oz),
np.max(oz),
num=mnum,
endpoint=True) # 设置显示数值范围和级数
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.jet)
elif color_mark == 2:
if mark1 == 0:
pic = plt.contourf(olon, olat, oz, cmap=plt.cm.rainbow)
else:
v = np.linspace(np.min(oz),
np.max(oz),
num=mnum,
endpoint=True)
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.rainbow)
elif color_mark == 3:
if mark1 == 0:
pic = plt.contourf(olon, olat, oz, cmap=plt.cm.gist_rainbow)
else:
v = np.linspace(np.min(oz),
np.max(oz),
num=mnum,
endpoint=True)
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.gist_rainbow)
elif color_mark == 4:
if mark1 == 0:
pic = plt.contourf(olon, olat, oz, cmap=plt.cm.OrRd)
else:
v = np.linspace(np.min(oz),
np.max(oz),
num=mnum,
endpoint=True)
pic = plt.contourf(olon, olat, oz, v, cmap=plt.cm.OrRd)
elif color_mark == 6: # 自定义颜色
# 判断出自定义颜色级数
jishu_colors = []
for index, r in enumerate(rgb):
if r == None:
num_color = index
break
else:
jishu_colors.append(r)
if mark2 == 1 and mark3 == 1: # mark2最小值；mark3最大值
v = np.linspace(mmin, mmax, num=num_color + 1,
endpoint=True) # 设置显示数值范围和级数
pic = plt.contourf(olon, olat, oz, v, colors=jishu_colors)
else:
v = np.linspace(np.min(oz),
np.max(oz),
num=len(jishu_colors) + 1,
endpoint=True)
pic = plt.contourf(olon, olat, oz, v, colors=jishu_colors)
for collection in pic.collections:
collection.set_clip_path(patch) # 设置显示区域
plt.scatter(x, y, marker='.', c='k', s=10) # 绘制站点
# 添加显示站名、数值等标签
for i in range(len(z)):
plt.text(x[i], y[i] + 0.05, df['站名'][i], size=5.5, weight=2, wrap=True)
# 添加单位标注
plt.text(117.75, 27.1, btn_legendunit.get(), size=8, weight=2)
fig = plt.gcf()
fig.set_size_inches(6, 4) # 设置图片大小
plt.axis('off') # 去除四边框框
if btn_style.get() == 'CMA_Rain':
position = fig.add_axes([0.65, 0.15, 0.03, 0.3]) # 位置
plt.colorbar(pic,
ticks=[0, 0.1, 10, 25, 50, 100, 250],
cax=position,
orientation='vertical')
else:
position = fig.add_axes([0.65, 0.15, 0.03, 0.3]) # 位置
plt.colorbar(pic, cax=position, orientation='vertical')
plt.savefig('pics_dpi100.png', dpi=100, bbox_inches='tight')
plt.savefig('pics_dpi300.png', dpi=300, bbox_inches='tight')
plt.close()
wifi_img = Image.open('pics_dpi100.png')
img = ImageTk.PhotoImage(wifi_img)
window.img = img # to prevent the image garbage collected.
