Remove deprecations and add docstring to `BaseImagingExtractorInterfa…

…ce` (#1126)

CHANGELOG.md

@@ -1,6 +1,7 @@
 # Upcoming
 
 ## Deprecations
+* Completely removed compression settings from most places[PR #1126](https://github.com/catalystneuro/neuroconv/pull/1126)
 
 ## Bug Fixes
 

src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py

@@ -1,6 +1,5 @@
 import json
 import re
-import warnings
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Optional, Union
@@ -210,8 +209,6 @@ def add_to_nwbfile(
         self,
         nwbfile: NWBFile,
         metadata: Optional[dict] = None,
-        compression: Optional[str] = None,  # TODO: remove completely after 10/1/2024
-        compression_opts: Optional[int] = None,  # TODO: remove completely after 10/1/2024
     ):
         """
         Parameters
@@ -223,17 +220,6 @@ def add_to_nwbfile(
         """
         import pandas as pd
 
-        # TODO: remove completely after 10/1/2024
-        if compression is not None or compression_opts is not None:
-            warnings.warn(
-                message=(
-                    "Specifying compression methods and their options at the level of tool functions has been deprecated. "
-                    "Please use the `configure_backend` tool function for this purpose."
-                ),
-                category=DeprecationWarning,
-                stacklevel=2,
-            )
-
         fictrac_data_df = pd.read_csv(self.file_path, sep=",", header=None, names=self.columns_in_dat_file)
 
         # Get the timestamps

src/neuroconv/datainterfaces/ecephys/baselfpextractorinterface.py

@@ -26,8 +26,6 @@ def add_to_nwbfile(
         starting_time: Optional[float] = None,
         write_as: Literal["raw", "lfp", "processed"] = "lfp",
         write_electrical_series: bool = True,
-        compression: Optional[str] = None,  # TODO: remove completely after 10/1/2024
-        compression_opts: Optional[int] = None,
         iterator_type: str = "v2",
         iterator_opts: Optional[dict] = None,
     ):
@@ -38,8 +36,6 @@ def add_to_nwbfile(
             starting_time=starting_time,
             write_as=write_as,
             write_electrical_series=write_electrical_series,
-            compression=compression,
-            compression_opts=compression_opts,
             iterator_type=iterator_type,
             iterator_opts=iterator_opts,
         )

src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py

@@ -308,8 +308,6 @@ def add_to_nwbfile(
         starting_time: Optional[float] = None,
         write_as: Literal["raw", "lfp", "processed"] = "raw",
         write_electrical_series: bool = True,
-        compression: Optional[str] = None,  # TODO: remove completely after 10/1/2024
-        compression_opts: Optional[int] = None,
         iterator_type: Optional[str] = "v2",
         iterator_opts: Optional[dict] = None,
         always_write_timestamps: bool = False,
@@ -388,8 +386,6 @@ def add_to_nwbfile(
             write_as=write_as,
             write_electrical_series=write_electrical_series,
             es_key=self.es_key,
-            compression=compression,
-            compression_opts=compression_opts,
             iterator_type=iterator_type,
             iterator_opts=iterator_opts,
             always_write_timestamps=always_write_timestamps,

src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py

@@ -1,6 +1,5 @@
 """Author: Ben Dichter."""
 
-import warnings
 from typing import Literal, Optional
 
 import numpy as np
@@ -46,17 +45,9 @@ def __init__(
         self.photon_series_type = photon_series_type
 
     def get_metadata_schema(
-        self, photon_series_type: Optional[Literal["OnePhotonSeries", "TwoPhotonSeries"]] = None
+        self,
     ) -> dict:
 
-        if photon_series_type is not None:
-            warnings.warn(
-                "The 'photon_series_type' argument is deprecated and will be removed in a future version. "
-                "Please set 'photon_series_type' during the initialization of the BaseImagingExtractorInterface instance.",
-                DeprecationWarning,
-                stacklevel=2,
-            )
-            self.photon_series_type = photon_series_type
         metadata_schema = super().get_metadata_schema()
 
         metadata_schema["required"] = ["Ophys"]
@@ -100,18 +91,9 @@ def get_metadata_schema(
         return metadata_schema
 
     def get_metadata(
-        self, photon_series_type: Optional[Literal["OnePhotonSeries", "TwoPhotonSeries"]] = None
+        self,
     ) -> DeepDict:
 
