anemoi-datasets 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

anemoi/datasets/grids.py

@@ -7,41 +7,65 @@
 # nor does it submit to any jurisdiction.
 #
 
+import logging
+
 import numpy as np
 
+LOG = logging.getLogger(__name__)
+
 
 def plot_mask(path, mask, lats, lons, global_lats, global_lons):
     import matplotlib.pyplot as plt
 
-    middle = (np.amin(lons) + np.amax(lons)) / 2
-    print("middle", middle)
     s = 1
 
-    # gmiddle = (np.amin(global_lons)+ np.amax(global_lons))/2
-
-    # print('gmiddle', gmiddle)
-    # global_lons = global_lons-gmiddle+middle
     global_lons[global_lons >= 180] -= 360
 
     plt.figure(figsize=(10, 5))
     plt.scatter(global_lons, global_lats, s=s, marker="o", c="r")
-    plt.savefig(path + "-global.png")
+    if isinstance(path, str):
+        plt.savefig(path + "-global.png")
 
     plt.figure(figsize=(10, 5))
     plt.scatter(global_lons[mask], global_lats[mask], s=s, c="k")
-    plt.savefig(path + "-cutout.png")
+    if isinstance(path, str):
+        plt.savefig(path + "-cutout.png")
 
     plt.figure(figsize=(10, 5))
     plt.scatter(lons, lats, s=s)
-    plt.savefig(path + "-lam.png")
+    if isinstance(path, str):
+        plt.savefig(path + "-lam.png")
     # plt.scatter(lons, lats, s=0.01)
 
     plt.figure(figsize=(10, 5))
     plt.scatter(global_lons[mask], global_lats[mask], s=s, c="r")
     plt.scatter(lons, lats, s=s)
-    plt.savefig(path + "-both.png")
+    if isinstance(path, str):
+        plt.savefig(path + "-both.png")
     # plt.scatter(lons, lats, s=0.01)
 
+    plt.figure(figsize=(10, 5))
+    plt.scatter(global_lons[mask], global_lats[mask], s=s, c="r")
+    plt.scatter(lons, lats, s=s)
+    plt.xlim(np.amin(lons) - 1, np.amax(lons) + 1)
+    plt.ylim(np.amin(lats) - 1, np.amax(lats) + 1)
+    if isinstance(path, str):
+        plt.savefig(path + "-both-zoomed.png")
+
+    plt.figure(figsize=(10, 5))
+    plt.scatter(global_lons[mask], global_lats[mask], s=s, c="r")
+    plt.xlim(np.amin(lons) - 1, np.amax(lons) + 1)
+    plt.ylim(np.amin(lats) - 1, np.amax(lats) + 1)
+    if isinstance(path, str):
+        plt.savefig(path + "-global-zoomed.png")
+
+
+def xyz_to_latlon(x, y, z):
+    return (
+        np.rad2deg(np.arcsin(np.minimum(1.0, np.maximum(-1.0, z)))),
+        np.rad2deg(np.arctan2(y, x)),
+    )
+
 
 def latlon_to_xyz(lat, lon, radius=1.0):
     # https://en.wikipedia.org/wiki/Geographic_coordinate_conversion#From_geodetic_to_ECEF_coordinates
@@ -121,6 +145,7 @@ def cutout_mask(
     global_lats,
     global_lons,
     cropping_distance=2.0,
+    neighbours=5,
     min_distance_km=None,
     plot=None,
 ):
@@ -164,58 +189,52 @@ def cutout_mask(
     xyx = latlon_to_xyz(lats, lons)
     lam_points = np.array(xyx).transpose()
 
