Add rechunking task to manifest

Author: jluethi

src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

@@ -33,7 +33,7 @@
             "default": false,
             "title": "Overwrite Input",
             "type": "boolean",
-            "description": "Whether"
+            "description": "Whether the existing iamge should be overwritten with the new OME-Zarr without the T dimension."
           }
         },
         "required": [
@@ -128,6 +128,73 @@
         "title": "Convert2dSegmentationTo3d"
       },
       "docs_link": "https://github.com/jluethi/fractal-helper-tasks"
+    },
+    {
+      "name": "Rechunk OME-Zarr",
+      "tags": [
+        "Rechunking",
+        "Many files"
+      ],
+      "docs_info": "### Purpose\n- Rechunks OME-Zarr to new chunking parameters: Changes whether the array is stored as many small files or few larger files.\n- Optionally applies the same rechunking to label images.\n\n### Outputs\n- A **new Zarr image** that is rechunked.\n",
+      "executable_parallel": "rechunk_zarr.py",
+      "meta_parallel": {
+        "cpus_per_task": 1,
+        "mem": 4000
+      },
+      "args_schema_parallel": {
+        "additionalProperties": false,
+        "properties": {
+          "zarr_url": {
+            "title": "Zarr Url",
+            "type": "string",
+            "description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server)."
+          },
+          "chunk_sizes": {
+            "additionalProperties": {
+              "type": "integer"
+            },
+            "title": "Chunk Sizes",
+            "type": "object",
+            "description": "Dictionary of chunk sizes to adapt. One can set any of the t, c, z, y, x axes that exist in the input image to be resized to a different chunk size. For example, {\"y\": 4000, \"x\": 4000} will set a new x & y chunking while maintaining the other chunk sizes. {\"z\": 10} will just change the Z chunking while keeping all other chunk sizes the same as the input."
+          },
+          "suffix": {
+            "default": "rechunked",
+            "title": "Suffix",
+            "type": "string",
+            "description": "Suffix of the rechunked image."
+          },
+          "rechunk_labels": {
+            "default": true,
+            "title": "Rechunk Labels",
+            "type": "boolean",
+            "description": "Whether to apply the same rechunking to all label images of the OME-Zarr as well."
+          },
+          "rebuild_pyramids": {
+            "default": true,
+            "title": "Rebuild Pyramids",
+            "type": "boolean",
+            "description": "Whether pyramids are built fresh in the rechunked image. This has a small performance overhead, but ensures that this task is save against off-by-one issues when pyramid levels aren't easily downsampled by 2."
+          },
+          "overwrite_input": {
+            "default": true,
+            "title": "Overwrite Input",
+            "type": "boolean",
+            "description": "Whether the old image without rechunking should be overwritten (to avoid duplicating the data needed)."
+          },
+          "overwrite": {
+            "default": false,
+            "title": "Overwrite",
+            "type": "boolean",
+            "description": "Whether to overwrite potential pre-existing output with the name zarr_url_suffix."
+          }
+        },
+        "required": [
+          "zarr_url"
+        ],
+        "type": "object",
+        "title": "RechunkZarr"
+      },
+      "docs_link": "https://github.com/jluethi/fractal-helper-tasks"
     }
   ],
   "has_args_schemas": true,

src/fractal_helper_tasks/dev/docs_info/rechunk_zarr.md

@@ -0,0 +1,6 @@
+### Purpose
+- Rechunks OME-Zarr to new chunking parameters: Changes whether the array is stored as many small files or few larger files.
+- Optionally applies the same rechunking to label images.
+
+### Outputs
+- A **new Zarr image** that is rechunked.

src/fractal_helper_tasks/dev/task_list.py

@@ -22,4 +22,14 @@
         ],
         docs_info="file:docs_info/2d_to_3d.md",
     ),
+    ParallelTask(
+        name="Rechunk OME-Zarr",
+        executable="rechunk_zarr.py",
+        meta={"cpus_per_task": 1, "mem": 4000},
+        tags=[
+            "Rechunking",
+            "Many files",
+        ],
+        docs_info="file:docs_info/rechunk_zarr.md",
+    ),
 ]