canvas.create_image(200, 180, anchor='center', image=img) # 设置生成的图片位置
def main(argv):
inps = cmdLineParse()
gps_file = inps.gps_file
geom_file = inps.geo_file
date = inps.date
datasetNames = ut.get_dataNames(gps_file)
meta0 = read_attr(gps_file)
meta = read_attr(geom_file)
WIDTH = int(meta['WIDTH'])
LENGTH = int(meta['LENGTH'])
date_list = read_hdf5(gps_file, datasetName='date')[0]
date_list = date_list.astype('U13')
date_list = list(date_list)
root_path = os.getcwd()
gig_dir = root_path + '/gigpy'
gig_atm_dir = gig_dir + '/atm'
gig_atm_raw_dir = gig_dir + '/atm/raw'
gig_atm_sar_raw_dir = gig_dir + '/atm/sar_raw'
gig_atm_sar_tzd_dir = gig_dir + '/atm/sar_tzd'
gig_atm_sar_wzd_dir = gig_dir + '/atm/sar_wzd'
if not os.path.isdir(gig_atm_sar_tzd_dir):
os.mkdir(gig_atm_sar_tzd_dir)
if not os.path.isdir(gig_atm_sar_wzd_dir):
os.mkdir(gig_atm_sar_wzd_dir)
if inps.out_file: OUT = inps.out_file
else: OUT = date + '_' + inps.type + '.h5'
if inps.type == 'tzd': OUT = gig_atm_sar_tzd_dir + '/' + OUT
elif inps.type == 'wzd': OUT = gig_atm_sar_wzd_dir + '/' + OUT
dem = read_hdf5(geom_file, datasetName='height')[0]
#inc = read_hdf5(geom_file,datasetName='incidenceAngle')[0]
dataNames = get_dataNames(geom_file)
if 'latitude' in dataNames:
grid_lat = read_hdf5(geom_file, datasetName='latitude')[0]
grid_lon = read_hdf5(geom_file, datasetName='longitude')[0]
else:
grid_lat, grid_lon = get_lat_lon(meta)
lats = grid_lat.flatten()
lons = grid_lon.flatten()
where_are_NaNs = np.isnan(lats)
lats[where_are_NaNs] = 0
where_are_NaNs = np.isnan(lons)
lons[where_are_NaNs] = 0
#print(grid_lat.shape)
# TWD, ZWD, TURB_Kriging, Turb_ITD, Trend, HgtCor,
k0 = date_list.index(date)
if 'wzd_turb' in datasetNames:
tzd_turb, wzd_turb, lat, lon = adjust_aps_lat_lon_unavco(gps_file,
epoch=k0)
else:
tzd_turb, lat, lon = adjust_aps_lat_lon_unr(gps_file, epoch=k0)
#print(inps.type)
if inps.type == 'tzd':
S0 = 'tzd'
turb = tzd_turb
elif inps.type == 'wzd':
S0 = 'wzd'
turb = wzd_turb
lat0, lon0, turb0 = remove_numb(lat, lon, turb, int(meta0['remove_numb']))
mean_lons = np.mean(lons)
lons0 = round((np.mean(lon0) - mean_lons) /
360) * 360 + lons # adjust to the same trend system
#lons0 = lons
lats0 = lats
#print(lats)
#print(lons)
if np.mean(lon0) > 180:
lon0 = lon0 - 360
#print(lat0)
#print(lon0)
variogram_para = read_hdf5(gps_file,
datasetName=S0 + '_variogram_parameter')[0]
trend_para = read_hdf5(gps_file, datasetName=S0 + '_trend_parameter')[0]
elevation_para = read_hdf5(gps_file,
datasetName=S0 + '_elevation_parameter')[0]
variogram_para0 = variogram_para[k0, :]
trend_para0 = trend_para[k0, :]
elevation_para0 = elevation_para[k0, :]
Trend0 = function_trend(lats0, lons0, trend_para0)
Trend0 = Trend0.reshape(LENGTH, WIDTH)
hei = dem.flatten()
elevation_function = model_dict[meta0['elevation_model']]
Dem_cor0 = elevation_function(elevation_para0, hei)
Dem_cor0 = Dem_cor0.reshape(LENGTH, WIDTH)
OK = OrdinaryKriging(lon0,
lat0,
turb0,
variogram_model=meta0['variogram_model'],
verbose=False,
enable_plotting=False)
para = variogram_para0[0:3]
#print(para)
para[1] = para[1] / 6371 / np.pi * 180
#print(para)
OK.variogram_model_parameters = para
Numb = inps.parallelNumb
zz = np.zeros((len(lats), ))
