Merge branch 'main' into dlc_csv

catalystneuro · Nov 13, 2024 · ec417c0 · ec417c0
2 parents 05591cd + 6960872
commit ec417c0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,10 +1,12 @@
 # Upcoming
 
 ## Deprecations
+* Completely removed compression settings from most places[PR #1126](https://github.com/catalystneuro/neuroconv/pull/1126)
 
 ## Bug Fixes
 
 ## Features
+* Imaging interfaces have a new conversion option `always_write_timestamps` that can be used to force writing timestamps even if neuroconv's heuristics indicates regular sampling rate [PR #1125](https://github.com/catalystneuro/neuroconv/pull/1125)
 * Added .csv support to DeepLabCutInterface [PR #1140](https://github.com/catalystneuro/neuroconv/pull/1140)
 
 ## Improvements
@@ -46,7 +48,7 @@
 * Added automated EFS volume creation and mounting to the `submit_aws_job` helper function. [PR #1018](https://github.com/catalystneuro/neuroconv/pull/1018)
 * Added a mock for segmentation extractors interfaces in ophys: `MockSegmentationInterface` [PR #1067](https://github.com/catalystneuro/neuroconv/pull/1067)
 * Added a `MockSortingInterface` for testing purposes. [PR #1065](https://github.com/catalystneuro/neuroconv/pull/1065)
-* BaseRecordingInterfaces have a new conversion options `always_write_timestamps` that ca be used to force writing timestamps even if neuroconv heuristic indicates regular sampling rate [PR #1091](https://github.com/catalystneuro/neuroconv/pull/1091)
+* BaseRecordingInterfaces have a new conversion options `always_write_timestamps` that can be used to force writing timestamps even if neuroconv heuristic indicates regular sampling rate [PR #1091](https://github.com/catalystneuro/neuroconv/pull/1091)
 
 
 ## Improvements

diff --git a/pyproject.toml b/pyproject.toml
@@ -270,50 +270,50 @@ icephys = [
 
 ## Ophys
 brukertiff = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
     "tifffile>=2023.3.21",
 ]
 caiman = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 cnmfe = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 extract = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 hdf5 = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 micromanagertiff = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
     "tifffile>=2023.3.21",
 ]
 miniscope = [
     "natsort>=8.3.1",
     "ndx-miniscope>=0.5.1",
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 sbx = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 scanimage = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
     "scanimage-tiff-reader>=1.4.1",
 ]
 sima = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 suite2p = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
 ]
 tdt_fp = [
     "ndx-fiber-photometry",
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.10",
     "tdt",
 ]
 tiff = [
-    "roiextractors>=0.5.7",
+    "roiextractors>=0.5.9",
     "tiffile>=2018.10.18",
 ]
 ophys = [

diff --git a/src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py b/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

diff --git a/src/neuroconv/datainterfaces/behavior/video/videodatainterface.py b/src/neuroconv/datainterfaces/behavior/video/videodatainterface.py
@@ -269,8 +269,6 @@ def add_to_nwbfile(
         chunk_data: bool = True,
         module_name: Optional[str] = None,
         module_description: Optional[str] = None,
-        compression: Optional[str] = "gzip",
-        compression_options: Optional[int] = None,
     ):
         """
         Convert the video data files to :py:class:`~pynwb.image.ImageSeries` and write them in the
@@ -431,17 +429,6 @@ def add_to_nwbfile(
                                 pbar.update(1)
                     iterable = video
 
-            # TODO: remove completely after 03/1/2024
-            if compression is not None or compression_options is not None:
-                warnings.warn(
-                    message=(
-                        "Specifying compression methods and their options for this interface has been deprecated. "
-                        "Please use the `configure_backend` tool function for this purpose."
-                    ),
-                    category=DeprecationWarning,
-                    stacklevel=2,
-                )
-
                 image_series_kwargs.update(data=iterable)
 
                 if timing_type == "starting_time and rate":

diff --git a/src/neuroconv/datainterfaces/ecephys/baselfpextractorinterface.py b/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,
         )
diff --git a/src/neuroconv/datainterfaces/ecephys/baserecordingextractorinterface.py b/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,

diff --git a/src/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py b/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()
@@ -146,7 +128,31 @@ def add_to_nwbfile(
         parent_container: Literal["acquisition", "processing/ophys"] = "acquisition",
         stub_test: bool = False,
         stub_frames: int = 100,
+        always_write_timestamps: bool = False,
     ):
+        """
+        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:
@@ -162,4 +168,5 @@ def add_to_nwbfile(
             photon_series_type=photon_series_type,
             photon_series_index=photon_series_index,
             parent_container=parent_container,
+            always_write_timestamps=always_write_timestamps,
         )
diff --git a/src/neuroconv/tools/neo/neo.py b/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)