Fix

docs/install.md

@@ -15,12 +15,26 @@ pip install siapy
 
 ### Alternative Installation Methods
 
-__Using Conda__
+__Python package and dependency managers__
 
-You can also install siapy using conda:
+You can also install siapy using other popular Python package and dependency managers:
+
+- PDM:
+
+```bash
+pdm add siapy
+```
+
+- Poetry:
+
+```bash
+poetry add siapy
+```
+
+- uv:
 
 ```bash
-conda install -c conda-forge siapy
+uv add siapy
 ```
 
 __Manually__

siapy/entities/imagesets.py

@@ -1,6 +1,6 @@
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Any, Iterator
+from typing import Any, Iterator, Sequence
 
 import numpy as np
 from rich.progress import track
@@ -31,8 +31,8 @@ def __getitem__(self, index) -> SpectralImage:
     def from_paths(
         cls,
         *,
-        header_paths: list[str | Path],
-        image_paths: list[str | Path] | None = None,
+        header_paths: Sequence[str | Path],
+        image_paths: Sequence[str | Path] | None = None,
     ):
         if image_paths is not None and len(header_paths) != len(image_paths):
             raise ValueError("The length of hdr_paths and img_path must be equal.")

siapy/entities/pixels.py

@@ -1,4 +1,5 @@
 from dataclasses import dataclass
+from pathlib import Path
 from typing import Annotated, ClassVar, Iterable, NamedTuple
 
 import numpy as np
@@ -28,10 +29,15 @@ def from_iterable(
                 Annotated[int, "v coordinate on the image"],
             ]
         ],
-    ):
+    ) -> "Pixels":
         df = pd.DataFrame(iterable, columns=[Pixels.coords.U, Pixels.coords.V])
         return cls(df)
 
+    @classmethod
+    def load_from_parquet(cls, filepath: str | Path) -> "Pixels":
+        df = pd.read_parquet(filepath)
+        return cls(df)
+
     @property
     def df(self) -> pd.DataFrame:
         return self._data
@@ -49,3 +55,6 @@ def v(self) -> pd.Series:
 
     def to_numpy(self) -> np.ndarray:
         return self.df.to_numpy()
+
+    def save_to_parquet(self, filepath: str | Path) -> None:
+        self.df.to_parquet(filepath, index=True)

siapy/entities/signatures.py

@@ -1,4 +1,5 @@
 from dataclasses import dataclass
+from pathlib import Path
 from typing import Any
 
 import numpy as np
@@ -13,6 +14,11 @@
 class Signals:
     _data: pd.DataFrame
 
+    @classmethod
+    def load_from_parquet(cls, filepath: str | Path) -> "Signals":
+        df = pd.read_parquet(filepath)
+        return cls(df)
+
     @property
     def df(self) -> pd.DataFrame:
         return self._data
@@ -23,6 +29,9 @@ def to_numpy(self) -> np.ndarray:
     def mean(self) -> np.ndarray:
         return np.nanmean(self.to_numpy(), axis=0)
 
+    def save_to_parquet(self, filepath: str | Path) -> None:
+        self.df.to_parquet(filepath, index=True)
+
 
 @dataclass
 class SignaturesFilter:
@@ -84,6 +93,11 @@ def from_dataframe(cls, dataframe: pd.DataFrame) -> "Signatures":
         signals = Signals(dataframe.drop(columns=[Pixels.coords.U, Pixels.coords.V]))
         return cls._create(pixels, signals)
 
+    @classmethod
+    def load_from_parquet(cls, filepath: str | Path) -> "Signatures":
+        df = pd.read_parquet(filepath)
+        return cls.from_dataframe(df)
+
     @property
     def pixels(self) -> Pixels:
         return self._pixels
@@ -100,3 +114,6 @@ def to_numpy(self) -> np.ndarray:
 
     def filter(self) -> SignaturesFilter:
         return SignaturesFilter(self.pixels, self.signals)
+
+    def save_to_parquet(self, filepath: str | Path) -> None:
+        self.to_dataframe().to_parquet(filepath, index=True)

siapy/utils/plots.py

@@ -1,4 +1,5 @@
 import sys
+from typing import Any
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -60,7 +61,9 @@ def onexit(event):
     return Pixels.from_iterable(coordinates)
 
