Add stitched geometry creation (#12)

* add static layer download and geometry creation

* add more types, fix pre-commits

* add tests and fix failing

* add tests and fix failing

* spacing

* try to fix pytet warning, io is optional

* install rastserio too

* try reverse

* try this version

* install deps correctly

* add another warning ignore, gdal 3.4

* gdal min is 3.5

* missing future import

* use `lru_cache` for py38

* add changelog, bump to py39

* remove `cast`

* back to `@cache`

.github/workflows/ci.yml

@@ -16,13 +16,17 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
         deps:
-            # Note: for now we're manually adding tophu deps,
-            # will change once it's on conda forge
           - label: Latest
-            spec: ""
+            spec: >-
+              rasterio
+              gdal
+              asf_search
           - label: Minimum
             spec: >-
-              python=3.8
+              python=3.9
+              rasterio=1.3
+              gdal=3.5
+              asf_search=6.7.2
 
       fail-fast: false
     name: ${{ matrix.os }} • ${{ matrix.deps.label }}

CHANGELOG.md

@@ -0,0 +1,22 @@
+# [Unreleased](https://github.com/opera-adt/opera-utils/compare/v0.1.4...main)
+
+**Added**
+- Based raster metadata convenience functions as `_io.get_raster_*`
+- Ability to download CSLC static layers and stitch into line-of-sight rasters
+
+
+**Requirements**
+Minimum python version is 3.9
+
+- click>=7.0
+- h5py>=1.10
+- numpy>=1.20
+- pooch>=1.7
+- pyproj>=3.3
+- shapely>=1.8
+- typing_extensions>=4
+
+For other interactions with geospatial rasters (i.e. reading metadata, creating geometries from Static Layers):
+- asf_search>=6.7.2
+- gdal>=3.5
+- rasterio>=1.3

LICENSE

@@ -1,3 +1,36 @@
+This software is licensed under either the BSD-3-Clause or Apache-2.0 license. Users may
+choose which license to apply. The terms of each license are reproduced below.
+
+---------------------------------------------------------------------------------------
+
+Copyright (c) 2023 California Institute of Technology ("Caltech"). U.S. Government
+sponsorship acknowledged.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are
+permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this list of
+  conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, this list of
+  conditions and the following disclaimer in the documentation and/or other materials
+  provided with the distribution.
+* Neither the name of Caltech nor its operating division, the Jet Propulsion Laboratory,
+  nor the names of its contributors may be used to endorse or promote products derived
+  from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+---------------------------------------------------------------------------------------
 
                                  Apache License
                            Version 2.0, January 2004
@@ -187,7 +220,8 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2023 Scott Staniewicz
+   Copyright 2023 California Institute of Technology (“Caltech”).
+   U.S. Government sponsorship acknowledged.
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

environment-geo.yml

@@ -1,6 +1,6 @@
 channels:
   - conda-forge
 dependencies:
-  - pyogrio>=0.5
-  - gdal>=3.3
-  - geopandas-base>=0.12
+  - asf_search>=6.7
+  - gdal>=3.5
+  - rasterio>=1.3

environment.yml

@@ -2,7 +2,7 @@ name: opera-utils-env
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8
+  - python>=3.9
   - pip>=21.3  # https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/#editable-installation
   - git  # for pip install, due to setuptools_scm
   - click>=7.0

pyproject.toml

@@ -9,13 +9,12 @@ authors = [
 ]
 description = "Miscellaneous utilities for working with OPERA data products"
 readme = { file = "README.md", content-type = "text/markdown" }
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 
 classifiers = [
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
@@ -71,7 +70,7 @@ preview = true
 
 [tool.isort]
 profile = "black"
-known_first_party = [" opera_utils"]
+known_first_party = ["opera_utils"]
 
 [tool.mypy]
 python_version = "3.10"
@@ -84,4 +83,9 @@ ignore = "D100,D102,D104,D105,D106,D107,D203,D204,D213,D413"
 [tool.pytest.ini_options]
 doctest_optionflags = "NORMALIZE_WHITESPACE NUMBER"
 addopts = "  --cov=opera_utils  --doctest-modules --randomly-seed=1234 --ignore=scripts --ignore=docs"
-filterwarnings = ["error"]
+filterwarnings = [
+  "error",
+  "ignore:h5py is running against HDF5.*:UserWarning",
+  # https://github.com/dateutil/dateutil/pull/1285 will be released, but not yet
+  "ignore:datetime.datetime.utcfromtimestamp.*:DeprecationWarning",
+]

src/opera_utils/__init__.py

@@ -4,7 +4,6 @@
 from __future__ import annotations
 
 from ._dates import *
-from ._io import *
 from ._version import version as __version__
 from .bursts import *
 from .burst_frame_db import *

src/opera_utils/_dates.py

@@ -4,10 +4,10 @@
 import itertools
 import re
 from collections import defaultdict
-from pathlib import Path
 from typing import Iterable, overload
 
 from ._types import DateOrDatetime, Filename, PathLikeT
+from ._utils import _get_path_from_gdal_str
 
