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----------
dims: str
A string containing a list of dimensions being requested. The default is to
return the six standard dims.
Returns
-------
size: Tuple[int]
A tuple with the requested dimensions filled in.
"""
# Ensure dims is an uppercase string
dims = dims.upper()
# Check that dims requested are all a part of the available dims in the package
if not (all(d in Dimensions.DefaultOrder for d in dims)):
raise InvalidDimensionOrderingError(f"Invalid dimensions requested: {dims}")
# Check that the dims requested are in the image dims
if not (all(d in self.dims for d in dims)):
raise InvalidDimensionOrderingError(f"Invalid dimensions requested: {dims}")
# Return the shape of the data for the dimensions requested
return tuple([self.dask_data.shape[self.dims.index(dim)] for dim in dims])
def dims(self, dims: str):
# Check amount of provided dims against data shape
if len(dims) != len(self.dask_data.shape):
raise exceptions.InvalidDimensionOrderingError(
f"Provided too many dimensions for the associated file. "
f"Received {len(dims)} dimensions [dims: {dims}] "
f"for image with {len(self.data.shape)} dimensions "
f"[shape: {self.data.shape}]."
)
# Set the dims
self._dims = dims
----------
dims: str
A string containing a list of dimensions being requested. The default is to
return the six standard dims.
Returns
-------
size: Tuple[int]
A tuple with the requested dimensions filled in.
"""
# Ensure dims is an uppercase string
dims = dims.upper()
# Check that dims requested are all a part of the available dims in the package
if not (all(d in Dimensions.DefaultOrder for d in dims)):
raise InvalidDimensionOrderingError(f"Invalid dimensions requested: {dims}")
# Check that the dims requested are in the image dims
if not (all(d in self.dims for d in dims)):
raise InvalidDimensionOrderingError(f"Invalid dimensions requested: {dims}")
# Return the shape of the data for the dimensions requested
return tuple([self.dask_data.shape[self.dims.index(dim)] for dim in dims])
def dims(self, dims: str):
# Check amount of provided dims against data shape
if len(dims) != len(self.dask_data.shape):
raise exceptions.InvalidDimensionOrderingError(
f"Provided too many dimensions for the associated file. "
f"Received {len(dims)} dimensions [dims: {dims}] "
f"for image with {len(self.data.shape)} dimensions "
f"[shape: {self.data.shape}]."
)
# Set the dims
self._dims = dims
... data = img.get_image_data("ZYX", S=0, T=0, C=0)
Notes
-----
When using the AICSImage context manager, the processing machine or container
must have networking capabilities enabled to function properly.
Constructor for AICSImage class intended for providing a unified interface for
dealing with microscopy images. To extend support to a new reader simply add a
new reader child class of Reader ([readers/reader.py]) and add the class to
SUPPORTED_READERS variable.
"""
# Check known dims
if known_dims is not None:
if not all([d in Dimensions.DefaultOrder for d in known_dims]):
raise InvalidDimensionOrderingError(
f"The provided dimension string to the 'known_dims' argument "
f"includes dimensions that AICSImage does not support. "
f"Received: '{known_dims}'. "
f"Supported dimensions: {Dimensions.DefaultOrderList}."
)
# Hold onto known dims until data is requested
self._known_dims = known_dims
# Dims should nearly always be default dim order unless explictly overridden
self.dims = Dimensions.DefaultOrder
# Determine reader class and create dask delayed array
reader_class = self.determine_reader(data=data)
self._reader = reader_class(data, **kwargs)
... data = img.get_image_data("ZYX", S=0, T=0, C=0)
Notes
-----
When using the AICSImage context manager, the processing machine or container
must have networking capabilities enabled to function properly.
Constructor for AICSImage class intended for providing a unified interface for
dealing with microscopy images. To extend support to a new reader simply add a
new reader child class of Reader ([readers/reader.py]) and add the class to
SUPPORTED_READERS variable.
"""
# Check known dims
if known_dims is not None:
if not all([d in Dimensions.DefaultOrder for d in known_dims]):
raise InvalidDimensionOrderingError(
f"The provided dimension string to the 'known_dims' argument "
f"includes dimensions that AICSImage does not support. "
f"Received: '{known_dims}'. "
f"Supported dimensions: {Dimensions.DefaultOrderList}."
)
# Hold onto known dims until data is requested
self._known_dims = known_dims
# Dims should nearly always be default dim order unless explictly overridden
self.dims = Dimensions.DefaultOrder
# Determine reader class and create dask delayed array
reader_class = self.determine_reader(data=data)
self._reader = reader_class(data, **kwargs)