-        if photon_series_type is not None:
-            warnings.warn(
-                "The 'photon_series_type' argument is deprecated and will be removed in a future version. "
-                "Please set 'photon_series_type' during the initialization of the BaseImagingExtractorInterface instance.",
-                DeprecationWarning,
-                stacklevel=2,
-            )
-            self.photon_series_type = photon_series_type
-
         from ...tools.roiextractors import get_nwb_imaging_metadata
 
         metadata = super().get_metadata()
@@ -147,6 +129,29 @@ def add_to_nwbfile(
         stub_test: bool = False,
         stub_frames: int = 100,
     ):
+        """
+        Add imaging data to the NWB file
+
+        Parameters
+        ----------
+        nwbfile : NWBFile
+            The NWB file where the imaging data will be added.
+        metadata : dict, optional
+            Metadata for the NWBFile, by default None.
+        photon_series_type : {"TwoPhotonSeries", "OnePhotonSeries"}, optional
+            The type of photon series to be added, by default "TwoPhotonSeries".
+        photon_series_index : int, optional
+            The index of the photon series in the provided imaging data, by default 0.
+        parent_container : {"acquisition", "processing/ophys"}, optional
+            Specifies the parent container to which the photon series should be added, either as part of "acquisition" or
+            under the "processing/ophys" module, by default "acquisition".
+        stub_test : bool, optional
+            If True, only writes a small subset of frames for testing purposes, by default False.
+        stub_frames : int, optional
+            The number of frames to write when stub_test is True. Will use min(stub_frames, total_frames) to avoid
+            exceeding available frames, by default 100.
+        """
+
         from ...tools.roiextractors import add_imaging_to_nwbfile
 
         if stub_test:

src/neuroconv/tools/neo/neo.py

@@ -214,7 +214,6 @@ def add_icephys_recordings(
     icephys_experiment_type: str = "voltage_clamp",
     stimulus_type: str = "not described",
     skip_electrodes: tuple[int] = (),
-    compression: Optional[str] = None,  # TODO: remove completely after 10/1/2024
 ):
     """
     Add icephys recordings (stimulus/response pairs) to nwbfile object.
@@ -230,16 +229,6 @@ def add_icephys_recordings(
     skip_electrodes : tuple, default: ()
         Electrode IDs to skip.
     """
-    # TODO: remove completely after 10/1/2024
-    if compression is not None:
-        warn(
-            message=(
-                "Specifying compression methods and their options at the level of tool functions has been deprecated. "
-                "Please use the `configure_backend` tool function for this purpose."
-            ),
-            category=DeprecationWarning,
-            stacklevel=2,
-        )
 
     n_segments = get_number_of_segments(neo_reader, block=0)
 
@@ -380,7 +369,6 @@ def add_neo_to_nwb(
     neo_reader,
     nwbfile: pynwb.NWBFile,
     metadata: dict = None,
-    compression: Optional[str] = None,  # TODO: remove completely after 10/1/2024
     icephys_experiment_type: str = "voltage_clamp",
     stimulus_type: Optional[str] = None,
     skip_electrodes: tuple[int] = (),
@@ -409,15 +397,6 @@ def add_neo_to_nwb(
     assert isinstance(nwbfile, pynwb.NWBFile), "'nwbfile' should be of type pynwb.NWBFile"
 
     # TODO: remove completely after 10/1/2024
-    if compression is not None:
-        warn(
-            message=(
-                "Specifying compression methods and their options at the level of tool functions has been deprecated. "
-                "Please use the `configure_backend` tool function for this purpose."
-            ),
-            category=DeprecationWarning,
-            stacklevel=2,
-        )
 
     add_device_from_metadata(nwbfile=nwbfile, modality="Icephys", metadata=metadata)
 