 __all__ = [
     "get_dates",
@@ -145,20 +145,6 @@ def _parse_date(datestr: str, fmt: str = DATE_FORMAT) -> datetime.datetime:
     return datetime.datetime.strptime(datestr, fmt)
 
 
-def _get_path_from_gdal_str(name: Filename) -> Path:
-    s = str(name)
-    if s.upper().startswith("DERIVED_SUBDATASET"):
-        # like DERIVED_SUBDATASET:AMPLITUDE:slc_filepath.tif
-        p = s.split(":")[-1].strip('"').strip("'")
-    elif ":" in s and (s.upper().startswith("NETCDF") or s.upper().startswith("HDF")):
-        # like NETCDF:"slc_filepath.nc":subdataset
-        p = s.split(":")[1].strip('"').strip("'")
-    else:
-        # Whole thing is the path
-        p = str(name)
-    return Path(p)
-
-
 def _date_format_to_regex(date_format: str) -> re.Pattern:
     r"""Convert a python date format string to a regular expression.
 

src/opera_utils/_io.py

@@ -0,0 +1,122 @@
+from __future__ import annotations
+
+from typing import Any
+
+import numpy as np
+import rasterio as rio
+from affine import Affine
+from pyproj import CRS
+
+from ._types import Bbox, PathOrStr
+
+
+def get_raster_nodata(filename: PathOrStr, band: int = 1) -> float | None:
+    """Get the nodata value from a file.
+
+    Parameters
+    ----------
+    filename : PathOrStr
+        Path to the file to load.
+    band : int, optional
+        Band to get nodata value for, by default 1.
+
+    Returns
+    -------
+    Optional[float]
+        Nodata value, or None if not found.
+    """
+    nodatas = _get_dataset_attr(filename, "nodatavals")
+    return nodatas[band - 1]
+
+
+def get_raster_crs(filename: PathOrStr) -> CRS:
+    """Get the CRS from a file.
+
+    Parameters
+    ----------
+    filename : PathOrStr
+        Path to the file to load.
+
+    Returns
+    -------
+    CRS
+        pyproj CRS for `filename`
+    """
+    return _get_dataset_attr(filename, "crs")
+
+
+def get_raster_transform(filename: PathOrStr) -> Affine:
+    """Get the rasterio `Affine` transform from a file.
+
+    Parameters
+    ----------
+    filename : PathOrStr
+        Path to the file to load.
+
+    Returns
+    -------
+    List[float]
+        6 floats representing a GDAL Geotransform.
+    """
+    return _get_dataset_attr(filename, "transform")
+
+
+def get_raster_gt(filename: PathOrStr) -> list[float]:
+    """Get the gdal geotransform from a file.
+
+    Parameters
+    ----------
+    filename : PathOrStr
+        Path to the file to load.
+
+    Returns
+    -------
+    Affine
+        Two dimensional affine transform for 2D linear mapping.
+    """
+    return get_raster_transform(filename).to_gdal()
+
+
+def get_raster_dtype(filename: PathOrStr, band: int = 1) -> np.dtype:
+    """Get the numpy data type from a raster file.
+
+    Parameters
+    ----------
+    filename : PathOrStr
+        Path to the file to load.
+    band : int, optional
+        Band to get nodata value for, by default 1.
+
+    Returns
+    -------
+    np.dtype
+        Data type.
+    """
+    dtype_per_band = _get_dataset_attr(filename, "dtypes")
+    return np.dtype(dtype_per_band[band - 1])
+
+
+def get_raster_driver(filename: PathOrStr) -> str:
+    """Get the GDAL driver `ShortName` from a file.
+
+    Parameters
+    ----------
+    filename : PathOrStr
+        Path to the file to load.
+
+    Returns
+    -------
+    str
+        Driver name.
+    """
+    return _get_dataset_attr(filename, "driver")
+
+
+def get_raster_bounds(filename: PathOrStr) -> Bbox:
+    """Get the (left, bottom, right, top) bounds of the image."""
+    return _get_dataset_attr(filename, "bounds")
+
+
+def _get_dataset_attr(filename: PathOrStr, attr_name: str) -> Any:
+    with rio.open(filename) as src:
+        return getattr(src, attr_name)