pysits 1.5.3.dev2__tar.gz → 2.0.0.dev0__tar.gz

{pysits-1.5.3.dev2 → pysits-2.0.0.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysits
-Version: 1.5.3.dev2
+Version: 2.0.0.dev0
 Summary: Python wrapper for the sits R package
 Project-URL: Homepage, https://github.com/e-sensing/pysits
 Project-URL: Issue Tracker, https://github.com/e-sensing/pysits/issues
@@ -34,6 +34,9 @@ Requires-Dist: ruff>=0.11.12; extra == 'dev'
 Provides-Extra: xarray
 Requires-Dist: affine>=2.4.0; extra == 'xarray'
 Requires-Dist: dask>=2025.3.0; extra == 'xarray'
+Requires-Dist: odc-stac>=0.5.3; extra == 'xarray'
+Requires-Dist: planetary-computer>=1.0.0; extra == 'xarray'
+Requires-Dist: pystac>=1.15.0; extra == 'xarray'
 Requires-Dist: rioxarray>=0.18.2; extra == 'xarray'
 Requires-Dist: xarray>=2025.3.0; extra == 'xarray'
 Description-Content-Type: text/markdown
@@ -42,7 +45,7 @@ Description-Content-Type: text/markdown
 
 Python wrapper for the [sits](https://github.com/e-sensing/sits) R package.
 
-## 📦 Installation
+## Installation
 
 To install `pysits` with pip:
 
@@ -58,7 +61,7 @@ pip install git+https://github.com/e-sensing/pysits.git
 
 > To use `pysits`, you must have [sits](https://github.com/e-sensing/sits) installed. For more information, refer to the [official sits documentation](https://e-sensing.github.io/sitsbook/setup.html).
 
-## 🛠 Development setup (for contributors)
+## Development setup (for contributors)
 
 To set up a local development environment:
 
@@ -82,7 +85,7 @@ source .venv/bin/activate  # or .venv\Scripts\activate on Windows
 uv pip install -e ".[dev]"
 ```
 
-### 🔍 Run tests
+### Run tests
 
 We use `pytest` for testing:
 
@@ -90,7 +93,7 @@ We use `pytest` for testing:
 pytest
 ```
 
-### 🧹 Code formatting
+### Code formatting
 
 To keep the codebase clean and consistent we use [ruff](https://github.com/astral-sh/ruff):
 
@@ -98,7 +101,7 @@ To keep the codebase clean and consistent we use [ruff](https://github.com/astra
 ruff format .
 ```
 
-### 🧪 Linting
+### Linting
 
 We use [ruff](https://github.com/astral-sh/ruff) for static analysis:
 
@@ -108,11 +111,11 @@ ruff check .
 
 > The `examples/` directory is excluded from linting.
 
-## 📚 Learn more
+## Learn more
 
 To learn all about `sits`, including its concepts, API, and real-world examples, we recommend accessing the [official sits book](https://e-sensing.github.io/sitsbook/). The book provides examples in both R and Python.
 
-## 🤝 Contributing
+## Contributing
 
 We welcome contributions! Please:
 
@@ -120,6 +123,6 @@ We welcome contributions! Please:
 - Create a feature branch
 - Submit a pull request with a clear description
 
-## 📄 License
+## License
 
 `pysits` is distributed under the GPL-2.0 license. See [LICENSE](./LICENSE) for more details.

{pysits-1.5.3.dev2 → pysits-2.0.0.dev0}/README.md

@@ -2,7 +2,7 @@
 
 Python wrapper for the [sits](https://github.com/e-sensing/sits) R package.
 
-## 📦 Installation
+## Installation
 
 To install `pysits` with pip:
 
@@ -18,7 +18,7 @@ pip install git+https://github.com/e-sensing/pysits.git
 
 > To use `pysits`, you must have [sits](https://github.com/e-sensing/sits) installed. For more information, refer to the [official sits documentation](https://e-sensing.github.io/sitsbook/setup.html).
 
-## 🛠 Development setup (for contributors)
+## Development setup (for contributors)
 
 To set up a local development environment:
 
@@ -42,7 +42,7 @@ source .venv/bin/activate  # or .venv\Scripts\activate on Windows
 uv pip install -e ".[dev]"
 ```
 
-### 🔍 Run tests
+### Run tests
 
 We use `pytest` for testing:
 
@@ -50,7 +50,7 @@ We use `pytest` for testing:
 pytest
 ```
 
-### 🧹 Code formatting
+### Code formatting
 
 To keep the codebase clean and consistent we use [ruff](https://github.com/astral-sh/ruff):
 
@@ -58,7 +58,7 @@ To keep the codebase clean and consistent we use [ruff](https://github.com/astra
 ruff format .
 ```
 
-### 🧪 Linting
+### Linting
 
 We use [ruff](https://github.com/astral-sh/ruff) for static analysis:
 
@@ -68,11 +68,11 @@ ruff check .
 