-    # Use a KDTree to find the nearest points
-    kdtree = KDTree(lam_points)
-    distances, indices = kdtree.query(global_points, k=3)
-
-    if min_distance_km is not None:
+    if isinstance(min_distance_km, (int, float)):
         min_distance = min_distance_km / 6371.0
     else:
-        # Estimnation of the minimum distance between two grib points
-
-        glats = sorted(set(global_lats_masked))
-        glons = sorted(set(global_lons_masked))
-        min_dlats = np.min(np.diff(glats))
-        min_dlons = np.min(np.diff(glons))
-
-        # Use the centre of the LAM grid as the reference point
-        centre = np.mean(lats), np.mean(lons)
-        centre_xyz = np.array(latlon_to_xyz(*centre))
-
-        pt1 = np.array(latlon_to_xyz(centre[0] + min_dlats, centre[1]))
-        pt2 = np.array(latlon_to_xyz(centre[0], centre[1] + min_dlons))
-        min_distance = (
-            min(
-                np.linalg.norm(pt1 - centre_xyz),
-                np.linalg.norm(pt2 - centre_xyz),
-            )
-            / 2.0
-        )
+        points = {"lam": lam_points, "global": global_points, None: global_points}[min_distance_km]
+        distances, _ = KDTree(points).query(points, k=2)
+        min_distance = np.min(distances[:, 1])
+
+        LOG.info(f"cutout_mask using min_distance = {min_distance * 6371.0} km")
+
+    # Use a KDTree to find the nearest points
+    distances, indices = KDTree(lam_points).query(global_points, k=neighbours)
 
+    # Centre of the Earth
     zero = np.array([0.0, 0.0, 0.0])
-    ok = []
+
+    # After the loop, 'inside_lam' will contain a list point to EXCLUDE
+    inside_lam = []
+
     for i, (global_point, distance, index) in enumerate(zip(global_points, distances, indices)):
-        t = Triangle3D(lam_points[index[0]], lam_points[index[1]], lam_points[index[2]])
-        # distance = np.min(distance)
-        # The point is inside the triangle if the intersection with the ray
-        # from the point to the centre of the Earth is not None
-        # (the direction of the ray is not important)
 
-        intersect = t.intersect(zero, global_point)
+        # We check more than one triangle in case te global point
+        # is near the edge of triangle, (the lam point and global points are colinear)
+
+        inside = False
+        for j in range(neighbours):
+            t = Triangle3D(
+                lam_points[index[j]], lam_points[index[(j + 1) % neighbours]], lam_points[index[(j + 2) % neighbours]]
+            )
+            inside = t.intersect(zero, global_point)
+            if inside:
+                break
+
         close = np.min(distance) <= min_distance
 
-        ok.append(intersect or close)
+        inside_lam.append(inside or close)
 
     j = 0
-    ok = np.array(ok)
+    inside_lam = np.array(inside_lam)
     for i, m in enumerate(mask):
         if not m:
             continue
 
-        mask[i] = ok[j]
+        mask[i] = inside_lam[j]
         j += 1
 
-    assert j == len(ok)
+    assert j == len(inside_lam)
 
     # Invert the mask, so we have only the points outside the cutout
     mask = ~mask
@@ -271,8 +290,7 @@ def thinning_mask(
     points = np.array(xyx).transpose()
 
     # Use a KDTree to find the nearest points
-    kdtree = KDTree(points)
-    _, indices = kdtree.query(global_points, k=1)
+    _, indices = KDTree(points).query(global_points, k=1)
 
     return np.array([i for i in indices])
 

