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Unify input output (ome#117)
* schemas: introduced central InputOutput object definition * tests: use correct InputOutput everywhere * docs: update examples for correct InputOutput syntax * chore: Updated version to 0.6.dev4 everywhere * specification: Unifiy input/output of transformations to object with name/path * chore: update version history * specification: improve clarity * chore: fix typos * Update index.md Co-authored-by: David Stansby <dstansby@gmail.com> * Update index.md Co-authored-by: David Stansby <dstansby@gmail.com> * specification: Clarify constraintsfor input/output in additional transforms * Update index.md Co-authored-by: David Stansby <dstansby@gmail.com> * Update index.md Co-authored-by: David Stansby <dstansby@gmail.com> * Update index.md Co-authored-by: David Stansby <dstansby@gmail.com> * Update index.md Co-authored-by: David Stansby <dstansby@gmail.com> * chore: Clearer on language * chore: Improve readability on multiscale transform input/output constraints * specification: allow sequence in labels transforms * doc: update and expand examples * enh: Add table with metadata fields * enh: avoid instances of "intrinsic before definition * enh: improve formatting of multiscales section * enh: combine labels examples into single example * chore: Update example title * specification: Weaken requirements regarding linkage of labels and image * enh: improve formatting * chore: typo * chore: clearer language * chore: language clarification * specification: Clarify omission of path * chore: update examples --------- Co-authored-by: David Stansby <dstansby@gmail.com>
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‎_version.py‎

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__version__ = '0.6.dev3'
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__version__ = '0.6.dev4'

‎examples/bf2raw/image.json‎

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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"bioformats2raw.layout": 3
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}
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}

‎examples/bf2raw/plate.json‎

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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"bioformats2raw.layout": 3,
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"plate": {
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"columns": [

‎examples/label_strict/colors_properties.json‎

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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"multiscales": [
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{
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"coordinateSystems": [
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{
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"name": "physical",
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"axes": [
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{"name": "z", "unit": "micrometer"},
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{"name": "y", "unit": "micrometer"},
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{"name": "x", "unit": "micrometer"}
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]
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}
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],
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"datasets": [
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{
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"path": "s0",
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"coordinateTransformations": [
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{
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"type": "scale",
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"scale": [0.5, 0.5, 1],
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"input": {"path": "s0"},
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"output": {"name": "physical"}
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}
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]
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}
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]
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}
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],
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"image-label": {
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"colors": [
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{

‎examples/multiscales_strict/multiscales_example.json‎

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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"multiscales": [
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{
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"name": "example",
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// and the time unit (0.1 milliseconds), which is the same for each scale level
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"type": "scale",
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"scale": [0.1, 1.0, 0.5, 0.5, 0.5],
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"input": "s0",
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"output": "intrinsic"
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"input": {"path": "s0"},
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"output": {"name": "intrinsic"}
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}
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]
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},
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// and the time unit (0.1 milliseconds), which is the same for each scale level
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"type": "scale",
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"scale": [0.1, 1.0, 1.0, 1.0, 1.0],
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"input": "s1",
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"output": "intrinsic"
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"input": {"path": "s1"},
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"output": {"name": "intrinsic"}
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}
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]
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},
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// and the time unit (0.1 milliseconds), which is the same for each scale level
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"type": "scale",
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"scale": [0.1, 1.0, 2.0, 2.0, 2.0],
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"input": "s2",
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"output": "intrinsic"
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"input": {"path": "s2"},
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"output": {"name": "intrinsic"}
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}
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]
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}

‎examples/multiscales_strict/multiscales_example_relative.json‎

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{
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"multiscales": [
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{
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"name": "example",
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"coordinateSystems" : [
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{
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"coordinateTransformations": [{
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"type": "scale",
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"scale": [1, 1, 1, 1, 1],
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"input": "s0",
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"output": "intrinsic"
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"input": {"path": "s0"},
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"output": {"name": "intrinsic"}
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}]
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},
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{
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// the second scale level (downscaled by a factor of 2 relative to "s0" in zyx)
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"type": "scale",
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"scale": [1, 1, 2, 2, 2],
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"input" : "s1",
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"output" : "intrinsic"
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"input" : {"path": "s1"},
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"output" : {"name": "intrinsic"}
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}]
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},
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{
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// the third scale level (downscaled by a factor of 4 relative to "s0" in zyx)
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"type": "scale",
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"scale": [1, 1, 4, 4, 4],
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"input" : "s2",
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"output" : "intrinsic"
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"input" : {"path": "s2"},
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"output" : {"name": "intrinsic"}
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}]
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}
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],
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"name": "additional_translation",
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"type": "translation",
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"translation": [0, 0, 10, 20, 30],
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"input": "intrinsic",
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"output": "world"
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"input": {"name": "intrinsic"},
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"output": {"name": "world"}
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}
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]
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}

‎examples/multiscales_strict/multiscales_reference_to_label.json‎

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{
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"ome": {
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"version": "0.6.dev4",
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"multiscales": [
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{
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"name": "Image",
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"datasets": [
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{
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"path": "s0",
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"coordinateTransformations": [
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{
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"type": "scale",
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"scale": [0.5, 0.5, 1],
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"input": {"path": "s0"},
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"output": {"name": "physical"}
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}
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]
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}
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],
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"coordinateSystems": [
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{
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"name": "physical",
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"axes": [
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{"name": "z", "unit": "micrometer"},
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{"name": "y", "unit": "micrometer"},
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{"name": "x", "unit": "micrometer"}
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]
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}
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],
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"coordinateTransformations": [
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{
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"type": "identity",
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"input": {"path": "labels/cell_segmentation","name": "physical"},
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"output": {"name": "physical"}
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}
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]
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}
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]
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}
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}

‎examples/multiscales_strict/multiscales_transformations.json‎

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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"multiscales": [
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{
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"coordinateSystems": [
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{
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"scale": [1, 1],
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"type": "scale",
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"input": "s0",
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"output": "intrinsic"
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"input": {"path": "s0"},
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"output": {"name": "intrinsic"}
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}
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]
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}
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{
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"scale": [10, 10],
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"type": "scale",
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"input": "intrinsic",
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"output": "physical"
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"input": {"name": "intrinsic"},
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"output": {"name": "physical"}
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}
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],
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"name": "image_with_coordinateTransformations",

‎examples/ome/series-2.json‎

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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"series": ["0", "1"]
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}
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}

‎examples/plate_strict/plate_2wells.json‎

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"node_type": "group",
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"attributes": {
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"ome": {
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"version": "0.6.dev3",
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"version": "0.6.dev4",
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"plate": {
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"acquisitions": [
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{

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