Merge pull request #50 from pflickin/feature/glc_layers

Add method for creating Copernicus Land Cover Layers.

.readthedocs.yml

@@ -25,6 +25,8 @@ python:
       path: stactools_aster/
     - method: pip
       path: stactools_corine/
+    - method: pip
+      path: stactools_cgls_lc100/
     - method: pip
       path: stactools_landsat/
     - method: pip

README.md

@@ -75,6 +75,7 @@ See the [documentation page](https://stactools.readthedocs.io/en/latest/) for th
 | `stactools_cli`               | Contains the command line interface (cli) for running the `stactools` command   |
 | `stactools_aster`             | Methods and commands for working with ASTER data                 |
 | `stactools_corine`            | Methods and commands for working with CORINE Land Cover data                 |
+| `stactools_cgls_lc100`        | Methods and commands for working with Copernicus Global Land Cover Layers                 |
 | `stactools_planet`            | Methods and commands for working with planet data                |
 | `stactools_landsat`           | Methods and commands for working with landsat data        |
 | `stactools_sentinel2`           | Methods and commands for working with Sentinel 2 data        |

cgls_lc100

@@ -0,0 +1 @@
+../stactools_cgls_lc100/stactools/cgls_lc100/

docker/Dockerfile

@@ -62,6 +62,10 @@ RUN pip install --no-build-isolation -r /tmp/aster/requirements.txt
 COPY stactools_corine/requirements.txt /tmp/corine/requirements.txt
 RUN pip install -r /tmp/corine/requirements.txt
 
+# Copernicus Global Land Cover Layers
+COPY stactools_cgls_lc100/requirements.txt /tmp/stactools_cgls_lc100/requirements.txt
+RUN pip install -r /tmp/stactools_cgls_lc100/requirements.txt
+
 # Landsat
 COPY stactools_landsat/requirements.txt /tmp/landsat/requirements.txt
 RUN pip install -r /tmp/landsat/requirements.txt

scripts/env

@@ -5,6 +5,7 @@ STACTOOLS_SUBPACKAGE_DIRS=(
     "stactools_cli"
     "stactools_aster"
     "stactools_corine"
+    "stactools_cgls_lc100"
     "stactools_landsat"
     "stactools_planet"
     "stactools_naip"
@@ -17,6 +18,7 @@ STACTOOLS_COVERAGE_DIRS=(
     "stactools_cli/stactools/cli"
     "stactools_aster/stactools/aster"
     "stactools_corine/stactools/corine"
+    "stactools_cgls_lc100/stactools/cgls_lc100"
     "stactools_landsat/stactools/landsat"
     "stactools_planet/stactools/planet"
     "stactools_naip/stactools/naip"

stactools/cgls_lc100

@@ -0,0 +1 @@
+../stactools_cgls_lc100/stactools/cgls_lc100/

stactools/glc_layers

@@ -0,0 +1 @@
+../stactools_glc_layers/stactools/glc_layers/

stactools_cgls_lc100/README.md

@@ -0,0 +1,3 @@
+# stactools_cgls_lc100
+
+A subpackage of stactools for working with Copernicus Global Land Cover Layers data.

stactools_cgls_lc100/requirements.txt

@@ -0,0 +1,2 @@
+rasterio==1.1.8 --no-binary=rasterio
+pyproj==3.0.0.post1

stactools_cgls_lc100/setup.py

@@ -0,0 +1,48 @@
+import os
+from os.path import (basename, splitext)
+from imp import load_source
+from setuptools import setup, find_namespace_packages
+from glob import glob
+import io
+
+name = 'stactools_cgls_lc100'
+description = (
+    "Subpackage for working with Copernicus Global Land Cover Layers data in stactools, "
+    "a command line tool and Python library for working with STAC.")
+
+__version__ = load_source(
+    'stactools.cgls_lc100.version',
+    os.path.join(os.path.dirname(__file__),
+                 'stactools/cgls_lc100/version.py')).__version__
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+# get the dependencies and installs
+with io.open(os.path.join(here, 'requirements.txt'), encoding='utf-8') as f:
+    install_requires = [line.split(' ')[0] for line in f.read().split('\n')]
+
+# Add stactools subpackage dependencies
+install_requires.extend(['stactools_core=={}'.format(__version__)])
+
+with open(os.path.join(here, 'README.md')) as readme_file:
+    readme = readme_file.read()
+
+setup(name=name,
+      description=description,
+      version=__version__,
+      long_description=readme,
+      long_description_content_type="text/markdown",
+      author="stac-utils",
+      author_email='stac@radiant.earth',
+      url='https://github.com/stac-utils/stactools.git',
+      packages=find_namespace_packages(),
+      py_modules=[
+          splitext(basename(path))[0] for path in glob('stactools/*.py')
+      ],
+      include_package_data=False,
+      install_requires=install_requires,
+      license="Apache Software License 2.0",
+      keywords=[
+          'stactools', 'psytac', 'CGLS_LC100', 'imagery', 'landcover',
+          'land cover', 'catalog', 'STAC', 'Copernicus'
+      ])

