def from_url(cls, url: str, baseurl: Optional[str], aligned_group: int = 0):
"""
Constructs an ImageStack object from a URL and a base URL.
The following examples will all load from the same location:
- url: https://www.example.com/images/primary_images.json baseurl: None
- url: https://www.example.com/images/primary_images.json baseurl: I_am_ignored
- url: primary_images.json baseurl: https://www.example.com/images
- url: images/primary_images.json baseurl: https://www.example.com
Parameters
----------
url : str
Either an absolute URL or a relative URL referring to the image to be read.
baseurl : Optional[str]
If url is a relative URL, then this must be provided. If url is an absolute URL, then
this parameter is ignored.
aligned_group: int
Which aligned tile group to load into the Imagestack, only applies if the
tileset is unaligned. Default 0 (the first group)
Returns
-------
ImageStack :
An ImageStack representing encapsulating the data from the TileSet.
"""
config = StarfishConfig()
tileset = Reader.parse_doc(url, baseurl, backend_config=config.slicedimage)
coordinate_groups = CropParameters.parse_aligned_groups(tileset)
crop_params = coordinate_groups[aligned_group]
return cls.from_tileset(tileset, crop_parameters=crop_params)
def __init__(
self, name: str,
image_tilesets: MutableMapping[str, TileSet]
) -> None:
self._images: MutableMapping[str, TileSet] = dict()
self._name = name
self.aligned_coordinate_groups: Dict[str, List[CropParameters]] = dict()
for name, tileset in image_tilesets.items():
self.aligned_coordinate_groups[name] = CropParameters.parse_coordinate_groups(tileset)
self._images = image_tilesets
def get_images(
self,
item: str,
rounds: Optional[Collection[int]] = None,
chs: Optional[Collection[int]] = None,
zplanes: Optional[Collection[int]] = None,
x: Optional[Union[int, slice]] = None,
y: Optional[Union[int, slice]] = None,
) -> Iterator[ImageStack]:
"""
Load into memory the an iterator of aligned Imagestacks for the given tileset and selected
axes.
Parameters
----------
item: str
The name of the tileset ex. 'primary' or 'nuclei'
rounds : Optional[Collection[int]]
The rounds in the original dataset to load into the ImageStack/s. If this is not set,
then all rounds are loaded into the ImageStack.
chs : Optional[Collection[int]]
The channels in the original dataset to load into the ImageStac/s. If this is not set,
then all channels are loaded into the ImageStack.
zplanes : Optional[Collection[int]]
The z-layers in the original dataset to load into the ImageStack/s. If this is not set,
then all z-layers are loaded into the ImageStack.
x : Optional[Union[int, slice]]
The x-range in the x-y tile that is loaded into the ImageStack/s. If this is not set,
then the entire x-y tile is loaded into the ImageStack.
y : Optional[Union[int, slice]]
The y-range in the x-y tile that is loaded into the ImageStack/s. If this is not set,
then the entire x-y tile is loaded into the ImageStack.
Returns
-------
AlignedImageStackIterator
The instantiated ImageStack or list of Imagestacks if the parameters given include
multiple aligned groups.
"""
# Parse the tileset into aligned groups, only include tiles from selected axes.
aligned_groups = CropParameters.parse_aligned_groups(
self._images[item],
rounds=rounds,
chs=chs,
zplanes=zplanes,
x=x,
y=y)
aligned_stack_iterator = AlignedImageStackIterator(
tileset=self._images[item], aligned_groups=aligned_groups)
return aligned_stack_iterator