Update pointcloud to use latests Pdal and Pystac dependencies

.github/workflows/continuous-integration.yml

@@ -25,7 +25,7 @@ jobs:
  runs-on: ubuntu-latest
  strategy:
  matrix:
- python-version: [3.6, 3.7, 3.8, 3.9]
+ python-version: ["3.8", "3.9", "3.10", "3.11"]
  defaults:
  run:
  shell: bash -l {0}

README.md

@@ -1,15 +1,42 @@
 # stactools-pointcloud
 
-Template repostitory for [stactools](https://github.com/stac-utils/stactools) packages.
-
-## How to use
-
-1. Clone this repository and name it `stactools-{NAME}`, where `NAME` is your package name.
- This name should be short, memorable, and a valid Python package name (i.e. it shouldn't start with a number, etc).
-2. Update `setup.cfg` with your package name, description, and such.
-3. Rename `src/stactools.pointcloud` to `src/stactools/{NAME}`.
-4. Rewrite this README to provide information about how to use your package.
-5. Update the LICENSE with your company's information (or whomever holds the copyright).
-6. Update the environment name in `environment.yml`.
-7. Update the environment variables in `.github/workflows/release.yml` to the appropriate values to publish for your organization.
-8. Update all scripts in the `docker` directory to refer to `stactools-{NAME}` and `stactools-{NAME}-dev`.
+Creates a STAC Item based on the header of a pointcloud.
+
+## Dependencies
+
+PDAL
+
+## Installation
+```bash
+pip install stactools-pointcloud
+```
+
+## Usage
+
+```
+stac pointcloud create-item [OPTIONS] HREF DST
+
+
+HREF is the pointcloud file. DST is directory that a STAC Item JSON file
+will be created in.
+
+Options:
+ -r, --reader TEXT Override the default PDAL reader.
+ -t, --pointcloud-type TEXT Set the pointcloud type (default: lidar)
+ --compute-statistics / --no-compute-statistics
+ Compute statistics for the pointcloud (could
+ take a while)
+ -p, --providers TEXT Path to JSON file containing array of
+ additional providers
+ --help Show this message and exit.
+stactools package for Pointcloud data.
+
+```
+
+## Example
+
+LAZ archive:
+
+```bash
+stac pointcloud create-item https://maps1.vcgov.org/LIDAR/LAZ/USGS_LPC_FL_Peninsular_2018_D18_LID2019_241594_E.laz .
+```

environment.yml

@@ -3,5 +3,8 @@ channels:
  - conda-forge
  - defaults
 dependencies:
- - gdal
- - pdal
+ - conda-forge::gdal>=3.3
+ - conda-forge::pdal>=2.5
+ - conda-forge::geos>=3.3
+ - conda-forge::rasterio>=1.3
+ - conda-forge::libstdcxx-ng # gdal dependency. Make sure it's from the same channel as gdal

setup.cfg

@@ -18,18 +18,18 @@ keywords =
 classifiers =
  Development Status :: 4 - Beta
  License :: OSI Approved :: Apache Software License
- Programming Language :: Python :: 3.6
- Programming Language :: Python :: 3.7
  Programming Language :: Python :: 3.8
  Programming Language :: Python :: 3.9
+ Programming Language :: Python :: 3.10
+ Programming Language :: Python :: 3.11
 
 [options]
 package_dir =
  = src
 packages = find_namespace:
 install_requires =
- stactools ~= 0.1
- pdal ~= 2.4
+ stactools ~= 0.5
+ pdal ~= 3.2
 
 [options.packages.find]
 where = src

src/stactools/pointcloud/commands.py

@@ -14,6 +14,7 @@ def create_pointcloud_command(cli):
  """Creates a command group for commands working with
  pointclouds.
  """
+
  @cli.group('pointcloud',
  short_help=("Commands for working with "
  "pointclouds."))

src/stactools/pointcloud/stac.py

@@ -4,18 +4,20 @@
 
 from pdal import Pipeline
 from pyproj import CRS
-from pystac import Item, Asset
-from pystac.extensions.pointcloud import PointcloudStatistic, PointcloudSchema
-from shapely.geometry import shape, box, mapping
-
+from pystac import Asset, Item
+from pystac.extensions.pointcloud import PointcloudExtension, Schema, Statistic
+from pystac.extensions.projection import ProjectionExtension
+from shapely.geometry import box, mapping, shape
 from stactools.core.projection import reproject_geom
 
 
-def create_item(href,
- pdal_reader=None,
- compute_statistics=False,
- pointcloud_type="lidar",
- additional_providers=None):
+def create_item(
+ href,
+ pdal_reader=None,
+ compute_statistics=False,
+ pointcloud_type="lidar",
+ additional_providers=None,
+):
  """Creates a STAC Item from a point cloud.
 
  Args:
@@ -41,7 +43,7 @@ def create_item(href,
  "count": 0
  }]))
  pipeline.execute()
- metadata = json.loads(pipeline.get_metadata())["metadata"]
+ metadata = pipeline.metadata["metadata"]
  try:
  reader_key = next(key for key in metadata.keys()
  if key.startswith("readers"))
@@ -53,7 +55,7 @@ def create_item(href,
  except StopIteration:
  raise Exception("could not find reader key in pipeline metadata")
  metadata = metadata[reader_key]
- schema = pipeline.get_schema()["schema"]["dimensions"]
+ schema = pipeline.schema["schema"]["dimensions"]
 
  id = os.path.splitext(os.path.basename(href))[0]
  encoding = os.path.splitext(href)[1][1:]
@@ -80,18 +82,19 @@ def create_item(href,
 
  item.add_asset(
  "pointcloud",
- Asset(href=href,
- media_type="application/octet-stream",
- roles=["data"],
- title="{} point cloud".format(encoding)))
+ Asset(
+ href=href,
+ media_type="application/octet-stream",
+ roles=["data"],
+ title="{} point cloud".format(encoding),
+ ),
+ )
 
