Merge pull request #744 from dcs4cop/forman-xxx-volumes_api

Experimental 3-D volume API

CHANGES.md

@@ -58,6 +58,9 @@
 
   - The `--show` option of `xcube serve` 
     now outputs various aspects of the server configuration. 
+
+  - Added experimental endpoint `/volumes`.
+    It is used by xcube Viewer to render 3-D volumes.
 
 * xcube Server is now more tolerant with respect to datasets it can not 
   open without errors. Implementation detail: It no longer fails if 

test/core/test_select.py

@@ -2,9 +2,8 @@
 import json
 import math
 import unittest
-from collections.abc import MutableMapping, Mapping
-from typing import Dict, KeysView, Iterator, Sequence, Any, Callable, \
-    Union
+from collections.abc import MutableMapping
+from typing import Dict, KeysView, Iterator, Sequence, Any
 
 import cftime
 import numpy as np
@@ -14,11 +13,11 @@
 from test.sampledata import create_highroc_dataset
 from xcube.core.gridmapping import GridMapping
 from xcube.core.new import new_cube
+from xcube.core.select import select_label_subset
 from xcube.core.select import select_spatial_subset
 from xcube.core.select import select_subset
 from xcube.core.select import select_temporal_subset
 from xcube.core.select import select_variables_subset
-from xcube.core.select import select_label_subset
 
 
 class SelectVariablesSubsetTest(unittest.TestCase):
@@ -99,9 +98,6 @@ def test_select_spatial_subset_with_gm(self):
         ds2 = select_spatial_subset(ds1, xy_bbox=(40., 40., 42., 42.),
                                     grid_mapping=GridMapping.from_dataset(ds1))
         self.assertEqual(((2,), (2,)), (ds2.lon.shape, ds2.lat.shape))
-        ds2 = select_spatial_subset(ds1, xy_bbox=(40., 40., 42., 42.),
-                                    geo_coding=GridMapping.from_dataset(ds1))
-        self.assertEqual(((2,), (2,)), (ds2.lon.shape, ds2.lat.shape))
 
 
 class SelectTemporalSubsetTest(unittest.TestCase):

test/server/test_server.py

@@ -110,6 +110,7 @@ def test_server_ctx(self):
                          server.ctx.config)
 
     def test_config_schema_effectively_merged(self):
+        self.maxDiff = None
         extension_registry = mock_extension_registry([
             (
                 "datasets",

test/util/test_cmaps.py

@@ -105,14 +105,15 @@ def test_colormaps(self):
         self.assertEqual('Perceptually Uniform Sequential',
                          colormap.cat_name)
         self.assertEqual('viridis', colormap.cm_name)
-        self.assertEqual('iVBORw0KGgoAAAANSUhEUgAAAQAAAAACCAYAAAC3zQLZ'
-                         'AAAAzklEQVR4nO2TQZLFIAhEX7dXmyPM/Y8SZwEqMcnU'
-                         '3/9QZTU8GszC6Ee/HQlk5FAsJIENqVGv/piZ3uqf3nX6'
-                         'Vtd+l8D8UwNOLhZL3+BLh796OXvMdWaqtrrqnZ/tjvuZ'
-                         'T/0XxnN/5f25z9X7tIMTKzV7/5yrME3NHoPlUzvplgOe'
-                         'vOcz6ZO5eCqzOmark1nHDQveHuuYaazZkTcdmE110HJu'
-                         '6doR3tgfPHyL51zNc0fd2xjf0vPukUPL36YBTcpcWArF'
-                         'yY0RTca88cYbXxt/gUOJC8yRF1kAAAAASUVORK5CYII=',
+        self.assertEqual('iVBORw0KGgoAAAANSUhEUgAAAQAAAAABCAYAAAA'
+                         'xWXB3AAAAxElEQVR4nI2TQZLEIAwDW+Jr84T5/1'
+                         'PCHGzAkGRrDynZbclwIPro25FARg7FQhLYkBr9m'
+                         'o/M9Fb/9K6vH32ddwnMHz3g5GKx9A2+dPirl91j'
+                         '7pmpOvqqT36OM54z//XfGO/zVff3OXfv2w42Vnr'
+                         'O+V6rME3NGYPlU9v0qAFP3vOZ9MlcPJVZHXP0ya'
+                         'zrgQVvr31kGis76qYLc6guWuaWrh3hjf3Bw7d45'
+                         'mqdO+rexrhLz7NHDS1/mwY0KWthKRQnN0Y0mR+s'
+                         'DYkJKNzLygAAAABJRU5ErkJggg==',
                          colormap.cmap_png_base64)
 
