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Add 0.4 schemas and examples #87
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f07a613
Add 0.4 schemas and examples
will-moore 1f584b0
ensure 'time' and 'space' axes have valid units
will-moore 78b1698
Require 'scale' or 'translation' transformation(s)
will-moore e92b6ef
Add new-lines to end of json examples
will-moore a434669
Rename to coordinateTransforms
will-moore eb2d997
Add example of dataset with missing scale element
sbesson b993d8b
Add containment requirement for scale element in coordinateTransforma…
sbesson df897f1
Merge pull request #1 from sbesson/scale_mandatory
will-moore 456afea
Add additional examples of valid/invalid axes
sbesson 6199e5c
Add requirement for 2/3 space axes via contains
sbesson cecafa8
Handle custom axes
sbesson ac87d92
Set axes maxItems to 5
sbesson 8a165d7
Add maxContains to coordinateTransformations to enforce only one scale
sbesson bd1618c
Move coordinateTransformations to
will-moore 3067dd9
Move axes into
will-moore 40a15df
duplicate_axes_name.json not invalid with schema
will-moore 95c20ed
Remove strict requirement for valid axis units
will-moore 36340be
Add uniqueItems to axes
will-moore 2459b15
validate multiscales:coordinateTransformations
will-moore File filter
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| Original file line number | Diff line number | Diff line change |
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@@ -13,6 +13,7 @@ jobs: | |
| - '0.1' | ||
| - '0.2' | ||
| - '0.3' | ||
| - '0.4' | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| }, | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } |
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|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "invalid", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [1, 1], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ], | ||
| "omero": { | ||
| "channels": [ | ||
| { | ||
| "active": true, | ||
| "coefficient": 1.0, | ||
| "color": 255, | ||
| "family": "linear", | ||
| "label": "1234", | ||
| "window": { | ||
| "end": 1765.0, | ||
| "max": 2555.0, | ||
| "min": 5.0, | ||
| "start": 0.0 | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ], | ||
| "omero": { | ||
| "channels": [ | ||
| { | ||
| "active": true, | ||
| "coefficient": 1.0, | ||
| "color": "ff0000", | ||
| "family": "linear", | ||
| "label": "1234", | ||
| "window": { | ||
| "end": "100", | ||
| "max": 2555.0, | ||
| "min": 5.0, | ||
| "start": 0.0 | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } |
39 changes: 39 additions & 0 deletions
39
0.4/examples/invalid/invalid_multiscales_transformations.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": ["invalid"], | ||
| "type": "scale" | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": 0, | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "scale" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| { | ||
| "multiscales": [ | ||
| { | ||
| "axes": [ | ||
| { | ||
| "name": "y", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| }, | ||
| { | ||
| "name": "x", | ||
| "type": "space", | ||
| "units": "micrometer" | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0", | ||
| "coordinateTransformations": [ | ||
| { | ||
| "scale": [ | ||
| 1, | ||
| 1 | ||
| ], | ||
| "type": "translation" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "version": "0.4" | ||
| } | ||
| ] | ||
| } |
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This is currently a SHOULD, see https://github.com/ome/ngff/blob/main/latest/index.bs#L217. Not sure how exactly we want to tackle this. I will leave a more general comment once I went through everything.
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Agreed, this should not fail validation but probably be flagged by the stricter schema. I propose to open a follow-up PR with the infrastructure to differentiate the two of them.
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Actually, re-reading this example, this should remain invalid.
As you rightfully mentioned
typeis a SHOULD and that is not sufficient ground to fail the strict schema. However there is only onespaceaxe within themultiscalesdictionaryThere was a problem hiding this comment.
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yes, you're right. But the name of this example is a bit misleading then.
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And in fact it is failing because
typeis notspace, channel or timerather than only-1-space-axis.So the schema should allow 1 'invalid' axis.
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I am not sure what you mean by this @will-moore. But I agree that this one should fail the strict spec because it has only 1 spatial axis, as @sbesson points out. But I would maybe rename the example to make that clear.
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Nods, that's probably more tests worth injecting but my understanding of the
typerestrictions is the following formultiscales.axes:There was a problem hiding this comment.
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with 3 spatial axes this would fail because we would have > 5 dim. Same for some of the other examples you bring up.
But otherwise I agree with your list.
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Heh the
orin between 1 channel and 1 time was meant to capture that but I certainly failed to write the different combinations in a concise way. Expanding a bit, all the following set of axes types should be valid according to the minimal schema but should fail the strict schema: