Source code for roiextractors.extractors.memmapextractors.memmapextractors
"""Defines the base class for memmapable imaging extractors.
Classes
-------
MemmapImagingExtractor
The base class for memmapable imaging extractors.
"""
import warnings
import numpy as np
from ...imagingextractor import ImagingExtractor
[docs]
class MemmapImagingExtractor(ImagingExtractor):
"""Abstract class for memmapable imaging extractors."""
extractor_name = "MemmapImagingExtractor"
def __init__(
self,
video,
) -> None:
"""Create a MemmapImagingExtractor instance.
Parameters
----------
video: numpy.ndarray
The video data.
"""
self._video = video
super().__init__()
[docs]
def get_series(self, start_sample: int | None = None, end_sample: int | None = None) -> np.ndarray:
if start_sample is None:
start_sample = 0
if end_sample is None:
end_sample = self._num_samples
sample_indices = range(start_sample, end_sample)
# Use channel=None to preserve the channel dimension
return self._video.take(indices=list(sample_indices), axis=0)
[docs]
def get_image_shape(self) -> tuple[int, int]:
"""Get the shape of the video frame (num_rows, num_columns).
Returns
-------
image_shape: tuple
Shape of the video frame (num_rows, num_columns).
"""
return (self._num_rows, self._num_columns)
[docs]
def get_channel_names(self) -> list:
"""Return the channel names (deprecated)."""
warnings.warn(
"get_channel_names is deprecated and will be removed in or after October 2026.",
FutureWarning,
stacklevel=2,
)
return [f"channel_{i}" for i in range(self._num_channels)]
[docs]
def get_volume_shape(self) -> tuple[int, int, int, int]:
"""Return the shape of the video data.
Returns
-------
video_shape: tuple[int, int, int, int]
The shape of the video data (num_samples, num_rows, num_columns, num_channels).
"""
return (self._num_samples, self._num_rows, self._num_columns, self._num_channels)
[docs]
def get_native_timestamps(
self, start_sample: int | None = None, end_sample: int | None = None
) -> np.ndarray | None:
# Memory-mapped imaging data does not have native timestamps
return None