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Merge pull request #2 from jo-mueller/omero_metadata_optional
Omero metadata optional
2 parents 4387a7a + facbf73 commit c0c1121

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‎index.md‎

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### "omero" metadata (transitional)
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(omero-md)=
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[=Transitional=] information specific to the channels of an image and how to render it can be found under the `omero` key in the group-level metadata:
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Information specific to the channels of an image and how to render it
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can be found under the `omero` key in the group-level metadata (i.e., under `"ome" > "omero"`):
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```json
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"id": 1, # ID in OMERO
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"name": "example.tif", # Name as shown in the UI
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"channels": [ # Array matching the c dimension size
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"id": 1, // ID in OMERO
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"name": "example.tif", // Name as shown in the UI
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"channels": [ // Array matching the c dimension size
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{
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"active": true,
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"coefficient": 1,
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}
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],
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"rdefs": {
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"defaultT": 0, # First timepoint to show the user
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"defaultZ": 118, # First Z section to show the user
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"model": "color" # "color" or "greyscale"
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"defaultT": 0, // First timepoint to show the user
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"defaultZ": 118, // First Z section to show the user
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"model": "color" // "color" or "greyscale"
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}
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```
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The `omero` metadata is optional, but if present it MUST contain the field `channels`,
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which is an array of objects describing the channels of the image.
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The `channels` array length SHOULD correspond to the size of the respective channels axis, if present.
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Each object in `channels` MAY contain the following fields:
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Each object in `channels` is optional and MAY contain the following fields:
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- `color` (string) String of 6 hexadecimal digits specifying the color of the channel in RGB format.
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- `label` (string) Channel name.
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- `active` (boolean) Indicates whether the channel should be displayed.
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- `coefficient`: (float) Value to multiply the pixel values of the channel by when rendering.
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- `family`: (string) Used transfer function family for rendering the channel, e.g. "linear", "log", "gamma".
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- `window` (dictionary) Values describing the windowing of the channel.
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If provided, `start` and `end` values MUST be specified.
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All values can be floating-point numbers, but will likely be integers for integer pixel types.

‎schemas/image.schema‎

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"label": {
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"type": "string"
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},
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"coefficient": {
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"type": "number"
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},
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"family": {
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"type": "string"
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},

‎tests/attributes/spec/invalid/omero/missing_channels.json‎

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{
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"ome": {
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"version": "0.6.dev3",
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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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{
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"name": "z",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "y",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "x",
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"type": "space",
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"unit": "micrometer"
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}
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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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"scale": [
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1,
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1,
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1
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],
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"input": "s0",
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"output": "physical",
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"type": "scale"
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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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"omero": {
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}
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},
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"_conformance": {
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"schema": {
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"id": "schemas/image.schema"
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},
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"valid": false
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}
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}

‎tests/attributes/spec/invalid/omero/missing_start_end.json‎

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{
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"ome": {
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"version": "0.6.dev3",
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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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{
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"name": "z",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "y",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "x",
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"type": "space",
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"unit": "micrometer"
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}
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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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"scale": [
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1,
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1,
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1
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],
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"input": "s0",
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"output": "physical",
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"type": "scale"
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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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"omero": {
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"channels": [
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{
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"label": "Channel:0",
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"color": "#ff0000",
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"active": true,
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"family": "linear",
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"coefficient": 1.0,
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"inverted": false,
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"window": {
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"min": 0,
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"max": 255
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}
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},
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{
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"label": "Channel:1",
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"color": "#00ff00",
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"active": true,
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"family": "log",
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"coefficient": 0.5,
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"inverted": true,
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"window": {
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"min": 0,
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"max": 255
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}
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},
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{
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"label": "Channel:2",
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"color": "#0000ff",
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"active": true,
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"family": "gamma",
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"coefficient": 2.0,
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"inverted": false,
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"window": {
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"min": 0,
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"max": 255
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}
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}
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]
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}
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},
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"_conformance": {
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"schema": {
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"id": "schemas/image.schema"
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},
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"valid": false
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}
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}

‎tests/attributes/spec/valid/omero/full_omero_metadata.json‎

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{
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"ome": {
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"version": "0.6.dev3",
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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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{
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"name": "z",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "y",
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"type": "space",
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"unit": "micrometer"
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},
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{
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"name": "x",
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"type": "space",
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"unit": "micrometer"
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}
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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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"scale": [
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1,
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1,
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1
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],
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"input": "s0",
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"output": "physical",
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"type": "scale"
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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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"omero": {
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"channels": [
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{
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"label": "Channel:0",
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"color": "#ff0000",
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"active": true,
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"family": "linear",
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"coefficient": 1.0,
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"inverted": false,
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"window": {
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"min": 0,
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"start": 100,
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"end": 200,
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"max": 255
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}
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},
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{
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"label": "Channel:1",
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"color": "#00ff00",
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"active": true,
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"family": "log",
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"coefficient": 0.5,
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"inverted": true,
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"window": {
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"min": 0,
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"start": 50,
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"end": 150,
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"max": 255
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}
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},
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{
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"label": "Channel:2",
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"color": "#0000ff",
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"active": true,
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"family": "gamma",
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"coefficient": 2.0,
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"inverted": false,
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"window": {
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"min": 0,
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"start": 25,
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"end": 125,
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"max": 255
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}
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}
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]
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}
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},
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"_conformance": {
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"schema": {
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"id": "schemas/image.schema"
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}
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}
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}

‎version_history.md‎

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- Updated version keys from `0.6.dev2` to `0.6.dev3` everywhere
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- style: Homogeneous use of backticks in spec document
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- spec: Released requirements for `omero` metadata in the spec document and in schemas.
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### Removed
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