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

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysits
-Version: 1.5.3.dev0
+Version: 1.5.3.dev2
 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
@@ -56,6 +56,8 @@ or the development version:
 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)
 
 To set up a local development environment:
@@ -108,7 +110,7 @@ ruff check .
 
 ## 📚 Learn more
 
-Explore the [examples](./examples) directory for usage demos and tutorials.
+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
 

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

@@ -16,6 +16,8 @@ or the development version:
 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)
 
 To set up a local development environment:
@@ -68,7 +70,7 @@ ruff check .
 
 ## 📚 Learn more
 
-Explore the [examples](./examples) directory for usage demos and tutorials.
+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
 

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

@@ -17,7 +17,7 @@
 
 [project]
 name = "pysits"
-version = "1.5.3.dev0"
+version = "1.5.3.dev2"
 description = "Python wrapper for the sits R package"
 readme = "README.md"
 requires-python = ">=3.10,<4"

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

@@ -42,6 +42,7 @@ from .sits.cube import (
     sits_confidence_sampling,
     sits_cube,
     sits_cube_copy,
+    sits_mosaic,
     sits_reclassify,
     sits_regularize,
     sits_texture,
@@ -71,6 +72,7 @@ from .sits.ml import (
     sits_formula_linear,
     sits_formula_logref,
     sits_kfold_validate,
+    sits_lightgbm,
     sits_lighttae,
     sits_mlp,
     sits_model_export,
@@ -83,7 +85,7 @@ from .sits.ml import (
     sits_xgboost,
 )
 from .sits.segment import sits_segment, sits_slic
-from .sits.tiles import sits_mgrs_to_roi, sits_tiles_to_roi
+from .sits.tiles import sits_mgrs_to_roi, sits_roi_to_tiles, sits_tiles_to_roi
 from .sits.ts import (
     sits_cluster_clean,
     sits_cluster_dendro,
@@ -113,7 +115,7 @@ from .sits.ts import (
 )
 from .sits.tuning import sits_tuning, sits_tuning_hparams
 from .sits.utils import (
-    load_samples_dataset,
+    load_samples,
     r_package_dir,
     r_set_seed,
     read_rds,
@@ -140,6 +142,7 @@ __all__ = (
     "sits_confidence_sampling",
     "sits_variance",
     "sits_texture",
+    "sits_mosaic",
     # Colors
     "sits_colors",
     "sits_colors_reset",
@@ -175,6 +178,7 @@ __all__ = (
     "sits_lighttae",
     "sits_svm",
     "sits_xgboost",
+    "sits_lightgbm",
     "sits_tae",
     "sits_kfold_validate",
     "sits_model_export",
@@ -209,6 +213,7 @@ __all__ = (
     # Tiles
     "sits_mgrs_to_roi",
     "sits_tiles_to_roi",
+    "sits_roi_to_tiles",
     # Segments
     "sits_segment",
     "sits_slic",
@@ -237,7 +242,7 @@ __all__ = (
     "read_rds",
     "r_package_dir",
     "r_set_seed",
-    "load_samples_dataset",
+    "load_samples",
     # Package settings
     "__version__",
 )

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

@@ -20,10 +20,25 @@
 from collections.abc import Callable
 from typing import Any
 
-from rpy2.robjects import r
+from rpy2.robjects import r as rpy2_r_interface
 from rpy2.robjects.packages import importr
 
 
+def load_package(name: str, min_version: str | None = None) -> Any:
+    """Load R package."""
+    if min_version:
+        has_min_version = rpy2_r_interface(
+            f'packageVersion("{name}") >= "{min_version}"'
+        )
+
+        if not has_min_version[0]:
+            raise RuntimeError(
+                f"`{name}` must have at least version {min_version} or greater."
+            )
+
+    return importr(name)
+
+
 def load_data_from_package(name: str, package: str, **kwargs) -> object:
     """Load data from package.
 
@@ -36,7 +51,7 @@ def load_data_from_package(name: str, package: str, **kwargs) -> object:
 
         **kwargs: Additional arguments to pass to the function.
     """
-    return r.data(name, package=package, **kwargs)
+    return rpy2_r_interface.data(name, package=package, **kwargs)
 
 
 def load_data_from_global(name: str) -> object:
@@ -47,7 +62,7 @@ def load_data_from_global(name: str) -> object:
     Args:
         name (str): Dataset name.
     """
-    return r[name]
+    return rpy2_r_interface[name]
 
 
 def load_function_from_package(name: str) -> Callable[..., Any]:

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

@@ -17,19 +17,20 @@
 
 """backend packages."""
 