 > The `examples/` directory is excluded from linting.
 
-## 📚 Learn more
+## Learn more
 
 To learn all about `sits`, including its concepts, API, and real-world examples, we recommend accessing the [official sits book](https://e-sensing.github.io/sitsbook/). The book provides examples in both R and Python.
 
-## 🤝 Contributing
+## Contributing
 
 We welcome contributions! Please:
 
@@ -80,6 +80,6 @@ We welcome contributions! Please:
 - Create a feature branch
 - Submit a pull request with a clear description
 
-## 📄 License
+## License
 
 `pysits` is distributed under the GPL-2.0 license. See [LICENSE](./LICENSE) for more details.

{pysits-1.5.3.dev2 → pysits-2.0.0.dev0}/pyproject.toml

@@ -17,7 +17,7 @@
 
 [project]
 name = "pysits"
-version = "1.5.3.dev2"
+version = "2.0.0.dev0"
 description = "Python wrapper for the sits R package"
 readme = "README.md"
 requires-python = ">=3.10,<4"
@@ -77,7 +77,10 @@ xarray = [
     "xarray>=2025.3.0",
     "dask>=2025.3.0",
     "rioxarray>=0.18.2",
-    "affine>=2.4.0"
+    "affine>=2.4.0",
+    "odc-stac>=0.5.3",
+    "pystac>=1.15.0",
+    "planetary-computer>=1.0.0"
 ]
 
 dev = [
@@ -93,7 +96,7 @@ dev = [
 exclude = ["examples", "_resources"]
 
 [tool.ruff.lint]
-ignore = ["PLC0415"]
+ignore = ["PLC0415", "PLW0108"]
 select = [
     "E",   # pycodestyle
     "F",   # pyflakes

