Using in-house GenericDataChunkIterator

CHANGELOG.md

@@ -1,10 +1,12 @@
 # Upcoming
 
+## Deprecations
+
 ## Bug Fixes
 
-## Deprecations
 
 ## Features
+* Using in-house `GenericDataChunkIterator` [PR #1068](https://github.com/catalystneuro/neuroconv/pull/1068)
 
 ## Improvements
 

src/neuroconv/datainterfaces/behavior/video/video_utils.py

@@ -2,10 +2,11 @@
 from typing import Optional, Tuple
 
 import numpy as np
-from hdmf.data_utils import GenericDataChunkIterator
 from pydantic import FilePath
 from tqdm import tqdm
 
+from neuroconv.tools.hdmf import GenericDataChunkIterator
+
 from ....tools import get_package
 
 

src/neuroconv/tools/nwb_helpers/_configuration_models/_base_dataset_io.py

@@ -9,7 +9,6 @@
 import numpy as np
 import zarr
 from hdmf import Container
-from hdmf.data_utils import GenericDataChunkIterator
 from hdmf.utils import get_data_shape
 from pydantic import (
     BaseModel,
@@ -25,7 +24,7 @@
 from neuroconv.utils.str_utils import human_readable_size
 
 from ._pydantic_pure_json_schema_generator import PureJSONSchemaGenerator
-from ...hdmf import SliceableDataChunkIterator
+from ...hdmf import GenericDataChunkIterator, SliceableDataChunkIterator
 
 
 def _recursively_find_location_in_memory_nwbfile(current_location: str, neurodata_object: Container) -> str:

src/neuroconv/tools/roiextractors/imagingextractordatachunkiterator.py

@@ -4,10 +4,11 @@
 from typing import Optional
 
 import numpy as np
-from hdmf.data_utils import GenericDataChunkIterator
 from roiextractors import ImagingExtractor
 from tqdm import tqdm
 
+from neuroconv.tools.hdmf import GenericDataChunkIterator
+
 
 class ImagingExtractorDataChunkIterator(GenericDataChunkIterator):
     """DataChunkIterator for ImagingExtractor objects primarily used when writing imaging data to an NWB file."""

src/neuroconv/tools/spikeinterface/spikeinterfacerecordingdatachunkiterator.py

@@ -1,9 +1,10 @@
 from typing import Iterable, Optional
 
-from hdmf.data_utils import GenericDataChunkIterator
 from spikeinterface import BaseRecording
 from tqdm import tqdm
 
+from neuroconv.tools.hdmf import GenericDataChunkIterator
+
 
 class SpikeInterfaceRecordingDataChunkIterator(GenericDataChunkIterator):
     """DataChunkIterator specifically for use on RecordingExtractor objects."""