Merge pull request #53 from siapy/develop

Develop

.github/PULL_REQUEST_TEMPLATE.md → .github/pull_request_template.md

@@ -20,4 +20,4 @@ Closes organization/repo#number
 
 <!-- List issues for GitHub to automatically close after merge to default branch. Type `#` and select from the list. See the [GitHub docs on linking PRs to issues](https://help.github.com/en/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue) for more. -->
 
-- [ ] I have reviewed the [Guidelines for Contributing](CONTRIBUTING.md) and the [Code of Conduct](CODE_OF_CONDUCT.md).
+- [ ] I have reviewed the [Guidelines for Contributing](../CONTRIBUTING.md) and the [Code of Conduct](../CODE_OF_CONDUCT.md).

.github/workflows/gitleaks.yml

@@ -7,7 +7,7 @@ jobs:
     name: gitleaks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: gitleaks/gitleaks-action@v2

.github/workflows/publish.yml

@@ -33,8 +33,8 @@ jobs:
       contents: read
       id-token: write
     steps:
-      - uses: actions/checkout@v3
-      - uses: pdm-project/setup-pdm@v3
+      - uses: actions/checkout@v4
+      - uses: pdm-project/setup-pdm@v4
         with:
           version: "head"
       - name: Publish package distributions to PyPI

SECURITY.md

@@ -0,0 +1,38 @@
+# Security Policy
+
+Security is very important for SiaPy and its community. 🔒
+
+Learn more about it below. 👇
+
+## Versions
+
+The latest version of SiaPy is supported.
+
+You are encouraged to update your SiaPy version frequently. This way you will benefit from the latest features, bug fixes, and **security fixes**.
+
+## Reporting a Vulnerability
+
+We take the security of our project seriously. If you have discovered a security vulnerability, we appreciate your cooperation in disclosing it to us in a responsible manner.
+
+Please report any security vulnerabilities by emailing us at [[email protected]]([email protected]).
+
+We will acknowledge receipt of your vulnerability report, assess it for validity and severity, and decide on the next steps. We ask that you do not publicly disclose the vulnerability until we have had a chance to address it.
+
+## What to include in your report
+
+To help us triage and prioritize the issue, please include as much information as possible, such as:
+
+- The version of our project you are using
+- A step-by-step description of how to reproduce the vulnerability
+- Any relevant logs or output
+- Any other information you think might be relevant
+
+## Public Discussions
+
+Please refrain from publicly discussing a potential security vulnerability.
+
+Discussing vulnerabilities in public forums before they are properly assessed and fixed can significantly increase the risk to the project and its users. It's better to discuss issues privately and work together to find a solution first, to limit the potential impact as much as possible. We appreciate your cooperation and understanding in handling sensitive matters with discretion.
+
+---
+
+Thank you for helping to keep SiaPy and its users safe. 🏅

siapy/entities/__init__.py

@@ -1,18 +1,12 @@
-from .containers import (
-    SpectralImageContainer,
-    SpectralImageContainerConfig,
-    SpectralImageMultiCameraContainer,
-)
 from .images import SpectralImage
+from .imagesets import SpectralImageSet
 from .pixels import Pixels
 from .shapes import Shape
 from .signatures import Signatures
 
 __all__ = [
     "SpectralImage",
-    "SpectralImageContainer",
-    "SpectralImageContainerConfig",
-    "SpectralImageMultiCameraContainer",
+    "SpectralImageSet",
     "Pixels",
     "Signatures",
     "Shape",

siapy/entities/images.py

@@ -125,9 +125,9 @@ def __str__(self) -> str:
 
     @classmethod
     def envi_open(
-        cls, *, hdr_path: str | Path, img_path: str | Path | None = None
+        cls, *, header_path: str | Path, image_path: str | Path | None = None
     ) -> "SpectralImage":
-        sp_file = sp.envi.open(file=hdr_path, image=img_path)
+        sp_file = sp.envi.open(file=header_path, image=image_path)
         if isinstance(sp_file, sp.io.envi.SpectralLibrary):
             raise ValueError("Opened file of type SpectralLibrary")
         return cls(sp_file)
@@ -165,18 +165,23 @@ def bands(self) -> int:
 