-from rpy2.robjects.packages import importr
+from pysits.backend.loaders import load_package
+from pysits.settings import __sitsver__
 
 # system pakage
-r_pkg_base = importr("base")
-r_pkg_grdevices = importr("grDevices")
+r_pkg_base = load_package("base")
+r_pkg_grdevices = load_package("grDevices")
 
 # sits package
-r_pkg_sits = importr("sits")
+r_pkg_sits = load_package("sits", min_version=__sitsver__)
 
 # sits-dependencies packages
-r_pkg_tibble = importr("tibble")
-r_pkg_leaflet = importr("leaflet")
-r_pkg_kohonen = importr("kohonen")
-r_pkg_sf = importr("sf")
-r_pkg_htmlwidgets = importr("htmlwidgets")
-r_pkg_arrow = importr("arrow")
+r_pkg_tibble = load_package("tibble")
+r_pkg_leaflet = load_package("leaflet")
+r_pkg_kohonen = load_package("kohonen")
+r_pkg_sf = load_package("sf")
+r_pkg_htmlwidgets = load_package("htmlwidgets")
+r_pkg_arrow = load_package("arrow")

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

@@ -25,7 +25,7 @@ from pandas import DataFrame as PandasDataFrame
 from pandas.core.generic import NDFrame as PandasNDFrame
 from pyarrow import feather
 from rpy2.rinterface_lib.sexp import NULLType
-from rpy2.robjects import StrVector
+from rpy2.robjects import StrVector, pandas2ri
 from rpy2.robjects import globalenv as rpy2_globalenv
 from rpy2.robjects import r as rpy2_r_interface
 from rpy2.robjects.vectors import DataFrame as RDataFrame
@@ -160,6 +160,10 @@ def _tibble_to_pandas_arrow(
     tmp_path = tmp.name
     tmp.close()
 
+    # Check if instance is a empty
+    if instance.nrow == 0:
+        return pandas2ri.rpy2py(instance)
+
     # Extract columns from the data
     data_columns = r_pkg_base.colnames(instance)
 

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/pysits/settings.py

@@ -36,9 +36,14 @@ rpy2.rinterface_lib.callbacks.consolewrite_warnerror = lambda x: None
 #
 os.environ["TORCH_INSTALL"] = "0"
 
+#
+# Compatible sits version
+#
+__sitsver__ = "1.5.3"
+
 #
 # Package version
 #
-__version__ = "1.5.3.dev0"
+__version__ = "1.5.3"
 
 __all__ = ("__version__",)

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/pysits/sits/context.py

@@ -17,20 +17,18 @@
 
 """Global objects from sits."""
 
-from pysits.sits.utils import load_samples_dataset
+from pysits.sits.utils import load_samples
 
 #
 # Samples objects
 #
-cerrado_2classes = load_samples_dataset("cerrado_2classes", package="sits")
+cerrado_2classes = load_samples("cerrado_2classes", package="sits")
 
-samples_modis_ndvi = load_samples_dataset("samples_modis_ndvi", package="sits")
-samples_l8_rondonia_2bands = load_samples_dataset(
-    "samples_l8_rondonia_2bands", package="sits"
-)
+samples_modis_ndvi = load_samples("samples_modis_ndvi", package="sits")
+samples_l8_rondonia_2bands = load_samples("samples_l8_rondonia_2bands", package="sits")
 
 
 #
 # Points objects
 #
-point_mt_6bands = load_samples_dataset("point_mt_6bands", package="sits")
+point_mt_6bands = load_samples("point_mt_6bands", package="sits")

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/pysits/sits/cube.py

@@ -72,6 +72,12 @@ def sits_cube_copy(*args, **kwargs) -> SITSCubeModel:
     """Copy cubes."""
 
