Coordinate transforms json-schema (request for feedback) #149
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| { | ||
| "schema": "schemas/coordinate_transforms.schema" | ||
| } |
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| { | ||
| "arrayCoordinateSystem" : { | ||
| "name" : "myDataArray", | ||
| "axes" : [ | ||
| {"name": "i", "type": "array"}, | ||
| {"name": "j", "type": "array"}, | ||
| {"name": "k", "type": "array"} | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| { | ||
| "multiscales": [ | ||
| { | ||
| "version": "0.5-dev", | ||
| "name": "example", | ||
| "coordinateSystems" : [ | ||
| { | ||
| "name" : "exampleCoordinateSystem", | ||
| "axes": [ | ||
| {"name": "t", "type": "time", "unit": "millisecond"}, | ||
| {"name": "c", "type": "channel"}, | ||
| {"name": "z", "type": "space", "unit": "micrometer"}, | ||
| {"name": "y", "type": "space", "unit": "micrometer"}, | ||
| {"name": "x", "type": "space", "unit": "micrometer"} | ||
| ] | ||
| } | ||
| ], | ||
| "datasets": [ | ||
| { | ||
| "path": "0" | ||
| // the transformation of other arrays are defined relative to this, the highest resolution, array | ||
|
There was a problem hiding this comment. The spec still says: "Each dictionary in "datasets" MUST contain the field "coordinateTransformations", which contains a list of transformations that map the data coordinates to the physical coordinates (as specified by "axes") for this resolution level. There was a problem hiding this comment. @bogovicj, assuming I should go with the spec over the example here? Out of interest, why does the pixel -> physical need to be replicated here? There was a problem hiding this comment. I think the spec just needs updating or clarifying at that point. Maybe now it's "Each dictionary in "datasets" except the first MUST contain the field "coordinateTransformations"... |
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| }, | ||
| { | ||
| "path": "1", | ||
| "coordinateTransformations": [{ | ||
| // the second scale level (downscaled by a factor of 2 relative to "0" in zyx) | ||
| "type": "scale", | ||
| "scale": [1, 1, 2, 2, 2], | ||
| "input" : "/1`", | ||
| "output" : "/0" | ||
| }] | ||
| }, | ||
| { | ||
| "path": "2", | ||
| "coordinateTransformations": [{ | ||
| // the third scale level (downscaled by a factor of 4 relative to "0" in zyx) | ||
| "type": "scale", | ||
| "scale": [1, 1, 4, 4, 4], | ||
| "input" : "/2", | ||
| "output" : "/0" | ||
| }] | ||
| } | ||
| ], | ||
| "coordinateTransformations": [{ | ||
| // the time unit (0.1 milliseconds), the voxel size for all spatial axes of "0" (0.5 micrometers) | ||
| "type": "scale", | ||
| "scale": [0.1, 1.0, 0.5, 0.5, 0.5], | ||
| "input" : "/0", | ||
| "output" : "xampleCoordinateSystem" | ||
|
There was a problem hiding this comment. |
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| }], | ||
| "type": "gaussian", | ||
| "metadata": { | ||
| "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given", | ||
| "method": "skimage.transform.pyramid_gaussian", | ||
| "version": "0.16.1", | ||
| "args": "[true]", | ||
| "kwargs": {"multichannel": true} | ||
| } | ||
| } | ||
| ] | ||
| } | ||
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| { | ||||||
| "coordinateSystems" : [ | ||||||
| { "name " : "in", "axes" : [ {"name" : "0", "name" : "1", "name": "2", "name": "3", "name": "4" }] }, | ||||||
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There was a problem hiding this comment. The axes list has a single dict with multiple "name" keys? Is is supposed to be There was a problem hiding this comment.