stactools_cgls_lc100/stactools/cgls_lc100/__init__.py

@@ -0,0 +1,16 @@
+# flake8: noqa
+
+from stactools.cgls_lc100.stac import create_item
+from stactools.cgls_lc100.cog import create_cogs
+
+import stactools.core
+
+stactools.core.use_fsspec()
+
+
+def register_plugin(registry):
+    # Register subcommands
+
+    from stactools.cgls_lc100 import commands
+
+    registry.register_subcommand(commands.create_cgls_lc100_command)

stactools_cgls_lc100/stactools/cgls_lc100/cog.py

@@ -0,0 +1,62 @@
+import logging
+import os
+from subprocess import Popen, PIPE, STDOUT
+
+import pystac
+
+from stactools.cgls_lc100.constants import (ITEM_COG_IMAGE_NAME,
+                                            ITEM_TIF_IMAGE_NAME)
+
+logger = logging.getLogger(__name__)
+
+
+def call(command):
+    def log_subprocess_output(pipe):
+        for line in iter(pipe.readline, b''):  # b'\n'-separated lines
+            logger.info(line.decode("utf-8").strip('\n'))
+
+    process = Popen(command, stdout=PIPE, stderr=STDOUT)
+    with process.stdout:
+        log_subprocess_output(process.stdout)
+    return process.wait()  # 0 means success
+
+
+def cogify(input_path, output_path):
+    call(['gdal_translate', '-of', 'COG', '-co', input_path, output_path])
+
+
+def _create_cog(item, cog_directory):
+    tif_asset = item.assets.get(ITEM_TIF_IMAGE_NAME)
+    cogify(tif_asset.href, cog_directory)
+
+    return cog_directory
+
+
+def create_cogs(item, cog_directory=None):
+    """Create COGs from the tif asset contained in the passed in STAC item.
+
+    Args:
+        item (pystac.Item): Land Cover Layers Item that contains an asset
+            with key equal to stactools.cgls_lc100.constants.ITEM_TIF_IMAGE_NAME,
+            which will be converted to COGs.
+        cog_directory (str): A URI of a directory to store COGs. This will be used
+            in conjunction with the file names based on the COG asset to store
+            the COG data. If not supplied, the directory of the Item's self HREF
+            will be used.
+
+    Returns:
+        pystac.Item: The same item, mutated to include assets for the
+            new COGs.
+    """
+    if cog_directory is None:
+        cog_directory = os.path.dirname(item.get_self_href())
+
+    cog_href = os.path.join(cog_directory, '{}-cog.tif'.format(item.id))
+    _create_cog(item, cog_href)
+
+    asset = pystac.Asset(href=cog_href,
+                         media_type=pystac.MediaType.COG,
+                         roles=['data'],
+                         title='Raster Dataset')
+
+    item.assets[ITEM_COG_IMAGE_NAME] = asset

stactools_cgls_lc100/stactools/cgls_lc100/commands.py

@@ -0,0 +1,50 @@
+import logging
+import os
+
+import click
+
+from stactools.cgls_lc100 import stac, cog
+
+logger = logging.getLogger(__name__)
+
+
+def create_cgls_lc100_command(cli):
+    """Creates a command group for commands working with
+    Copernicus Global Land Cover Layers data.
+    """
+    @cli.group('cgls_lc100',
+               short_help=("Commands for working with "
+                           "Copernicus Global Land Cover Layers data."))
+    def cgls_lc100():
+        pass
+
+    @cgls_lc100.command('create-item',
+                        short_help=("Create a STAC Item from a Copernicus "
+                                    "Global Land Cover Layers tif file."))
+    @click.argument('tif_href')
+    @click.argument('dst')
+    @click.option('-c',
+                  '--cogify',
+                  is_flag=True,
+                  help='Convert the tif into COG.')
+    def create_item_command(tif_href, dst, cogify):
+        """Creates a STAC Item based on metadata from a tif
+        Copernicus Global Land Cover Layers file.
+
+        TIF_REF is the Copernicus Global Land Cover Layers tif file.
+        DST is directory that a STAC Item JSON file will be created
+        in. This will have a filename that matches the ID, which will
+        is the name of the tif_REF, without it's file extension.
+        """
+
+        item = stac.create_item(tif_href)
+
+        item_path = os.path.join(dst, '{}.json'.format(item.id))
+        item.set_self_href(item_path)
+
+        if cogify:
+            cog.create_cogs(item)
+
+        item.save_object()
+
+    return cgls_lc100