 
+@function_call(r_pkg_sits.sits_mosaic, SITSCubeModel)
+@attach_doc("sits_mosaic")
+def sits_mosaic(*args, **kwargs) -> SITSCubeModel:
+    """Mosaic classified cubes."""
+
+
 #
 # Probability and metrics
 #

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/pysits/sits/ml.py

@@ -73,6 +73,8 @@ sits_resnet = closure_factory("sits_resnet", converters=dl_converters)
 sits_rfor = closure_factory("sits_rfor")
 sits_svm = closure_factory("sits_svm")
 sits_xgboost = closure_factory("sits_xgboost")
+sits_lightgbm = closure_factory("sits_lightgbm")
+
 
 #
 # Extra parameters - SVM

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/pysits/sits/tiles.py

@@ -20,6 +20,7 @@
 from pysits.backend.pkgs import r_pkg_sits
 from pysits.conversions.decorators import function_call
 from pysits.docs import attach_doc
+from pysits.models.data.frame import SITSFrameSF
 from pysits.models.data.vector import SITSNamedVector
 
 
@@ -33,3 +34,9 @@ def sits_mgrs_to_roi(*args, **kwargs) -> SITSNamedVector:
 @attach_doc("sits_tiles_to_roi")
 def sits_tiles_to_roi(*args, **kwargs) -> SITSNamedVector:
     """Convert tiles to ROI."""
+
+
+@function_call(r_pkg_sits.sits_roi_to_tiles, SITSFrameSF)
+@attach_doc("sits_roi_to_tiles")
+def sits_roi_to_tiles(*args, **kwargs) -> SITSFrameSF:
+    """Find tiles of a given ROI and Grid System."""

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/pysits/sits/utils.py

@@ -106,7 +106,7 @@ def r_package_dir(content_dir: str, package: str) -> Path | None:
     return None if not dir_path.exists() else dir_path
 
 
-def load_samples_dataset(name: str, package: str, **kwargs) -> SITSTimeSeriesModel:
+def load_samples(name: str, package: str, **kwargs) -> SITSTimeSeriesModel:
     """Load sits data from package.
 
     Args:

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/pysits/visualization/base.py

@@ -104,7 +104,8 @@ def _base_plot(
         # Assuming a plot is a list of elements, we always have many elements.
         # Cases where we have a single element indicates that the plot object is
         # inside a list.
-        while len(plots) == 1:
+        # This is only true when the object is not a ggplot object
+        while "ggplot2::ggplot" not in list(plots.rclass) and len(plots) == 1:
             plots = plots[0]
 
         # Create a temporary file

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/tests/test_models.py

@@ -31,6 +31,7 @@ from pysits.sits.data import sits_labels, sits_select
 from pysits.sits.ml import (
     sits_formula_linear,
     sits_formula_logref,
+    sits_lightgbm,
     sits_lighttae,
     sits_mlp,
     sits_model_export,
@@ -55,6 +56,7 @@ ALL_MODELS = [
     sits_rfor,
     sits_svm,
     sits_xgboost,
+    sits_lightgbm,
 ]
 
 

{pysits-1.5.3.dev0 → pysits-1.5.3.dev2}/uv.lock

@@ -1068,7 +1068,7 @@ wheels = [
 
 [[package]]
 name = "pysits"
-version = "0.0.1"
+version = "1.5.3.dev1"
 source = { editable = "." }
 dependencies = [
     { name = "geopandas" },

pysits-1.5.3.dev0/examples/apply.py

@@ -1,80 +0,0 @@
-#
-# 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/>.
-#
-
-"""apply example."""
-
-import os
-
-from pysits import *
-
-#
-# General definition
-#
-# Output directory
-output_dir = "data/output/apply"
-
-# Cube directory
-cube_dir = "data/cube/"
-
-
-#
-# 1. Create directory
-#
-os.makedirs(output_dir, exist_ok=True)
-
-
-#
-# 2. Load cube
-#
-cube = sits_cube(
-    source="BDC",
-    collection="MOD13Q1-6.1",
-    data_dir=cube_dir,
-)
-
-
-#
-# 3. Apply
-#
-
-# NDVI Median
-cube_apply = sits_apply(
-    data=cube,
-    NDVIMEDIAN="w_median(NDVI)",
-    window_size=5,
-    output_dir=output_dir,
-    multicores=4,
-)
-
-# NDVI / 2
-cube_apply = sits_apply(
-    data=cube_apply,
-    NDVIDIV="NDVI / 2",
-    window_size=5,
-    output_dir=output_dir,
-    multicores=4,
-)
-
-#
-# 4. Plot
-#
-
-# NDVI Median
-plot(cube_apply, band="NDVIMEDIAN")
-
-# NDVI / 2
-plot(cube_apply, band="NDVIDIV")