{pysits-1.5.3.dev2 → pysits-2.0.0.dev0}/pysits/__init__.py

@@ -27,7 +27,13 @@ from .sits.colors import (
     sits_colors_set,
     sits_colors_show,
 )
-from .sits.config import sits_config, sits_config_show, sits_config_user_file
+from .sits.config import (
+    sits_config,
+    sits_config_show,
+    sits_config_user_file,
+    sits_config_value,
+    sits_parallel,
+)
 from .sits.context import (
     cerrado_2classes,
     point_mt_6bands,
@@ -67,8 +73,15 @@ from .sits.data import (
 )
 from .sits.data import sits_summary as summary
 from .sits.exporters import sits_as_geopandas, sits_as_xarray, sits_to_csv, sits_to_xlsx
-from .sits.impute import impute_linear, sits_impute
+from .sits.impute import (
+    impute_linear,
+    impute_mean,
+    impute_mean_window,
+    impute_median,
+)
 from .sits.ml import (
+    sits_barlow_twins,
+    sits_contrastive_learning,
     sits_formula_linear,
     sits_formula_logref,
     sits_kfold_validate,
@@ -76,20 +89,25 @@ from .sits.ml import (
     sits_lighttae,
     sits_mlp,
     sits_model_export,
+    sits_pre_train,
     sits_resnet,
     sits_rfor,
+    sits_ssl_lejepa,
+    sits_ssl_mae,
+    sits_ssl_vicreg,
     sits_svm,
     sits_tae,
     sits_tempcnn,
     sits_train,
     sits_xgboost,
 )
-from .sits.segment import sits_segment, sits_slic
-from .sits.tiles import sits_mgrs_to_roi, sits_roi_to_tiles, sits_tiles_to_roi
+from .sits.segment import sits_segment, sits_slic, sits_snic
+from .sits.tiles import sits_roi_to_tiles, sits_tiles_to_roi
 from .sits.ts import (
     sits_cluster_clean,
     sits_cluster_dendro,
     sits_cluster_frequency,
+    sits_encode,
     sits_geo_dist,
     sits_get_class,
     sits_get_data,
@@ -103,7 +121,6 @@ from .sits.ts import (
     sits_reduce_imbalance,
     sits_sample,
     sits_sampling_design,
-    sits_sgolay,
     sits_show_prediction,
     sits_som_clean_samples,
     sits_som_evaluate_cluster,
@@ -111,7 +128,6 @@ from .sits.ts import (
     sits_stats,
     sits_stratified_sampling,
     sits_validate,
-    sits_whittaker,
 )
 from .sits.tuning import sits_tuning, sits_tuning_hparams
 from .sits.utils import (
@@ -152,6 +168,8 @@ __all__ = (
     "sits_config",
     "sits_config_show",
     "sits_config_user_file",
+    "sits_config_value",
+    "sits_parallel",
     # Data management
     "sits_bands",
     "sits_timeline",
@@ -184,13 +202,19 @@ __all__ = (
     "sits_model_export",
     "sits_formula_linear",
     "sits_formula_logref",
+    "sits_ssl_mae",
+    "sits_ssl_lejepa",
+    "sits_ssl_vicreg",
+    "sits_barlow_twins",
+    "sits_contrastive_learning",
+    "sits_pre_train",
     # Impute
-    "sits_impute",
     "impute_linear",
+    "impute_mean",
+    "impute_median",
+    "impute_mean_window",
     # Time-series
     "sits_show_prediction",
-    "sits_sgolay",
-    "sits_whittaker",
     "sits_get_data",
     "sits_get_class",
     "sits_get_probs",
@@ -210,13 +234,14 @@ __all__ = (
     "sits_reduce_imbalance",
     "sits_sampling_design",
     "sits_stratified_sampling",
+    "sits_encode",
     # Tiles
-    "sits_mgrs_to_roi",
     "sits_tiles_to_roi",
     "sits_roi_to_tiles",
     # Segments
     "sits_segment",
     "sits_slic",
+    "sits_snic",
     # Apply
     "sits_apply",
     # Exporters

{pysits-1.5.3.dev2 → pysits-2.0.0.dev0}/pysits/backend/functions.py

@@ -17,7 +17,10 @@
 
 """backend functions."""
 
-from pysits.backend.loaders import load_function_from_package
+from pysits.backend.loaders import (
+    load_function_from_package,
+    load_internal_function_from_package,
+)
 
 # Base - plot
 r_fnc_plot = load_function_from_package("base::plot")
@@ -40,6 +43,9 @@ r_fnc_set_seed = load_function_from_package("base::set_seed")
 # Base - class (base)
 r_fnc_class = load_function_from_package("base::class")
 
+# Base - eval (base)
+r_fnc_eval = load_function_from_package("base::eval")
+
 # Base - as.data.frame (base)
 r_fnc_as_data_frame = load_function_from_package("base::as_data_frame")
 
@@ -48,3 +54,6 @@ r_fnc_colnames = load_function_from_package("base::colnames")
 
 # Base - rownames (base)
 r_fnc_rownames = load_function_from_package("base::rownames")
+
+# sits - configuration (internal)
+r_fnc_sits_conf = load_internal_function_from_package("sits:::.conf")

{pysits-1.5.3.dev2 → pysits-2.0.0.dev0}/pysits/backend/loaders.py

@@ -105,3 +105,42 @@ def load_function_from_package(name: str) -> Callable[..., Any]:
 
     # Return function
     return getattr(pkg, func_name)
+
+
+def load_internal_function_from_package(name: str) -> Callable[..., Any]:
+    """Load an internal R function from a specified package.
+
+    Internal functions are those not exported by a package. They are addressed
+    in R with the ``package:::function`` notation.
+
+    Args:
+        name (str): The fully qualified name of the R function in the format
+                    'package:::function'. For example, 'sits:::.conf'.
+
+    Returns:
+        Callable[..., Any]: A Python callable that wraps the R function.
+                            The exact signature depends on the underlying R function.
+
+    Raises:
+        ValueError: If the ``name`` doesn't follow the 'package:::function' format.
+
+        PackageNotFoundError: If the specified R package is not installed.
+
+    Examples:
+        >>> conf = load_internal_function_from_package('sits:::.conf')
+        >>> scale = conf('sources', 'BDC', 'collections', 'MOD13Q1-6.1')
+    """
+    # Parse package and function
+    package_name, _, func_name = name.partition(":::")
+
+    if not package_name or not func_name:
+        raise ValueError(
+            f"Invalid function name format: {name}. "
+            "Expected format: 'package:::function'"
+        )
+
+    # Import the package
+    importr(package_name, on_conflict="warn")
+
+    # Return function
+    return rpy2_r_interface(name)

