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Unify input output #117

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d4c1c2c
schemas: introduced central InputOutput object definition
jo-mueller Mar 26, 2026
d453396
tests: use correct InputOutput everywhere
jo-mueller Mar 26, 2026
82f6c8f
docs: update examples for correct InputOutput syntax
jo-mueller Mar 26, 2026
0ab6faf
chore: Updated version to 0.6.dev4 everywhere
jo-mueller Mar 26, 2026
34fa54c
specification: Unifiy input/output of transformations to object with …
jo-mueller Mar 26, 2026
d883e55
chore: update version history
jo-mueller Mar 26, 2026
38f9334
specification: improve clarity
jo-mueller Mar 26, 2026
85056a3
chore: fix typos
jo-mueller Mar 26, 2026
9849a4c
Update index.md
jo-mueller Mar 27, 2026
98a4d56
Update index.md
jo-mueller Mar 27, 2026
9c7dae2
specification: Clarify constraintsfor input/output in additional tran…
jo-mueller Mar 27, 2026
3076fb7
Update index.md
jo-mueller Mar 27, 2026
80703fc
Update index.md
jo-mueller Mar 27, 2026
8c0674c
Update index.md
jo-mueller Mar 27, 2026
b0108b2
Update index.md
jo-mueller Mar 30, 2026
2ab8a28
chore: Clearer on language
jo-mueller Mar 30, 2026
0bd9da6
chore: Improve readability on multiscale transform input/output const…
jo-mueller Mar 30, 2026
bd5175d
specification: allow sequence in labels transforms
jo-mueller Apr 1, 2026
8a32f83
Merge remote-tracking branch 'upstream/main' into unify-input-output
jo-mueller Apr 2, 2026
e05ff89
doc: update and expand examples
jo-mueller Apr 2, 2026
e9f012e
enh: Add table with metadata fields
jo-mueller Apr 2, 2026
64e7cb6
enh: avoid instances of "intrinsic before definition
jo-mueller Apr 2, 2026
45458b8
enh: improve formatting of multiscales section
jo-mueller Apr 2, 2026
aacc2b7
enh: combine labels examples into single example
jo-mueller Apr 2, 2026
236a31c
chore: Update example title
jo-mueller Apr 2, 2026
3e1e3de
specification: Weaken requirements regarding linkage of labels and image
jo-mueller Apr 2, 2026
c50ef5b
enh: improve formatting
jo-mueller Apr 2, 2026
2b9b823
chore: typo
jo-mueller Apr 2, 2026
38b7849
chore: clearer language
jo-mueller Apr 2, 2026
9ae08ed
chore: language clarification
jo-mueller Apr 2, 2026
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2 changes: 1 addition & 1 deletion _version.py
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@@ -1 +1 @@
__version__ = '0.6.dev3'
__version__ = '0.6.dev4'
2 changes: 1 addition & 1 deletion examples/bf2raw/image.json
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Expand Up @@ -3,7 +3,7 @@
"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"bioformats2raw.layout": 3
}
}
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2 changes: 1 addition & 1 deletion examples/bf2raw/plate.json
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Expand Up @@ -3,7 +3,7 @@
"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"bioformats2raw.layout": 3,
"plate": {
"columns": [
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2 changes: 1 addition & 1 deletion examples/label_strict/colors_properties.json
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Expand Up @@ -3,7 +3,7 @@
"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"image-label": {
"colors": [
{
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14 changes: 7 additions & 7 deletions examples/multiscales_strict/multiscales_example.json
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"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"multiscales": [
{
"name": "example",
Expand All @@ -28,8 +28,8 @@
// and the time unit (0.1 milliseconds), which is the same for each scale level
"type": "scale",
"scale": [0.1, 1.0, 0.5, 0.5, 0.5],
"input": "s0",
"output": "intrinsic"
"input": {"path": "s0"},
"output": {"name": "intrinsic"}
}
]
},
Expand All @@ -41,8 +41,8 @@
// and the time unit (0.1 milliseconds), which is the same for each scale level
"type": "scale",
"scale": [0.1, 1.0, 1.0, 1.0, 1.0],
"input": "s1",
"output": "intrinsic"
"input": {"path": "s1"},
"output": {"name": "intrinsic"}
}
]
},
Expand All @@ -54,8 +54,8 @@
// and the time unit (0.1 milliseconds), which is the same for each scale level
"type": "scale",
"scale": [0.1, 1.0, 2.0, 2.0, 2.0],
"input": "s2",
"output": "intrinsic"
"input": {"path": "s2"},
"output": {"name": "intrinsic"}
}
]
}
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18 changes: 9 additions & 9 deletions examples/multiscales_strict/multiscales_example_relative.json
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@@ -1,7 +1,7 @@
{
"multiscales": [
{
"version": "0.6.dev3",
"version": "0.6.dev4",
"name": "example",
"coordinateSystems" : [
{
Expand Down Expand Up @@ -33,8 +33,8 @@
"coordinateTransformations": [{
"type": "scale",
"scale": [1, 1, 1, 1, 1],
"input": "s0",
"output": "intrinsic"
"input": {"path": "s0"},
"output": {"name": "intrinsic"}
}]
},
{
Expand All @@ -43,8 +43,8 @@
// the second scale level (downscaled by a factor of 2 relative to "s0" in zyx)
"type": "scale",
"scale": [1, 1, 2, 2, 2],
"input" : "s1",
"output" : "intrinsic"
"input" : {"path": "s1"},
"output" : {"name": "intrinsic"}
}]
},
{
Expand All @@ -53,8 +53,8 @@
// the third scale level (downscaled by a factor of 4 relative to "s0" in zyx)
"type": "scale",
"scale": [1, 1, 4, 4, 4],
"input" : "s2",
"output" : "intrinsic"
"input" : {"path": "s2"},
"output" : {"name": "intrinsic"}
}]
}
],
Expand All @@ -63,8 +63,8 @@
"name": "additional_translation",
"type": "translation",
"translation": [0, 0, 10, 20, 30],
"input": "intrinsic",
"output": "world"
"input": {"name": "intrinsic"},
"output": {"name": "world"}
}
]
}
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10 changes: 5 additions & 5 deletions examples/multiscales_strict/multiscales_transformations.json