zz_sigma = np.zeros((len(lats), ))
#print(len(lats))
n_jobs = inps.parallelNumb
# split dataset into multiple subdata
split_numb = 1000
idx_list = split_lat_lon_kriging(len(lats), processors=split_numb)
#print(idx_list[split_numb-1])
print(
'------------------------------------------------------------------------------'
)
if inps.type == 'tzd':
print(
'Start to interpolate the high-resolution tropospheric delay for SAR acquisition: '
+ date)
print('Total number of the available GPS stations: %s' % str(len(lat)))
elif inps.type == 'wzd':
print(
'Start to interpolate the high-resolution atmospheric water vapor for SAR acquisition: '
+ date)
print('Total number of the available GPS stations: %s' % str(len(lat)))
if inps.method == 'kriging':
np0 = inps.kriging_points_numb
data = []
for i in range(split_numb):
data0 = (OK, lats[idx_list[i]], lons[idx_list[i]], np0)
data.append(data0)
future = ut.parallel_process(data,
OK_function,
n_jobs=Numb,
use_kwargs=False)
elif inps.method == 'weight_distance':
data = []
for i in range(split_numb):
data0 = (lat0, lon0, turb0, lats[idx_list[i]], lons[idx_list[i]])
data.append(data0)
future = ut.parallel_process(data,
dist_weight_interp,
n_jobs=Numb,
use_kwargs=False)
for i in range(split_numb):
id0 = idx_list[i]
gg = future[i]
zz[id0] = gg[0]
turb = zz.reshape(LENGTH, WIDTH)
datasetDict = dict()
aps = Dem_cor0 + Trend0 + turb
datasetDict['hgt_sar'] = Dem_cor0
datasetDict['trend_sar'] = Trend0
datasetDict['turb_sar'] = turb
datasetDict['aps_sar'] = aps
if inps.method == 'kriging':
for i in range(split_numb):
id0 = idx_list[i]
gg = future[i]
zz_sigma[id0] = gg[1]
sigma = zz_sigma.reshape(LENGTH, WIDTH)
datasetDict['turb_sar_sigma'] = sigma
meta['DATA_TYPE'] = inps.type
meta['interp_method'] = inps.method
for key, value in meta0.items():
meta[key] = str(value)
ut.write_h5(datasetDict,
OUT,
metadata=meta,
ref_file=None,
compression=None)
sys.exit(1)
[1.80, 0.76], [1.93, 0.68], [2.03, 0.03], [2.12, 0.31],
[2.23, -0.14], [2.31, -0.88], [2.40, -1.25], [2.50, -1.62],
[2.63, -1.37], [2.72, -0.99], [2.80, -1.92], [2.83, -1.94],
[2.91, -1.32], [3.00, -1.69], [3.13, -1.84], [3.21, -2.05],
[3.30, -1.69], [3.41, -0.53], [3.52, -0.55], [3.63, -0.92],
[3.72, -0.76], [3.80, -0.41], [3.91, 0.12], [4.04, 0.25],
[4.13, 0.16], [4.24, 0.26], [4.32, 0.62], [4.44, 1.69],
[4.52, 1.11], [4.65, 0.36], [4.74, 0.79], [4.84, 0.87],
[4.93, 1.01], [5.02, 0.55]]).T
# fmt: on
X_pred = np.linspace(-6, 6, 200)
# pykrige doesn't support 1D data for now, only 2D or 3D
# adapting the 1D input to 2D
uk = OrdinaryKriging(X, np.zeros(X.shape), y, variogram_model="gaussian")
y_pred, y_std = uk.execute("grid", X_pred, np.array([0.0]))
y_pred = np.squeeze(y_pred)
y_std = np.squeeze(y_std)
fig, ax = plt.subplots(1, 1, figsize=(10, 4))
ax.scatter(X, y, s=40, label="Input data")
ax.plot(X_pred, y_pred, label="Predicted values")
ax.fill_between(
X_pred,
y_pred - 3 * y_std,
y_pred + 3 * y_std,
alpha=0.3,
def main(argv):
inps = cmdLineParse()
gps_h5 = inps.gps_file
FILE = gps_h5
R = 6371 # Radius of the Earth (km)
if inps.out: OUT = inps.out
else: OUT = 'gps_delay_variogram.h5'
print('')
print('Start to estimate the variogram (i.e. variance) samples ...')
