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IndexedSource and ImageSource bug fixes #891

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Merged
merged 1 commit into from
Mar 23, 2023
Merged

IndexedSource and ImageSource bug fixes #891

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19 changes: 17 additions & 2 deletions src/aspire/source/image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -269,6 +269,8 @@ def angles(self, values):
:param values: Rotation angles in radians, as a n x 3 array
:return: None
"""

values = values.astype(self.dtype)
self._rotations = Rotation.from_euler(values)
self.set_metadata(
["_rlnAngleRot", "_rlnAngleTilt", "_rlnAnglePsi"], np.rad2deg(values)
Expand All @@ -282,6 +284,8 @@ def rotations(self, values):
:param values: Rotation matrices as a n x 3 x 3 array
:return: None
"""

values = values.astype(self.dtype)
self._rotations = Rotation.from_matrix(values)
self.set_metadata(
["_rlnAngleRot", "_rlnAngleTilt", "_rlnAnglePsi"],
Expand Down Expand Up @@ -1080,7 +1084,7 @@ def __init__(self, src, indices, memory=None):
# here, but it returns a Numpy array, which would need to be
# converted back into Pandas for use below. So here we'll just
# use `loc` to return a dataframe.
metadata = self.src._metadata.loc[self.index_map]
metadata = self.src._metadata.loc[self.index_map].copy()

# Construct a fully formed ImageSource with this metadata
super().__init__(
Expand All @@ -1091,6 +1095,11 @@ def __init__(self, src, indices, memory=None):
memory=memory,
)

# Create filter indices, these are required to pass unharmed through filter eval code
# that is potentially called by other methods later.
self.filter_indices = np.zeros(self.n, dtype=int)
self.unique_filters = [IdentityFilter()]

def _images(self, indices):
"""
Returns images from `self.src` corresponding to `indices`
Expand All @@ -1100,7 +1109,13 @@ def _images(self, indices):
:return: An `Image` object.
"""
mapped_indices = self.index_map[indices]
return self.src.images[mapped_indices]
# Load previous source image data and apply any transforms
# belonging to this IndexedSource. Note the previous source
# requires remapped indices, while the current source uses the
# `indices` arg directly.
return self.generation_pipeline.forward(
self.src.images[mapped_indices], indices
)

def __repr__(self):
return f"{self.__class__.__name__} mapping {self.n} of {self.src.n} indices from {self.src.__class__.__name__}."
Expand Down