transform_coordinates tests

README.md

@@ -104,6 +104,13 @@ repo in [PR #5](https://github.com/clbarnes/oztest/pull/5). The script used for
 from the `ngff-spec` repo at commit [5c76733](https://github.com/ome/ngff-spec/commit/5c76733fe3a1f97a3957909c879b15d57689f74e).
 The script used for this import is under `scripts/import_v06_cases.py`.
 
+## Custom test cases
+
+If you extend your implementation to include metadata not in the OME-Zarr spec, you can use oztest too.
+
+Structure your test cases in the same directory hierarchy
+and use the `--custom-cases` argument to have them included in test discovery.
+
 ## Versioning
 
 This project is currently in alpha (`0.x` series).

cases/transform_coordinates/README.md

@@ -8,30 +8,38 @@ They do NOT test implementations' capability to transform images on the basis of
 Each test case is an OME-Zarr hierarchy with a Scene in the root node.
 This Scene contains a graph of coordinate systems joined by coordinate transformations.
 
-At the root of each OME-Zarr hierarchy is a `conformance.toml` file, which lays out:
-
-```toml
-description = "The first case of my comprehensive and totally correct test suite."
-
-# result should be within 0.000_001 of expected value
-absolute_tolerance = 1e-06
-
-# result should be within 0.1% of expected value
-relative_tolerance = 0.001
-
-[source]
-name = "inputSystem"  # name of the input coordinate system
-coordinates = [
-  [ -1, -1, -1 ],  # first 3D input coordinate
-  [ 0, 0, 0 ],  # second 3D input coordinate
-]
-
-[target]
-name = "outputSystem"  # name of the output coordinate system
-coordinates = [
-  [ 18, 57, 16 ],  # first 3D expected output coordinate
-  [ 20, 60, 120 ],  # second 3D expected output coordinate
-]
+At the root of each OME-Zarr hierarchy is an `oztest.json` file, which lays out:
+
+```jsonc
+{
+    "description": "The first case of my comprehensive and totally correct test suite.",
+    "transform_coordinates": {
+        "tolerance": {  // optional, defaults as shown
+            "relative": 0.00001,  // optional, default as shown
+            "absolute": 0.00000001  // optional, default as shown
+        },
+        "source": {
+            // input coordinate system name
+            "name": "mySourceCoordinateSystem",
+            "coordinates": [
+                // first input coordinate
+                [-1, -1, -1],
+                // second input coordinate
+                [0, 0, 0]
+            ]
+        },
+        "target": {
+            // output coordinate system name
+            "name": "myTargetCoordinateSystem",
+            "coordinates": [
+                // expected result of transforming first input coordinate
+                [ 18, 57, 16 ],
+                // expected result of transforming second input coordinate
+                [ 20, 60, 120 ]
+            ]
+        }
+    }
+}
 ```
 
 Users of the conformance tests should
@@ -41,7 +49,8 @@ Users of the conformance tests should
 3. construct the coordinate system graph
 4. find a path through the graph from the input to the output coordinate system
 5. apply the resulting coordinate transform sequence to the input coordinates
-6. check that the resulting coordinates equal the given output coordinates, to within the given tolerances
+6. check that the resulting coordinates are close to the given output coordinates, using the `numpy.allclose` algorithm
+    `|a - b| <= (absolute + relative * |b|)`
 
 raising an error if any of these steps are not possible.
 
@@ -79,7 +88,6 @@ The dingus MUST then
 5. exit with status code 0
 
 If any of the above steps are not supported by the implementation, the dingus MUST exit with a status code other than 0.
-In this case, it MAY print to STDOUT a JSON-serialised [Error](#object-response) object.
 
 For the example above, a passing test would exit with status code 0 after printing
 
@@ -93,9 +101,4 @@ For the example above, a passing test would exit with status code 0 after printi
 | ----- | --------- | ---- | ----------- |
 | coordinates | MUST | array of array of number | The resulting coordinates from transforming the input. |
 | message | MAY | string | Free-text details. |
-
-### Object: Error
-
-| field | necessity | type | description |
-| ----- | --------- | ---- | ----------- |
-| message | MAY | string | Free-text description of error. |
+| xfail | MAY | boolean, default `false` | Whether the dingus expected to fail this test. |

cases/transform_coordinates/v0.6/core/valid/identity.ome.zarr/oztest.json

@@ -0,0 +1,27 @@
+{
+  "description": "Identity transformation.",
+  "transform_coordinates": {
+    "source": {
+      "coordinates": [
+        [
+          1,
+          2
+        ]
+      ],
+      "name": "input"
+    },
+    "target": {
+      "coordinates": [
+        [
+          1,
+          2
+        ]
+      ],
+      "name": "output"
+    },
+    "tolerance": {
+      "absolute": 1e-6,
+      "relative": 0.001
+    }
+  }
+}

cases/transform_coordinates/v0.6/core/valid/identity.ome.zarr/zarr.json

