Merge pull request #195 from siapy/fix

chore: remove unnecessary blank line in pyproject.toml

Author: janezlapajne

.github/copilot-instructions.md

@@ -0,0 +1,54 @@
+# SiaPy Style Guide
+
+## Type Hints & Python Version
+
+- Use Python 3.10+ type hints (prefer `x | y` over `Union[x, y]`)
+- Include type hints for all functions and class members
+
+## Code Style
+
+- 4-space indentation (PEP 8)
+- No docstrings needed
+- Define `__all__` directly under imports
+
+## Class Design
+
+- Use dataclasses for data-oriented classes
+- Use pydantic for data validation
+- Prefer property decorators for read-only access
+
+## Method Naming
+
+- Properties: simple noun (e.g. `name`, `value`)
+- Expensive getters: prefix with `get_` (e.g. `get_statistics()`)
+- Constructors: prefix with `from_` (e.g. `from_point()`)
+- Data converters: prefix with `to_` (e.g. `to_numpy()`)
+- File loaders: prefix with `open_` (e.g. `open_shapefile()`)
+- File savers: prefix with `save_` (e.g. `save_to_csv()`)
+- Actions/operations: use verbs (e.g. `calculate()`, `process()`)
+- Batch operations: use plural nouns (e.g. `process_items()`)
+- Boolean queries: prefix with `is_`, `has_` or `can_` (e.g. `is_valid()`, `has_data()`)
+- Factory methods: prefix with `create_` (e.g. `create_instance()`)
+
+## Class Organization
+
+1. Dunder methods
+2. Class methods
+3. Properties
+4. Instance methods
+
+## Error Handling
+
+- Use custom exceptions from `siapy.core.exceptions`:
+  - InvalidFilepathError
+  - InvalidInputError
+  - InvalidTypeError
+  - ProcessingError
+  - ConfigurationError
+  - MethodNotImplementedError
+  - DirectInitializationError
+
+## Other
+
+- Use `from siapy.core import logger` for logging
+- Use Protocol/ABC for interfaces where appropriate

docs/api/entities/shapefiles.md

@@ -0,0 +1 @@
+::: siapy.entities.shapes.shape

docs/api/entities/shapes.md

@@ -88,10 +88,9 @@ nav:
               - Rasterio Library: api/entities/images/rasterio_lib.md
               - Spectral Library: api/entities/images/spectral_lib.md
               - Spectral Images: api/entities/images/spimage.md
+          - Shape: api/entities/shapes/shape.md
           - Image Sets: api/entities/imagesets.md
           - Pixels: api/entities/pixels.md
-          - Shapefiles: api/entities/shapefiles.md
-          - Shapes: api/entities/shapes.md
           - Signatures: api/entities/signatures.md
       - Features:
           - Features: api/features/features.md

docs/api/entities/shapes/shape.md

@@ -44,6 +44,7 @@ dependencies = [
     "rasterio>=1.4.3",
     "xarray>=2025.1.2",
     "rioxarray>=0.18.2",
+    "shapely>=2.0.7",
 ]
 
 [dependency-groups]
@@ -109,7 +110,6 @@ ignore_missing_imports = true
 module = "geopandas.*"
 ignore_missing_imports = true
 
-
 [[tool.mypy.overrides]]
 module = "rasterio.*"
 ignore_missing_imports = true

mkdocs.yml

@@ -11,6 +11,7 @@
 
 __all__ = [
     "SpectralLibType",
+    "XarrayType",
     "ImageType",
     "ImageSizeType",
     "ImageDataType",

pdm.lock

@@ -22,6 +22,7 @@ class MetaDataEntity(BaseModel):
     shape_idx: int
     shape_type: str
     shape_label: str | None
+    geometry_idx: int
 
 
 class TabularDataEntity(MetaDataEntity):
@@ -61,17 +62,20 @@ def process_image_data(self):
         self.data_entities.clear()
         for image_idx, image in enumerate(self.image_set):
             for shape_idx, shape in enumerate(image.geometric_shapes.shapes):
-                signatures = image.to_signatures(shape.convex_hull())
-                entity = TabularDataEntity(
-                    image_idx=image_idx,
-                    shape_idx=shape_idx,
-                    image_filepath=image.filepath,
-                    camera_id=image.camera_id,
-                    shape_type=shape.shape_type,
-                    shape_label=shape.label,
-                    signatures=signatures,
-                )
-                self.data_entities.append(entity)
+                convex_hulls = shape.get_pixels_within_convex_hull()
+                for geometry_idx, pixels in enumerate(convex_hulls):
+                    signatures = image.to_signatures(pixels)
+                    entity = TabularDataEntity(
+                        image_idx=image_idx,
+                        shape_idx=shape_idx,
+                        geometry_idx=geometry_idx,
+                        image_filepath=image.filepath,
+                        camera_id=image.camera_id,
+                        shape_type=shape.shape_type,
+                        shape_label=shape.label,
+                        signatures=signatures,
+                    )
+                    self.data_entities.append(entity)
 
     def generate_dataset_data(self, mean_signatures=True) -> TabularDatasetData:
         self._check_data_entities()
@@ -92,6 +96,7 @@ def generate_dataset_data(self, mean_signatures=True) -> TabularDatasetData:
                     "shape_idx": [str(entity.shape_idx)] * signatures_len,
                     "shape_type": [entity.shape_type] * signatures_len,
                     "shape_label": [entity.shape_label] * signatures_len,
+                    "geometry_idx": [str(entity.geometry_idx)] * signatures_len,
                 }
             )
 

pyproject.toml

@@ -1,13 +1,13 @@
 from .images import SpectralImage
 from .imagesets import SpectralImageSet
 from .pixels import Pixels
-from .shapes import Shapefile
+from .shapes import Shape
 from .signatures import Signatures
 
 __all__ = [
     "SpectralImage",
     "SpectralImageSet",
     "Pixels",
     "Signatures",
-    "Shapefile",
+    "Shape",
 ]