feat: Added MedVol code

README.md

@@ -1,25 +1,40 @@
-# medvol
+# MedVol
 
 [![License Apache Software License 2.0](https://img.shields.io/pypi/l/medvol.svg?color=green)](https://github.com/Karol-G/medvol/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/medvol.svg?color=green)](https://pypi.org/project/medvol)
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-[![tests](https://github.com/Karol-G/medvol/workflows/tests/badge.svg)](https://github.com/Karol-G/medvol/actions)
-![Unit Tests](https://github.com/Karol-G/medvol/actions/workflows/test_and_deploy.yml/badge.svg?branch=main)
-[![codecov](https://codecov.io/gh/Karol-G/medvol/branch/main/graph/badge.svg)](https://codecov.io/gh/Karol-G/medvol)
 
 A wrapper for loading medical 3D image volumes such as NIFTI or NRRD images.
 
-----------------------------------
-
-Project description...
-
 ## Installation
 
 You can install `medvol` via [pip](https://pypi.org/project/medvol/):
 
     pip install medvol
 
+## Example
+
+```python
+from medvol import MedVol
+
+# Load NIFTI image
+image = MedVol("path/to/image.nifti")
+
+# Print some metadata
+print("Spacing: ", image.spacing)
+print("Affine: ", image.affine)
+print("Header: ", image.header)
+
+# Access and modify the image array
+arr = image.array
+arr[0, 0, 0] = 1
+
+# Create a new image with the new array, a new spacing, but copy all remaining metadata
+new_image = MedVol(arr, spacing=[2, 2, 2], copy=image)
 
+# Save the new image as NRRD
+new_image.save("path/to/new_image.nrrd")
+```
 
 
 ## Contributing

medvol/__init__.py

@@ -1 +1,3 @@
 __version__ = "0.0.1"
+
+from medvol.medvol import MedVol

medvol/medvol.py

@@ -0,0 +1,82 @@
+import SimpleITK as sitk
+from dataclasses import dataclass, field
+from typing import Dict, Optional, Union
+import numpy as np
+
+
+@dataclass
+class MedVol:
+    array: Union[np.ndarray, str]
+    spacing: Optional[np.ndarray] = None
+    origin: Optional[np.ndarray] = None
+    direction: Optional[np.ndarray] = None
+    header: Optional[Dict] = None
+    copy: Optional['MedVol'] = field(default=None, repr=False)
+
+    def __post_init__(self):
+        # Validate array: Must be a 3D array
+        if not ((isinstance(self.array, np.ndarray) and self.array.ndim == 3) or isinstance(self.array, str)):
+            raise ValueError("array must be a 3D numpy array or a filepath string")
+
+        if isinstance(self.array, str):
+            self._load(self.array)
+
+        # Validate spacing: Must be None or a 1D array with three floats
+        if self.spacing is not None:
+            if not (isinstance(self.spacing, np.ndarray) and self.spacing.shape == (3,) and np.issubdtype(self.spacing.dtype, np.floating)):
+                raise ValueError("spacing must be None or a 1D numpy array with three floats")
+
+        # Validate origin: Must be None or a 1D array with three floats
+        if self.origin is not None:
+            if not (isinstance(self.origin, np.ndarray) and self.origin.shape == (3,) and np.issubdtype(self.origin.dtype, np.floating)):
+                raise ValueError("origin must be None or a 1D numpy array with three floats")
+
+        # Validate direction: Must be None or a 3x3 array of floats
+        if self.direction is not None:
+            if not (isinstance(self.direction, np.ndarray) and self.direction.shape == (3, 3) and np.issubdtype(self.direction.dtype, np.floating)):
+                raise ValueError("direction must be None or a 3x3 numpy array of floats")
+
+        # Validate header: Must be None or a dictionary
+        if self.header is not None and not isinstance(self.header, dict):
+            raise ValueError("header must be None or a dictionary")
+
+        # If copy is set, copy fields from the other Nifti instance
+        if self.copy is not None:
+            self._copy_fields_from(self.copy)
+
+    @property
+    def affine(self) -> np.ndarray:
+        if self.spacing is None or self.origin is None or self.direction is None:
+            raise ValueError("spacing, origin, and direction must all be set to compute the affine.")
+
+        affine = np.eye(4)
+        affine[:3, :3] = self.direction @ np.diag(self.spacing)
+        affine[:3, 3] = self.origin
+        return affine
+
+    def _copy_fields_from(self, other: 'MedVol'):
+        if self.spacing is None:
+            self.spacing = other.spacing
+        if self.origin is None:
+            self.origin = other.origin
+        if self.direction is None:
+            self.direction = other.direction
+        if self.header is None:
+            self.header = other.header
+
+    def _load(self, filepath):
+        image_sitk = sitk.ReadImage(filepath)
+        self.array = sitk.GetArrayFromImage(image_sitk)
+        self.spacing = np.array(image_sitk.GetSpacing()[::-1])
+        self.origin = np.array(image_sitk.GetOrigin()[::-1])
+        self.direction = np.array(image_sitk.GetDirection()[::-1]).reshape(3, 3)
+        self.header = {key: image_sitk.GetMetaData(key) for key in image_sitk.GetMetaDataKeys()}
+
+    def save(self, filepath):
+        image_sitk = sitk.GetImageFromArray(self.array)
+        image_sitk.SetSpacing(self.spacing.tolist()[::-1])
+        image_sitk.SetOrigin(self.origin.tolist()[::-1])
+        image_sitk.SetDirection(self.direction.flatten().tolist()[::-1])
+        for key, value in self.header.items():
+            image_sitk.SetMetaData(key, value) 
+        sitk.WriteImage(image_sitk, filepath)