Fix illumination correction test (ref #116)

tests/data/generate_zarr_ones.py

@@ -1,21 +1,33 @@
 import json
+import os
+import shutil
 
 import dask.array as da
 import numpy as np
+import pandas as pd
+import zarr
+from anndata.experimental import write_elem
+
+from fractal.tasks.lib_regions_of_interest import prepare_FOV_ROI_table
 
 
 num_C = 2
 num_Z = 1
 num_Y = 2
 num_X = 1
 num_levels = 5
+cxy = 2
+
 
 x = da.ones(
     (num_C, num_Z, num_Y * 2160, num_X * 2560), chunks=(1, 1, 2160, 2560)
 ).astype(np.uint16)
 
 
 zarrurl = "plate_ones.zarr/"
+
+if os.path.isdir(zarrurl):
+    shutil.rmtree(zarrurl)
 component = "B/03/0/"
 
 for ind_level in range(num_levels):
@@ -27,14 +39,78 @@
         zarrurl, component=f"{component}{ind_level}", dimension_separator="/"
     )
 
+pxl_x = 0.1625
+pxl_y = 0.1625
+pxl_z = 1.0
+
+axes = [
+    {"name": "c", "type": "channel"},
+    {"name": "z", "type": "space", "unit": "micrometer"},
+    {"name": "y", "type": "space", "unit": "micrometer"},
+    {"name": "x", "type": "space", "unit": "micrometer"},
+]
+
+cT = "coordinateTransformations"
 zattrs = {
     "multiscales": [
         {
-            "axes": [],
-            "datasets": [{"path": level} for level in range(num_levels)],
+            "axes": axes,
+            "datasets": [
+                {
+                    "path": level,
+                    cT: [
+                        {
+                            "type": "scale",
+                            "scale": [
+                                pxl_z,
+                                pxl_y * cxy**level,
+                                pxl_x * cxy**level,
+                            ],
+                        }
+                    ],
+                }
+                for level in range(num_levels)
+            ],
             "version": "0.3",
         }
     ]
 }
 with open(f"{zarrurl}{component}.zattrs", "w") as jsonfile:
     json.dump(zattrs, jsonfile)
+
+
+pixel_size_z = 1.0
+pixel_size_y = 0.1625
+pixel_size_x = 0.1625
+
+df = pd.DataFrame(np.zeros((2, 10)), dtype=int)
+df.index = ["FOV1", "FOV2"]
+df.columns = [
+    "x_micrometer",
+    "y_micrometer",
+    "z_micrometer",
+    "x_pixel",
+    "y_pixel",
+    "z_pixel",
+    "pixel_size_x",
+    "pixel_size_y",
+    "pixel_size_z",
+    "bit_depth",
+]
+df["x_micrometer"] = [0.0, 0.0]
+df["y_micrometer"] = [0.0, 351.0]
+df["z_micrometer"] = [0.0, 0.0]
+df["x_pixel"] = [2560] * 2
+df["y_pixel"] = [2160] * 2
+df["z_pixel"] = [num_Z] * 2
+df["pixel_size_x"] = [pxl_x] * 2
+df["pixel_size_y"] = [pxl_y] * 2
+df["pixel_size_z"] = [pxl_z] * 2
+df["bit_depth"] = [16.0, 16.0]
+
+
+FOV_ROI_table = prepare_FOV_ROI_table(df)
+print(FOV_ROI_table.to_df())
+
+group_tables = zarr.group(f"{zarrurl}{component}/tables")
+write_elem(group_tables, "FOV_ROI_table", FOV_ROI_table)

tests/data/plate_ones.zarr/B/03/0/.zattrs

@@ -1 +1 @@
-{"multiscales": [{"axes": [], "datasets": [{"path": 0}, {"path": 1}, {"path": 2}, {"path": 3}, {"path": 4}], "version": "0.3"}]}
+{"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": [{"path": 0, "coordinateTransformations": [{"type": "scale", "scale": [1.0, 0.1625, 0.1625]}]}, {"path": 1, "coordinateTransformations": [{"type": "scale", "scale": [1.0, 0.325, 0.325]}]}, {"path": 2, "coordinateTransformations": [{"type": "scale", "scale": [1.0, 0.65, 0.65]}]}, {"path": 3, "coordinateTransformations": [{"type": "scale", "scale": [1.0, 1.3, 1.3]}]}, {"path": 4, "coordinateTransformations": [{"type": "scale", "scale": [1.0, 2.6, 2.6]}]}], "version": "0.3"}]}

tests/data/plate_ones.zarr/B/03/0/tables/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "anndata",
+    "encoding-version": "0.1.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/X/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        2,
+        6
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<f4",
+    "fill_value": 0.0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        2,
+        6
+    ],
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/X/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "array",
+    "encoding-version": "0.2.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/layers/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "dict",
+    "encoding-version": "0.1.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/layers/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obs/.zattrs

@@ -0,0 +1,6 @@
+{
+    "_index": "_index",
+    "column-order": [],
+    "encoding-type": "dataframe",
+    "encoding-version": "0.2.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obs/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obs/_index/.zarray

@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        2
+    ],
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obs/_index/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "string-array",
+    "encoding-version": "0.2.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obsm/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "dict",
+    "encoding-version": "0.1.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obsm/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obsp/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "dict",
+    "encoding-version": "0.1.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/obsp/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/uns/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "dict",
+    "encoding-version": "0.1.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/uns/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/var/.zattrs

@@ -0,0 +1,6 @@
+{
+    "_index": "_index",
+    "column-order": [],
+    "encoding-type": "dataframe",
+    "encoding-version": "0.2.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/var/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/var/_index/.zarray

@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        6
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        6
+    ],
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/var/_index/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "string-array",
+    "encoding-version": "0.2.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/varm/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "dict",
+    "encoding-version": "0.1.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/varm/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/varp/.zattrs

@@ -0,0 +1,4 @@
+{
+    "encoding-type": "dict",
+    "encoding-version": "0.1.0"
+}

tests/data/plate_ones.zarr/B/03/0/tables/FOV_ROI_table/varp/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

tests/test_unit_illumination_correction.py

@@ -13,7 +13,6 @@
 
 
 @pytest.mark.parametrize("overwrite", [True, False])
-@pytest.mark.skip("Missing ROIs table in test data")
 def test_illumination_correction(
     overwrite: bool,
     tmp_path: pathlib.Path,