@@ -443,7 +422,6 @@ def write_neo_to_nwb(
     overwrite: bool = False,
     nwbfile=None,
     metadata: dict = None,
-    compression: Optional[str] = None,  # TODO: remove completely after 10/1/2024
     icephys_experiment_type: Optional[str] = None,
     stimulus_type: Optional[str] = None,
     skip_electrodes: Optional[tuple] = (),
@@ -499,9 +477,6 @@ def write_neo_to_nwb(
 
         Note that data intended to be added to the electrodes table of the NWBFile should be set as channel
         properties in the RecordingExtractor object.
-    compression: str (optional, defaults to "gzip")
-        Type of compression to use. Valid types are "gzip" and "lzf".
-        Set to None to disable all compression.
     icephys_experiment_type: str (optional)
         Type of Icephys experiment. Allowed types are: 'voltage_clamp', 'current_clamp' and 'izero'.
         If no value is passed, 'voltage_clamp' is used as default.
@@ -518,17 +493,6 @@ def write_neo_to_nwb(
 
     assert save_path is None or nwbfile is None, "Either pass a save_path location, or nwbfile object, but not both!"
 
-    # TODO: remove completely after 10/1/2024
-    if compression is not None:
-        warn(
-            message=(
-                "Specifying compression methods and their options at the level of tool functions has been deprecated. "
-                "Please use the `configure_backend` tool function for this purpose."
-            ),
-            category=DeprecationWarning,
-            stacklevel=2,
-        )
-
     if metadata is None:
         metadata = get_nwb_metadata(neo_reader=neo_reader)
 

src/neuroconv/tools/spikeinterface/spikeinterface.py

@@ -749,8 +749,6 @@ def add_electrical_series(
     write_as: Literal["raw", "processed", "lfp"] = "raw",
     es_key: str = None,
     write_scaled: bool = False,
-    compression: Optional[str] = None,
-    compression_opts: Optional[int] = None,
     iterator_type: Optional[str] = "v2",
     iterator_opts: Optional[dict] = None,
 ):
@@ -772,8 +770,6 @@ def add_electrical_series(
         write_as=write_as,
         es_key=es_key,
         write_scaled=write_scaled,
-        compression=compression,
-        compression_opts=compression_opts,
         iterator_type=iterator_type,
         iterator_opts=iterator_opts,
     )
@@ -810,8 +806,6 @@ def add_electrical_series_to_nwbfile(
     write_as: Literal["raw", "processed", "lfp"] = "raw",
     es_key: str = None,
     write_scaled: bool = False,
-    compression: Optional[str] = None,
-    compression_opts: Optional[int] = None,
     iterator_type: Optional[str] = "v2",
     iterator_opts: Optional[dict] = None,
     always_write_timestamps: bool = False,
@@ -847,7 +841,6 @@ def add_electrical_series_to_nwbfile(
     write_scaled : bool, default: False
         If True, writes the traces in uV with the right conversion.
         If False , the data is stored as it is and the right conversions factors are added to the nwbfile.
-        Only applies to compression="gzip". Controls the level of the GZIP.
     iterator_type: {"v2",  None}, default: 'v2'
         The type of DataChunkIterator to use.
         'v1' is the original DataChunkIterator of the hdmf data_utils.
@@ -868,16 +861,6 @@ def add_electrical_series_to_nwbfile(
     Missing keys in an element of metadata['Ecephys']['ElectrodeGroup'] will be auto-populated with defaults
     whenever possible.
     """
-    # TODO: remove completely after 10/1/2024
-    if compression is not None or compression_opts is not None:
-        warnings.warn(
-            message=(
-                "Specifying compression methods and their options at the level of tool functions has been deprecated. "
-                "Please use the `configure_backend` tool function for this purpose."
-            ),
-            category=DeprecationWarning,
-            stacklevel=2,
-        )
 