print('Output file name: %s' % OUT)
print('Remove outliers number: %s' % inps.remove_numb)
print('')
print(' Date Stations')
BIN_NUMB = inps.bin_numb
datasetNames = ut.get_dataNames(FILE)
if 'wzd_turb' in datasetNames:
wzd_turb = read_hdf5(FILE, datasetName='wzd_turb')[0]
wzd_turb_trend = read_hdf5(FILE, datasetName='wzd_turb_trend')[0]
date_list, meta = read_hdf5(FILE, datasetName='date')
tzd_turb = read_hdf5(FILE, datasetName='tzd_turb')[0]
tzd_turb_trend = read_hdf5(FILE, datasetName='tzd_turb_trend')[0]
Lag = np.zeros((len(date_list), BIN_NUMB), dtype=np.float32)
Variance = np.zeros((len(date_list), BIN_NUMB), dtype=np.float32)
Variance_trend = np.zeros((len(date_list), BIN_NUMB), dtype=np.float32)
Variance_wzd = np.zeros((len(date_list), BIN_NUMB), dtype=np.float32)
Variance_wzd_trend = np.zeros((len(date_list), BIN_NUMB), dtype=np.float32)
for i in range(len(date_list)):
#print(date_list[i])
if 'wzd_turb' in datasetNames:
tzd_turb, wzd_turb, tzd_turb_trend, wzd_turb_trend, lat, lon = adjust_aps_lat_lon_unavco(
FILE, epoch=i)
else:
tzd_turb, tzd_turb_trend, lat, lon = adjust_aps_lat_lon_unr(
FILE, epoch=i)
lat = np.asarray(lat, dtype=np.float32)
lon = np.asarray(lon, dtype=np.float32)
lat0, lon0, tzd_turb0, fg0 = remove_numb(lat,
lon,
tzd_turb,
numb=inps.remove_numb)
#print(tzd_turb0*1000)
print(' ' + date_list[i].astype(str) + ' ' + str(len(lat0[0])))
#uk = OrdinaryKriging(lon, lat, tzd_turb, coordinates_type = 'geographic', nlags=BIN_NUMB)
uk = OrdinaryKriging(lon0,
lat0,
tzd_turb0,
coordinates_type='geographic',
nlags=BIN_NUMB)
#print(len((uk.lags)))
Lags = (uk.lags) / 180 * np.pi * R
Semivariance = 2 * (uk.semivariance)
#print(Semivariance)
y0 = np.asarray(tzd_turb_trend, dtype=np.float32)
tzd_turb_trend0 = y0[fg0]
#lat0, lon0, tzd_turb_trend0 = remove_numb(lat,lon,tzd_turb_trend,numb=inps.remove_numb)
uk = OrdinaryKriging(lon0,
lat0,
tzd_turb_trend0,
coordinates_type='geographic',
nlags=BIN_NUMB)
Semivariance_trend = 2 * (uk.semivariance)
Lag[i, 0:len(Lags)] = Lags
Variance[i, 0:len(Lags)] = Semivariance
Variance_trend[i, 0:len(Lags)] = Semivariance_trend
if 'wzd_turb' in datasetNames:
lat0, lon0, wzd_turb0, fg0 = remove_numb(lat,
lon,
wzd_turb,
numb=inps.remove_numb)
uk = OrdinaryKriging(lon0,
lat0,
wzd_turb0,
coordinates_type='geographic',
nlags=BIN_NUMB)
Semivariance_wzd = 2 * (uk.semivariance)
#lat0, lon0, wzd_turb_trend0, fg0 = remove_numb(lat,lon,wzd_turb_trend,numb=inps.remove_numb)
y0 = np.asarray(wzd_turb_trend, dtype=np.float32)
