Merge pull request #69 from will-moore/salad

NGFF json validation
ome · Nov 26, 2021 · 37a4238 · 37a4238
2 parents 3ec8d61 + dd312a8
commit 37a4238
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diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
@@ -0,0 +1,21 @@
+name: Validation
+on:
+  push:
+  pull_request:
+
+jobs:
+
+  validate:
+    name: Validation
+    strategy:
+      matrix:
+        ngff:
+          - '0.3'
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+      - run: python -mpip install --upgrade wheel tox
+      - run: cd ${{matrix.ngff}} && tox
diff --git a/0.3/examples/invalid/invalid_axes.json b/0.3/examples/invalid/invalid_axes.json
@@ -0,0 +1,22 @@
+{
+    "@id": "#my-image",
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "@id": "#my-pyramid",
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "@id": "#my-full-resolution",
+                    "path": "path/to/0"
+                }
+            ],
+            "axes": [
+                "z",
+                "y",
+                "ct"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/invalid_axes_count.json b/0.3/examples/invalid/invalid_axes_count.json
@@ -0,0 +1,20 @@
+{
+    "@id": "#my-image",
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "@id": "#my-pyramid",
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "@id": "#my-full-resolution",
+                    "path": "path/to/0"
+                }
+            ],
+            "axes": [
+                "y"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/invalid_axes_order.json b/0.3/examples/invalid/invalid_axes_order.json
@@ -0,0 +1,22 @@
+{
+    "@id": "#my-image",
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "@id": "#my-pyramid",
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "@id": "#my-full-resolution",
+                    "path": "path/to/0"
+                }
+            ],
+            "axes": [
+                "y",
+                "t",
+                "c"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/invalid_channels_color.json b/0.3/examples/invalid/invalid_channels_color.json
@@ -0,0 +1,36 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                }
+            ],
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ],
+    "omero": {
+        "channels": [
+            {
+                "active": true,
+                "coefficient": 1.0,
+                "color": 255,
+                "family": "linear",
+                "label": "1234",
+                "window": {
+                    "end": 1765.0,
+                    "max": 2555.0,
+                    "min": 5.0,
+                    "start": 0.0
+                }
+            }
+        ]
+    }
+}
diff --git a/0.3/examples/invalid/invalid_channels_window.json b/0.3/examples/invalid/invalid_channels_window.json
@@ -0,0 +1,36 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                }
+            ],
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ],
+    "omero": {
+        "channels": [
+            {
+                "active": true,
+                "coefficient": 1.0,
+                "color": "ff0000",
+                "family": "linear",
+                "label": "1234",
+                "window": {
+                    "end": "100",
+                    "max": 2555.0,
+                    "min": 5.0,
+                    "start": 0.0
+                }
+            }
+        ]
+    }
+}
diff --git a/0.3/examples/invalid/invalid_path.json b/0.3/examples/invalid/invalid_path.json
@@ -0,0 +1,22 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                },
+                {
+                    "path": 0
+                }
+            ],
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/missing_axes.json b/0.3/examples/invalid/missing_axes.json
@@ -0,0 +1,14 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                }
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/missing_datasets.json b/0.3/examples/invalid/missing_datasets.json
@@ -0,0 +1,14 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/missing_name.json b/0.3/examples/invalid/missing_name.json
@@ -0,0 +1,33 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                },
+                {
+                    "path": 0
+                }
+            ],
+            "type": "gaussian",
+            "metadata": {
+                "method": "skimage.transform.pyramid_gaussian",
+                "version": "0.16.1",
+                "args": [
+                    "true",
+                    "false"
+                ],
+                "kwargs": {
+                    "multichannel": true
+                }
+            },
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/missing_path.json b/0.3/examples/invalid/missing_path.json
@@ -0,0 +1,22 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "foo": "path/to/0"
+                },
+                {
+                    "path": "1"
+                }
+            ],
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/missing_version.json b/0.3/examples/invalid/missing_version.json
@@ -0,0 +1,18 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "name": "example",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                }
+            ],
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/no_axes.json b/0.3/examples/invalid/no_axes.json
@@ -0,0 +1,15 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                }
+            ],
+            "axes": []
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/no_datasets.json b/0.3/examples/invalid/no_datasets.json
@@ -0,0 +1,15 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [],
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/invalid/no_multiscales.json b/0.3/examples/invalid/no_multiscales.json
@@ -0,0 +1,4 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": []
+}
diff --git a/0.3/examples/valid/image.json b/0.3/examples/valid/image.json
@@ -0,0 +1,17 @@
+{
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {"path": "path/to/0"},
+                {"path": "1"},
+                {"path": "2"}
+            ],
+            "axes": [
+                "z", "y", "x"
+            ]
+        }
+    ]
+}
diff --git a/0.3/examples/valid/image_metadata.json b/0.3/examples/valid/image_metadata.json
@@ -0,0 +1,33 @@
+{
+    "@id": "top",
+    "@type": "ngff:Image",
+    "multiscales": [
+        {
+            "@id": "inner",
+            "version": "0.3",
+            "name": "example",
+            "datasets": [
+                {
+                    "path": "path/to/0"
+                }
+            ],
+            "type": "gaussian",
+            "metadata": {
+                "method": "skimage.transform.pyramid_gaussian",
+                "version": "0.16.1",
+                "args": [
+                    "true",
+                    "false"
+                ],
+                "kwargs": {
+                    "multichannel": true
+                }
+            },
+            "axes": [
+                "z",
+                "y",
+                "x"
+            ]
+        }
+    ]
+}