def _read_immediate(self) -> da.core.Array:
# Init temp czi
czi = CziFile(self._file)
# Safely construct the numpy array or catch any exception
try:
# Get image dims indicies
image_dim_indices = czi.dims_shape()
# Catch inconsistent scene dimension sizes
if len(image_dim_indices) > 1:
# Choose the provided scene
log.info(
f"File contains variable dimensions per scene, "
f"selected scene: {self.specific_s_index} for data retrieval."
)
# Get the specific scene
if self.specific_s_index < len(image_dim_indices):
data, _ = czi.read_image(
**{Dimensions.Scene: self.specific_s_index})
else:
raise exceptions.InconsistentShapeError(
f"The CZI image provided has variable dimensions per scene. "
f"Please provide a valid index to the 'S' parameter to create "
f"a dask array for the index provided. "
f"Provided scene index: {self.specific_s_index}. "
f"Scene index range: 0-{len(image_dim_indices)}.")
else:
# If the list is length one that means that all the scenes in the image
# have the same dimensions
# Read all data in the image
data, _ = czi.read_image()
# A really bad way to close any connection to the CZI object
czi._bytes = None
czi.reader = None
except Exception as e:
# A really bad way to close any connection to the CZI object
czi._bytes = None
czi.reader = None
raise e
return data
def _daread_safe(
img: Union[str, Path],
chunk_by_dims: List[str] = [
Dimensions.SpatialZ,
Dimensions.SpatialY,
Dimensions.SpatialX,
],
S: int = 0,
) -> Tuple[da.core.Array, str]:
"""
Safely read a CZI image file as a delayed dask array where certain dimensions
act as the chunk size.
Parameters
----------
img: Union[str, Path]
The filepath to read.
chunk_by_dims: List[str]
The dimensions to use as the for mapping the chunks / blocks.
Default: [Dimensions.SpatialZ, Dimensions.SpatialY, Dimensions.SpatialX]
Note: SpatialY and SpatialX will always be added to the list if not present.
S: int
If the image has different dimensions on any scene from another, the dask
array construction will fail.
In that case, use this parameter to specify a specific scene to construct a
dask array for.
Default: 0 (select the first scene)
Returns
-------
img: dask.array.core.Array
The constructed dask array where certain dimensions are chunked.
dims: str
The dimension order as a string.
"""
# Resolve image path
img = CziReader._resolve_image_path(img)
# Init temp czi
czi = CziFile(img)
# Safely construct the dask array or catch any exception
try:
return CziReader._daread(img=img,
czi=czi,
chunk_by_dims=chunk_by_dims,
S=S)
except Exception as e:
# A really bad way to close any connection to the CZI object
czi._bytes = None
czi.reader = None
raise e