{anemoi_datasets-0.4.3.dist-info → anemoi_datasets-0.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: anemoi-datasets
-Version: 0.4.3
+Version: 0.4.5
 Summary: A package to hold various functions to support training of ML models on ECMWF data.
 Author-email: "European Centre for Medium-Range Weather Forecasts (ECMWF)" <software.support@ecmwf.int>
 License: Apache License
@@ -223,7 +223,7 @@ Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Requires-Python: >=3.9
 License-File: LICENSE
-Requires-Dist: anemoi-utils[provenance] >=0.3.13
+Requires-Dist: anemoi-utils[provenance] >=0.3.15
 Requires-Dist: numpy
 Requires-Dist: pyyaml
 Requires-Dist: semantic-version
@@ -235,7 +235,7 @@ Requires-Dist: boto3 ; extra == 'all'
 Requires-Dist: earthkit-data[mars] >=0.9 ; extra == 'all'
 Requires-Dist: earthkit-geo >=0.2 ; extra == 'all'
 Requires-Dist: earthkit-meteo ; extra == 'all'
-Requires-Dist: ecmwflibs >=0.6.3 ; extra == 'all'
+Requires-Dist: eccodes >=2.37 ; extra == 'all'
 Requires-Dist: entrypoints ; extra == 'all'
 Requires-Dist: gcsfs ; extra == 'all'
 Requires-Dist: kerchunk ; extra == 'all'
@@ -246,7 +246,7 @@ Provides-Extra: create
 Requires-Dist: earthkit-data[mars] >=0.9 ; extra == 'create'
 Requires-Dist: earthkit-geo >=0.2 ; extra == 'create'
 Requires-Dist: earthkit-meteo ; extra == 'create'
-Requires-Dist: ecmwflibs >=0.6.3 ; extra == 'create'
+Requires-Dist: eccodes >=2.37 ; extra == 'create'
 Requires-Dist: entrypoints ; extra == 'create'
 Requires-Dist: pyproj ; extra == 'create'
 Provides-Extra: dev
@@ -255,7 +255,7 @@ Requires-Dist: boto3 ; extra == 'dev'
 Requires-Dist: earthkit-data[mars] >=0.9 ; extra == 'dev'
 Requires-Dist: earthkit-geo >=0.2 ; extra == 'dev'
 Requires-Dist: earthkit-meteo ; extra == 'dev'
-Requires-Dist: ecmwflibs >=0.6.3 ; extra == 'dev'
+Requires-Dist: eccodes >=2.37 ; extra == 'dev'
 Requires-Dist: entrypoints ; extra == 'dev'
 Requires-Dist: gcsfs ; extra == 'dev'
 Requires-Dist: kerchunk ; extra == 'dev'

