ndx-hed 0.1.0__py3-none-any.whl

ndx_hed/__init__.py

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+import os
+from pynwb import load_namespaces, get_class
+
+# Set path of the namespace.yaml file to the expected install location
+ndx_hed_specpath = os.path.join(
+    os.path.dirname(__file__),
+    'spec',
+    'ndx-hed.namespace.yaml'
+)
+
+# If the extension has not been installed yet but we are running directly from
+# the git repo
+if not os.path.exists(ndx_hed_specpath):
+    ndx_hed_specpath = os.path.abspath(os.path.join(
+        os.path.dirname(__file__),
+        '..', '..', '..',
+        'spec',
+        'ndx-hed.namespace.yaml'
+    ))
+
+# Load the namespace
+load_namespaces(ndx_hed_specpath)
+# 
+# from . import io as __io  # noqa: E402,F401
+# from .hed_models import NWBHedVersion
+# 
+# try:
+#     from importlib.resources import files
+# except ImportError:
+#     # TODO: Remove when python 3.9 becomes the new minimum
+#     from importlib_resources import files
+# 
+#     
+# 
+# # Get path to the namespace.yaml file with the expected location when installed not in editable mode
+# __location_of_this_file = files(__name__)
+# __spec_path = __location_of_this_file / "spec" / "ndx-hed.namespace.yaml"
+# 
+# # If that path does not exist, we are likely running in editable mode. Use the local path instead
+# if not os.path.exists(__spec_path):
+#     __spec_path = __location_of_this_file.parent.parent.parent / "spec" / "ndx-hed.namespace.yaml"
+# 
+# # Load the namespace
+# load_namespaces(str(__spec_path))
+# 
+# # TODO: Define your classes here to make them accessible at the package level.
+# # 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")
+# HedVersion = get_class("HedVersion", "ndx-hed")
+# 
+# # Remove these functions from the package
+del load_namespaces, get_class
+
+from .hed_tags import HedTags

ndx_hed/hed_tags.py

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+
+from hdmf.common import VectorData
+from hdmf.utils import docval, getargs, get_docval, popargs
+from hed.errors import get_printable_issue_string
+from hed.schema import load_schema_version
+from hed.models import HedString
+from pynwb import register_class
+
+
+@register_class('HedTags', 'ndx-hed')
+class HedTags(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__ = ('_hed_schema', 'hed_version')
+
+    @docval({'name': 'hed_version', 'type': 'str', 'doc': 'The version of HED used by this data.'},
+            {'name': 'name', 'type': str, 'doc': 'The name of this VectorData', 'default': 'HED'},
+            {'name': 'description', 'type': str, 'doc': 'a description for this column',
+             'default': "Column that stores HED tags as text annotating their respective row."},
+            *get_docval(VectorData.__init__, 'data'))
+    def __init__(self, **kwargs):
+        hed_version = popargs('hed_version', kwargs)
+        super().__init__(**kwargs)
+        self.hed_version = hed_version
+        self._init_internal()
+
+    def _init_internal(self):
+        """
+        This loads (a private pointer to) the HED schema and validates the HED data.
+        """
+        self._hed_schema = load_schema_version(self.hed_version)
+        issues = []
+        for index in range(len(self.data)):
+            hed_obj = HedString(self.get(index), self._hed_schema)
+            these_issues = hed_obj.validate()
+            if these_issues:
+                issues.append(f"line {str(index)}: {get_printable_issue_string(these_issues)}")
+        if issues:
+            issue_str = "\n".join(issues)
+            raise ValueError(f"InvalidHEDData {issue_str}")
+
+    @docval({'name': 'val', 'type': str,
+             'doc': 'the value to add to this column. Should be a valid HED string -- just forces string.'})
+    def add_row(self, **kwargs):
+        """Append a data value to this column."""
+        val = getargs('val', kwargs)
+        hed_obj = HedString(val, self._hed_schema)
+        these_issues = hed_obj.validate()
+        if these_issues:
+            raise ValueError(f"InvalidHEDValue [{str(val)}] issues: {get_printable_issue_string(these_issues)}")
+        super().append(val)
+
+    def get_hed_version(self):
+        return self.hed_version
+
+    def get_hed_schema(self):
+        return self._hed_schema

