self review cleanup

Author: garrettwrong

src/aspire/image/image.py

@@ -130,10 +130,10 @@ def load_tiff(filepath):
 
     # Future todo, extract `voxel_size` if available in TIFF tags (custom tag?)
     # For now, default to `None`.
-    voxel_size = None
+    pixel_size = None
 
     # Cast image data as numpy array
-    return np.array(img), voxel_size
+    return np.array(img), pixel_size
 
 
 class Image:
@@ -160,7 +160,7 @@ def __init__(self, data, pixel_size=None, dtype=None):
 
         :param data: Numpy array containing image data with shape
             `(..., resolution, resolution)`.
-        :param pixel_size: Optional pixel size in Angstroms.
+        :param pixel_size: Optional pixel size in angstroms.
             When provided will be saved with `mrc` metadata.
             Default of `None` will not write to file,
             but will be considered unit pixels (1) for FSC.

src/aspire/source/image.py

@@ -170,7 +170,7 @@ def __init__(
             The path of the base directory to use as a data store or None. If None is given, no caching is performed.
         :param symmetry_group: A SymmetryGroup instance or string indicating the underlying symmetry of the molecule.
             Defaults to the `IdentitySymmetryGroup`, which represents an asymmetric particle, if none provided.
-        :param pixel_size: Pixel size of the images in Angstroms, default `None`.
+        :param pixel_size: Pixel size of the images in angstroms, default `None`.
         """
 
         # Instantiate the accessor for the `images` property
@@ -1673,6 +1673,7 @@ def __init__(
         :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`.
         :param symmetry_group: A SymmetryGroup instance or string indicating the underlying symmetry of the molecule.
+        :param pixel_size: Pixel size of the images in angstroms, default `None`.
         """
 
         if not isinstance(im, Image):

src/aspire/source/micrograph.py

@@ -122,6 +122,7 @@ def __init__(self, micrographs, dtype=None, pixel_size=None):
             Currently only `float32` and `float64` are supported.
             Note, due to limitations of common MRC implementations,
             saving is limited to single precision.
+        :param pixel_size: Pixel size of the images in angstroms, default `None`.
         """
 
         # Check micrographs is an array

src/aspire/source/simulation.py

@@ -80,7 +80,7 @@ def __init__(
         :param noise_adder: Optionally append instance of `NoiseAdder`
             to generation pipeline.
         :param symmetry_group: A SymmetryGroup instance or string indicating symmetry of the molecule.
-        :param pixel_size: Pixel size of the images in Angstroms, default `None`.
+        :param pixel_size: Pixel size of the images in angstroms, default `None`.
 
         :return: A Simulation object.
         """

src/aspire/volume/volume.py

@@ -76,7 +76,7 @@ def __init__(self, data, dtype=None, pixel_size=None, symmetry_group=None):
             `(..., resolution, resolution, resolution)`.
         :param dtype: Optionally cast `data` to this dtype.
             Defaults to `data.dtype`.
-        :param pixel_size: Optional voxel_size in Angstroms.
+        :param pixel_size: Optional voxel_size in angstroms.
             When provided will be saved with `map`/`mrc` metadata.
             Default of `None` will not write to file,
             but will be considered unit pixels (1) for FSC.
@@ -262,7 +262,7 @@ def stack_reshape(self, *args):
     def __repr__(self):
         px_msg = "."
         if self.pixel_size is not None:
-            px_msg = f" with pixel_size={self.pixel_size} Angstroms."
+            px_msg = f" with pixel_size={self.pixel_size} angstroms."
 
         msg = (
             f"{self.n_vols} {self.dtype} volumes arranged as a {self.stack_shape} stack"
@@ -420,7 +420,6 @@ def project(self, rot_matrices):
             im_f[:, :, 0] = 0
 
         im_f = fft.centered_ifft2(im_f)
-        # todo add pixel_size to Image
         return aspire.image.Image(xp.asnumpy(im_f.real), pixel_size=self.pixel_size)
 
     def to_vec(self):

src/aspire/volume/volume_synthesis.py

@@ -48,7 +48,7 @@ def __init__(
         :param C: Number of Volumes to generate.
         :param K: Number of Gaussian blobs used to construct the Volume(s).
         :param alpha: Scaling factor for variance of Gaussian blobs. Default=1.
-        :param pixel_size: Optional voxel_size in Angstroms. Default=1.
+        :param pixel_size: Optional voxel_size in angstroms. Default=1.
         :param seed: Random seed for generating random Gaussian blobs.
         :param dtype: dtype for Volume(s)
         """
@@ -184,7 +184,7 @@ def __init__(
         :param C: Number of Volumes to generate.
         :param order: An integer representing the cyclic order of the Volume(s).
         :param K: Number of Gaussian blobs used to construct the Volume(s).
-        :param pixel_size: Optional voxel_size in Angstroms. Default=1.
+        :param pixel_size: Optional voxel_size in angstroms. Default=1.
         :param seed: Random seed for generating random Gaussian blobs.
         :param dtype: dtype for Volume(s)
         """