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Lift 5d requirement for images and move multiscales description into spec #39

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Lift 5d requirement for images and move multiscales description into spec #39

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e1a5168
Lift 5d requirement for images
constantinpape Mar 13, 2021
9fae845
Move multiscales definition into spec
constantinpape Mar 13, 2021
4223549
Address reviews: make axes MUST; bump version to 0.2
constantinpape Mar 16, 2021
7b664a9
Address review comments
constantinpape Mar 17, 2021
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52 changes: 48 additions & 4 deletions latest/index.bs
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Original file line number Diff line number Diff line change
Expand Up @@ -124,8 +124,8 @@ multiple levels of resolutions and optionally associated labels.
├── n # The name of the array is arbitrary with the ordering defined by
│ │ # by the "multiscales" metadata, but is often a sequence starting at 0.
│ │
│ ├── .zarray # All image arrays are 5-dimensional
│ │ # with dimension order (t, c, z, y, x).
│ ├── .zarray # All image arrays are up to 5-dimensional with dimension order (t, c, z, y, x).
│ │ # An image without time dimension has axes (c, z, y, x) etc.
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Is a 3D array interpreted as (z, y, x)?

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If we promote "axes" to MUST, then the interpretation always depends on the metadata, i.e. on the values in "axes".

│ │
│ ├── 0.0.0.0.0 # Chunks are stored with the flat directory layout.
│ │ ... # Each dotted component of the chunk file represents
Expand Down Expand Up @@ -207,8 +207,52 @@ keys as specified below for discovering certain types of data, especially images

Metadata about the multiple resolution representations of the image can be
found under the "multiscales" key in the group-level metadata.
The specification for the multiscale (i.e. "resolution") metadata is provided
in [zarr-specs#50](https://github.com/zarr-developers/zarr-specs/issues/50).
"multiscales" contains a list of dictionaries where each entry describes a multiscale image.
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"multiscales" MUST contain the field "datasets", which is a list of dictionaries describing
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the arrays storing the individual resolution levels. Each dictionary in "datasets" MUST
contain the field "path", whose value contains the path to the array for this resolution relative
to the current zarr group. The "path"s MUST be ordered from largest (i.e. highest resolution) to smallest.

It MUST contain the field "axes", which is a list of dimension names of the axes.
The values MUST be unique and one of `{"t", "c", "z", "y", "x"}`.
The number of values MUST be the same as the number of dimensions of the arrays corresponding to this image.

It SHOULD contain the field "name".

It SHOULD contain the field "version", which indicates the version of the
multiscale metadata of this image (current version is 0.2).

It SHOULD contain the field "type", which gives the type of downscaling method used to generate the multiscale image pyramid.
It SHOULD contain the field "metadata", which contains a dictionary with additional information about the downscaling method.

```json
{
"multiscales": [
{
"version": "0.2",
"name": "example",
"datasets": [
{"path": "0"},
{"path": "1"},
{"path": "2"}
],
"axes": [
"t", "c", "z", "y", "z"
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],
"type": "gaussian",
"metadata": { # the fields in metadata depend on the downscaling implementation
"method": "skimage.transform.pyramid_gaussian", # here, the paramters passed to the skimage function are given
"version": "0.16.1",
"args": "[true]",
"kwargs": {"multichannel": true}
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}
}
]
}
```


If only one multiscale is provided, use it. Otherwise, the user can choose by
name, using the first multiscale as a fallback:

Expand Down