ndx_hed/spec/ndx-hed.extensions.yaml

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+datasets:
+- neurodata_type_def: HedTags
+  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.
+  attributes:
+  - name: hed_version
+    dtype: text
+    doc: "The version of the HED schema used to validate the HED tags, e.g., '8.2.0'.
+      (Required). "

ndx_hed/spec/ndx-hed.namespace.yaml

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+namespaces:
+- author:
+  - Ryan Ly
+  - Oliver Ruebel
+  - Kay Robbins
+  - Ian Callanan
+  contact:
+  - rly@lbl.gov
+  - oruebel@lbl.gov
+  - kay.robbins@utsa.edu
+  - ianrcallanan@gmail.com
+  doc: NWB extension for HED data
+  name: ndx-hed
+  schema:
+  - namespace: core
+    neurodata_types:
+    - VectorData
+  - source: ndx-hed.extensions.yaml
+  version: 0.1.0

ndx_hed-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.3
+Name: ndx-hed
+Version: 0.1.0
+Summary: NWB extension for HED data
+Project-URL: Homepage, https://github.com/hed-standard/ndx-hed
+Project-URL: Documentation, https://https://www.hed-resources.org/en/latest/HedAnnotationInNWB.html
+Project-URL: Bug Tracker, https://github.com/hed-standard/ndx-hed/issues
+Project-URL: Discussions, https://github.com/hed-standard/ndx-hed/discussions
+Project-URL: Changelog, https://github.com/hed-standard/ndx-hed/CHANGELOG.md
+Author-email: Ryan Ly <rly@lbl.gov>, Oliver Ruebel <oruebel@lbl.gov>, Kay Robbins <kay.robbins@utsa.edu>, Ian Callanan <ianrcallanan@gmail.com>
+License: BSD-3
+License-File: LICENSE.txt
+Keywords: NWB,NeurodataWithoutBorders,ndx-extension,nwb-extension
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.8
+Requires-Dist: hdmf>=3.14.1
+Requires-Dist: hedtools>=0.5.0
+Requires-Dist: pynwb>=2.8.0
+Description-Content-Type: text/markdown
+
+# ndx-hed Extension for NWB
+
+[**Neurodata Without Borders (NWB)**](https://www.nwb.org/) is a data standard for organizing neurophysiology data.
+NWB is used extensively as the data representation for single cell and animal recordings as well as
+human neuroimaging modalities such as IEEG. HED (Hierarchical Event Descriptors) is a system of
+standardized vocabularies and supporting tools that allows fine-grained annotation of data.
+HED annotations can now be used in NWB to provide a column of HED annotations for any NWB
+dynamic table. 
+
+The [**HED annotation in NWB**](https://www.hed-resources.org/en/latest/HedAnnotationInNWB.html)
+user guide explains in more detail how to use this extension for HED.
+
+
+## Installation
+
+**Python:**
+```bash
+pip install -U ndx-hed
+```
+
+**Matlab:**  The Matlab extension is under development

ndx_hed-0.1.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+ndx_hed/spec/ndx-hed.extensions.yaml,sha256=Ujh24UBAJCSGKn7WI-h5THllp4qIkXBTEOgi8Wnat4k,452
+ndx_hed/spec/ndx-hed.namespace.yaml,sha256=zmo5P0jNvIz7mwzr6cWmnsSNq_UhfB6GUJ4lbBEmtbw,374
+ndx_hed/__init__.py,sha256=Ep4kOLhuG81AfZ-3ZLvpkgRAJmbB4bJEJfmvYrm7bkA,1971
+ndx_hed/hed_tags.py,sha256=3VMBpVvPY1cnp82agJHPnCl-L8n_qbzvkqoFOFI7mTI,2618
+ndx_hed-0.1.0.dist-info/METADATA,sha256=r9sHAnjfedHRj45NuP5JVLMlthsz6YHvkgE2f6bvEGY,2194
+ndx_hed-0.1.0.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+ndx_hed-0.1.0.dist-info/licenses/LICENSE.txt,sha256=ogc7sj95gG_7TUtmjl1fBMf0bk9KVI76BgcApFqTxhw,1572
+ndx_hed-0.1.0.dist-info/RECORD,,

ndx_hed-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.25.0
+Root-Is-Purelib: true
+Tag: py3-none-any

ndx_hed-0.1.0.dist-info/licenses/LICENSE.txt

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+BSD 3-Clause License
+
+Copyright (c) 2024, Ryan Ly, Oliver Ruebel, Kay Robbins
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.