bioformats2raw metadata support

.isort.cfg

@@ -1,5 +1,5 @@
 [settings]
-known_third_party = dask,numcodecs,numpy,pytest,scipy,setuptools,skimage,zarr
+known_third_party = dask,entrypoints,numcodecs,numpy,pytest,scipy,setuptools,skimage,zarr
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0

ome_zarr/reader.py

@@ -6,7 +6,9 @@
 from typing import Any, Dict, Iterator, List, Optional, Type, Union, cast, overload
 
 import dask.array as da
+import entrypoints
 import numpy as np
+import zarr
 from dask import delayed
 
 from .axes import Axes
@@ -45,21 +47,44 @@ def __init__(
         self.post_nodes: List[Node] = []
 
         # TODO: this should be some form of plugin infra over subclasses
+        found: List[Spec] = []
         if Labels.matches(zarr):
-            self.specs.append(Labels(self))
+            found.append(Labels(self))
+            self.specs.append(found[-1])
         if Label.matches(zarr):
-            self.specs.append(Label(self))
+            found.append(Label(self))
+            self.specs.append(found[-1])
         if Multiscales.matches(zarr):
-            self.specs.append(Multiscales(self))
+            found.append(Multiscales(self))
+            self.specs.append(found[-1])
         if OMERO.matches(zarr):
-            self.specs.append(OMERO(self))
+            found.append(OMERO(self))
+            self.specs.append(found[-1])
         if plate_labels:
-            self.specs.append(PlateLabels(self))
+            found.append(PlateLabels(self))
+            self.specs.append(found[-1])
         elif Plate.matches(zarr):
-            self.specs.append(Plate(self))
+            found.append(Plate(self))
+            self.specs.append(found[-1])
             # self.add(zarr, plate_labels=True)
         if Well.matches(zarr):
-            self.specs.append(Well(self))
+            found.append(Well(self))
+            self.specs.append(found[-1])
+
+        for key, value in entrypoints.get_group_named("ome_zarr.spec").items():
+            cls = value.load()
+            if cls.matches(zarr):
+                found.append(cls(self))
+                self.specs.append(found[-1])
+
+        if not found:
+            self.specs.append(Implicit(self))
+
+        # Load up the hierarchy
+        if Leaf.matches(zarr):
+            self.specs.append(Leaf(self))
+        else:
+            self.specs.append(Root(self))
 
     @overload
     def first(self, spectype: Type["Well"]) -> Optional["Well"]:
@@ -178,6 +203,60 @@ def lookup(self, key: str, default: Any) -> Any:
         return self.zarr.root_attrs.get(key, default)
 
 
+class Implicit(Spec):
+    """
+    A spec-type which simply iterates over available zgroups.
+    """
+
+    @staticmethod
+    def matches(zarr: ZarrLocation) -> bool:
+        """Always return true"""
+        return True
+
+    def __init__(self, node: Node) -> None:
+        super().__init__(node)
+
+        for name in zarr.group(self.zarr.store).group_keys():
+            child_zarr = self.zarr.create(name)
+            if child_zarr.exists():
+                node.add(child_zarr)
+
+
+class Leaf(Spec):
+    """
+    A non-root level of the Zarr hierarchy
+    """
+
+    @staticmethod
+    def matches(zarr: ZarrLocation) -> bool:
+        """Return if the parent directory is within the zarr fileset"""
+
+        parent_zarr = zarr.create("..")
+        return bool(parent_zarr.exists() and (parent_zarr.zgroup or parent_zarr.zarray))
+
+    def __init__(self, node: Node) -> None:
+        super().__init__(node)
+        parent_zarr = node.zarr.create("..")
+        if parent_zarr.exists() and (parent_zarr.zgroup or parent_zarr.zarray):
+            node.add(parent_zarr)
+
+
+class Root(Spec):
+    """
+    Root of the Zarr fileset
+    """
+
+    @staticmethod
+    def matches(zarr: ZarrLocation) -> bool:
+        """Return if the parent directory is not within the zarr fileset"""
+
+        parent_zarr = zarr.create("..")
+        return parent_zarr.exists() and not (parent_zarr.zgroup or parent_zarr.zarray)
+
+    def __init__(self, node: Node) -> None:
+        super().__init__(node)
+
+
 class Labels(Spec):
     """Relatively small specification for the well-known "labels" group which only
     contains the name of subgroups which should be loaded as labeled images."""

requirements/requirements-dev.txt

@@ -1,6 +1,7 @@
 black
 cython >= 0.29.16
 numpy >= 1.16.0
+entrypoints
 pre-commit
 tox
 wheel

setup.py

@@ -24,6 +24,7 @@ def read(fname):
 install_requires += (["requests"],)
 install_requires += (["scikit-image"],)
 install_requires += (["toolz"],)
+install_requires += (["entrypoints"],)
 
 
 setup(