Skip to content

Commit

Permalink
Extract the multiscales snippet into a JSON file validated by the schema
Browse files Browse the repository at this point in the history
  • Loading branch information
sbesson committed Feb 8, 2022
1 parent a516207 commit 4a319ba
Show file tree
Hide file tree
Showing 2 changed files with 42 additions and 39 deletions.
37 changes: 37 additions & 0 deletions 0.4/examples/valid_strict/multiscales_example.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
{
"multiscales": [
{
"version": "0.4",
"name": "example",
"axes": [
{"name": "t", "type": "time", "unit": "millisecond"},
{"name": "c", "type": "channel"},
{"name": "z", "type": "space", "unit": "micrometer"},
{"name": "y", "type": "space", "unit": "micrometer"},
{"name": "x", "type": "space", "unit": "micrometer"}
],
"datasets": [
{
"path": "0",
"coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 0.5, 0.5, 0.5]}] # the voxel size for the first scale level (0.5 micrometer)
}
{
"path": "1",
"coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 1.0, 1.0, 1.0]}] # the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
},
{
"path": "2",
"coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 2.0, 2.0, 2.0]}] # the voxel size for the second scale level (downscaled by a factor of 4 -> 2 micrometer)
}
],
"coordinateTransformations": [{"type": "scale", "scale": [0.1, 1.0, 1.0, 1.0, 1.0]], # the time unit (0.1 milliseconds), which is the same for each scale level
"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}
}
}
]
}
44 changes: 5 additions & 39 deletions 0.4/index.bs
Original file line number Diff line number Diff line change
Expand Up @@ -285,45 +285,11 @@ Each "multiscales" dictionary SHOULD contain the field "name". It SHOULD contain
Each "multiscales" dictionary 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.

```
{
"multiscales": [
{
"version": "0.4",
"name": "example",
"axes": [
{"name": "t", "type": "time", "unit": "millisecond"},
{"name": "c", "type": "channel"},
{"name": "z", "type": "space", "unit": "micrometer"},
{"name": "y", "type": "space", "unit": "micrometer"},
{"name": "x", "type": "space", "unit": "micrometer"}
],
"datasets": [
{
"path": "0",
"coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 0.5, 0.5, 0.5]}] # the voxel size for the first scale level (0.5 micrometer)
}
{
"path": "1",
"coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 1.0, 1.0, 1.0]}] # the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
},
{
"path": "2",
"coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.0, 2.0, 2.0, 2.0]}] # the voxel size for the second scale level (downscaled by a factor of 4 -> 2 micrometer)
}
],
"coordinateTransformations": [{"type": "scale", "scale": [0.1, 1.0, 1.0, 1.0, 1.0]], # the time unit (0.1 milliseconds), which is the same for each scale level
"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}
}
}
]
}
```
<pre class=include-code>
path: examples/valid_strict/multiscales_example.json
highlight: json
</pre>


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

0 comments on commit 4a319ba

Please sign in to comment.