working on grpah loading of nwb files

nwb_linkml/pdm.lock

@@ -5,7 +5,7 @@
 groups = ["default", "dev", "plot", "tests"]
 strategy = ["inherit_metadata"]
 lock_version = "4.5.0"
-content_hash = "sha256:aaf3c34a5f39fc7db0c5dce91a0693eb78358a255d6b0a72f2e1f988eb7e899f"
+content_hash = "sha256:1c297e11f6dc9e4f6b8d29df872177d2ce65bbd334c0b65aa5175dfb125c4d9f"
 
 [[metadata.targets]]
 requires_python = ">=3.10,<3.13"
@@ -996,7 +996,7 @@ name = "networkx"
 version = "3.3"
 requires_python = ">=3.10"
 summary = "Python package for creating and manipulating graphs and networks"
-groups = ["dev", "tests"]
+groups = ["default", "dev", "tests"]
 files = [
     {file = "networkx-3.3-py3-none-any.whl", hash = "sha256:28575580c6ebdaf4505b22c6256a2b9de86b316dc63ba9e93abde3d78dfdbcf2"},
     {file = "networkx-3.3.tar.gz", hash = "sha256:0c127d8b2f4865f59ae9cb8aafcd60b5c70f3241ebd66f7defad7c4ab90126c9"},

nwb_linkml/pyproject.toml

@@ -25,6 +25,7 @@ dependencies = [
     "numpydantic>=1.3.3",
     "black>=24.4.2",
     "pandas>=2.2.2",
+    "networkx>=3.3",
 ]
 
 [project.urls]

nwb_linkml/src/nwb_linkml/io/hdf5.py

@@ -22,6 +22,7 @@ Other TODO:
 
 import json
 import os
+import re
 import shutil
 import subprocess
 import sys
@@ -31,11 +32,12 @@ from types import ModuleType
 from typing import TYPE_CHECKING, Dict, List, Optional, Union, overload
 
 import h5py
+import networkx as nx
 import numpy as np
 from pydantic import BaseModel
 from tqdm import tqdm
 
-from nwb_linkml.maps.hdf5 import ReadPhases, ReadQueue, flatten_hdf
+from nwb_linkml.maps.hdf5 import ReadPhases, ReadQueue, flatten_hdf, get_references
 
 if TYPE_CHECKING:
     from nwb_linkml.providers.schema import SchemaProvider
@@ -47,6 +49,85 @@ else:
     from typing_extensions import Never
 
 
+def hdf_dependency_graph(h5f: Path | h5py.File) -> nx.DiGraph:
+    """
+    Directed dependency graph of dataset and group nodes in an NWBFile such that
+    each node ``n_i`` is connected to node ``n_j`` if
+
+    * ``n_j`` is ``n_i``'s child
+    * ``n_i`` contains a reference to ``n_j``
+
+    Resolve references in
+
+    * Attributes
+    * Dataset columns
+    * Compound dtypes
+
+    Args:
+        h5f (:class:`pathlib.Path` | :class:`h5py.File`): NWB file to graph
+
+    Returns:
+        :class:`networkx.DiGraph`
+    """
+    # detect nodes to skip
+    skip_pattern = re.compile("^/specifications.*")
+
+    if isinstance(h5f, (Path, str)):
+        h5f = h5py.File(h5f, "r")
+
+    g = nx.DiGraph()
+
+    def _visit_item(name: str, node: h5py.Dataset | h5py.Group) -> None:
+        if skip_pattern.match(name):
+            return
+        # find references in attributes
+        refs = get_references(node)
+        if isinstance(node, h5py.Group):
+            refs.extend([child.name for child in node.values()])
+        refs = set(refs)
+
+        # add edges
+        edges = [(node.name, ref) for ref in refs]
+        g.add_edges_from(edges)
+
+        # ensure node added to graph
+        if len(edges) == 0:
+            g.add_node(node.name)
+
+        # store attrs in node
+        g.nodes[node.name].update(node.attrs)
+
+    # apply to root
+    _visit_item(h5f.name, h5f)
+
+    h5f.visititems(_visit_item)
+    return g
+
+
+def filter_dependency_graph(g: nx.DiGraph) -> nx.DiGraph:
+    """
+    Remove nodes from a dependency graph if they
+
+    * have no neurodata type AND
+    * have no outbound edges
+
+    OR
+
+    * are a VectorIndex (which are handled by the dynamictable mixins)
+    """
+    remove_nodes = []
+    node: str
+    for node in g.nodes.keys():
+        ndtype = g.nodes[node].get("neurodata_type", None)
+        if ndtype == "VectorData":
+            remove_nodes.append(node)
+        elif not ndtype and g.out_degree(node) == 0:
+            remove_nodes.append(node)
+
+    g.remove_nodes_from(remove_nodes)
+    return g
+
+
 class HDF5IO:
     """
     Read (and eventually write) from an NWB HDF5 file.

nwb_linkml/src/nwb_linkml/maps/hdf5.py

@@ -859,7 +859,7 @@ def get_references(obj: h5py.Dataset | h5py.Group) -> List[str]:
             # scalar
             if isinstance(obj[()], h5py.h5r.Reference):
                 refs.append(obj[()])
-        elif isinstance(obj[0], h5py.h5r.Reference):
+        elif len(obj) > 0 and isinstance(obj[0], h5py.h5r.Reference):
             # single-column
             refs.extend(obj[:].tolist())
         elif len(obj.dtype) > 1:

nwb_linkml/tests/data/test_nwb.yaml

@@ -1,46 +1,28 @@
 # manually transcribed target version of nwb-linkml dataset
 # matching the one created by fixtures.py:nwb_file
----
+meta:
-id: my_dataset
+  id: my_dataset
 
