Add test for HCS datset (#76)

* Add basic test data layout * Add test with a real HCS dataset * Add HCS to docs * Remove tables from test data
BioImageTools · Dec 10, 2024 · 4a6851e · 4a6851e
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Showing 15 changed files with 353 additions and 3 deletions.
diff --git a/docs/api/v04/other.md b/docs/api/v04/other.md
@@ -14,9 +14,9 @@ These are models that live further down the hierarchy.
 
 ::: ome_zarr_models.v04.multiscales
 
-## plate
+## hcs
 
-::: ome_zarr_models.v04.plate
+::: ome_zarr_models.v04.hcs
 
 ## image_label
 
@@ -26,6 +26,10 @@ These are models that live further down the hierarchy.
 
 ::: ome_zarr_models.v04.omero
 
+## plate
+
+::: ome_zarr_models.v04.plate
+
 ## well
 
 ::: ome_zarr_models.v04.well
diff --git a/src/ome_zarr_models/v04/hcs.py b/src/ome_zarr_models/v04/hcs.py
@@ -1,9 +1,20 @@
 from pydantic_zarr.v2 import ArraySpec, GroupSpec
 
+from ome_zarr_models.base import Base
 from ome_zarr_models.v04.plate import Plate
 
+__all__ = ["HCSAttrs"]
 
-class HCS(GroupSpec[Plate, ArraySpec | GroupSpec]):
+
+class HCSAttrs(Base):
+    """
+    HCS metadtata attributes.
+    """
+
+    plate: Plate
+
+
+class HCS(GroupSpec[HCSAttrs, ArraySpec | GroupSpec]):
     """
     An OME-zarr high-content screening (HCS) dataset representing a single plate.
     """
diff --git a/tests/v04/data/hcs_example.ome.zarr/.zattrs b/tests/v04/data/hcs_example.ome.zarr/.zattrs
@@ -0,0 +1,28 @@
+{
+    "plate": {
+        "acquisitions": [
+            {
+                "id": 0,
+                "name": "20200812-CardiomyocyteDifferentiation14-Cycle1"
+            }
+        ],
+        "columns": [
+            {
+                "name": "03"
+            }
+        ],
+        "rows": [
+            {
+                "name": "B"
+            }
+        ],
+        "version": "0.4",
+        "wells": [
+            {
+                "columnIndex": 0,
+                "path": "B/03",
+                "rowIndex": 0
+            }
+        ]
+    }
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/.zgroup b/tests/v04/data/hcs_example.ome.zarr/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/.zgroup b/tests/v04/data/hcs_example.ome.zarr/B/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/.zattrs b/tests/v04/data/hcs_example.ome.zarr/B/03/.zattrs
@@ -0,0 +1,10 @@
+{
+    "well": {
+        "images": [
+            {
+                "path": "0"
+            }
+        ],
+        "version": "0.4"
+    }
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/.zgroup b/tests/v04/data/hcs_example.ome.zarr/B/03/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/0/.zattrs b/tests/v04/data/hcs_example.ome.zarr/B/03/0/.zattrs
@@ -0,0 +1,118 @@
+{
+    "multiscales": [
+        {
+            "axes": [
+                {
+                    "name": "c",
+                    "type": "channel"
+                },
+                {
+                    "name": "z",
+                    "type": "space",
+                    "unit": "micrometer"
+                },
+                {
+                    "name": "y",
+                    "type": "space",
+                    "unit": "micrometer"
+                },
+                {
+                    "name": "x",
+                    "type": "space",
+                    "unit": "micrometer"
+                }
+            ],
+            "datasets": [
+                {
+                    "coordinateTransformations": [
+                        {
+                            "scale": [
+                                1,
+                                1.0,
+                                0.1625,
+                                0.1625
+                            ],
+                            "type": "scale"
+                        }
+                    ],
+                    "path": "0"
+                },
+                {
+                    "coordinateTransformations": [
+                        {
+                            "scale": [
+                                1,
+                                1.0,
+                                0.325,
+                                0.325
+                            ],
+                            "type": "scale"
+                        }
+                    ],
+                    "path": "1"
+                },
+                {
+                    "coordinateTransformations": [
+                        {
+                            "scale": [
+                                1,
+                                1.0,
+                                0.65,
+                                0.65
+                            ],
+                            "type": "scale"
+                        }
+                    ],
+                    "path": "2"
+                },
+                {
+                    "coordinateTransformations": [
+                        {
+                            "scale": [
+                                1,
+                                1.0,
+                                1.3,
+                                1.3
+                            ],
+                            "type": "scale"
+                        }
+                    ],
+                    "path": "3"
+                },
+                {
+                    "coordinateTransformations": [
+                        {
+                            "scale": [
+                                1,
+                                1.0,
+                                2.6,
+                                2.6
+                            ],
+                            "type": "scale"
+                        }
+                    ],
+                    "path": "4"
+                }
+            ],
+            "version": "0.4"
+        }
+    ],
+    "omero": {
+        "channels": [
+            {
+                "color": "00FFFF",
+                "label": "DAPI",
+                "wavelength_id": "A01_C01",
+                "window": {
+                    "end": 800,
+                    "max": 65535,
+                    "min": 0,
+                    "start": 110
+                }
+            }
+        ],
+        "id": 1,
+        "name": "TBD",
+        "version": "0.4"
+    }
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/0/.zgroup b/tests/v04/data/hcs_example.ome.zarr/B/03/0/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/0/0/.zarray b/tests/v04/data/hcs_example.ome.zarr/B/03/0/0/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1,
+        1,
+        2160,
+        2560
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<u2",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        1,
+        2,
+        2160,
+        5120
+    ],
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/0/1/.zarray b/tests/v04/data/hcs_example.ome.zarr/B/03/0/1/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1,
+        1,
+        1080,
+        2560
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<u2",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        1,
+        2,
+        1080,
+        2560
+    ],
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/0/2/.zarray b/tests/v04/data/hcs_example.ome.zarr/B/03/0/2/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1,
+        1,
+        540,
+        1280
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<u2",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        1,
+        2,
+        540,
+        1280
+    ],
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/0/3/.zarray b/tests/v04/data/hcs_example.ome.zarr/B/03/0/3/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1,
+        1,
+        270,
+        640
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<u2",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        1,
+        2,
+        270,
+        640
+    ],
+    "zarr_format": 2
+}
diff --git a/tests/v04/data/hcs_example.ome.zarr/B/03/0/4/.zarray b/tests/v04/data/hcs_example.ome.zarr/B/03/0/4/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1,
+        1,
+        135,
+        320
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<u2",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        1,
+        2,
+        135,
+        320
+    ],
+    "zarr_format": 2
+}