Merge pull request #4 from VisLab/main

Did some renaming of classes

.gitignore

@@ -14,6 +14,8 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
+bin/
 build/
 develop-eggs/
 dist/
@@ -164,7 +166,8 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
+/venv/
 
 # Mac finder
 .DS_Store

requirements-dev.txt

@@ -5,6 +5,7 @@ codespell==2.2.6
 coverage==7.3.2
 hdmf==3.10.0
 hdmf-docutils==0.4.6
+hedtools==0.4.0
 pre-commit==3.4.0
 pynwb==2.5.0
 pytest==7.4.2

requirements-min.txt

@@ -3,3 +3,4 @@
 # NOTE: it may be possible to relax these minimum requirements
 pynwb==2.5.0
 hdmf==3.10.0
+hedtools==0.4.0

spec/ndx-hed.extensions.yaml

@@ -1,19 +1,27 @@
-datasets:
-- neurodata_type_def: HedAnnotations
-  neurodata_type_inc: VectorData
-  dtype: text
-  doc: An extension of VectorData for Hierarchical Event Descriptor (HED) tags. If
-    HED tags are used, the HED schema version must be specified in the NWB file using
-    the HedMetadata type.
-groups:
-- neurodata_type_def: HedMetadata
-  neurodata_type_inc: LabMetaData
-  name: HedMetadata
-  doc: An extension of LabMetaData to store the Hierarchical Event Descriptor (HED)
-    schema version. TODO When merged with core, this will no longer inherit from LabMetaData
-    but from NWBContainer and be placed optionally in /general.
-  attributes:
-  - name: hed_schema_version
-    dtype: text
-    doc: The version of the HED schema used to validate the HED tags, e.g., '8.2.0'.
-      Required if HED tags are used in the NWB file.
+datasets:
+- neurodata_type_def: HedAnnotations
+  neurodata_type_inc: VectorData
+  dtype: text
+  doc: An extension of VectorData for Hierarchical Event Descriptor (HED) tags. If
+    HED tags are used, the HED schema version must be specified in the NWB file using
+    the HedVersion type.
+  attributes:
+  - name: sub_name
+    dtype: text
+    doc: The smallest possible difference between two event times. Usually 1 divided
+      by the event time sampling rate on the data acquisition system.
+    required: false
+groups:
+- neurodata_type_def: HedVersion
+  neurodata_type_inc: LabMetaData
+  name: hed_version
+  doc: An extension of LabMetaData to store the Hierarchical Event Descriptor (HED)
+    schema version. TODO When merged with core, this will no longer inherit from LabMetaData
+    but from NWBContainer and be placed optionally in /general.
+  attributes:
+  - name: version
+    dtype: text
+    shape:
+    - null
+    doc: The version of the HED schema used to validate the HED tags, e.g., '8.2.0'.
+      Required if HED tags are used in the NWB file.

spec/ndx-hed.namespace.yaml

@@ -1,17 +1,17 @@
-namespaces:
-- author:
-  - Ryan Ly
-  - Oliver Ruebel
-  - Kay Robbins
-  - Ian Callanan
-  contact:
-  - [email protected]
-  - [email protected]
-  - [email protected]
-  - [email protected]
-  doc: NWB extension for HED data
-  name: ndx-hed
-  schema:
-  - namespace: core
-  - source: ndx-hed.extensions.yaml
-  version: 0.1.0
+namespaces:
+- author:
+  - Ryan Ly
+  - Oliver Ruebel
+  - Kay Robbins
+  - Ian Callanan
+  contact:
+  - [email protected]
+  - [email protected]
+  - [email protected]
+  - [email protected]
+  doc: NWB extension for HED data
+  name: ndx-hed
+  schema:
+  - namespace: core
+  - source: ndx-hed.extensions.yaml
+  version: 0.1.0

src/pynwb/ndx_hed/__init__.py

@@ -22,8 +22,9 @@
 # Either have PyNWB generate a class from the spec using `get_class` as shown
 # below or write a custom class and register it using the class decorator
 # `@register_class("TetrodeSeries", "ndx-hed")`
-HedAnnotations = get_class("HedAnnotations", "ndx-hed")
-HedMetadata = get_class("HedMetadata", "ndx-hed")
+# HedAnnotations = get_class("HedAnnotations", "ndx-hed")
+# HedVersion = get_class("HedVersion", "ndx-hed")
 