     def test_to_json(self):
@@ -144,15 +145,16 @@ def test_colormaps_ocean(self):
         self.assertIsInstance(colormap, Colormap)
         self.assertEqual("Ocean", colormap.cat_name)
         self.assertEqual("thermal", colormap.cm_name)
-        self.assertEqual('iVBORw0KGgoAAAANSUhEUgAAAQAAAAACCAYAAAC3zQLZ'
-                         'AAAA2klEQVR4nO2S6xHDMAiDP+FROkL3Xy30RwBju52g'
-                         '8V0OIcnyKxqvtwsD5SfAUPZNE6M4VR2hJTdQeBX6UhlY'
-                         '8xgDY8V24A15pMuIXcQHJo4qwOQYIHlojpT6zWnzqDxR'
-                         'o+/+zFZbR7H2Tx3WvMPf1qDvq+17zz/m7TV97YxHbefE'
-                         'W27ve+7Oe9xZZu3cdXCdr17XokurfvYOcmTXxHJkE2P3'
-                         '2ei8eVxww1WJecRlBxZr/cndj+T5MKULbzqm5pnY56MF'
-                         'jnkmPH7cb7xXzvR49RRO3njGM57xt+MDC391Pt11tkYA'
-                         'AAAASUVORK5CYII=',
+        self.assertEqual('iVBORw0KGgoAAAANSUhEUgAAAQAAAAABCAYAAAA'
+                         'xWXB3AAAAz0lEQVR4nHWSyZUEIQxDv0woHULnn1'
+                         'p5DiWDgekDz7IkxKrx+aYIUA0BgapvmhiT06zDW'
+                         'nED2SvrW2UQzRMMgh3HhQ+UTlfgXXhAiKsKCCUB'
+                         'SGktkUp/OR0eTY+r++6vbLV15LV/6rDnXf62Bn1'
+                         'fbd9n/jXvrOVrZ7xqOyfZcnvfc08+fWeVdXLPxX'
+                         'V+9no2Xdr1u09QongWVqJYmHjPRucjfcENz4rn4'
+                         'cs2Fnv9yb2PlPUwUxfZdELNs3CuRzP2vBDpj/sf'
+                         'nzNneXL2TFz8H4K3dTwq9eoAAAAAAElFTkSuQmC'
+                         'C',
                          colormap.cmap_png_base64)
 
     def test_load_snap_cpd_colormap(self):
@@ -220,13 +222,12 @@ def test_cmap_png_base64(self):
         self.assertIsInstance(base64, str)
         self.assertIs(base64, self.colormap.cmap_png_base64)
         self.assertEqual(
-            'iVBORw0KGgoAAAANSUhEUgAAAQAAAAACCAYAAAC3zQLZAAAA'
-            'yUlEQVR4nO2SsWFEIQxDZY+VGW7o7HVBSgEGG7gidT6NZenJ'
-            'Ffb1+paZwdzh3mfsNnbP+5U1eNLmdnR8dnMe93HllsbizTYe'
-            'qYdxG7VnmNyhDYWrHqq36eppy3VqZH/wSDvihhYLXffZy/tF'
-            'e2jwzMPX0OKH2TXCU2WgNMHimQSkWVjx8CDCGOzywLiz9J6J'
-            'p3dkJDQmpO5PpuZzUrMvVi76mpwg7V7K/qDZqt/34TWBwTf2'
-            'rCWuCSSht8Af3ee7/6vnPe95//T9Ai79U+7uqc9UAAAAAElF'
-            'TkSuQmCC',
+            'iVBORw0KGgoAAAANSUhEUgAAAQAAAAABCAYAAAAxWXB3AAAA'
+            'u0lEQVR4nJWMwQEDIAwCScbqDB26e7VCHxpN1D76gsARezxf'
+            'MjOYO9y7xm3j9nxfWYMnb27Hxuc29/EfV255LN5s45F2GL9R'
+            'd4bJHd5QuJqhZpuvmbZep0fOB490I35osdD1nrt8X7yHB88+'
+            'cg0v/tDuEZkqAyUFS2YSkLSw4pFBhDHYlYHxZ/m9E8/s6Eho'
+            'KKSeT6b2U6m5FysXe01OkPYsdX94tpr3e2RNYPCNvWuJawJJ'
+            '6C3wo7u+hS8PX1PsPRnqDgAAAABJRU5ErkJggg==',
             base64
         )

test/webapi/volumes/__init__.py

@@ -0,0 +1,20 @@
+# The MIT License (MIT)
+# Copyright (c) 2022 by the xcube team and contributors
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.

