Merge pull request #449 from ComputationalCryoEM/aspire_image_source_403

ArrayImageSource admit numpy

Author: j-c-c

src/aspire/source/image.py

@@ -763,11 +763,22 @@ class ArrayImageSource(ImageSource):
     def __init__(self, im, metadata=None, angles=None):
         """
         Initialize from an `Image` object
-        :param im: An `Image` object representing image data served up by this `ImageSource`
+        :param im: An `Image` or Numpy array object representing image data served up by this `ImageSource`.
+        In the case of a Numpy array, attempts to create an 'Image' object.
         :param metadata: A Dataframe of metadata information corresponding to this ImageSource's images
         :param angles: Optional n-by-3 array of rotation angles corresponding to `im`.
         """
 
+        if not isinstance(im, Image):
+            logger.info("Attempting to create an Image object from Numpy array.")
+            try:
+                im = Image(im)
+            except Exception as e:
+                raise RuntimeError(
+                    "Creating Image object from Numpy array failed."
+                    f" Original error: {str(e)}"
+                )
+
         super().__init__(
             L=im.res, n=im.n_images, dtype=im.dtype, metadata=metadata, memory=None
         )

tests/test_adaptive_support.py

@@ -6,7 +6,6 @@
 import pytest
 
 from aspire.denoising import adaptive_support
-from aspire.image import Image
 from aspire.source import ArrayImageSource
 from aspire.utils import gaussian_2d
 
@@ -37,7 +36,7 @@ def testAdaptiveSupportBadThreshold(self):
         """
 
         discs = np.empty((self.size, self.size))  # Intentional Dummy Data
-        img_src = ArrayImageSource(Image(discs))
+        img_src = ArrayImageSource(discs)
 
         with pytest.raises(ValueError, match=r"Given energy_threshold.*"):
             _ = adaptive_support(img_src, -0.5)
@@ -69,7 +68,7 @@ def test_adaptive_support_F(self):
         )
 
         # Setup ImageSource like objects
-        img_src = ArrayImageSource(Image(imgs))
+        img_src = ArrayImageSource(imgs)
 
         for ref, threshold in self.references.items():
             c, R = adaptive_support(img_src, threshold)

tests/test_array_image_source.py

@@ -55,6 +55,32 @@ def testArrayImageSource(self):
         im = src.images(start=0, num=np.inf)  # returns Image instance
         self.assertTrue(np.allclose(im.asnumpy(), self.ims_np))
 
+    def testArrayImageSourceFromNumpy(self):
+        """
+        An Array can be wrapped in an ArrayImageSource when we need to deal with ImageSource objects.
+
+        This checks round trip conversion does not crash and returns identity.
+        """
+
+        # Create an ArrayImageSource directly from Numpy array
+        src = ArrayImageSource(self.ims_np)
+
+        # Ask the Source for all images in the stack as a Numpy array
+        ims_np = src.images(start=0, num=np.inf).asnumpy()
+
+        # Comparison should be yield identity
+        self.assertTrue(np.allclose(ims_np, self.ims_np))
+
+    def testArrayImageSourceNumpyError(self):
+        """
+        Test that ArrayImageSource when instantiated with incorrect input
+        gives appropriate error.
+        """
+
+        # Test we raise with expected message from getter.
+        with raises(RuntimeError, match=r"Creating Image object from Numpy.*"):
+            _ = ArrayImageSource(np.empty((3, 2, 1)))
+
     def testArrayImageSourceAngGetterError(self):
         """
         Test that ArrayImageSource when instantiated without required