Skip to content

Broaden scope of mapAxis #156

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jo-mueller wants to merge 1 commit into
base: main
Choose a base branch
from
+156 −15
Open

Broaden scope of mapAxis #156

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion examples/transformations/mapAxis2.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
{
"name": "projection up",
"type": "mapAxis",
"mapAxis": [1, 1, 0],
"mapAxis": [null, 0, 1],
"input": {"name": "in"},
"output": {"name": "out_up"}
}
Expand Down
20 changes: 11 additions & 9 deletions index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -741,18 +741,20 @@ y = j
##### mapAxis
(mapAxis-md)=

`mapAxis` transformations describe axis permutations as a transpose vector of integers.
`mapAxis` transformations describe axis permutations, adding or dropping of axes as a vector of integers or nulls.
Transformations MUST include a `mapAxis` field
whose value is an array of integers that specifies the new ordering in terms of indices of the old order.
The length of the array MUST equal the number of dimensions in both the input and output coordinate systems.
whose value is an array of unique integers or nulls that specifies the new ordering in terms of indices of the old order.
Each integer in the array MUST be a valid zero-based index into the input coordinate system's axes
(i.e., between 0 and N-1 for an N-dimensional input).
Each index MUST appear exactly once in the array.
The value at position `i` in the array indicates which input axis becomes the `i`-th output axis.
`mapAxis` transforms are invertible.
`mapAxis` transforms are invertible if the array contains no nulls
and its length corresponds to the number of dimensions in both the input and output coordinate systems.

If the value `null` is used in a `mapAxis` transformation,
this corresponds to adding the value zero in the coordinate vector at the position of the null.

**mapAxis**
: The axis permutation stored as a JSON array of integers.
: The axis permutation stored as a JSON array of integers or nulls.


:::{dropdown} Example 1
Expand Down Expand Up @@ -792,9 +794,9 @@ x = b
and the `projection_up` transformation defines the function:

```
x = a
y = b
z = b
x = b
y = a
z = 0
```
:::

Expand Down
16 changes: 11 additions & 5 deletions schemas/coordinate_transformations.schema
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -119,14 +119,20 @@
"mapAxis": {
"type": "array",
"items": {
"type": "integer",
"minimum": 0,
"maximum": 4
"anyOf": [
{
"type": "integer",
"minimum": 0,
"maximum": 4
},
{
"type": "null"
}
]
},
"minItems": 2,
"maxItems": 5,
"uniqueItems": true,
"description": "An array of integers representing the new axis order as zero-based indices of the input axes."
"description": "An array of integers or nulls representing the new axis order as zero-based indices of the input axes."
}
},
"required": [
Expand Down
133 changes: 133 additions & 0 deletions tests/attributes/spec/valid/transforms/mapAxis_up.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,133 @@
{
"ome": {
"version": "0.6.dev4",
"multiscales": [
{
"name": "multiscales",
"coordinateSystems": [
{
"name": "world",
"axes": [
{
"type": "space",
"name": "z",
"unit": "micrometer",
"discrete": false
},
{
"type": "space",
"name": "y",
"unit": "micrometer",
"discrete": false
},
{
"type": "space",
"name": "x",
"unit": "micrometer",
"discrete": false
}
]
},
{
"name": "physical",
"axes": [
{
"type": "space",
"name": "y",
"unit": "micrometer",
"discrete": false
},
{
"type": "space",
"name": "x",
"unit": "micrometer",
"discrete": false
}
]
}
],
"datasets": [
{
"path": "s0",
"coordinateTransformations": [
{
"type": "sequence",
"output": {"name": "physical"},
"input": {"path": "s0"},
"name": "scale0_to_physical",
"transformations": [
{
"type": "scale",
"scale": [1, 1]
},
{
"type": "translation",
"translation": [0, 0]
}
]
}
]
},
{
"path": "s1",
"coordinateTransformations": [
{
"type": "sequence",
"output": {"name": "physical"},
"input": {"path": "s1"},
"name": "scale1_to_physical",
"transformations": [
{
"type": "scale",
"scale": [2, 2]
},
{
"type": "translation",
"translation": [0.7071, 0.7071]
}
]
}
]
},
{
"path": "s2",
"coordinateTransformations": [
{
"type": "sequence",
"output": {"name": "physical"},
"input": {"path": "s2"},
"name": "scale2_to_physical",
"transformations": [
{
"type": "scale",
"scale": [4, 4]
},
{
"type": "translation",
"translation": [2.1213, 2.1213]
}
]
}
]
}
],
"coordinateTransformations": [
{
"type": "mapAxis",
"name": "physical-to-world",
"input": {"name": "physical"},
"output": {"name": "world"},
"mapAxis": [null, 0, 1]
}
]
}
]
},
"_conformance": {
"schema": {
"id": "schemas/image.schema"
},
"description": "Tests for a JSON document with a mapAxis transformation",
"valid": true
}
}
Loading