pysits-1.5.3.dev0/examples/classification.py

@@ -1,120 +0,0 @@
-#
-# 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/>.
-#
-
-"""classification example."""
-
-import os
-
-from pysits import *
-
-#
-# General definition
-#
-
-# Output directory
-output_dir = "data/output/classification"
-
-# Cube directory
-cube_dir = "data/cube/"
-
-# Samples file
-samples_file = "data/samples/samples_sinop_crop.csv"
-
-
-#
-# 1. Create directory
-#
-os.makedirs(output_dir, exist_ok=True)
-
-
-#
-# 2. Load cube
-#
-cube = sits_cube(
-    source="BDC",
-    collection="MOD13Q1-6.1",
-    data_dir=cube_dir,
-)
-
-#
-# 3. Get cube bands
-#
-sits_bands(cube)
-
-
-#
-# 4. Get cube timeline
-#
-sits_timeline(cube)
-
-
-#
-# 5. Get time series
-#
-samples_ts = sits_get_data(
-    cube=cube,
-    samples=samples_file,
-)
-
-
-#
-# 6. Train model
-#
-rfor_model = sits_train(
-    samples=samples_ts,
-    ml_method=sits_rfor(),
-)
-
-
-#
-# 7. Classify cube
-#
-probs_cube = sits_classify(
-    data=cube,
-    ml_model=rfor_model,
-    output_dir=output_dir,
-)
-
-
-#
-# 8. Smooth classification
-#
-bayes_cube = sits_smooth(
-    cube=probs_cube,
-    output_dir=output_dir,
-)
-
-
-#
-# 9. Label classification
-#
-label_cube = sits_label_classification(
-    cube=bayes_cube,
-    output_dir=output_dir,
-)
-
-
-#
-# 10. Plot
-#
-plot(label_cube)
-
-
-#
-# 11. Classification labels
-#
-sits_labels(label_cube)

pysits-1.5.3.dev0/examples/cube-copy.py

@@ -1,58 +0,0 @@
-#
-# 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/>.
-#
-
-"""classification example."""
-
-import os
-
-from pysits import *
-
-#
-# General definitions
-#
-output_dir = "data/output/copy"
-
-
-#
-# 1. Create directory
-#
-os.makedirs(output_dir, exist_ok=True)
-
-
-#
-# 2. Define cube
-#
-bdc_cube = sits_cube(
-    source="BDC",
-    collection="CBERS-WFI-16D",
-    tiles=["007004", "007005"],
-    bands=["B15", "CLOUD"],
-    start_date="2018-01-01",
-    end_date="2018-01-12",
-)
-
-
-#
-# 3. Copy from remote to local
-#
-cube_local = sits_cube_copy(
-    cube=bdc_cube,
-    output_dir=output_dir,
-    roi=dict(lon_min=-46.5, lat_min=-45.5, lon_max=-15.5, lat_max=-14.6),
-    multicores=2,
-    res=250,
-)

pysits-1.5.3.dev0/examples/data/samples/samples_sinop_crop.csv

@@ -1,19 +0,0 @@
-id,longitude,latitude,start_date,end_date,label
-1,-55.65931,-11.76267,2013-09-14,2014-08-29,Pasture
-2,-55.64833,-11.76385,2013-09-14,2014-08-29,Pasture
-3,-55.66738,-11.78032,2013-09-14,2014-08-29,Forest
-4,-55.64747,-11.75276,2013-09-14,2014-08-29,Pasture
-5,-55.65742,-11.78788,2013-09-14,2014-08-29,Forest
-6,-55.63168,-11.74771,2013-09-14,2014-08-29,Forest
-7,-55.68369,-11.73679,2013-09-14,2014-08-29,Soy_Corn
-8,-55.69004,-11.73343,2013-09-14,2014-08-29,Soy_Corn
-9,-55.67854,-11.74519,2013-09-14,2014-08-29,Soy_Corn
-10,-55.64215,-11.77595,2013-09-14,2014-08-29,Soy_Corn
-11,-55.63219,-11.77259,2013-09-14,2014-08-29,Soy_Corn
-12,-55.62223,-11.78653,2013-09-14,2014-08-29,Soy_Corn
-13,-55.75218,-11.73225,2013-09-14,2014-08-29,Cerrado
-14,-55.75218,-11.68855,2013-09-14,2014-08-29,Cerrado
-15,-55.68764,-11.61525,2013-09-14,2014-08-29,Cerrado
-16,-55.63614,-11.63110,2013-09-14,2014-08-29,Soy_Corn
-17,-55.37384,-11.71746,2013-09-14,2014-08-29,Soy_Corn
-18,-55.52284,-11.58296,2013-09-14,2014-08-29,Pasture