Suggested change
@bogovicj, should changes to the examples happen here or in your PR? I haven't modified these from your branch, but also could add tests for the subspace directory. There was a problem hiding this comment. |
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| { "name " : "out", "axes" : [ {"name" : "x", "name" : "y", "name" : "z" }] } | ||||||
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| ], | ||||||
| "coordinateTransformations" : [ | ||||||
| { | ||||||
| "type" : "sequence", | ||||||
| "name" : "5D-to-3D", | ||||||
|
There was a problem hiding this comment. Does this combination of |
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| "input" : "in", | ||||||
| "output" : "out", | ||||||
| "transformations" : [ | ||||||
| { | ||||||
| "type": "mapIndex", | ||||||
| "inputAxes" : ["0", "1"], | ||||||
| "outputAxes" : ["x", "y"] | ||||||
| }, | ||||||
| { | ||||||
| "type": "scale", | ||||||
| "scale" : [2], | ||||||
| "inputAxes" : ["3"], | ||||||
| "outputAxes" : ["z"] | ||||||
| } | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "type" : "sequence", | ||||||
| "name" : "5D-to-3D-not-contiguous", | ||||||
| "input" : "in", | ||||||
| "output" : "out", | ||||||
| "transformations" : [ | ||||||
| { | ||||||
| "type": "mapIndex", | ||||||
| "inputAxes" : ["0", "2"], | ||||||
| "outputAxes" : ["x", "z"] | ||||||
| }, | ||||||
| { | ||||||
| "type": "scale", | ||||||
| "scale" : [2], | ||||||
| "inputAxes" : ["1"], | ||||||
| "outputAxes" : ["y"] | ||||||
| } | ||||||
| ] | ||||||
| }, | ||||||
| { | ||||||
| "type" : "sequence", | ||||||
| "name" : "5D-to-3D-not-contiguous", | ||||||
| "input" : "in", | ||||||
| "output" : "out", | ||||||
| "transformations" : [ | ||||||
| { | ||||||
| "type": "mapAxes", | ||||||
| "map" : {"0":"x", "2":"z"} | ||||||
| }, | ||||||
| { | ||||||
| "type": "scale", | ||||||
| "scale" : [2], | ||||||
| "inputAxes" : ["1"], | ||||||
| "outputAxes" : ["y"] | ||||||
| } | ||||||
| ] | ||||||
| } | ||||||
| ] | ||||||
| } | ||||||
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| { | ||
| "coordinateSystems" : [ | ||
| { "name " : "in", "axes" : [ {"name" : "i", "name" : "j" }] }, | ||
| { "name " : "out", "axes" : [ {"name" : "x", "name" : "y" }] } | ||
| ], | ||
| "coordinateTransformations" : [ | ||
| { | ||
| "type" : "sequence", | ||
| "input" : "in", | ||
| "output" : "out", | ||
| "transformations" : [ | ||
| { | ||
| "type": "identity", | ||
| "inputAxes" : ["j"], | ||
| "outputAxes" : ["x"] | ||
| }, | ||
| { | ||
| "type": "scale", | ||
| "scale" : [2], | ||
| "inputAxes" : ["i"], | ||
| "outputAxes" : ["y"] | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| { | ||
| "schema": "schemas/coordinate_transforms.schema" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,14 @@ | ||
| { | ||
| "coordinateSystems" : [ | ||
| { "name": "ij", "axes": [{"name": "i"}, {"name": "j"}] }, | ||
| { "name": "xy", "axes": [{"name": "x"}, {"name": "y"}] } | ||
| ], | ||
| "coordinateTransformations" : [ | ||
| { | ||
| "type": "affine", | ||
| "affine": [1, 2, 3, 4, 5, 6], | ||
| "input": "ij", | ||
| "output": "xy" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,14 @@ | ||
| { | ||
| "coordinateSystems": [ | ||
| { "name": "ij", "axes": [{"name": "i"}, {"name": "j"}] }, | ||
| { "name": "xyz", "axes": [{"name": "x"}, {"name": "y"}, {"name": "z"}] } | ||
| ], | ||
| "coordinateTransformations": [ | ||
| { | ||
| "type": "affine", | ||
| "affine": [1, 2, 3, 4, 5, 6, 7, 8, 9], | ||
| "input": "ij", | ||
| "output": "xyz" | ||
| } | ||
| ] | ||
| } |
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| { | ||
| "coordinateSystems": [ | ||
