Zarr v3

latest/examples/coordSystems/arrayCoordSys.json

@@ -0,0 +1,10 @@
+{
+    "arrayCoordinateSystem" : {
+        "name" : "myDataArray",
+        "axes" : [
+            {"name": "i", "type": "array"},
+            {"name": "j", "type": "array"},
+            {"name": "k", "type": "array"}
+        ]
+    }
+}

latest/examples/multiscales_strict/multiscales_example.json

@@ -3,44 +3,50 @@
         {
             "version": "0.5-dev",
             "name": "example",
-            "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"}
+            "coordinateSystems" : [
+                {
+                    "name" : "example",
+                    "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",
                     "coordinateTransformations": [{
-                        // the voxel size for the first scale level (0.5 micrometer)
+                        // the voxel size for the first scale level (0.5 micrometer), time unit (0.1 milliseconds)
                         "type": "scale",
-                        "scale": [1.0, 1.0, 0.5, 0.5, 0.5]
+                        "scale": [0.1, 1.0, 0.5, 0.5, 0.5],
+                        "input" : "/0",
+                        "output" : "example"
                     }]
                 },
                 {
                     "path": "1",
                     "coordinateTransformations": [{
-                        // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
+                        // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer), time unit (0.1 milliseconds)
                         "type": "scale",
-                        "scale": [1.0, 1.0, 1.0, 1.0, 1.0]
+                        "scale": [0.1, 1.0, 1.0, 1.0, 1.0],
+                        "input" : "/1`",
+                        "output" : "example"
                     }]
                 },
                 {
                     "path": "2",
                     "coordinateTransformations": [{
-                        // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
+                        // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer), time unit (0.1 milliseconds)
                         "type": "scale",
-                        "scale": [1.0, 1.0, 2.0, 2.0, 2.0]
+                        "scale": [0.1, 1.0, 2.0, 2.0, 2.0],
+                        "input" : "/2",
+                        "output" : "example"
                     }]
                 }
             ],
-            "coordinateTransformations": [{
-                // the time unit (0.1 milliseconds), which is the same for each scale level
-                "type": "scale",
-                "scale": [0.1, 1.0, 1.0, 1.0, 1.0]
-            }],
             "type": "gaussian",
             "metadata": {
                 "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given",
@@ -51,4 +57,4 @@
             }
         }
     ]
-}
+}

latest/examples/multiscales_strict/multiscales_example_relative.json

@@ -0,0 +1,61 @@
+{
+    "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}
+            }
+        }
+    ]
+}

latest/examples/subspace/subspaceMultidim.json

@@ -0,0 +1,64 @@
+{
+    "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"]
+                }
+            ]
+        }
+    ]
+}

latest/examples/subspace/subspacePermute.json

@@ -0,0 +1,26 @@
+{
+    "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"]
+                }
+            ]
+        }
+    ]
+}

latest/examples/transformations/affine2d2d.json

@@ -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"
+        }
+    ]
+}

latest/examples/transformations/affine2d3d.json

@@ -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"
+        }
+    ]
+}

latest/examples/transformations/affine2d3d_nested.json

@@ -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"
+        }
+    ]
+}

latest/examples/transformations/bijection.json

@@ -0,0 +1,15 @@
+{
+    "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"
+        }
+    ]
+}

latest/examples/transformations/bijection_verbose.json

@@ -0,0 +1,7 @@
+{
+    "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"
+}

latest/examples/transformations/byDimension1.json

@@ -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"]}
+            ]
+        }
+    ]
+}

latest/examples/transformations/byDimension2.json

@@ -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"]}
+            ]
+        }
+    ]
+}

latest/examples/transformations/byDimensionInvalid1.json

@@ -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"]}
+            ]
+        }
+    ]
+}

latest/examples/transformations/byDimensionInvalid2.json

@@ -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"]}
+            ]
+        }
+    ]
+}

latest/examples/transformations/coordinates1d.json

@@ -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"
+    }]
+}