 
-def pixels_select_lasso(image: ImageType) -> list[Pixels]:
+def pixels_select_lasso(
+    image: ImageType, selector_props: dict[str, Any] | None = None
+) -> list[Pixels]:
     image_display = validate_image_to_numpy_3channels(image)
 
     x, y = np.meshgrid(
@@ -100,7 +103,12 @@ def accept(event):
             enter_clicked = 1
             plt.close()
 
-    lasso = LassoSelector(ax, onselect)  # noqa: F841
+    props = (
+        selector_props
+        if selector_props is not None
+        else {"color": "red", "linewidth": 2, "linestyle": "-"}
+    )
+    lasso = LassoSelector(ax, onselect, props=props)  # noqa: F841
     fig.canvas.mpl_connect("button_release_event", onrelease)
     fig.canvas.mpl_connect("close_event", onexit)
     fig.canvas.mpl_connect("key_press_event", accept)

tests/entities/test_entities_pixels.py

@@ -1,3 +1,7 @@
+import os
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
 import numpy as np
 import pandas as pd
 
@@ -51,3 +55,14 @@ def test_to_numpy():
     pixels = Pixels(df)
     expected_array = df.to_numpy()
     assert np.array_equal(pixels.to_numpy(), expected_array)
+
+
+def test_save_and_load_to_parquet():
+    pixels = Pixels.from_iterable(iterable)
+    with TemporaryDirectory() as tmpdir:
+        parquet_file = Path(tmpdir, "test_pixels.parquet")
+        pixels.save_to_parquet(parquet_file)
+        assert os.path.exists(parquet_file)
+        loaded_pixels = Pixels.load_from_parquet(parquet_file)
+        assert isinstance(loaded_pixels, Pixels)
+        assert loaded_pixels.df.equals(pixels.df)

tests/entities/test_entities_signatures.py

@@ -1,3 +1,7 @@
+import os
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
 import numpy as np
 import pandas as pd
 import pytest
@@ -22,6 +26,18 @@ def test_signals_mean():
     assert signals_mean.shape == (4,)
 
 
+def test_signals_save_and_load_to_parquet():
+    signals_df = pd.DataFrame([[1, 2, 4, 6], [3, 4, 3, 5]])
+    signals = Signals(signals_df)
+    with TemporaryDirectory() as tmpdir:
+        parquet_file = Path(tmpdir, "test_signals.parquet")
+        signals.save_to_parquet(parquet_file)
+        assert os.path.exists(parquet_file)
+        loaded_signals = Signals.load_from_parquet(parquet_file)
+        assert isinstance(loaded_signals, Signals)
+        assert loaded_signals.df.equals(signals.df)
+
+
 def test_signatures_filter_create():
     pixels_df = pd.DataFrame({"u": [0, 1], "v": [0, 1]})
     signals_df = pd.DataFrame([[1, 2], [3, 4]])
@@ -140,3 +156,15 @@ def test_signatures_from_dataframe():
 
     with pytest.raises(ValueError):
         Signatures.from_dataframe(df_missing_v)
+
+
+def test_signatures_save_and_load_to_parquet():
+    df = pd.DataFrame({"u": [0, 1], "v": [0, 1], "0": [1, 2], "1": [3, 4]})
+    signatures = Signatures.from_dataframe(df)
+    with TemporaryDirectory() as tmpdir:
+        parquet_file = Path(tmpdir, "test_signatures.parquet")
+        signatures.save_to_parquet(parquet_file)
+        assert os.path.exists(parquet_file)
+        loaded_signatures = Signatures.load_from_parquet(parquet_file)
+        assert isinstance(loaded_signatures, Signatures)
+        assert loaded_signatures.to_dataframe().equals(signatures.to_dataframe())

tests/utils/test_utils_plots.py

@@ -23,7 +23,7 @@ def test_pixels_select_click_manual(spectral_images):
 @pytest.mark.manual
 def test_pixels_select_lasso_manual(spectral_images):
     image_vnir = spectral_images.vnir
-    selected_areas = pixels_select_lasso(image_vnir)
+    selected_areas = pixels_select_lasso(image_vnir, selector_props={"color": "blue"})
     display_image_with_areas(image_vnir, selected_areas, color="blue")