test/webapi/volumes/test_config.py

@@ -0,0 +1,65 @@
+# The MIT License (MIT)
+# Copyright (c) 2022 by the xcube team and contributors
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+import unittest
+
+import jsonschema
+import pytest
+
+# noinspection PyProtectedMember
+from xcube.webapi.volumes.config import CONFIG_SCHEMA
+
+
+class VolumesAccessConfigTest(unittest.TestCase):
+    def test_config_ok(self):
+        self.assertIsNone(CONFIG_SCHEMA.validate_instance({}))
+
+        self.assertIsNone(CONFIG_SCHEMA.validate_instance({
+            "VolumesAccess": {}
+        }))
+
+        self.assertIsNone(CONFIG_SCHEMA.validate_instance({
+            "VolumesAccess": {
+                "MaxVoxelCount": 100 ** 3
+            }
+        }))
+
+    def test_config_fails(self):
+        with pytest.raises(jsonschema.exceptions.ValidationError):
+            CONFIG_SCHEMA.validate_instance({
+                "VolumesAccess": {
+                    "MaxVoxelCount": 1
+                }
+            })
+
+        with pytest.raises(jsonschema.exceptions.ValidationError):
+            CONFIG_SCHEMA.validate_instance({
+                "VolumesAccess": {
+                    "MaxVoxelCount": True
+                }
+            })
+
+        with pytest.raises(jsonschema.exceptions.ValidationError):
+            CONFIG_SCHEMA.validate_instance({
+                "VolumesAccess": {
+                    "MaxPoxelCount": 100 ** 3
+                }
+            })

test/webapi/volumes/test_routes.py

@@ -0,0 +1,37 @@
+# The MIT License (MIT)
+# Copyright (c) 2022 by the xcube team and contributors
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+from ..helpers import RoutesTestCase
+
+
+class VolumesRoutesTest(RoutesTestCase):
+
+    def test_fetch_dataset_volume_ok(self):
+        response = self.fetch('/volumes/demo/conc_chl?bbox=1.0,51.0,2.0,51.5')
+        self.assertResponseOK(response)
+
+    def test_fetch_dataset_volume_404(self):
+        response = self.fetch('/volumes/demo/conc_x?bbox=1.0,51.0,2.0,51.5')
+        self.assertResourceNotFoundResponse(response)
+
+    def test_fetch_dataset_volume_400(self):
+        response = self.fetch('/volumes/demo/conc_chl?bbox=1.0,51.0')
+        self.assertBadRequestResponse(response)

xcube/core/select.py

@@ -19,15 +19,16 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
+import warnings
+from typing import Collection, Optional, Tuple, Callable, Dict, Any, \
+    List, Mapping
+from typing import Union
+
 import cftime
 import dask.array as da
 import numpy as np
 import pandas as pd
-import warnings
 import xarray as xr
-from typing import Collection, Optional, Tuple, Callable, Dict, Any, \
-    List, Mapping
-from typing import Union
 
 from xcube.core.gridmapping import GridMapping
 from xcube.util.assertions import assert_given
@@ -38,11 +39,14 @@
                   Tuple[Optional[pd.Timestamp], Optional[pd.Timestamp]]]
 