wzd_turb_trend0 = y0[fg0]
uk = OrdinaryKriging(lon0,
lat0,
wzd_turb_trend0,
coordinates_type='geographic',
nlags=BIN_NUMB)
Semivariance_wzd_trend = 2 * (uk.semivariance)
Variance_wzd[i, :] = Semivariance
Variance_wzd_trend[i, :] = Semivariance_trend
#datasetNames = ['date','gps_name','gps_lat','gps_lon','gps_height','hzd','wzd','tzd','wzd_turb_trend','tzd_turb_trend','wzd_turb','tzd_turb','station','tzd_elevation_parameter', 'wzd_elevation_parameter','tzd_trend_parameter', 'wzd_trend_parameter']
datasetDict = dict()
meta['remove_numb'] = inps.remove_numb
for dataName in datasetNames:
datasetDict[dataName] = read_hdf5(FILE, datasetName=dataName)[0]
datasetDict['Lags'] = Lag
datasetDict['Semivariance'] = Variance
datasetDict['Semivariance_trend'] = Variance_trend
if 'wzd_turb' in datasetNames:
datasetDict['Semivariance_wzd'] = Variance_wzd
datasetDict['Semivariance_wzd_trend'] = Variance_wzd_trend
ut.write_h5(datasetDict,
OUT,
metadata=meta,
ref_file=None,
compression=None)
sys.exit(1)
lista = []
for x in range(1, 101, 1):
print('Archivo ', x)
file = '..\\database\\dataSet60_' + str(x) + '.csv'
data = np.array(np.loadtxt(file, delimiter=','))
dataOld = np.array(
pd.read_csv('..\\database\\ptr.water.csv', delimiter=','))
dataInt = open('..\\database\\dataSetInterpolatedKringing.csv', 'w')
gridx = np.arange(0.0, 72, 0.5)
gridy = np.arange(0.0, 37, 0.5)
OK = OrdinaryKriging(data[:, 0],
data[:, 1],
data[:, 2],
variogram_model='linear',
verbose=False,
enable_plotting=False)
z, ss = OK.execute('grid', gridx, gridy)
kt.write_asc_grid(gridx, gridy, z, filename="output.asc")
valor = 0
suma = 0
for k in range(1, 2, 1):
print('Iteracion ', k)
for i in range(0, 72, 1):
for j in range(0, 144, 1):
valor = round(data[i][j], 4)
valorOld = round(dataOld[i][j], 4)
if (i == 0 and j < 143) or (j == 0 and j < 143):
dataInt.write(str(valor) + ',')
[2.91, -1.32], [3.00, -1.69], [3.13, -1.84], [3.21, -2.05],
[3.30, -1.69], [3.41, -0.53], [3.52, -0.55], [3.63, -0.92],
[3.72, -0.76], [3.80, -0.41], [3.91, 0.12], [4.04, 0.25],
[4.13, 0.16], [4.24, 0.26], [4.32, 0.62], [4.44, 1.69],
[4.52, 1.11], [4.65, 0.36], [4.74, 0.79], [4.84, 0.87],
[4.93, 1.01], [5.02, 0.55]]).T
from pykrige import OrdinaryKriging
X_pred = np.linspace(-6, 6, 200)
# pykrige doesn't support 1D data for now, only 2D or 3D
# adapting the 1D input to 2D
uk = OrdinaryKriging(
X,
np.zeros(X.shape),
y,
variogram_model='gaussian',
)
y_pred, y_std = uk.execute('grid', X_pred, np.array([0.]))