 # Remove these functions from the package
 del load_namespaces, get_class
+from .hed_annotations import HedVersion, HedAnnotations

src/pynwb/ndx_hed/hed_annotations.py

@@ -0,0 +1,104 @@
+from collections.abc import Iterable
+from hdmf.common import VectorData
+from hdmf.utils import docval, getargs, get_docval, popargs
+from hed.schema import HedSchema, HedSchemaGroup, load_schema_version
+from pynwb import register_class
+from pynwb.file import LabMetaData
+
+
+@register_class('HedAnnotations', 'ndx-hed')
+class HedAnnotations(VectorData):
+    """
+    Column storing HED (Hierarchical Event Descriptors) annotations for a row. A HED string is a comma-separated,
+    and possibly parenthesized list of HED tags selected from a valid HED vocabulary as specified by the
+    NWBFile field HEDVersion.
+
+    """
+
+    __nwbfields__ = ('sub_name')
+
+    @docval(*get_docval(VectorData.__init__))
+    def __init__(self, **kwargs):
+        # kwargs['name'] = 'HED'
+        super().__init__(**kwargs)
+        self._init_internal()
+
+    def _init_internal(self):
+        """
+        This finds the HED schema object of use in this NWBFile.
+
+        TODO: How should errors be handled if this file doesn't have a HedVersion object in the LabMetaData?
+
+        """
+        self.sub_name = "HED"
+        root = self
+        # parent = root.parent
+        # while parent is not None:
+        #     root = parent
+        #     parent = root.parent
+        # hed_version = parent.get_lab_meta_data("HedVersion")
+        # if hed_version:
+        #     self.hed_schema = hed_version.get_schema()
+
+    @docval({'name': 'val', 'type': str,
+             'doc': 'the value to add to this column. Should be a valid HED string.'})
+    def add_row(self, **kwargs):
+        """Append a data value to this column."""
+        val = getargs('val', kwargs)
+        # val.check_types()
+        # TODO how to validate
+        #
+        # if val is not None and self.validate(val):
+        #     if self.term_set.validate(term=val):
+        #         self.append(val)
+        #     else:
+        #         msg = ("%s is not in the term set." % val)
+        #         raise ValueError(msg)
+        #
+        # else:
+        #     self.append(val)
+        super().append(val)
+
+    @docval({'name': 'key', 'type': 'str', 'doc': 'the value to add to this column'})
+    def get(self, key):
+        """
+        Retrieve elements from this object.
+
+        """
+        # TODO: Can key be more than a single value?  Do we need to check validity of anything?
+        vals = super().get(key)
+        return vals
+
+    @docval({'name': 'val', 'type': 'str', 'doc': 'the value to validate'},
+            {'name': 'return', 'type': 'list', 'doc': 'list of issues or none'})
+    def validate(self, **kwargs):
+        """Validate this HED string"""
+        val = getargs('val', kwargs)
+        return True
+
+
+@register_class("HedVersion", "ndx-hed")
+class HedVersion(LabMetaData):
+    """
+    The class containing the HED versions and HED schema used in this data file.
+
+    """
+
+    __nwbfields__ = ('name', 'description', 'version')
+
+    @docval({'name': 'version', 'type': (str, list),  'doc': 'HED strings of type str'})
+    def __init__(self, version):
+        kwargs = {'name': 'hed_version'}
+        super().__init__(**kwargs)
+        self.version = version
+        self._init_internal()
+
+    def _init_internal(self):
+        """
+        Create a HedSchema or HedSchemaGroup object from the HED Versions
+        """
+        self._hed_schema = load_schema_version(self.version)
+
+    @docval(returns='The HED schema or schema group object for this version', rtype=(HedSchema, HedSchemaGroup))
+    def get_hed_schema(self):
+        return self._hed_schema