| { "name": "in", "axes": [ {"name": "i"}, {"name": "j"} ] }, | ||
| { "name": "out", "axes": [ {"name": "x"}, {"name": "y"} ] } | ||
| ], | ||
| "coordinateTransformations": [ | ||
| { | ||
| "type": "byDimension", | ||
| "input": "in", | ||
| "output": "out", | ||
| "transformations": [ | ||
| { "type": "translation", "translation": [-1.0], "input": ["i"], "output": ["x"]}, | ||
| { "type": "scale", "scale": [2.0], "input": ["j"], "output": ["y"]} | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,17 @@ | ||
| { | ||
| "coordinateSystems": [ | ||
| { "name": "in", "axes": [ {"name": "i"}, {"name": "j"}, {"name": "k"}, {"name": "l"}] }, | ||
| { "name": "out", "axes": [ {"name": "x"}, {"name": "y"}, {"name": "z"} ] } | ||
| ], | ||
| "coordinateTransformations": [ | ||
| { | ||
| "type": "byDimension", | ||
| "input": "in", | ||
| "output": "out", | ||
| "transformations" : [ | ||
| { "type": "translation", "translation": [1, 3], "input": ["i", "k" ], "output": ["y", "x"]}, | ||
| { "type": "scale", "scale": [2.0], "input": ["j"], "output": ["z"]} | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,17 @@ | ||
| { | ||
| "coordinateSystems": [ | ||
| { "name": "in", "axes": [ {"name": "i"}, {"name": "j"} ] }, | ||
| { "name": "out", "axes": [ {"name": "x"}, {"name": "y"} ] } | ||
| ], | ||
| "coordinateTransformations": [ | ||
| { | ||
| "type": "byDimension", | ||
| "input": "in", | ||
| "output": "out", | ||
| "transformations": [ | ||
| { "type": "translation", "translation": [-1.0], "input": ["i"], "output": ["z"]}, | ||
| { "type": "scale", "scale": [2.0], "input": ["0"], "output": ["y"]} | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| { | ||
| "coordinateSystems": [ | ||
| { "name": "in", "axes": [ {"name": "i"}, {"name": "j"} ] }, | ||
| { "name": "out", "axes": [ {"name": "x"}, {"name": "y"} ] } | ||
| ], | ||
| "coordinateTransformations": [ | ||
| { | ||
| "type": "byDimension", | ||
| "input": "in", | ||
| "output": "out", | ||
| "transformations": [ | ||
| { "type": "translation", "translation": [-1.0], "input": ["i"], "output": ["x"]}, | ||
| { "type": "scale", "scale": [2.0], "input": ["i"], "output": ["x"]} | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| { | ||
| "coordinateSystems": [ | ||
| { "name": "i", "axes": [{"name": "i"}] }, | ||
| { "name": "x", "axes": [{"name": "x"}] } | ||
| ], | ||
| "coordinateTransformations": [{ | ||
| "name": "a coordinate field transform", | ||
| "type": "coordinates", | ||
| "path": "i2xCoordinates", | ||
| "input": "i", | ||
| "output": "x", | ||
| "interpolation": "nearest" | ||
| }] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| { | ||
| "coordinateSystems": [ | ||
| { "name": "i", "axes": [{"name": "i"}] }, | ||
| { "name": "x", "axes": [{"name": "x"}] } | ||
| ], | ||
| "coordinateTransformations": [{ | ||
| "name": "a displacement field transform", | ||
| "type": "displacements", | ||
| "path": "i2xCoordinates", | ||
| "input": "i", | ||
| "output": "x", | ||
| "interpolation": "nearest" | ||
| }] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| { | ||
| "coordinateSystems": [ | ||
| { "name": "in", "axes": [ {"name": "i"}, {"name": "j"} ]}, | ||
| { "name": "out", "axes": [ {"name": "x"}, {"name": "y"} ]} | ||
| ], | ||
| "coordinateTransformations": [ | ||
| { "type": "identity", "input": "in", "output": "out" } | ||
| ] | ||
| } |
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Is the top-level multiscales coordinateTransformations no-longer valid? If it is, then this is a useful example. If not then the spec wording needs to be changed.
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It will still be valid - I'll edit this example showing how.