{pysits-1.5.3.dev2 → pysits-2.0.0.dev0}/pysits/conversions/common.py

@@ -25,8 +25,10 @@ from geopandas import GeoDataFrame as GeoPandasDataFrame
 from pandas import DataFrame as PandasDataFrame
 from rpy2.rinterface_lib.sexp import NULLType
 from rpy2.robjects import pandas2ri
+from rpy2.robjects.language import LangVector
 from rpy2.robjects.robject import RObjectMixin
 
+from pysits.backend.functions import r_fnc_eval
 from pysits.backend.pkgs import r_pkg_tibble
 from pysits.conversions.dsl.base import DSLObject
 from pysits.conversions.tibble import geopandas_to_tibble, pandas_to_tibble
@@ -179,6 +181,22 @@ def convert_to_r(obj):
     raise TypeError(f"Cannot convert object of type {obj_type} to R format")
 
 
+def eval_r_language(obj):
+    """Evaluate an unevaluated R expression.
+
+    Args:
+        obj: The R object to evaluate.
+
+    Returns:
+        The evaluated R object. Objects that are not R expressions are returned
+        unchanged.
+    """
+    if isinstance(obj, LangVector):
+        return r_fnc_eval(obj)
+
+    return obj
+
+
 def convert_to_python(obj, as_type="str"):
     """Convert an R object to a Python representation.
 
@@ -206,6 +224,9 @@ def convert_to_python(obj, as_type="str"):
     def _convert(value, type_):
         result = []
 
+        # R expressions must be evaluated to be converted
+        value = eval_r_language(value)
+
         if isinstance(value, ro.ListVector):
             for k, v in value.items():
                 result.append(

