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Fix typo on Nathalie Gaudreault's name
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rfc/5/versions/1/index.md

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@@ -54,7 +54,7 @@ This RFC is currently in RFC state `R1` (send for review).
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- 2024-08-22
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-
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* - Reviewer
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- Dan Toloudis, David Feng, Forrest Collman, Nathalie GAudreault, Gideon Dunster
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- Dan Toloudis, David Feng, Forrest Collman, Nathalie Gaudreault, Gideon Dunster
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- toloudis, dyf, fcollman
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- Allen Institutes
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- 2024-11-28
@@ -90,7 +90,7 @@ to enable:
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reverse transformations as needed for different analysis purposes. This flexibility is critical for tasks such as
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longitudinal studies, multi-modal imaging, and comparative analysis across different subjects or experimental conditions.
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Toward these goals, this RFC expands the set of transformations in the OME-Zarr spec covering many of the use cases
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Toward these goals, this RFC expands the set of transformations in the OME-Zarr spec covering many of the use cases
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requested in [this github issue](https://github.com/ome/ngff/issues/84). It also adds "coordinate systems" - named
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sets of "axes." Related the relationship of discrete arrays to physical coordinates and the interpretation and motivation for
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axis types.
@@ -157,12 +157,12 @@ The dimensionality of each array coordinate system equals the dimensionality of
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name `"dim_i"` is the ith element of the `"axes"` list. The axes and their order align with the `shape`
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attribute in the zarr array attributes (in `.zarray`), and whose data depends on the byte order used to store
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chunks. As described in the [zarr array metadata](https://zarr.readthedocs.io/en/stable/spec/v2.html#arrays),
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the last dimension of an array in "C" order are stored contiguously on disk or in-memory when directly loaded.
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the last dimension of an array in "C" order are stored contiguously on disk or in-memory when directly loaded.
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The name and axes names MAY be customized by including a `arrayCoordinateSystem` field in
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the user-defined attributes of the array whose value is a coordinate system object. The length of
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`axes` MUST be equal to the dimensionality. The value of `"type"` for each object in the
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`axes` MUST be equal to the dimensionality. The value of `"type"` for each object in the
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axes array MUST equal `"array"`.
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@@ -183,7 +183,7 @@ half-open interval `[-0.5, 0.5) x [-0.5, 0.5)` (i.e., -0.5 is included, +0.5 is
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"coordinateTransformations" describe the mapping between two coordinate systems (defined by "axes").
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For example, to map an array's discrete coordinate system to its corresponding physical coordinates.
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Coordinate transforms are in the "forward" direction. They represent functions from *points* in the
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input space to *points* in the output space.
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input space to *points* in the output space.
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- MUST contain the field "type".
@@ -195,7 +195,7 @@ input space to *points* in the output space.
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<table>
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<tr><th><code>identity</code>
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<td>
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<td>
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<td>The identity transformation is the default transformation and is typically not explicitly defined.
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<tr><th><code>mapAxis</code>
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<td><code>"mapAxis":Dict[String:String]</code>
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#### <a name="mapAxis">mapAxis</a>
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`mapAxis` transformations describe axis permutations as a mapping of axis names. Transformations MUST include a `mapAxis` field
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whose value is an object, all of whose values are strings. If the object contains `"x":"i"`, then the transform sets the value
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whose value is an object, all of whose values are strings. If the object contains `"x":"i"`, then the transform sets the value
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of the output coordinate for axis "x" to the value of the coordinate of input axis "i" (think `x = i`). For every axis in its output coordinate
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system, the `mapAxis` MUST have a corresponding field. For every value of the object there MUST be an axis of the input
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coordinate system with that name. Note that the order of the keys could be reversed.
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#### <a name="translation">translation</a>
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`translation` transformations are special cases of affine transformations. When possible, a
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`translation` transformations are special cases of affine transformations. When possible, a
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translation transformation should be preferred to its equivalent affine. Input and output dimensionality MUST be
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identical and MUST equal the the length of the "translation" array (N). `translation` transformations are
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invertible.
@@ -443,11 +443,11 @@ result of the sequence.
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The transformations included in the `transformations` array may omit their `input` and `output` fields under the conditions
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outlined below:
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- The `input` and `output` fields MAY be omitted for the following transformation types:
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- The `input` and `output` fields MAY be omitted for the following transformation types:
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- `identity`, `scale`, `translation`, `rotation`, `affine`, `displacements`, `coordinates`
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- The `input` and `output` fields MAY be omitted for `inverseOf` transformations if those fields may be omitted for the
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transformation it wraps
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- The `input` and `output` fields MAY be omitted for `bijection` transformations if the fields may be omitted for
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- The `input` and `output` fields MAY be omitted for `bijection` transformations if the fields may be omitted for
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both its `forward` and `inverse` transformations
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- The `input` and `output` fields MAY be omitted for `sequence` transformations if the fields may be omitted for
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all transformations in the sequence after flattening the nested sequence lists.