-prefixes:
+  prefixes:
-  nwbfile:
+    nwbfile:
-    - path: "test_nwb.nwb"
+      - path: "test_nwb.nwb"
-    - hash: "blake2b:blahblahblahblah"
+      - hash: "blake2b:blahblahblahblah"
 
-imports:
+  imports:
-  core:
+    core:
-    as: nwb
+      as: nwb
-    version: "2.7.0"
+      version: "2.7.0"
-    from:
+      from:
-      - pypi:
+        - pypi:
-          package: nwb-models
+            package: nwb-models
----
+    hdmf-common:
-
+      as: hdmf
-  hdmf-common:
+      version: "1.8.0"
-    as: hdmf
+      from:
-    version: "1.8.0"
+        - pypi:
-    from:
+            package: nwb-models
-      - pypi:
-          package: nwb-models
----
 
 extracellular_ephys: &ecephys
-  electrodes:
-    group:
-      - @shank{{i}}
-      - @shank{{i}}
-      - @shank{{i}}
-      # could have expression here like { range(3) } => i
-      # - ... { range(3) } => i
-      # or blank ... implies use expression from outer scope
-      - ...
-    shank{{i}}:
-      device: @general.devices.array
-    ...: { range(3) } => i
-
-# expands to
-extracellular_ephys:
   electrodes:
     group:
       - @shank0
@@ -54,7 +36,7 @@ extracellular_ephys:
       device: @general.devices.array
     # etc.
 
-data: !{{ nwb.NWBFile }} <== :nwbfile
+data: !nwb.NWBFile
   file_create_date: [ 2024-01-01 ]
   identifier: "1111-1111-1111-1111"
   session_description: All that you touch, you change.
@@ -63,11 +45,12 @@ data: !{{ nwb.NWBFile }} <== :nwbfile
     devices:
       - Heka ITC-1600:
       - Microscope:
+          description: My two-photon microscope
+          manufacturer: The best microscope manufacturer
       - array:
           description: old reliable
           manufacturer: diy
-    extracellular_ephys: *ecephys
+    extracellular_ephys: nwbfile:/general/extracellular_ephys
-
     experiment_description: All that you change, changes you.
     experimenter: [ "Lauren Oya Olamina" ]
     institution: Earthseed Research Institute

nwb_linkml/tests/data/test_nwb_condensed_sketch.yaml

@@ -0,0 +1,76 @@
+# Sketch of a condensed expression syntax for creation with nwb-linkml
+# just a sketch! keeping here for continued work but currentl unused.
+---
+id: my_dataset
+
+prefixes:
+  nwbfile:
+    - path: "test_nwb.nwb"
+    - hash: "blake2b:blahblahblahblah"
+
+imports:
+  core:
+    as: nwb
+    version: "2.7.0"
+    from:
+      - pypi:
+          package: nwb-models
+  hdmf-common:
+    as: hdmf
+    version: "1.8.0"
+    from:
+      - pypi:
+          package: nwb-models
+---
+
+extracellular_ephys: &ecephys
+  electrodes:
+    group:
+      - @shank{{i}}
+      - @shank{{i}}
+      - @shank{{i}}
+      # could have expression here like { range(3) } => i
+      # - ... { range(3) } => i
+      # or blank ... implies use expression from outer scope
+      - ...
+    shank{{i}}:
+      device: @general.devices.array
+    ...: { range(3) } => i
+
+# expands to
+extracellular_ephys:
+  electrodes:
+    group:
+      - @shank0
+      - @shank0
+      - @shank0
+      - @shank1
+      - # etc.
+    shank0:
+      device: @general.devices.array
+    shank1:
+      device: @general.devices.array
+    # etc.
+
+data: !{{ nwb.NWBFile }} <== :nwbfile
+  file_create_date: [ 2024-01-01 ]
+  identifier: "1111-1111-1111-1111"
+  session_description: All that you touch, you change.
+  session_start_time: 2024-01-01T01:01:01
+  general:
+    devices:
+      - Heka ITC-1600:
+      - Microscope:
+      - array:
+          description: old reliable
+          manufacturer: diy
+    extracellular_ephys: *ecephys
+
+    experiment_description: All that you change, changes you.
+    experimenter: [ "Lauren Oya Olamina" ]
+    institution: Earthseed Research Institute
+    keywords:
+      - behavior
+      - belief
+    related_publications: doi:10.1016/j.neuron.2016.12.011
+

nwb_linkml/tests/fixtures.py

@@ -349,6 +349,8 @@ def nwb_file(tmp_output_dir) -> Path:
     generator = np.random.default_rng()
 
     nwb_path = tmp_output_dir / "test_nwb.nwb"
+    if nwb_path.exists():
+        return nwb_path
 
     nwbfile = NWBFile(
         session_description="All that you touch, you change.",  # required

nwb_linkml/tests/test_io/test_io_hdf5.py

@@ -4,7 +4,7 @@ import h5py
 import numpy as np
 import pytest
 
-from nwb_linkml.io.hdf5 import HDF5IO, truncate_file
+from nwb_linkml.io.hdf5 import HDF5IO, truncate_file, hdf_dependency_graph, filter_dependency_graph
 
 
 @pytest.mark.skip()
@@ -98,3 +98,12 @@ def test_flatten_hdf():
     assert not any(["specifications" in v.path for v in flat.values()])
     pdb.set_trace()
     raise NotImplementedError("Just a stub for local testing for now, finish me!")
+
+
+def test_dependency_graph(nwb_file):
+    """
+    dependency graph is correctly constructed from an HDF5 file
+    """
+    graph = hdf_dependency_graph(nwb_file)
+    graph = filter_dependency_graph(graph)
+    pass