Coordinate systems and new coordinate transformations proposal

0.5/tests/test_validation.py

@@ -60,6 +60,11 @@ def pytest_generate_tests(metafunc):
     if "suite" in metafunc.fixturenames:
         suites: List[Schema] = []
         ids: List[str] = []
+        schema_store = {}
+        for filename in glob.glob("schemas/*.schema"):
+            with open(filename) as o:
+                schema = json.load(o)
+            schema_store[schema["$id"]] = schema
 
         # Validation
         for filename in glob.glob("tests/*.json"):

0.6-dev/copyright.include

@@ -0,0 +1,4 @@
+Copyright © 2020-[YEAR]
+<a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup>
+(<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
+OME trademark rules apply.

0.6-dev/examples/bf2raw/.config.json

@@ -0,0 +1,3 @@
+{
+    "schema": "schemas/bf2raw.schema"
+}

0.6-dev/examples/bf2raw/image.json

@@ -0,0 +1,10 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "bioformats2raw.layout": 3
+    }
+  }
+}

0.6-dev/examples/bf2raw/plate.json

@@ -0,0 +1,36 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "bioformats2raw.layout": 3,
+      "plate": {
+        "columns": [
+          {
+            "name": "1"
+          }
+        ],
+        "name": "Plate Name 0",
+        "wells": [
+          {
+            "path": "A/1",
+            "rowIndex": 0,
+            "columnIndex": 0
+          }
+        ],
+        "field_count": 1,
+        "rows": [
+          {
+            "name": "A"
+          }
+        ],
+        "acquisitions": [
+          {
+            "id": 0
+          }
+        ]
+      }
+    }
+  }
+}

0.6-dev/examples/coordSystems/.config.json

@@ -0,0 +1,3 @@
+{
+  "schema": "schemas/coordinate_systems_and_transforms.schema"
+}

0.6-dev/examples/label_strict/.config.json

@@ -0,0 +1,3 @@
+{
+    "schema": "schemas/strict_label.schema"
+}

0.6-dev/examples/label_strict/colors_properties.json

@@ -0,0 +1,37 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "image-label": {
+        "colors": [
+          {
+            "label-value": 0,
+            "rgba": [0, 0, 128, 128]
+          },
+          {
+            "label-value": 1,
+            "rgba": [0, 128, 0, 128]
+          }
+        ],
+        "properties": [
+          {
+            "label-value": 0,
+            "area (pixels)": 1200,
+            "class": "intercellular space"
+          },
+          {
+            "label-value": 1,
+            "area (pixels)": 1650,
+            "class": "cell",
+            "cell type": "neuron"
+          }
+        ],
+        "source": {
+          "image": "../../"
+        }
+      }
+    }
+  }
+}

0.6-dev/examples/multiscales_strict/.config.json

@@ -0,0 +1,3 @@
+{
+    "schema": "schemas/strict_image.schema"
+}

0.6-dev/examples/multiscales_strict/multiscales_example.json

@@ -0,0 +1,69 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "multiscales": [
+        {
+          "name": "example",
+          "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",
+              "coordinateTransformation": {
+                // the voxel size for the first scale level (0.5 micrometer)
+                // and the time unit (0.1 milliseconds), which is the same for each scale level
+                "type": "scale",
+                "scale": [0.1, 1.0, 0.5, 0.5, 0.5],
+                "input": "0",
+                "output": "example"
+              }
+            },
+            {
+              "path": "1",
+              "coordinateTransformation": {
+                // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
+                // and 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],
+                "input": "1",
+                "output": "example"
+              }
+            },
+            {
+              "path": "2",
+              "coordinateTransformation": {
+                // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
+                // and the time unit (0.1 milliseconds), which is the same for each scale level
+                "type": "scale",
+                "scale": [0.1, 1.0, 2.0, 2.0, 2.0],
+                "input": "2",
+                "output": "example"
+              }
+            }
+          ],
+          "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 }
+          }
+        }
+      ]
+    }
+  }
+}

0.6-dev/examples/multiscales_strict/multiscales_example_relative.json

@@ -0,0 +1,76 @@
+{
+    "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"}
+                    ]
+                },
+                {
+                    "name" : "array_0",
+                    "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
+                    "coordinateTransformations": [{
+                        "type": "identity",
+                        "input": "/0",
+                        "output": "array_0"
+                    }]
+                },
+                {
+                    "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" : "array_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" : "array_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" : "array_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}
+            }
+        }
+    ]
+}

0.6-dev/examples/multiscales_strict/multiscales_example_twoCoordSystems.json

@@ -0,0 +1,85 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "multiscales": [
+        {
+          "name": "example",
+          "coordinateSystems": [
+              {
+                "name": "default",
+                "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" }
+                ]
+              },
+              {
+                "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",
+              "coordinateTransformation": {
+                // the voxel size for the first scale level (0.5 micrometer)
+                "type": "scale",
+                "scale": [1.0, 1.0, 0.5, 0.5, 0.5],
+                "input": "0",
+                "output": "default"
+              }
+            },
+            {
+              "path": "1",
+              "coordinateTransformation": {
+                // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer)
+                "type": "scale",
+                "scale": [1.0, 1.0, 1.0, 1.0, 1.0],
+                "input": "1",
+                "output": "default"
+              }
+            },
+            {
+              "path": "2",
+              "coordinateTransformation": {
+                // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer)
+                "type": "scale",
+                "scale": [1.0, 1.0, 2.0, 2.0, 2.0],
+                "input": "2",
+                "output": "default"
+              }
+            }
+          ],
+          "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],
+              "input": "default",
+              "output": "example"
+            }
+          ],
+          "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 }
+          }
+        }
+      ]
+    }
+  }
+}

0.6-dev/examples/multiscales_strict/multiscales_transformations.json

@@ -0,0 +1,47 @@
+{
+  "zarr_format": 3,
+  "node_type": "group",
+  "attributes": {
+    "ome": {
+      "version": "0.5",
+      "multiscales": [
+        {
+          "axes": [
+            {
+              "name": "y",
+              "type": "space",
+              "unit": "micrometer"
+            },
+            {
+              "name": "x",
+              "type": "space",
+              "unit": "micrometer"
+            }
+          ],
+          "datasets": [
+            {
+              "path": "0",
+              "coordinateTransformations": [
+                {
+                  "scale": [1, 1],
+                  "type": "scale"
+                }
+              ]
+            }
+          ],
+          "coordinateTransformations": [
+            {
+              "scale": [10, 10],
+              "type": "scale"
+            }
+          ],
+          "name": "image_with_coordinateTransformations",
+          "type": "foo",
+          "metadata": {
+            "key": "value"
+          }
+        }
+      ]
+    }
+  }
+}