{anemoi_datasets-0.4.3.dist-info → anemoi_datasets-0.4.5.dist-info}/RECORD

@@ -1,27 +1,34 @@
 anemoi/datasets/__init__.py,sha256=Z1gqZWhecLcT0RZQqYBLlz01MUlUZd0kWEj_RavbITM,782
 anemoi/datasets/__main__.py,sha256=cLA2PidDTOUHaDGzd0_E5iioKYNe-PSTv567Y2fuwQk,723
-anemoi/datasets/_version.py,sha256=mDTy6z4iq5XKGigbX2Q9ub9_BzxGHksMlMjpkDAl_hE,411
-anemoi/datasets/grids.py,sha256=3YBMMJodgYhavarXPAlMZHaMtDT9v2IbTmAXZTqf8Qo,8481
+anemoi/datasets/_version.py,sha256=XyejXnBNtqNdR37CiSnJ022K8vUHKAlzN9lbcpmmftA,411
+anemoi/datasets/grids.py,sha256=xgvIbpMGuN2GKi2wIBhOLEMzj940nY9PH-toD0rCmPo,8980
 anemoi/datasets/commands/__init__.py,sha256=qAybFZPBBQs0dyx7dZ3X5JsLpE90pwrqt1vSV7cqEIw,706
+anemoi/datasets/commands/cleanup.py,sha256=_BkzGPUgvSqnuleymBfBx-sIyIM55hjK61m-v7yK0T8,1062
 anemoi/datasets/commands/compare.py,sha256=svEhyR7pOS1847_RJr1I6vF7ZDPB9AVlcrhy_gxQVms,3263
 anemoi/datasets/commands/copy.py,sha256=SxAeN51owyN5gwtwpt30xhJSIJRlJb9YOUt_4K4m-D8,11780
-anemoi/datasets/commands/create.py,sha256=iAXm7b1zeFEbVyTSqgSdCXwYtgIi8XUN96muv-btC0w,3868
-anemoi/datasets/commands/inspect.py,sha256=rEBzR5LmrPzkNrlGS471Q7Ma9O8Djiml2mxAlxvSl0U,18676
+anemoi/datasets/commands/create.py,sha256=jdwgzUvZBkXROkJ-LSbi28mVWnnZ5F1xr0IOciktfrU,5012
+anemoi/datasets/commands/finalise-additions.py,sha256=876K37hVjslHJiu9VXZfre4YJhS2_t9rLhmNWqlKGGk,1158
+anemoi/datasets/commands/finalise.py,sha256=oPul5za7E__eJqkf5fRwvdL_0n2nG5Xk3JraRZQe64k,913
+anemoi/datasets/commands/init-additions.py,sha256=K3eKH5V_6ERiBKKyqIUuI1cfvAsjWV9ZAFzbtjIDyjs,1146
+anemoi/datasets/commands/init.py,sha256=7BpWaZ4gzMMiRqD9djHRciQNa0W2R4cOzoy5R-UJ0ck,2033
+anemoi/datasets/commands/inspect.py,sha256=g2H_Ey47szeRp6sfaXkbAuk2JWW-LL4GXpssJIsWKVo,18675
+anemoi/datasets/commands/load-additions.py,sha256=Tg4FX0xealmwyB--zv03ZBrqTAGddkT0rKrHlcu4VW0,1234
+anemoi/datasets/commands/load.py,sha256=3jhL3DKUg07C8D6L8RsRWciq8korYsJ40_9atp-p68U,1304
+anemoi/datasets/commands/patch.py,sha256=gHY16r46GHxARItaAUHVjKSOm0Q7ZyZvSZmXqg1Wnig,841
 anemoi/datasets/commands/scan.py,sha256=MaTdne4JrtlqO3LhOUr43DZhZ6O-RZwC7uQ7C6PG7Os,2910
 anemoi/datasets/compute/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-anemoi/datasets/compute/recentre.py,sha256=oIqhENljB9ad-wnMJCJ3P0Xf1v76zQjqYCu1TuySgSI,4919
-anemoi/datasets/create/__init__.py,sha256=_XMODLz0xpVf06Tu7x2c1HhFcuBYJ0xeux6dn9dgTXg,6830
-anemoi/datasets/create/check.py,sha256=TAZOrq8QbS9F5kuR779FAuZPJXA7MXsS_DU1kVotq5Q,5838
+anemoi/datasets/compute/recentre.py,sha256=CMvRxTMv2H1hF1KqaZHT3Maa9P01GtsgAxr1YHbvH_o,4939
+anemoi/datasets/create/__init__.py,sha256=8eYVI0QAkdAIdxVDrqQAY34yDlLAAsr92DL-e_nhHCM,35163
+anemoi/datasets/create/check.py,sha256=9If6iAXILExjzX1YAWCDekV821BquHdjDaUSb_S_gp0,6008
 anemoi/datasets/create/chunks.py,sha256=1Inh3sIBn-2sNguErb-BsLns6W_HtDiOJAjIb29lp-U,2442
-anemoi/datasets/create/config.py,sha256=vZ-t50mHgrEnxJoaooWrZKzVGeEQrg__rCOrhi5Q4nU,7122
