glue_genes.glue_genomics_data.multires_data.MultiResolutionData#

class glue_genes.glue_genomics_data.multires_data.MultiResolutionData(label='', coords=None, all_resolutions=[], reduced_dims=[], **kwargs)#

A data class that supports multi-resolution n-dimensional datasets. If these multiple resolutions are accessed as DaskArrays this provides a memory-efficient way to browse very high-resolution images.

The basic scheme is to use the highest resolution dataset for setting up components but to store the lower-resolution versions as a list of Data objects. Then, whenever we need a chunk of the data, we calculate whether we can use one of the lower-resolution images instead. The lower-resolution versions are not part of the DataCollection and so we can’t use the general linking framework, but as they are all different views of the same data we can do this manually.

Currently this class assumes OME-Zarr datasets where the multi-resolution datasets are stored from highest to lowest resolution with each lower resolution version downsampled by a factor of two.

Since the MultiResolutionData set contains the full data, we do not need to override get_mask or get_data.

__init__(label='', coords=None, all_resolutions=[], reduced_dims=[], **kwargs)#

Methods

`__init__`([label, coords, all_resolutions, ...])
`add_component`(component, label)	Add a new component to this data set.
`add_component_link`(link[, label])	Shortcut method for generating a new `DerivedComponent` from a ComponentLink object, and adding it to a data set.
`add_subset`(subset[, label])	Assign a pre-existing subset to this data object.
`broadcast`(attribute)	Send a `DataUpdateMessage` to the hub
`component_ids`()	Equivalent to `Data.components`
`compute_fixed_resolution_buffer`(args, *kwargs)	Get a fixed_resolution_buffer from the smallest resolution dataset that we can glue flips x/y relative to ome-zarr, so we read in the data as tczxy
`compute_histogram`(cids[, weights, range, ...])	We want to pass the compute_histogram calls to whatever reduced resolution dataset has sufficient number of points.
`compute_statistic`(statistic, cid, **kwargs)	random_views_for_dask_array (used if random_subset is set and we have a dask array) has a problem if there is structure in the image that corresponds to the chunk size.
`dtype`(cid)	Lookup the dtype for the data associated with a ComponentID
`find_component_id`(label)	Retrieve component_ids associated by label name.
`get_component`(component_id)	Fetch the component corresponding to component_id.
`get_data`(cid[, view])	Get the data values for a given component
`get_kind`(cid)	Get the kind of data for a given component.
`get_mask`(subset_state[, view])	Get a boolean mask for a given subset state.
`get_object`([cls])	Get the dataset represented as a non-glue object, using the translation infrastructure.
`get_selection_definition`([subset_id, format])	Get subset state represented as a non-glue object, using the translation infrastructure.
`get_subset_object`([subset_id, cls])	Get a subset represented as a non-glue object, using the translation infrastructure.
`join_on_key`(other, cid, cid_other)	Create an element mapping to another dataset, by joining on values of ComponentIDs in both datasets.
`new_subset`([subset])	Create a new subset, and attach to self.
`register_to_hub`(hub)	Connect to a hub.
`remove_component`(component_id)	Remove a component from a data set
`reorder_components`(component_ids)	Reorder the components using a list of component IDs.
`setup_cid_lookups`()
`to_dataframe`([index])	Convert the Data object into a `pandas.DataFrame` object.
`update_components`(mapping)	Change the numerical data associated with some of the Components in this Data object.
`update_id`(old, new)	Reassign a component to a different `glue.core.component_id.ComponentID`
`update_values_from_data`(data)	Replace numerical values in data to match values from another dataset.

Attributes

`components`	All `ComponentIDs` in the Data.
`coordinate_components`	The ComponentIDs associated with a `CoordinateComponent`.
`coordinate_links`	A list of the ComponentLinks that connect pixel and world.
`coords`	The coordinates object for the data.
`data`
`derived_components`	The ComponentIDs for each `DerivedComponent`.
`derived_links`	A list of the links present inside all of the DerivedComponent objects in this dataset.
`externally_derivable_components`
`label`	The name of the dataset
`links`	A list of all the links internal to the dataset.
`main_components`
`ndim`	The number of dimensions of the data, as an integer.
`pixel_aligned_data`	Information about other datasets in the same data collection that have matching or a subset of pixel component IDs.
`pixel_component_ids`	The `ComponentIDs` for each pixel coordinate.
`primary_components`	The ComponentIDs not associated with a `DerivedComponent`
`shape`	The n-dimensional shape of the dataset, as a tuple.
`size`	The size of the data (the product of the shape dimensions), as an integer.
`subsets`	Tuple of subsets attached to this dataset.
`visible_components`	All `ComponentIDs` in the Data that aren't coordinates.
`world_component_ids`	The `ComponentIDs` for each world coordinate.