stactools_cgls_lc100/stactools/cgls_lc100/constants.py

@@ -0,0 +1,92 @@
+PROVIDER_NAME = 'European Environment Agency (EEA) under the framework of the Copernicus programme'
+
+ITEM_COG_IMAGE_NAME = 'cog_image'
+ITEM_TIF_IMAGE_NAME = 'tif_image'
+
+DISCRETE_CLASSIFICATION_CLASS_NAMES = {
+    0: "Unknown.",
+    20:
+    """Shrubs. Woody perennial plants with persistent and woody stems and without
+         any defined main stem being less than 5 m tall. The shrub foliage can be either
+         evergreen or deciduous.""",
+    30:
+    """Herbaceous vegetation. Plants without persistent stem or shoots above ground and
+         lacking definite firm structure. Tree and shrub cover is less than 10 %.""",
+    40:
+    """Cultivated and managed vegetation / agriculture. Lands covered with temporary crops
+         followed by harvest and a bare soil period (e.g., single and multiple cropping systems).
+         Note that perennial woody crops will be classified as the appropriate forest or shrub
+         land cover type.""",
+    50:
+    "Urban / built up. Land covered by buildings and other man-made structures.",
+    60:
+    """Bare / sparse vegetation. Lands with exposed soil, sand, or rocks and never has more
+         than 10 % vegetated cover during any time of the year.""",
+    70: "Snow and ice. Lands under snow or ice cover throughout the year.",
+    80:
+    """Permanent water bodies. Lakes, reservoirs, and rivers. Can be either fresh or
+         salt-water bodies.""",
+    90:
+    """Herbaceous wetland. Lands with a permanent mixture of water and herbaceous or woody
+         vegetation. The vegetation can be present in either salt, brackish, or fresh water.""",
+    100: "Moss and lichen.",
+    111:
+    """Closed forest, evergreen needle leaf. Tree canopy >70 %, almost all needle leaf trees
+         remain green all year. Canopy is never without green foliage.""",
+    112:
+    """Closed forest, evergreen broad leaf. Tree canopy >70 %, almost all broadleaf trees remain
+         green year round. Canopy is never without green foliage.""",
+    113:
+    """Closed forest, deciduous needle leaf. Tree canopy >70 %, consists of seasonal needle
+         leaf tree communities with an annual cycle of leaf-on and leaf-off periods.""",
+    114:
+    """Closed forest, deciduous broad leaf. Tree canopy >70 %, consists of seasonal broadleaf
+         tree communities with an annual cycle of leaf-on and leaf-off periods.""",
+    115: "Closed forest, mixed.",
+    116: "Closed forest, not matching any of the other definitions.",
+    121:
+    """Open forest, evergreen needle leaf. Top layer- trees 15-70 and second layer- mixed of
+         shrubs and grassland, almost all needle leaf trees remain green all year. Canopy is never
+         without green foliage.""",
+    122:
+    """Open forest, evergreen broad leaf. Top layer- trees 15-70 and second layer- mixed of
+         shrubs and grassland, almost all broadleaf trees remain green year round. Canopy is never
+         without green foliage.""",
+    123:
+    """Open forest, deciduous needle leaf. Top layer- trees 15-70 and second layer- mixed of
+         shrubs and grassland, consists of seasonal needle leaf tree communities with an
+         annual cycle of leaf-on and leaf-off periods.""",
+    124:
+    """Open forest, deciduous broad leaf. Top layer- trees 15-70 and second layer- mixed of
+         shrubs and grassland, consists of seasonal broadleaf tree communities with an
+         annual cycle of leaf-on and leaf-off periods.""",
+    125: "Open forest, mixed.",
+    126: "Open forest, not matching any of the other definitions.",
+    200: "Oceans, seas. Can be either fresh or salt-water bodies."
+}
+
+DISCRETE_CLASSIFICATION_CLASS_PALETTE = {
+    0: '282828',
+    1: 'FFBB22',
+    2: 'FFFF4C',
+    3: 'F096FF',
+    4: 'FA0000',
+    5: 'B4B4B4',
+    6: 'F0F0F0',
+    7: '0032C8',
+    8: '0096A0',
+    9: 'FAE6A0',
+    10: '58481F',
+    11: '009900',
+    12: '70663E',
+    13: '00CC00',
+    14: '4E751F',
+    15: '007800',
+    16: '666000',
+    17: '8DB400',
+    18: '8D7400',
+    19: 'A0DC00',
+    20: '929900',
+    21: '648C00',
+    22: '000080'
+}