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Finalize axes & initial transformation #85

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merged 9 commits into from
Feb 2, 2022
Merged

Finalize axes & initial transformation #85

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af0f626
Rename transformations to coordinateTransformations
constantinpape Jan 27, 2022
97d66fb
Remove axis indices
constantinpape Jan 27, 2022
b863e0e
Further clarifications
constantinpape Jan 27, 2022
f3dc3f1
Rename transformations to coordinateTransformations in example
constantinpape Jan 27, 2022
0241254
Mandatory scale transformation for datasets
constantinpape Jan 28, 2022
c9d2e3e
Clarify the multiscale level transformation
constantinpape Feb 1, 2022
4b376a3
Update latest/index.bs
sbesson Feb 2, 2022
37e64a1
Update latest/index.bs
sbesson Feb 2, 2022
cc76444
Update latest/index.bs
sbesson Feb 2, 2022
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37 changes: 17 additions & 20 deletions latest/index.bs
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Expand Up @@ -222,10 +222,11 @@ keys as specified below for discovering certain types of data, especially images
If part of [[#multiscale-md]], the length of "axes" MUST be equal to the number of dimensions of the arrays that contain the image data.


"transformations" metadata {#trafo-md}
"coordinateTransformations" metadata {#trafo-md}
-------------------------------------

"transformations" describes a series of transformations, e.g. to map discrete data space of an array to the corresponding physical space.
"coordinateTransformations" describe a series of transformations that map between two coordinate spaces (defined by "axes").
For example, to map a discrete data space of an array to the corresponding physical space.
It is a list of dictionaries. Each entry describes a single transformation and MUST contain the field "type".
The value of "type" MUST be one of the elements of the `type` column in the table below.
Additional fields for the entry depend on "type" and are defined by the column `fields`.
Expand All @@ -236,9 +237,6 @@ Additional fields for the entry depend on "type" and are defined by the column `
| `translation` | one of: `"translation":List[float]`, `"path":str` | translation vector, stored either as a list of floats (`"translation"`) or as binary data at a location in this container (`path`). The length of vector defines number of dimensions. |
| `scale` | one of: `"scale":List[float]`, `"path":str` | scale vector, stored either as a list of floats (`scale`) or as binary data at a location in this container (`path`). The length of vector defines number of dimensions. |
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It looks like this table still isn't rendered correctly:
table-rendering
I don't understand why. Could someone with more bikeshed experience give this a shot? cc @joshmoore @will-moore @sbesson

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I think I tried this way back on the previous PR, but didn't get much joy. I think @joshmoore suggested using an HTML table?


In addition, the field "axisIndices" MAY be given to specify the subset of axes that the transformation is applied to, leaving other axes unchanged. If not given, the transformation is applied to all axes. The length of "axisIndices" MUST be equal to the dimensionality of the transformation. If "axisIndices" are not given, the dimensionality of the transformation MUST be equal to the number of dimensions of the space that the transformation is applied to.
If given, "axisIndices" MUST be given in increasing order. It uses zero-based indexing.

The transformations in the list are applied sequentally and in order.
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Expand All @@ -263,17 +261,16 @@ Each dictionary in "datasets" MUST contain the field "path", whose value contain
to the current zarr group. The "path"s MUST be ordered from largest (i.e. highest resolution) to smallest.

Each "datasets" dictionary MUST have the same number of dimensions and MUST NOT have more than 5 dimensions. The number of dimensions and order MUST correspond to number and order of "axes".
Each dictionary MAY contain the field "transformations", which contains a list of transformations that map the data coordinates to the physical coordinates (as specified by "axes") for this resolution level.
The transformations are defined according to [[#trafo-md]]. In addition, the transformation types MUST only be `identity`, `translation` or `scale`.
They MUST contain at most one `scale` transformation per axis that specifies the pixel size in physical units.
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The "per axis" should be kept if we keep the 'global' transformation.

It also MUST contain at most one `translation` per axis that specifies the offset from the origin in physical units.
If both `scale` and `translation` are given `translation` must be listed after `scale` to ensure that it is given in physical coordinates. If "transformations" is not given, the identity transformation is assumed.
The requirements (only `scale` and `translation`, restrictions on order) are in place to provide a simple mapping from data coordinates to physical coordinates while
being compatible with the general transformation spec.

Each "multiscales" dictionary MAY contain the field "transformations", describing transformations that are applied to each resolution level.
The transformations MUST follow the same rules about allowed types, order, etc. as in "datasets:transformations".
These transformations are applied after the per resolution level transformations specified in "datasets". They can for example be used to specify the `scale` for a dimension that is the same for all resolutions.
Each dictionary MUST contain the field "coordinateTransformations", which contains a list of transformations that map the data coordinates to the physical coordinates (as specified by "axes") for this resolution level.
The transformations are defined according to [[#trafo-md]]. The transformation types MUST only be `translation` or `scale`.
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They MUST contain exactly one `scale` transformation that specifies the pixel size in physical units or time duration. If scaling information is not available or applicable for one of the axes set it to 1.
It MAY contain exactly one `translation` that specifies the offset from the origin in physical units. If `translation` is given it must be listed after `scale` to ensure that it is given in physical coordinates.
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The length of the `scale` and `translation` array MUST be the same as the length of "axes".
The requirements (only `scale` and `translation`, restrictions on order) are in place to provide a simple mapping from data coordinates to physical coordinates while being compatible with the general transformation spec.

Each "multiscales" dictionary MAY contain the field "coordinateTransformations", describing transformations that are applied to all resolution levels in the same manner.
The transformations MUST follow the same rules about allowed types, order, etc. as in "datasets:coordinateTransformations" and are applied after them.
They can for example be used to specify the `scale` for a dimension that is the same for all resolutions.

Each "multiscales" dictionary 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 0.4).

Expand All @@ -296,18 +293,18 @@ It SHOULD contain the field "metadata", which contains a dictionary with additio
"datasets": [
{
"path": "0",
"transformations": [{"type": "scale", "scale": [0.5, 0.5, 0.5], "axisIndices": [2, 3, 4]}] # the voxel size for the first scale level (0.5 micrometer)
"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",
"transformations": [{"type": "scale", "scale": [1.0, 1.0, 1.0], "axisIndices": [2, 3, 4]}] # the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
"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",
"transformations": [{"type": "scale", "scale": [2.0, 2.0, 2.0], "axisIndices": [2, 3, 4]}] # the voxel size for the second scale level (downscaled by a factor of 4 -> 2 micrometer)
"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)
}
],
"transformations": [{"type": "scale", "scale": [0.1], "axisIndices": [0]], # the time unit (0.1 milliseconds), which is the same for each scale level
"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
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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
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