-anemoi/datasets/create/input.py,sha256=BJiGFR-imZcChdij3fodyz8XSHMUs-__ZfoCeMHuhUo,32472
-anemoi/datasets/create/loaders.py,sha256=tosx8Zms7OAEScw9JxHw6BLq6xZSDCNPYKeqFWP5O3Y,32504
+anemoi/datasets/create/config.py,sha256=ojynLQTX7BmJRZ18rhjUTmuMOh0rYAx9M5d6gY8wRH0,8872
+anemoi/datasets/create/input.py,sha256=LArEOIxa6Y42rneF0VUva25zOvks_BwVDfBNOSERpYA,33924
 anemoi/datasets/create/patch.py,sha256=c8cWoqxFzcY9mKREosLjuQCUeJMJL6sbNNkoVvhCZDA,3800
 anemoi/datasets/create/persistent.py,sha256=wfNnNSY8VLO2EyEOQL9umI3sbQqETjJP7bPCiVF6Cko,4291
 anemoi/datasets/create/size.py,sha256=k4COEjs3wud0oKHH5P3n8Fap35xddXs002ucPjpBC88,1040
 anemoi/datasets/create/template.py,sha256=1t8EKGQcZGFUpgQw9a9oEy6ZWlfnow5e0vs1SOelUNc,3148
 anemoi/datasets/create/trace.py,sha256=J-8jDy28wNZa4aSV1KIQMwc1KolcoH3R2xjLl-_eLzM,2183
-anemoi/datasets/create/utils.py,sha256=WRuUbEaP4FRSKzkQpuRaisML84uQAEDqvvACd3pnMVs,2613
+anemoi/datasets/create/utils.py,sha256=mgin7LF-JkfXMr22IIIEQjfUHFkwPwMJHca4Fek3F6Q,2639
 anemoi/datasets/create/writer.py,sha256=G1qAPvdn8anGnpWYhvSSP4u3Km_tHKPdMXm0G4skKSk,1379
 anemoi/datasets/create/zarr.py,sha256=Pb57mZn5s4JTA1o6_satrvG7C8XQhgPFhpTGvlaC_kg,5340
 anemoi/datasets/create/functions/__init__.py,sha256=5HmelLkXDjFOhNhX0Z78aV3ZlW2txiJliJwT4jfLEN4,945
@@ -32,55 +39,58 @@ anemoi/datasets/create/functions/filters/rename.py,sha256=02p6zj2g0Qp866RrXeZG9D
 anemoi/datasets/create/functions/filters/rotate_winds.py,sha256=E0P5scdX0lwTMdcFDYfBzQ_X_4A6EvnrtFvF55-56Hk,2414
 anemoi/datasets/create/functions/filters/unrotate_winds.py,sha256=hiIwgWi_2lk_ntxsPFMyZ6Ku8_5p91ht36VN_2kHYDA,2414
 anemoi/datasets/create/functions/sources/__init__.py,sha256=83G1-DD2IV4VJP3MVN9512_CN4D3IVDZHUKa2ghVgKo,1246
-anemoi/datasets/create/functions/sources/accumulations.py,sha256=Rzn9ocBR4CHdws4s6GuKiV4IqVQo0rCQLyPQNBsTGXY,12493
+anemoi/datasets/create/functions/sources/accumulations.py,sha256=nz09rezfNvXdTBtSQAKnsOeoiWwB8v1ecAayrJZq9rE,11947
 anemoi/datasets/create/functions/sources/constants.py,sha256=9MNxjkXAjtIq7X-T7GgKGVzH-V-FBcTxj0gLLJYoXTI,903
 anemoi/datasets/create/functions/sources/empty.py,sha256=ZrXGs8Y3VrLSV8C8YlJTJcHV7Bmi7xPiUlrq8R0JZQY,485
 anemoi/datasets/create/functions/sources/forcings.py,sha256=tF3EyIs5AGF1Ppvp6dIExONM-kGF-wcnMO1sZc_wDuo,646
 anemoi/datasets/create/functions/sources/grib.py,sha256=MbHSAJAkvUsQT5uo_-mEqzN-0-aOygMwFIds42kXcqg,1750
-anemoi/datasets/create/functions/sources/hindcasts.py,sha256=TRe25E6Xb_fBUsyOnzB_Bm1cTZ4H99viplf1ccWzZv8,3154
+anemoi/datasets/create/functions/sources/hindcasts.py,sha256=xgE4a-diiy8rP8cmgAT12cBsQZiGk0cRzUswtZM7i_0,3607
 anemoi/datasets/create/functions/sources/mars.py,sha256=Wrxm15-7QUQ_xCe7eqmxHLLkYo5RDM0GKUoeEP8BZS4,6603
 anemoi/datasets/create/functions/sources/netcdf.py,sha256=8uug0oAdGBJIKKws-EflA4ZgjQye_sWCBymUVv1TEW4,532