     assert write_as in [
         "raw",
@@ -1042,8 +1025,6 @@ def add_recording(
     es_key: Optional[str] = None,
     write_electrical_series: bool = True,
     write_scaled: bool = False,
-    compression: Optional[str] = "gzip",
-    compression_opts: Optional[int] = None,
     iterator_type: str = "v2",
     iterator_opts: Optional[dict] = None,
 ):
@@ -1065,8 +1046,6 @@ def add_recording(
         es_key=es_key,
         write_electrical_series=write_electrical_series,
         write_scaled=write_scaled,
-        compression=compression,
-        compression_opts=compression_opts,
         iterator_type=iterator_type,
         iterator_opts=iterator_opts,
     )
@@ -1081,8 +1060,6 @@ def add_recording_to_nwbfile(
     es_key: Optional[str] = None,
     write_electrical_series: bool = True,
     write_scaled: bool = False,
-    compression: Optional[str] = "gzip",
-    compression_opts: Optional[int] = None,
     iterator_type: str = "v2",
     iterator_opts: Optional[dict] = None,
     always_write_timestamps: bool = False,
@@ -1163,8 +1140,6 @@ def add_recording_to_nwbfile(
                 write_as=write_as,
                 es_key=es_key,
                 write_scaled=write_scaled,
-                compression=compression,
-                compression_opts=compression_opts,
                 iterator_type=iterator_type,
                 iterator_opts=iterator_opts,
                 always_write_timestamps=always_write_timestamps,
@@ -1183,8 +1158,6 @@ def write_recording(
     es_key: Optional[str] = None,
     write_electrical_series: bool = True,
     write_scaled: bool = False,
-    compression: Optional[str] = "gzip",
-    compression_opts: Optional[int] = None,
     iterator_type: Optional[str] = "v2",
     iterator_opts: Optional[dict] = None,
 ):
@@ -1209,8 +1182,6 @@ def write_recording(
         es_key=es_key,
         write_electrical_series=write_electrical_series,
         write_scaled=write_scaled,
-        compression=compression,
-        compression_opts=compression_opts,
         iterator_type=iterator_type,
         iterator_opts=iterator_opts,
     )
@@ -1228,8 +1199,6 @@ def write_recording_to_nwbfile(
     es_key: Optional[str] = None,
     write_electrical_series: bool = True,
     write_scaled: bool = False,
-    compression: Optional[str] = "gzip",
-    compression_opts: Optional[int] = None,
     iterator_type: Optional[str] = "v2",
     iterator_opts: Optional[dict] = None,
 ) -> pynwb.NWBFile:
@@ -1303,11 +1272,6 @@ def write_recording_to_nwbfile(
         and electrodes are written to NWB.
     write_scaled: bool, default: True
         If True, writes the scaled traces (return_scaled=True)
-    compression: {None, 'gzip', 'lzp'}, default: 'gzip'
-        Type of compression to use. Set to None to disable all compression.
-        To use the `configure_backend` function, you should set this to None.
-    compression_opts: int, optional, default: 4
-        Only applies to compression="gzip". Controls the level of the GZIP.
     iterator_type: {"v2", "v1",  None}
         The type of DataChunkIterator to use.
         'v1' is the original DataChunkIterator of the hdmf data_utils.
@@ -1348,8 +1312,6 @@ def write_recording_to_nwbfile(
             es_key=es_key,
             write_electrical_series=write_electrical_series,
             write_scaled=write_scaled,
-            compression=compression,
-            compression_opts=compression_opts,
             iterator_type=iterator_type,
             iterator_opts=iterator_opts,
         )

src/neuroconv/tools/testing/mock_interfaces.py

@@ -265,9 +265,9 @@ def __init__(
         self.verbose = verbose
         self.photon_series_type = photon_series_type
 
-    def get_metadata(self, photon_series_type: Optional[Literal["OnePhotonSeries", "TwoPhotonSeries"]] = None) -> dict:
+    def get_metadata(self) -> dict:
         session_start_time = datetime.now().astimezone()
-        metadata = super().get_metadata(photon_series_type=photon_series_type)
+        metadata = super().get_metadata()
         metadata["NWBFile"]["session_start_time"] = session_start_time
         return metadata