 
-def select_subset(dataset: xr.Dataset,
-                  *,
-                  var_names: Collection[str] = None,
-                  bbox: Bbox = None,
-                  time_range: TimeRange = None):
+def select_subset(
+        dataset: xr.Dataset,
+        *,
+        var_names: Optional[Collection[str]] = None,
+        bbox: Optional[Bbox] = None,
+        time_range: Optional[TimeRange] = None,
+        grid_mapping: Optional[GridMapping] = None
+):
     """
     Create a subset from *dataset* given *var_names*,
     *bbox*, *time_range*.
@@ -58,20 +62,29 @@ def select_subset(dataset: xr.Dataset,
     :param bbox: Optional bounding box in the dataset's
         CRS coordinate units.
     :param time_range: Optional time range
+    :param grid_mapping: Optional dataset grid mapping.
     :return: a subset of *dataset*, or unchanged *dataset*
         if no keyword-arguments are used.
     """
     if var_names is not None:
-        dataset = select_variables_subset(dataset, var_names=var_names)
+        dataset = select_variables_subset(
+            dataset, var_names=var_names
+        )
     if bbox is not None:
-        dataset = select_spatial_subset(dataset, xy_bbox=bbox)
+        dataset = select_spatial_subset(
+            dataset, xy_bbox=bbox, grid_mapping=grid_mapping
+        )
     if time_range is not None:
-        dataset = select_temporal_subset(dataset, time_range=time_range)
+        dataset = select_temporal_subset(
+            dataset, time_range=time_range
+        )
     return dataset
 
 
-def select_variables_subset(dataset: xr.Dataset,
-                            var_names: Collection[str] = None) -> xr.Dataset:
+def select_variables_subset(
+        dataset: xr.Dataset,
+        var_names: Optional[Collection[str]] = None
+) -> xr.Dataset:
     """
     Select data variable from given *dataset* and create new dataset.
 
@@ -88,15 +101,14 @@ def select_variables_subset(dataset: xr.Dataset,
     return dataset.drop_vars(dropped_variables)
 
 
-def select_spatial_subset(dataset: xr.Dataset,
-                          ij_bbox: Tuple[int, int, int, int] = None,
-                          ij_border: int = 0,
-                          xy_bbox: Tuple[float, float, float, float] = None,
-                          xy_border: float = 0.,
-                          grid_mapping: GridMapping = None,
-                          geo_coding: GridMapping = None,
-                          xy_names: Tuple[str, str] = None) \
-        -> Optional[xr.Dataset]:
+def select_spatial_subset(
+        dataset: xr.Dataset,
+        ij_bbox: Optional[Tuple[int, int, int, int]] = None,
+        ij_border: int = 0,
+        xy_bbox: Optional[Tuple[float, float, float, float]] = None,
+        xy_border: float = 0.,
+        grid_mapping: Optional[GridMapping] = None,
+) -> Optional[xr.Dataset]:
     """
     Select a spatial subset of *dataset* for the
     bounding box *ij_bbox* or *xy_bbox*.
@@ -113,9 +125,6 @@ def select_spatial_subset(dataset: xr.Dataset,
     :param xy_bbox: The bounding box in x,y coordinates.
     :param xy_border: Border in units of the x,y coordinates.
     :param grid_mapping: Optional dataset grid mapping.
-    :param geo_coding: Deprecated. Use *grid_mapping* instead.
-    :param xy_names: Optional tuple of the x- and y-coordinate
-        variables in *dataset*. Ignored if *geo_coding* is given.
     :return: Spatial dataset subset
     """
 
@@ -124,12 +133,6 @@ def select_spatial_subset(dataset: xr.Dataset,
     if ij_bbox and xy_bbox:
         raise ValueError('Only one of ij_bbox and xy_bbox can be given')
 
-    if geo_coding:
-        warnings.warn('keyword "geo_coding" has been deprecated,'
-                      ' use "grid_mapping" instead',
-                      DeprecationWarning)
-
-    grid_mapping = grid_mapping or geo_coding
     if grid_mapping is None:
         grid_mapping = GridMapping.from_dataset(dataset)
     x_name, y_name = grid_mapping.xy_var_names

xcube/plugin.py

@@ -225,6 +225,7 @@ def _register_server_apis(ext_registry: extension.ExtensionRegistry):
         'datasets',
         'tiles',
         'timeseries',
+        'volumes',
         'ows.wmts',
         's3',
         'viewer',

xcube/util/cmaps.py

@@ -470,7 +470,7 @@ def get_alpha_cmap(cm_name: str, cmap: matplotlib.colors.Colormap) \
 
 def get_cmap_png_base64(cmap: matplotlib.colors.Colormap) -> str:
     gradient = np.linspace(0, 1, 256)
-    gradient = np.vstack((gradient, gradient))
+    gradient = np.vstack((gradient,))
     image_data = cmap(gradient, bytes=True)
     image = Image.fromarray(image_data, 'RGBA')