Coordinate systems and new coordinate transformations proposal #138
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| { | ||
| "arrayCoordinateSystem" : { | ||
| "name" : "myDataArray", | ||
| "axes" : [ | ||
| {"name": "i", "type": "array"}, | ||
| {"name": "j", "type": "array"}, | ||
| {"name": "k", "type": "array"} | ||
| ] | ||
| } | ||
| } |
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|---|---|---|
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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 | ||
| }, | ||
| { | ||
| "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" : "exampleCoordinateSystem" | ||
| }], | ||
| "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" }] }, | ||
| { "name " : "out", "axes" : [ {"name" : "x", "name" : "y", "name" : "z" }] } | ||
| ], | ||
| "coordinateTransformations" : [ | ||
| { | ||
| "type" : "sequence", | ||
| "name" : "5D-to-3D", | ||
| "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" : "byDimension", | ||
| "input" : "in", | ||
| "output" : "out", | ||
| "transformations" : [ | ||
| { | ||
| "type": "identity", | ||
| "input" : ["j"], | ||
| "output" : ["x"] | ||
| }, | ||
| { | ||
| "type": "scale", | ||
| "scale" : [2], | ||
| "input" : ["i"], | ||
| "output" : ["y"] | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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| { | ||
| "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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| { | ||
| "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" | ||
| } | ||
| ] | ||
| } | ||
|
There was a problem hiding this comment. This is the first example where I really don't know at first glance what's going on...? There was a problem hiding this comment. Related: #146 (comment) (please @bogovicj close the issue if the nested representation is adopted) |
||
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| @@ -0,0 +1,15 @@ | ||
| { | ||
| "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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| { | ||
| "coordinateSystems" : [ | ||
| { "name": "src", "axes": [{"name": "i"}, {"name": "j"}] }, | ||
| { "name": "tgt", "axes": [{"name": "x"}, {"name": "y"}] } | ||
| ], | ||
| "coordinateTransformations" : [ | ||
| { | ||
| "type": "bijection", | ||
| "forward": { "type" : "coordinates", "path" : "/forward_coordinates" }, | ||
| "inverse": { "type" : "coordinates", "path" : "/inverse_coordinates" }, | ||
| "input": "src", | ||
| "output": "tgt" | ||
| } | ||
| ] | ||
| } |
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| { | ||
| "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" | ||
| } |
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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": ["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 |
|---|---|---|
| @@ -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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Trying to integrate the proposal from #114 which is orthognal to this proposal but is scheduled for discussion at the upcoming OME-NGFF call, how would this be modified?
Would the input still point at the relative path to the resolution group or should it point at the relative path to the resolution array i.e. `"/0/image"?
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A secondary concern is whether this nomenclature is redundant with the
multiscales.datasets.pathmetadata which also defines the path to the array?