@@ -481,7 +481,7 @@ The `i`th value of the array along the `coordinate` or `displacement` axis refer
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of the `i`th output axis. See the example below.
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`coordinates` and `displacements` transformations are not invertible in general, but implementations MAY approximate their
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inverses. Metadata for these coordinate transforms have the following field:
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inverses. Metadata for these coordinate transforms have the following field:
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<dl>
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<dt><strong>path</strong></dt>
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<dl>
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<dt><strong>transformations</strong></dt>
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<dd> A list of transformations, each of which applies to a (non-strict) subset of input and output dimensions (axes).
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<dd> A list of transformations, each of which applies to a (non-strict) subset of input and output dimensions (axes).
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The values of <code>input</code> and <code>output</code> fields MUST be an array of strings.
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Every axis name in <code>input</code> MUST correspond to a name of some axis in this parent object's <code>input</code> coordinate system.
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Every axis name in the parent byDimension's <code>output</code> MUST appear in exactly one of its child transformations' <code>output</code>.
@@ -626,7 +626,7 @@ This RFC has been discussed in:
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Many RFCs have an "implementation" section which details how the implementation
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will work. This section should explain the rough specification changes. The
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goal is to give an idea to reviewers about the subsystems that require change
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and the surface area of those changes.
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and the surface area of those changes.
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This knowledge can result in recommendations for alternate approaches that
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perhaps are idiomatic to the project or result in less packages touched. Or, it
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transformations of arbitrary dimension and axis type, where there is not a strong convention we are aware of.
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An early consideration was to use axis names to indicate correspondence across different coordinate systems (i.e. if two
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coordinate systems both have the "x" axis, then it is "the same" axis. We abandoned this for several reasons. It was
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coordinate systems both have the "x" axis, then it is "the same" axis. We abandoned this for several reasons. It was
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restrictive - it is useful to have many coordinate systems with an "x" axis without requiring that they be "identical." Under our
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early idea, every set of spatial axes would need unique names ("x1", "x2", ...), and this seemed burdensome. As well, this
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approach would have also made transformations less explicit and likely would have required more complicated implementations.
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* thin-plate spline
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* b-spline
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* velocity fields
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* by-coordinate
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* by-coordinate
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## Performance
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rfc/5/versions/2/index.md

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@@ -27,7 +27,7 @@ This RFC is currently in RFC state `R4` (authors prepare responses).
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| **Endorser** | Will Moore | @will-moore | University of Dundee | 2025-10-23 | Implemented |
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| **Endorser** | David Stansby | @dstansby | University College London | 2025-10-23 | Implemented |
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| **Endorser** | Norman Rzepka | @normanrz | Scalable Minds | 2024-08-22 | |
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| **Reviewer** | Dan Toloudis, David Feng, Forrest Collman, Nathalie GAudreault, Gideon Dunster | toloudis, dyf, fcollman | Allen Institutes | 2024-11-28 | [Review](rfcs:rfc5:review1) |
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| **Reviewer** | Dan Toloudis, David Feng, Forrest Collman, Nathalie Gaudreault, Gideon Dunster | toloudis, dyf, fcollman | Allen Institutes | 2024-11-28 | [Review](rfcs:rfc5:review1) |
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| **Reviewer** | Will Moore, Jean-Marie Burel, Jason Swedlow | will-moore, jburel, jrswedlow | University of Dundee | 2025-01-22 | [Review](rfcs:rfc5:review2)|
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## Overview
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transformations are applied consistently across different platforms and applications.
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This FAIR capability is a cornerstone of scientific research,
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and having standardized formats and tools facilitates verification of results by independent researchers.
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2. Integration with Analysis Workflows:
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2. Integration with Analysis Workflows:
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Having spatial transformations as a first-class citizen within file formats
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allows for seamless integration with various image analysis workflows.
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Registration transformations can be used in subsequent image analysis steps
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The axes of a coordinate system (see below) give information
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about the types, units, and other properties of the coordinate system's dimensions.
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Axis names may contain semantically meaningful information, but can be arbitrary.
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As a result, two coordinate systems that have identical axes in the same order
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As a result, two coordinate systems that have identical axes in the same order
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may not be "the same" in the sense that measurements at the same point
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refer to different physical entities and therefore should not be analyzed jointly.
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Tasks that require images, annotations, regions of interest, etc.,
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The axes and their order align with the shape of the corresponding zarr array,
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and whose data depends on the byte order used to store chunks.