- item.ext.enable("pointcloud")
- item.ext.pointcloud.count = metadata["count"]
- item.ext.pointcloud.type = pointcloud_type
- item.ext.pointcloud.encoding = encoding
- item.ext.pointcloud.schemas = [
- PointcloudSchema(schema) for schema in schema
- ]
+ pointcloud_ext = PointcloudExtension.ext(item, add_if_missing=True)
+ pointcloud_ext.count = metadata["count"]
+ pointcloud_ext.type = pointcloud_type
+ pointcloud_ext.encoding = encoding
+ pointcloud_ext.schemas = [Schema(schema) for schema in schema]
  # TODO compute density.
  #
  # Do we just divide point clount by bounding box area? That's too low. But
@@ -100,22 +103,21 @@ def create_item(href,
  # quick-and-dirty? But then densities mean different things depending on
  # the processing history of the STAC file, which seems inconsistant.
  if compute_statistics:
- item.ext.pointcloud.statistics = _compute_statistics(reader)
+ pointcloud_ext.statistics = _compute_statistics(reader)
 
+ projection_ext = ProjectionExtension.ext(item, add_if_missing=True)
  epsg = spatialreference.to_epsg()
  if epsg:
- item.ext.enable("projection")
- item.ext.projection.epsg = epsg
- item.ext.projection.wkt2 = spatialreference.to_wkt()
- item.ext.projection.bbox = list(original_bbox.bounds)
+ projection_ext.epsg = epsg
+ projection_ext.wkt2 = spatialreference.to_wkt()
+ projection_ext.bbox = list(original_bbox.bounds)
 
  return item
 
 
 def _compute_statistics(reader):
  pipeline = Pipeline(json.dumps([reader, {"type": "filters.stats"}]))
  pipeline.execute()
- stats = json.loads(
- pipeline.get_metadata())["metadata"]["filters.stats"]["statistic"]
- stats = [PointcloudStatistic(stats) for stats in stats]
+ stats = pipeline.metadata["metadata"]["filters.stats"]["statistic"]
+ stats = [Statistic(stats) for stats in stats]
  return stats

tests/test_commands.py

@@ -1,21 +1,25 @@
 import os
+import unittest
+
 from tempfile import TemporaryDirectory
 
 import pystac
 
+from click import Group
+from click.testing import CliRunner
 from stactools.pointcloud.commands import create_pointcloud_command
-from tests.utils import (TestData, CliTestCase)
 
 
-class CreateItemTest(CliTestCase):
- def create_subcommand_functions(self):
- return [create_pointcloud_command]
+class CreateItemTest(unittest.TestCase):
 
  def test_create_item(self):
- href = TestData.get_path('data-files/pointcloud/autzen_trim.las')
+ href = f"{os.path.dirname(__file__)}/data-files/autzen_trim.las"
  with TemporaryDirectory() as directory:
- cmd = ['pointcloud', 'create-item', href, directory]
- self.run_command(cmd)
+ runner = CliRunner()
+ runner.invoke(
+ create_pointcloud_command(Group()),
+ ["create-item", href, directory],
+ )
  jsons = [p for p in os.listdir(directory) if p.endswith('.json')]
  self.assertEqual(len(jsons), 1)
  item_path = os.path.join(directory, jsons[0])

tests/test_stac.py

@@ -1,33 +1,35 @@
 import datetime
+import os
 import unittest
 
-from tests.utils import TestData
+from pystac.extensions.pointcloud import PointcloudExtension
+from pystac.extensions.projection import ProjectionExtension
 from stactools.pointcloud.stac import create_item
 
 
 class StacTest(unittest.TestCase):
+
  def test_create_item(self):
- path = TestData.get_path("data-files/pointcloud/autzen_trim.las")
+ path = f"{os.path.dirname(__file__)}/data-files/autzen_trim.las"
  item = create_item(path)
  self.assertEqual(item.id, "autzen_trim")
  self.assertEqual(item.datetime, datetime.datetime(2015, 9, 10))
 
- item.ext.enable("projection")
- self.assertEqual(item.ext.projection.epsg, 2994)
-
- item.ext.enable("pointcloud")
- self.assertEqual(item.ext.pointcloud.count, 110000)
- self.assertEqual(item.ext.pointcloud.type, "lidar")
- self.assertEqual(item.ext.pointcloud.encoding, "las")
- self.assertEqual(item.ext.pointcloud.statistics, None)
- self.assertTrue(item.ext.pointcloud.schemas)
+ ProjectionExtension.validate_has_extension(item)
+ pointcloud_ext = PointcloudExtension.ext(item)
+ self.assertEqual(pointcloud_ext.count, 110000)
+ self.assertEqual(pointcloud_ext.type, "lidar")
+ self.assertEqual(pointcloud_ext.encoding, "las")
+ self.assertEqual(pointcloud_ext.statistics, None)
+ self.assertTrue(pointcloud_ext.schemas)
 
  item.validate()
 
  def test_create_item_with_statistic(self):
- path = TestData.get_path("data-files/pointcloud/autzen_trim.las")
+ path = f"{os.path.dirname(__file__)}/data-files/autzen_trim.las"
  item = create_item(path, compute_statistics=True)
- self.assertNotEqual(item.ext.pointcloud.statistics, None)
+ pointcloud_ext = PointcloudExtension.ext(item, add_if_missing=True)
+ self.assertNotEqual(pointcloud_ext.statistics, None)
 
  def test_create_item_from_url(self):
  url = "https://github.com/PDAL/PDAL/raw/2.2.0/test/data/las/autzen_trim.las"