@@ -0,0 +1,51 @@
+{
+  "attributes": {
+    "ome": {
+      "scene": {
+        "coordinateSystems": [
+          {
+            "axes": [
+              {
+                "name": "y",
+                "type": "space"
+              },
+              {
+                "name": "x",
+                "type": "space"
+              }
+            ],
+            "name": "input"
+          },
+          {
+            "axes": [
+              {
+                "name": "y",
+                "type": "space"
+              },
+              {
+                "name": "x",
+                "type": "space"
+              }
+            ],
+            "name": "output"
+          }
+        ],
+        "coordinateTransformations": [
+          {
+            "input": {
+              "name": "input"
+            },
+            "name": "inputToOutput",
+            "output": {
+              "name": "output"
+            },
+            "type": "identity"
+          }
+        ]
+      },
+      "version": "0.6"
+    }
+  },
+  "node_type": "group",
+  "zarr_format": 3
+}

cases/transform_coordinates/v0.6/core/valid/identity_inverse.ome.zarr/oztest.json

@@ -0,0 +1,27 @@
+{
+  "description": "Identity transformation. (inverse)",
+  "transform_coordinates": {
+    "source": {
+      "coordinates": [
+        [
+          1,
+          2
+        ]
+      ],
+      "name": "output"
+    },
+    "target": {
+      "coordinates": [
+        [
+          1,
+          2
+        ]
+      ],
+      "name": "input"
+    },
+    "tolerance": {
+      "absolute": 1e-6,
+      "relative": 0.001
+    }
+  }
+}

cases/transform_coordinates/v0.6/core/valid/identity_inverse.ome.zarr/zarr.json

@@ -0,0 +1,51 @@
+{
+  "attributes": {
+    "ome": {
+      "scene": {
+        "coordinateSystems": [
+          {
+            "axes": [
+              {
+                "name": "y",
+                "type": "space"
+              },
+              {
+                "name": "x",
+                "type": "space"
+              }
+            ],
+            "name": "input"
+          },
+          {
+            "axes": [
+              {
+                "name": "y",
+                "type": "space"
+              },
+              {
+                "name": "x",
+                "type": "space"
+              }
+            ],
+            "name": "output"
+          }
+        ],
+        "coordinateTransformations": [
+          {
+            "input": {
+              "name": "input"
+            },
+            "name": "inputToOutput",
+            "output": {
+              "name": "output"
+            },
+            "type": "identity"
+          }
+        ]
+      },
+      "version": "0.6"
+    }
+  },
+  "node_type": "group",
+  "zarr_format": 3
+}

cases/transform_coordinates/v0.6/core/valid/scale.ome.zarr/oztest.json

@@ -0,0 +1,27 @@
+{
+  "description": "Simple scale.",
+  "transform_coordinates": {
+    "source": {
+      "coordinates": [
+        [
+          1,
+          2
+        ]
+      ],
+      "name": "input"
+    },
+    "target": {
+      "coordinates": [
+        [
+          10,
+          40
+        ]
+      ],
+      "name": "output"
+    },
+    "tolerance": {
+      "absolute": 1e-6,
+      "relative": 0.001
+    }
+  }
+}

cases/transform_coordinates/v0.6/core/valid/scale.ome.zarr/zarr.json

@@ -0,0 +1,55 @@
+{
+  "attributes": {
+    "ome": {
+      "scene": {
+        "coordinateSystems": [
+          {
+            "axes": [
+              {
+                "name": "y",
+                "type": "space"
+              },
+              {
+                "name": "x",
+                "type": "space"
+              }
+            ],
+            "name": "input"
+          },
+          {
+            "axes": [
+              {
+                "name": "y",
+                "type": "space"
+              },
+              {
+                "name": "x",
+                "type": "space"
+              }
+            ],
+            "name": "output"
+          }
+        ],
+        "coordinateTransformations": [
+          {
+            "input": {
+              "name": "input"
+            },
+            "name": "inputToOutput",
+            "output": {
+              "name": "output"
+            },
+            "scale": [
+              10,
+              20
+            ],
+            "type": "scale"
+          }
+        ]
+      },
+      "version": "0.6"
+    }
+  },
+  "node_type": "group",
+  "zarr_format": 3
+}

cases/transform_coordinates/v0.6/core/valid/scale_inverse.ome.zarr/oztest.json

@@ -0,0 +1,27 @@
+{
+  "description": "Simple scale. (inverse)",
+  "transform_coordinates": {
+    "source": {
+      "coordinates": [
+        [
+          10,
+          40
+        ]
+      ],
+      "name": "output"
+    },
+    "target": {
+      "coordinates": [
+        [
+          1,
+          2
+        ]
+      ],
+      "name": "input"
+    },
+    "tolerance": {
+      "absolute": 1e-6,
+      "relative": 0.001
+    }
+  }
+}