Add base methods for iterator serialization (#924)

Co-authored-by: Ryan Ly <[email protected]>

Author: CodyCBakerPhD

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### New features and minor improvements
 - Increase raw data chunk cache size for reading HDF5 files from 1 MiB to 32 MiB. @bendichter, @rly [#925](https://github.com/hdmf-dev/hdmf/pull/925)
 - Increase default chunk size for `GenericDataChunkIterator` from 1 MB to 10 MB. @bendichter, @rly [#925](https://github.com/hdmf-dev/hdmf/pull/925)
+- Added the magic `__reduce__` method as well as two private semi-abstract helper methods to enable pickling of the `GenericDataChunkIterator`. @codycbakerphd [#924](https://github.com/hdmf-dev/hdmf/pull/924)
 
 ## HDMF 3.8.1 (July 25, 2023)
 

src/hdmf/backends/io.py

@@ -74,8 +74,7 @@ def read(self, **kwargs):
 
         return container
 
-    @docval({'name': 'container', 'type': Container, 'doc': 'the Container object to write'},
-            allow_extra=True)
+    @docval({'name': 'container', 'type': Container, 'doc': 'the Container object to write'}, allow_extra=True)
     def write(self, **kwargs):
         """Write a container to the IO source."""
         container = popargs('container', kwargs)

src/hdmf/data_utils.py

@@ -3,7 +3,7 @@
 from abc import ABCMeta, abstractmethod
 from collections.abc import Iterable
 from warnings import warn
-from typing import Tuple
+from typing import Tuple, Callable
 from itertools import product, chain
 
 import h5py
@@ -190,9 +190,10 @@ def __init__(self, **kwargs):
         HDF5 recommends chunk size in the range of 2 to 16 MB for optimal cloud performance.
         https://youtu.be/rcS5vt-mKok?t=621
         """
-        buffer_gb, buffer_shape, chunk_mb, chunk_shape, self.display_progress, self.progress_bar_options = getargs(
+        buffer_gb, buffer_shape, chunk_mb, chunk_shape, self.display_progress, progress_bar_options = getargs(
             "buffer_gb", "buffer_shape", "chunk_mb", "chunk_shape", "display_progress", "progress_bar_options", kwargs
         )
+        self.progress_bar_options = progress_bar_options or dict()
 
         if buffer_gb is None and buffer_shape is None:
             buffer_gb = 1.0
@@ -264,15 +265,13 @@ def __init__(self, **kwargs):
         )
 
         if self.display_progress:
-            if self.progress_bar_options is None:
-                self.progress_bar_options = dict()
-
             try:
                 from tqdm import tqdm
 
                 if "total" in self.progress_bar_options:
                     warn("Option 'total' in 'progress_bar_options' is not allowed to be over-written! Ignoring.")
                     self.progress_bar_options.pop("total")
+
                 self.progress_bar = tqdm(total=self.num_buffers, **self.progress_bar_options)
             except ImportError:
                 warn(
@@ -345,12 +344,6 @@ def _get_default_buffer_shape(self, **kwargs) -> Tuple[int, ...]:
             ]
         )
 
-    def recommended_chunk_shape(self) -> Tuple[int, ...]:
-        return self.chunk_shape
-
-    def recommended_data_shape(self) -> Tuple[int, ...]:
-        return self.maxshape
-
     def __iter__(self):
         return self
 
@@ -371,6 +364,11 @@ def __next__(self):
                 self.progress_bar.write("\n")  # Allows text to be written to new lines after completion
             raise StopIteration
 
+    def __reduce__(self) -> Tuple[Callable, Iterable]:
+        instance_constructor = self._from_dict
+        initialization_args = (self._to_dict(),)
+        return (instance_constructor, initialization_args)
+
     @abstractmethod
     def _get_data(self, selection: Tuple[slice]) -> np.ndarray:
         """
@@ -391,24 +389,42 @@ def _get_data(self, selection: Tuple[slice]) -> np.ndarray:
         """
         raise NotImplementedError("The data fetching method has not been built for this DataChunkIterator!")
 
-    @property
-    def maxshape(self) -> Tuple[int, ...]:
-        return self._maxshape
-
     @abstractmethod
     def _get_maxshape(self) -> Tuple[int, ...]:
         """Retrieve the maximum bounds of the data shape using minimal I/O."""
         raise NotImplementedError("The setter for the maxshape property has not been built for this DataChunkIterator!")
 
-    @property
-    def dtype(self) -> np.dtype:
-        return self._dtype
-
     @abstractmethod
     def _get_dtype(self) -> np.dtype:
         """Retrieve the dtype of the data using minimal I/O."""
         raise NotImplementedError("The setter for the internal dtype has not been built for this DataChunkIterator!")
 
