Merge pull request #149 from siapy/develop

Develop

.github/FUNDING.yml

@@ -1 +1,5 @@
-github: [janezlapajne]
+github:
+  - janezlapajne
+  - siapy
+ko_fi: janezlapajne
+custom: buymeacoffee.com/janezlapajne

mkdocs.yml

@@ -98,7 +98,7 @@ nav:
           - Plots: api/utils/plots.md
   - Contributing: contributing.md
   - Release Notes: changelog.md
-  - License: license.md
+  - License: permit.md
 
 markdown_extensions:
   # Python Markdown

siapy/entities/images.py

@@ -220,6 +220,23 @@ def to_signatures(self, pixels: "Pixels") -> Signatures:
         signatures = Signatures.from_array_and_pixels(image_arr, pixels)
         return signatures
 
+    def to_subarray(self, pixels: "Pixels") -> np.ndarray:
+        image_arr = self.to_numpy()
+        u_max = pixels.u().max()
+        u_min = pixels.u().min()
+        v_max = pixels.v().max()
+        v_min = pixels.v().min()
+        # create new image
+        image_arr_area = np.nan * np.ones(
+            (v_max - v_min + 1, u_max - u_min + 1, self.bands)
+        )
+        # convert original coordinates to coordinates for new image
+        v_norm = pixels.v() - v_min
+        u_norm = pixels.u() - u_min
+        # write values from original image to new image
+        image_arr_area[v_norm, u_norm, :] = image_arr[pixels.v(), pixels.u(), :]
+        return image_arr_area
+
     def mean(self, axis: int | tuple[int] | None = None) -> float | np.ndarray:
         image_arr = self.to_numpy()
         return np.nanmean(image_arr, axis=axis)

siapy/entities/signatures.py

@@ -76,7 +76,7 @@ def _create(cls, pixels: Pixels, signals: Signals) -> "Signatures":
     def from_array_and_pixels(cls, image: np.ndarray, pixels: Pixels) -> "Signatures":
         u = pixels.u()
         v = pixels.v()
-        signals_list = list(image[v, u, :])
+        signals_list = image[v, u, :]
         signals = Signals(pd.DataFrame(signals_list))
         return cls._create(pixels, signals)
 

tests/entities/test_entities_images.py

@@ -7,6 +7,7 @@
 
 from siapy.entities import Pixels, Shape, SpectralImage
 from siapy.entities.images import GeometricShapes, _parse_description
+from siapy.utils.plots import pixels_select_lasso
 
 
 def test_envi_open(configs):
@@ -180,6 +181,29 @@ def test_to_signatures(spectral_images):
     assert np.array_equal(signatures.pixels.df.iloc[2].to_numpy(), iterable[2])
 
 
+@pytest.mark.manual
+def test_to_signatures_perf(spectral_images):
+    spectral_image_vnir = spectral_images.vnir
+    selected_areas_vnir = pixels_select_lasso(spectral_image_vnir)
+    spectral_image_vnir.to_signatures(selected_areas_vnir[0]).signals.to_numpy()
+    pass
+
+
+def test_to_subarray(spectral_images):
+    spectral_image_vnir = spectral_images.vnir
+    iterable = [(1, 2), (3, 4), (2, 4)]
+    pixels = Pixels.from_iterable(iterable)
+    subarray = spectral_image_vnir.to_subarray(pixels)
+    expected_subarray = np.full((3, 3, spectral_image_vnir.bands), np.nan)
+    image_array = spectral_image_vnir.to_numpy()
+    expected_subarray[0, 0, :] = image_array[2, 1, :]
+    expected_subarray[2, 2, :] = image_array[4, 3, :]
+    expected_subarray[2, 1, :] = image_array[4, 2, :]
+
+    assert expected_subarray.shape == (3, 3, spectral_image_vnir.bands)
+    assert np.array_equal(subarray, expected_subarray, equal_nan=True)
+
+
 def test_mean(spectral_images):
     spectral_image_vnir = spectral_images.vnir