 anemoi/datasets/create/functions/sources/opendap.py,sha256=0Bs0PytUvI1WZGn2OdmnJuFDGAQypxN8v44nl106QjY,531
 anemoi/datasets/create/functions/sources/recentre.py,sha256=t07LIXG3Hp9gmPkPriILVt86TxubsHyS1EL1lzwgtXY,1810
 anemoi/datasets/create/functions/sources/source.py,sha256=J3O4M0nB1a-67IJuY_aWqDDqyNGXB_uzxVbicFldO4U,1422
-anemoi/datasets/create/functions/sources/tendencies.py,sha256=OIYKdRTabDvxnBXCcffWWBcorVlhZVNj3VkcVuQjIYA,4088
+anemoi/datasets/create/functions/sources/tendencies.py,sha256=4hFPGU51KnxXp-KteSp5WLb8v586sDq2ePPd8CfUFjA,4108
 anemoi/datasets/create/functions/sources/xarray_kerchunk.py,sha256=JsuGjTs5BQdJIPRI8TuUNde680UQkT4GbUhOt6wYy38,1432
 anemoi/datasets/create/functions/sources/xarray_zarr.py,sha256=qI_fEKo28hu_B_qMPx67gigysw8qw5ePMU9P0wbDcIc,531
 anemoi/datasets/create/functions/sources/zenodo.py,sha256=n7_sfZHJVDjVnSwc07muO9kS7TwOM4S8DIlJf5pnDiU,1237
-anemoi/datasets/create/functions/sources/xarray/__init__.py,sha256=cOhyFoD_1e_asJXcYJFy13SIbndWvzXZJnUj39FF5xc,2494
-anemoi/datasets/create/functions/sources/xarray/coordinates.py,sha256=pW3DoFYL55fapNE2KmRYSGid3Y_KstkqsRXrqVCrsc0,5734
-anemoi/datasets/create/functions/sources/xarray/field.py,sha256=JYtwQMB_QzML2x68wZDGOckjy0MbRR7jMgkHLY6hYco,3206
-anemoi/datasets/create/functions/sources/xarray/fieldlist.py,sha256=RfFQZ6FexgeZ3dAKtRojzEJROkJFztMaxOWkNXrX39w,5604
-anemoi/datasets/create/functions/sources/xarray/flavour.py,sha256=7gdnJlMtQ2AtAP7mPGg1O0DBr7IKI73DKwn2_Bg3I1g,9901
+anemoi/datasets/create/functions/sources/xarray/__init__.py,sha256=XcP072AgDX_aiK3t_rWM-C3MnAuX-mhYO5-wSLyaxPo,2805
+anemoi/datasets/create/functions/sources/xarray/coordinates.py,sha256=iwnGIinuLoP0jk2s4ro9_ihJ6CoJcZ9HaRGyWh2gm8M,5893
+anemoi/datasets/create/functions/sources/xarray/field.py,sha256=bUTgod2XuV3OGDaK7kcGiUqC5oQ6tuCWbHb67fo9lsY,3186
+anemoi/datasets/create/functions/sources/xarray/fieldlist.py,sha256=B0toXCiYFBFF0fvxpy5bxnan2dfptWMl51_JO8TrH3A,5557
+anemoi/datasets/create/functions/sources/xarray/flavour.py,sha256=_tVSrvDPJ5pXAJhmha3UA1a0Gr2FrPhcjRFoAMtX-EU,10538
 anemoi/datasets/create/functions/sources/xarray/grid.py,sha256=KSlhXj5dHeRQVeZd26CChMyC1iqYsH5XqxPC2VA_YJc,1169
-anemoi/datasets/create/functions/sources/xarray/metadata.py,sha256=tKMY7dYd8e6SGZM8wXH2OovfqSViePrnMVKrezD00cI,4757
-anemoi/datasets/create/functions/sources/xarray/time.py,sha256=w3mQ34KEJIXwp35_eF7I8RN5lDKP4Mp1ujfavSdaTBE,3487
-anemoi/datasets/create/functions/sources/xarray/variable.py,sha256=pb-xPaRFwqV6p6YuGQM8TB2rNgcwJ7x1yDYclyB32ZI,5331
-anemoi/datasets/create/statistics/__init__.py,sha256=U5aoqAgy0MzY_DSIU1Mz2kwBSw_mPRGh8xtA9DI3YA8,12672
+anemoi/datasets/create/functions/sources/xarray/metadata.py,sha256=_HQgAY5qI39M-5JhEx2q3APgqqmXE0Ed3GqoUvttNuE,4721
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 Root-Is-Purelib: true
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