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Expand Up @@ -3,7 +3,7 @@
"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"multiscales": [
{
"coordinateSystems": [
Expand Down Expand Up @@ -45,8 +45,8 @@
{
"scale": [1, 1],
"type": "scale",
"input": "s0",
"output": "intrinsic"
"input": {"path": "s0"},
"output": {"name": "intrinsic"}
}
]
}
Expand All @@ -55,8 +55,8 @@
{
"scale": [10, 10],
"type": "scale",
"input": "intrinsic",
"output": "physical"
"input": {"name": "intrinsic"},
"output": {"name": "physical"}
}
],
"name": "image_with_coordinateTransformations",
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2 changes: 1 addition & 1 deletion examples/ome/series-2.json
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"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"series": ["0", "1"]
}
}
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2 changes: 1 addition & 1 deletion examples/plate_strict/plate_2wells.json
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"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"plate": {
"acquisitions": [
{
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2 changes: 1 addition & 1 deletion examples/plate_strict/plate_6wells.json
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"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"plate": {
"acquisitions": [
{
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2 changes: 1 addition & 1 deletion examples/scene/scene_registration.json
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"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"scene": {
"coordinateTransformations": [
{
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2 changes: 1 addition & 1 deletion examples/scene/scene_stitching.json
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Expand Up @@ -3,7 +3,7 @@
"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"scene": {
"coordinateTransformations": [
{
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87 changes: 0 additions & 87 deletions examples/subspace/subspaceMultidim.json
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10 changes: 5 additions & 5 deletions examples/subspace/subspacePermute.json
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Expand Up @@ -3,7 +3,7 @@
"node_type": "group",
"attributes": {
"ome": {
"version": "0.6.dev3",
"version": "0.6.dev4",
"multiscales": [
{
"name": "multiscales",
Expand Down Expand Up @@ -47,8 +47,8 @@
"coordinateTransformations": [
{
"type": "scale",
"output": "array_coordinates",
"input": "array",
"output": {"name": "array_coordinates"},
"input": {"path": "array"},
"name": "default-scale",
"scale": [1, 1]
}
Expand All @@ -58,8 +58,8 @@
"coordinateTransformations": [
{
"type": "mapAxis",
"output": "physical",
"input": "array_coordinates",
"output": {"name": "physical"},
"input": {"name": "array_coordinates"},
"name": "transform-name",
"mapAxis": [1, 0]
}
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4 changes: 2 additions & 2 deletions examples/transformations/affine2d2d.json
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Expand Up @@ -7,8 +7,8 @@
{
"type": "affine",
"affine": [[1, 2, 3], [4, 5, 6]],
"input": "ji",
"output": "yx"
"input": {"name": "ji"},
"output": {"name": "yx"}
}
]
}
4 changes: 2 additions & 2 deletions examples/transformations/affine2d2d_with_channel.json
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Expand Up @@ -25,8 +25,8 @@
[0, 1, 2, 3],
[0, 4, 5, 6]
],
"input": "cji",
"output": "cyx"
"input": {"name": "cji"},
"output": {"name": "cyx"}
}
]
}
4 changes: 2 additions & 2 deletions examples/transformations/affine2d3d.json
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Expand Up @@ -7,8 +7,8 @@
{
"type": "affine",
"affine": [[1, 0, 0], [2, 3, 4], [5, 6, 7]],
"input": "ij",
"output": "zyx"
"input": {"name": "ij"},
"output": {"name": "zyx"}
}
]
}
4 changes: 2 additions & 2 deletions examples/transformations/bijection.json
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Expand Up @@ -14,8 +14,8 @@
"type" : "coordinates",
"path" : "inverse_coordinates"
},
"input": "src",
"output": "tgt"
"input": {"name": "src"},
"output": {"name": "tgt"}
}
]
}
8 changes: 4 additions & 4 deletions examples/transformations/bijection_verbose.json
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@@ -1,7 +1,7 @@
{
"type": "bijection",
"forward": { "type" : "coordinates", "path" : "forward_coordinates", "input" : "src", "output" : "tgt" },
"inverse": { "type" : "coordinates", "path" : "inverse_coordinates", "input" : "tgt", "output" : "src" },
"input": "src",
"output": "tgt"
"forward": { "type" : "coordinates", "path" : "forward_coordinates", "input" : {"name": "src"}, "output" : {"name": "tgt"} },
"inverse": { "type" : "coordinates", "path" : "inverse_coordinates", "input" : {"name": "tgt"}, "output" : {"name": "src"} },
"input": {"name": "src"},
"output": {"name": "tgt"}
}
4 changes: 2 additions & 2 deletions examples/transformations/byDimension1.json
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Expand Up @@ -6,8 +6,8 @@
"coordinateTransformations": [
{
"type": "byDimension",
"input": "in",
"output": "out",
"input": {"name": "in"},
"output": {"name": "out"},
"transformations": [
{
"transformation": {
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4 changes: 2 additions & 2 deletions examples/transformations/byDimension2.json
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Expand Up @@ -21,8 +21,8 @@
"coordinateTransformations": [
{
"type": "byDimension",
"input": "in",
"output": "out",
"input": {"name": "in"},
"output": {"name": "out"},
"transformations": [
{
"transformation": {
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