y_pred = np.squeeze(y_pred)
y_std = np.squeeze(y_std)
fig, ax = plt.subplots(1, 1, figsize=(10, 4))
ax.scatter(X, y, s=40, label='Input data')
ax.plot(X_pred, y_pred, label='Predicted values')
ax.fill_between(X_pred,
y_pred - 3 * y_std,
y_pred + 3 * y_std,
co2 = (10**6) * co2
co2 = co2.flatten()
#co2=co2.transpose()
print(co2)
gridx = np.linspace(70.0, 75.0, 737)
#print(gridx)
gridy = np.linspace(22.0, 26.0, 448)
#print(gridy)
coords = np.transpose(
[np.tile(gridx, len(gridy)),
np.repeat(gridy, len(gridx))])
model = OrdinaryKriging(lon,
lat,
co2,
variogram_model='linear',
enable_plotting=True)
z, ss = model.execute('grid', gridx, gridy)
#
##read data from tif images for fpar values
fpar = rasterio.open('2010_01_01.tif')
#print(fpar.width)
fpar = fpar.read(1)
fpar = fpar.flatten()
print(len(fpar))
#
ndvi = rasterio.open('2010_01_01-737x448-ndvi.tif')
ndvi = ndvi.read(1)
ndvi = ndvi.flatten()
[2.12 , 0.31], [2.23 ,-0.14], [2.31 ,-0.88], [2.40 ,-1.25], [2.50 ,-1.62],
[2.63 ,-1.37], [2.72 ,-0.99], [2.80 ,-1.92], [2.83 ,-1.94], [2.91 ,-1.32],
[3.00 ,-1.69], [3.13 ,-1.84], [3.21 ,-2.05], [3.30 ,-1.69], [3.41 ,-0.53],
[3.52 ,-0.55], [3.63 ,-0.92], [3.72 ,-0.76], [3.80 ,-0.41], [3.91 , 0.12],
[4.04 , 0.25], [4.13 , 0.16], [4.24 , 0.26], [4.32 , 0.62], [4.44 , 1.69],
[4.52 , 1.11], [4.65 , 0.36], [4.74 , 0.79], [4.84 , 0.87], [4.93 , 1.01],
[5.02 , 0.55]]).T
from pykrige import OrdinaryKriging
X_pred = np.linspace(-6, 6, 200)
# pykrige doesn't support 1D data for now, only 2D or 3D
# adapting the 1D input to 2D
uk = OrdinaryKriging(X, np.zeros(X.shape), y, variogram_model='gaussian',)
y_pred, y_std = uk.execute('grid', X_pred, np.array([0.]))
y_pred = np.squeeze(y_pred)
y_std = np.squeeze(y_std)
fig, ax = plt.subplots(1, 1, figsize=(10, 4))
ax.scatter(X, y, s=40, label='Input data')
ax.plot(X_pred, y_pred, label='Predicted values')
ax.fill_between(X_pred, y_pred - 3*y_std, y_pred + 3*y_std, alpha=0.3, label='Confidence interval')
ax.legend(loc=9)
ax.set_xlabel('x')
ax.set_ylabel('y')
datetime = df_TAHMO.index.values
x = lon_u
y = lat_u
nx = len(x)
ny = len(y)
# Interpolation of (TAHMO) stations on the regular grid
v = np.zeros((nt, 37, 37))
for k in range(nt):
OK = OrdinaryKriging(lon_v,
lat_v,
np.sqrt(v_station[k, :]),
variogram_model='exponential',
variogram_parameters={
'sill': 1.0,
'range': 2,
'nugget': 0.01
},
nlags=50,
verbose=False,
enable_plotting=False,
weight=True,
coordinates_type='geographic')
z, ss = OK.execute('grid', lon_u, lat_u)
v[k, :, :] = (z**2).T
u_input = u.copy()
v_input = v.copy()
#==================================================================
# Pre-processing
print('\nPre-processing')
nc.variables.keys()
lat = nc.variables['latitude'][:].data
print(lat[:8], type(lat[:8]))
lon = nc.variables['longitude'][:].data
print((((68 < lon) & (lon < 75)) & (20 < lat) & (lat < 25)).sum())
print(lon[(68 < lon) & (lon < 75) & (20 < lat) & (lat < 25)])
co2 = nc.variables['xco2'][:].data
print(co2)
import pandas as pd
import numpy as np
from pykrige import OrdinaryKriging
model = OrdinaryKriging(lon, lat, co2, variogram_model='gaussian')
#print(model)
# grid around gujarat
gridx = np.arange(68.1862489922972372, 74.4766299192354495, 0.1)
print(gridx.ndim)
print(gridx.shape)
print(len(gridx))
gridy = np.arange(20.1209430201043347, 24.7084824408120198, 0.1)
print(gridy.shape)
coords = np.transpose(
[np.tile(gridx, len(gridy)),
np.repeat(gridy,
len(gridx))]) #for every combination of lat and long together.
#array([[1, 5],
# [2, 5],