pysits-2.0.0.dev0/pysits/conversions/stac.py

@@ -0,0 +1,233 @@
+#
+# Copyright (C) 2025 sits developers.
+#
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <https://www.gnu.org/licenses/>.
+#
+
+"""STAC conversions."""
+
+from __future__ import annotations
+
+from urllib.parse import urlparse, urlunparse
+
+import pystac
+from affine import Affine
+from numpy import datetime64
+from odc.geo.geobox import GeoBox
+from odc.geo.geom import CRS
+from pandas import DataFrame as PandasDataFrame
+from rasterio.warp import transform_bounds
+
+#
+# Prefix used by GDAL to read files through HTTP
+#
+VSICURL_PREFIX = "/vsicurl/"
+
+#
+# Host used by Microsoft Planetary Computer to store data
+#
+MPC_HOST_SUFFIX = "blob.core.windows.net"
+
+
+#
+# Grid operations
+#
+def files_geobox(files: PandasDataFrame) -> GeoBox:
+    """Create the geobox covering all files of a grid group.
+
+    The geobox uses the native resolution and CRS of the files, so data is read
+    without resampling.
+
+    Args:
+        files (PandasDataFrame): Files of a single grid group.
+
+    Returns:
+        GeoBox: Geobox covering all files.
+    """
+    xres = float(files["xres"].iloc[0])
+    yres = float(files["yres"].iloc[0])
+
+    # Extent covering all files of the group
+    xmin = float(files["xmin"].min())
+    xmax = float(files["xmax"].max())
+    ymin = float(files["ymin"].min())
+    ymax = float(files["ymax"].max())
+
+    # Shape (rounded, as files of a group share the same grid)
+    width = int(round((xmax - xmin) / xres))
+    height = int(round((ymax - ymin) / yres))
+
+    return GeoBox(
+        shape=(height, width),
+        affine=Affine(xres, 0.0, xmin, 0.0, -yres, ymax),
+        crs=CRS(str(files["crs"].iloc[0])),
+    )
+
+
+def grid_group_name(files: PandasDataFrame, index: int) -> str:
+    """Create a name for a grid group.
+
+    Args:
+        files (PandasDataFrame): Files of a single grid group.
+
+        index (int): Position of the group, used when the CRS has no EPSG code.
+
+    Returns:
+        str: Group name (e.g., ``epsg32720-10m``).
+    """
+    crs = CRS(str(files["crs"].iloc[0]))
+    resolution = float(files["xres"].iloc[0])
+
+    try:
+        crs_name = f"epsg{crs.epsg}" if crs.epsg else f"grid{index}"
+
+    except Exception:
+        crs_name = f"grid{index}"
+
+    return f"{crs_name}-{resolution:g}m"
+
+
+#
+# STAC items
+#
+def stac_items_from_files(files: PandasDataFrame) -> list[pystac.Item]:
+    """Create STAC Items from cube files.
+
+    One item is created for each ``(tile, date)``, with one asset per band. All
+    item properties come from the cube metadata: no file is read.
+
+    Cubes can have more than one file for the same tile, date and band, as
+    collections may have multiple versions of an acquisition. Each version is
+    described as its own item, so all of them are used when data is read.
+
+    Args:
+        files (PandasDataFrame): Files of a single grid group.
+
+    Returns:
+        list[pystac.Item]: Items describing the files.
+    """
+    items = []
+
+    # Files of the same tile, date and band are versions of an acquisition
+    files = files.copy()
+    files["version"] = files.groupby(["tile", "date", "band"]).cumcount()
+
+    for (tile, date, version), group in files.groupby(
+        ["tile", "date", "version"], sort=True
+    ):
+        crs = str(group["crs"].iloc[0])
+        assets = {}
+
+        for _, file in group.iterrows():
+            transform = Affine(
+                a=float(file["xres"]),
+                b=0.0,
+                c=float(file["xmin"]),
+                d=0.0,
+                e=-float(file["yres"]),
+                f=float(file["ymax"]),
+            )
+
+            # Create asset
+            asset = pystac.Asset(
+                href=str(file["path"]),
+                roles=["data"],
+            )
+
+            # Define extra fields
+            asset.extra_fields.update(
+                {
+                    "proj:wkt2": crs,
+                    "proj:shape": [int(file["nrows"]), int(file["ncols"])],
+                    "proj:transform": [*list(transform)[:6], 0.0, 0.0, 1.0],
+                }
+            )
+
+            # Save band
+            assets[str(file["band"])] = asset
+
+        # Footprint, in geographic coordinates (required by STAC)
+        bbox = list(
+            transform_bounds(
+                src_crs=crs,
+                dst_crs="EPSG:4326",
+                left=float(group["xmin"].min()),
+                bottom=float(group["ymin"].min()),
+                right=float(group["xmax"].max()),
+                top=float(group["ymax"].max()),
+            )
+        )
+
+        # Create item
+        item = pystac.Item(
+            id=f"{tile}_{date}_{version}",
+            geometry={
+                "type": "Polygon",
+                "coordinates": [
+                    [
+                        [bbox[0], bbox[1]],
+                        [bbox[2], bbox[1]],
+                        [bbox[2], bbox[3]],
+                        [bbox[0], bbox[3]],
+                        [bbox[0], bbox[1]],
+                    ]
+                ],
+            },
+            bbox=bbox,
+            datetime=datetime64(str(date)).astype("datetime64[s]").item(),
+            properties={"tile": tile},
+        )
+
+        # Add assets
+        for band, asset in assets.items():
+            item.add_asset(band, asset)
+
+        # Save item
+        items.append(item)
+
+    # Return!
+    return items
+
+
+#
+# Data access
+#
+def signature_file_url(url: str) -> str:
+    """Refresh the credentials of a file URL.
+
+    Cubes store the credentials available when they were created. As these
+    credentials expire, they are refreshed before data is read.
+
+    Args:
+        url (str): File URL.
+
+    Returns:
+        str: URL with refreshed credentials, if required.
+    """
+    prefix = VSICURL_PREFIX if url.startswith(VSICURL_PREFIX) else ""
+    address = url[len(prefix) :]
+
+    parsed = urlparse(address)
+
+    # Only data with expiring credentials is refreshed
+    if not parsed.netloc.endswith(MPC_HOST_SUFFIX) or not parsed.query:
+        return url
+
+    try:
+        from planetary_computer import sign
+
+    except ImportError:
+        return url
+
+    return prefix + sign(urlunparse(parsed._replace(query="")))