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As described in the [Zarr array metadata](https://zarr.readthedocs.io/en/stable/spec/v3.html#arrays),
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the last dimension of an array in "C" order are stored contiguously on disk or in-memory when directly loaded.
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the last dimension of an array in "C" order are stored contiguously on disk or in-memory when directly loaded.
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The name and axes names MAY be customized by including a `arrayCoordinateSystem` field
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in the user-defined attributes of the array whose value is a coordinate system object.
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| [`byDimension`](#bydimension) | `"transformations":List[Transformation]`, <br> `"input_axes": List[str]`, <br> `"output_axes": List[str]` | A high dimensional transformation using lower dimensional transformations on subsets of dimensions. |
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Implementations SHOULD prefer to store transformations as a sequence of less expressive transformations where possible
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(e.g., sequence[translation, rotation], instead of affine transformation with translation/rotation).
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(e.g., sequence[translation, rotation], instead of affine transformation with translation/rotation).
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````{admonition} Example
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(example:coordinate_transformation_scale)=
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{ "name": "in", "axes": [{"name": "j"}, {"name": "i"}] },
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{ "name": "out", "axes": [{"name": "y"}, {"name": "x"}] }
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],
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"coordinateTransformations": [
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"coordinateTransformations": [
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{
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"type": "scale",
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"scale": [2, 3.12],
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- SHOULD be able to apply transformations to images;
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Coordinate transformations can be stored in multiple places to reflect different usecases.
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- Transformations in individual multiscale datasets represent a special case of transformations
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and are explained [below](#multiscales-metadata).
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- Additional transformations for single multiscale images MUST be stored under a field `coordinateTransformations`
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The indexes of axis dimensions correspond to indexes into transformation parameter arrays.
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When rendering transformed images and interpolating,
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implementations may need the "inverse" transformation -
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implementations may need the "inverse" transformation -
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from the output to the input coordinate system.
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Inverse transformations will not be explicitly specified
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when they can be computed in closed form from the forward transformation.
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#### Transformation types
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Input and output dimensionality may be determined by the coordinate system referred to by the `input` and `output` fields, respectively.
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Input and output dimensionality may be determined by the coordinate system referred to by the `input` and `output` fields, respectively.
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If the value of `input` is a path to an array, its shape gives the input dimension,
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otherwise it is given by the length of `axes` for the coordinate system with the name of the `input`.
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If the value of `output` is an array, its shape gives the output dimension,
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`coordinates` and `displacements` transformations are not invertible in general,
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but implementations MAY approximate their inverses.
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Metadata for these coordinate transforms have the following fields:
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Metadata for these coordinate transforms have the following fields:
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<dl>
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<dt><strong>path</strong></dt>
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The transformation is defined according to [transformations metadata](#transformation-types).
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The transformation MUST take as input points in the array coordinate system
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corresponding to the Zarr array at location `path`.
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The value of "input" MUST equal the value of `path`,
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The value of "input" MUST equal the value of `path`,
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implementations should always treat the value of `input` as if it were equal to the value of `path`.
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The value of the transformation’s `output` MUST be the name of the "intrinsic" [coordinate system](#coordinatesystems-metadata).
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Many RFCs have an "implementation" section which details how the implementation
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will work. This section should explain the rough specification changes. The
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goal is to give an idea to reviewers about the subsystems that require change
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and the surface area of those changes.
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and the surface area of those changes.
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This knowledge can result in recommendations for alternate approaches that
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perhaps are idiomatic to the project or result in less packages touched. Or, it
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transformations of arbitrary dimension and axis type, where there is not a strong convention we are aware of.
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An early consideration was to use axis names to indicate correspondence across different coordinate systems (i.e. if two
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coordinate systems both have the "x" axis, then it is "the same" axis. We abandoned this for several reasons. It was
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coordinate systems both have the "x" axis, then it is "the same" axis. We abandoned this for several reasons. It was
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restrictive - it is useful to have many coordinate systems with an "x" axis without requiring that they be "identical." Under our
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early idea, every set of spatial axes would need unique names ("x1", "x2", ...), and this seemed burdensome. As well, this
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approach would have also made transformations less explicit and likely would have required more complicated implementations.
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* thin-plate spline
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* b-spline
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* velocity fields
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* by-coordinate
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* by-coordinate
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## Performance
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| Date | Description | Link |
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| ---------- | ---------------------------- | ---------------------------------------------------------------------------- |
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| 2024-10-08 | RFC assigned and published | [https://github.com/ome/ngff/pull/255](https://github.com/ome/ngff/pull/255) |
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| 2024-10-08 | RFC assigned and published | [https://github.com/ome/ngff/pull/255](https://github.com/ome/ngff/pull/255) |

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