+    def _to_dict(self) -> dict:
+        """Optional method to add in child classes to enable pickling (required for multiprocessing)."""
+        raise NotImplementedError(
+            "The `._to_dict()` method for pickling has not been defined for this DataChunkIterator!"
+        )
+
+    @staticmethod
+    def _from_dict(self) -> Callable:
+        """Optional method to add in child classes to enable pickling (required for multiprocessing)."""
+        raise NotImplementedError(
+            "The `._from_dict()` method for pickling has not been defined for this DataChunkIterator!"
+        )
+
+    def recommended_chunk_shape(self) -> Tuple[int, ...]:
+        return self.chunk_shape
+
+    def recommended_data_shape(self) -> Tuple[int, ...]:
+        return self.maxshape
+
+    @property
+    def maxshape(self) -> Tuple[int, ...]:
+        return self._maxshape
+    @property
+    def dtype(self) -> np.dtype:
+        return self._dtype
+
 
 class DataChunkIterator(AbstractDataChunkIterator):
     """

tests/unit/utils_test/test_core_GenericDataChunkIterator.py

@@ -1,12 +1,14 @@
 import unittest
+import pickle
 import numpy as np
 from pathlib import Path
 from tempfile import mkdtemp
 from shutil import rmtree
-from typing import Tuple, Iterable
+from typing import Tuple, Iterable, Callable
 from sys import version_info
 
 import h5py
+from numpy.testing import assert_array_equal
 
 from hdmf.data_utils import GenericDataChunkIterator
 from hdmf.testing import TestCase
@@ -18,6 +20,30 @@
     TQDM_INSTALLED = False
 
 
+class TestPickleableNumpyArrayDataChunkIterator(GenericDataChunkIterator):
+    def __init__(self, array: np.ndarray, **kwargs):
+        self.array = array
+        self._kwargs = kwargs
+        super().__init__(**kwargs)
+
+    def _get_data(self, selection) -> np.ndarray:
+        return self.array[selection]
+
+    def _get_maxshape(self) -> Tuple[int, ...]:
+        return self.array.shape
+
+    def _get_dtype(self) -> np.dtype:
+        return self.array.dtype
+
+    def _to_dict(self) -> dict:
+        return dict(array=pickle.dumps(self.array), kwargs=self._kwargs)
+
+    @staticmethod
+    def _from_dict(dictionary: dict) -> Callable:
+        array = pickle.loads(dictionary["array"])
+        return TestPickleableNumpyArrayDataChunkIterator(array=array, **dictionary["kwargs"])
+
+
 class GenericDataChunkIteratorTests(TestCase):
     class TestNumpyArrayDataChunkIterator(GenericDataChunkIterator):
         def __init__(self, array: np.ndarray, **kwargs):
@@ -204,6 +230,29 @@ def test_progress_bar_assertion(self):
                 progress_bar_options=dict(total=5),
             )
 
+    def test_private_to_dict_assertion(self):
+        with self.assertRaisesWith(
+            exc_type=NotImplementedError,
+            exc_msg="The `._to_dict()` method for pickling has not been defined for this DataChunkIterator!"
+        ):
+            iterator = self.TestNumpyArrayDataChunkIterator(array=self.test_array)
+            _ = iterator._to_dict()
+
+    def test_private_from_dict_assertion(self):
+        with self.assertRaisesWith(
+            exc_type=NotImplementedError,
+            exc_msg="The `._from_dict()` method for pickling has not been defined for this DataChunkIterator!"
+        ):
+            _ = self.TestNumpyArrayDataChunkIterator._from_dict(dict())
+
+    def test_direct_pickle_assertion(self):
+        with self.assertRaisesWith(
+            exc_type=NotImplementedError,
+            exc_msg="The `._to_dict()` method for pickling has not been defined for this DataChunkIterator!"
+        ):
+            iterator = self.TestNumpyArrayDataChunkIterator(array=self.test_array)
+            _ = pickle.dumps(iterator)
+
     def test_maxshape_attribute_contains_int_type(self):
         """Motivated by issues described in https://github.com/hdmf-dev/hdmf/pull/780 & 781 regarding return types."""
         self.check_all_of_iterable_is_python_int(
@@ -377,3 +426,12 @@ def test_tqdm_not_installed(self):
                 display_progress=True,
             )
             self.assertFalse(dci.display_progress)
+
+    def test_pickle(self):
+        pre_dump_iterator = TestPickleableNumpyArrayDataChunkIterator(array=self.test_array)
+        post_dump_iterator = pickle.loads(pickle.dumps(pre_dump_iterator))
+
+        assert isinstance(post_dump_iterator, TestPickleableNumpyArrayDataChunkIterator)
+        assert post_dump_iterator.chunk_shape == pre_dump_iterator.chunk_shape
+        assert post_dump_iterator.buffer_shape == pre_dump_iterator.buffer_shape
+        assert_array_equal(post_dump_iterator.array, pre_dump_iterator.array)