     @property
     def default_bands(self) -> list[int]:
-        if "default bands" not in self.metadata.keys():
-            return []
-        db = self.metadata["default bands"]
+        db = self.metadata.get("default bands", [])
         return list(map(int, db))
 
     @property
     def wavelengths(self) -> list[float]:
-        if "wavelength" not in self.metadata.keys():
-            return []
-        wavelength_data = self.metadata["wavelength"]
+        wavelength_data = self.metadata.get("wavelength", [])
         return list(map(float, wavelength_data))
 
+    @property
+    def description(self) -> dict[str, Any]:
+        description_str = self.metadata.get("description", {})
+        return _parse_description(description_str)
+
+    @property
+    def camera_id(self) -> str:
+        return self.description.get("ID", "")
+
     @property
     def geometric_shapes(self) -> GeometricShapes:
         return self._geometric_shapes
@@ -212,3 +217,32 @@ def _remove_nan(self, image: np.ndarray, nan_value: float = 0.0) -> np.ndarray:
         image_mask = np.bitwise_not(np.bool_(np.isnan(image).sum(axis=2)))
         image[~image_mask] = nan_value
         return image
+
+
+def _parse_description(description: str) -> dict[str, Any]:
+    def _parse():
+        data_dict = {}
+        for line in description.split("\n"):
+            key, value = line.split("=", 1)
+            key = key.strip()
+            value = value.strip()
+            if "," in value:  # Special handling for values with commas
+                value = [
+                    float(v) if v.replace(".", "", 1).isdigit() else v
+                    for v in value.split(",")
+                ]
+            elif value.isdigit():
+                value = int(value)
+            elif value.replace(".", "", 1).isdigit():
+                value = float(value)
+            data_dict[key] = value
+        return data_dict
+
+    try:
+        return _parse()
+    except ValueError as e:
+        raise ValueError(f"Error parsing description: {e}") from e
+    except KeyError as e:
+        raise KeyError(f"Missing key in description: {e}") from e
+    except Exception as e:
+        raise Exception(f"Unexpected error parsing description: {e}") from e

siapy/entities/imagesets.py

@@ -0,0 +1,59 @@
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Iterator
+
+from rich.progress import track
+
+from siapy.core import logger
+
+from .images import SpectralImage
+
+
+@dataclass
+class SpectralImageSet:
+    def __init__(self, spectral_images: list[SpectralImage] | None = None):
+        self._images = spectral_images if spectral_images is not None else []
+
+    def __len__(self) -> int:
+        return len(self.images)
+
+    def __str__(self) -> str:
+        return f"<{self.__class__.__name__} object with {len(self)} spectral images>"
+
+    def __iter__(self) -> Iterator[SpectralImage]:
+        return iter(self.images)
+
+    def __getitem__(self, index) -> SpectralImage:
+        return self.images[index]
+
+    @classmethod
+    def from_paths(
+        cls,
+        *,
+        header_paths: list[str | Path],
+        image_paths: list[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.")
+
+        if image_paths is None:
+            spectral_images = [
+                SpectralImage.envi_open(header_path=hdr_path)
+                for hdr_path in track(
+                    header_paths, description="Loading spectral images..."
+                )
+            ]
+        else:
+            spectral_images = [
+                SpectralImage.envi_open(header_path=hdr_path, image_path=img_path)
+                for hdr_path, img_path in track(
+                    zip(header_paths, image_paths),
+                    description="Loading spectral images...",
+                )
+            ]
+        logger.info("Spectral images loaded into memory.")
+        return cls(spectral_images)
+
+    @property
+    def images(self) -> list[SpectralImage]:
+        return self._images

siapy/utils/plots.py

@@ -96,7 +96,7 @@ def accept(event):
             enter_clicked = 1
             plt.close()
 
-    LassoSelector(ax, onselect)
+    lasso = LassoSelector(ax, onselect)  # 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)