roiextractors.extractors.suite2p package

Submodules

roiextractors.extractors.suite2p.suite2psegmentationextractor module

A segmentation extractor for Suite2p.

Classes

Suite2pSegmentationExtractor

A segmentation extractor for Suite2p.

class Suite2pSegmentationExtractor(folder_path: str | Path, channel_name: str | None = None, plane_name: str | None = None, combined: bool | None = None, plane_no: int | None = None)

Bases: SegmentationExtractor

A segmentation extractor for Suite2p.

Create SegmentationExtractor object out of suite 2p data type.

Parameters:

• folder_path (str or Path) – The path to the ‘suite2p’ folder.

• channel_name (str, optional) – The name of the channel to load, to determine what channels are available use Suite2pSegmentationExtractor.get_available_channels(folder_path).

• plane_name (str, optional) – The name of the plane to load, to determine what planes are available use Suite2pSegmentationExtractor.get_available_planes(folder_path).

extractor_name = 'Suite2pSegmentationExtractor'

installed = True

is_writable = False

mode = 'folder'

installation_mesg = ''

classmethod get_available_channels(folder_path: str | Path)

Get the available channel names from the folder paths produced by Suite2p.

Parameters:

folder_path (PathType) – Path to Suite2p output path.

Returns:

channel_names – List of channel names.

Return type:

list

classmethod get_available_planes(folder_path: str | Path)

Get the available plane names from the folder produced by Suite2p.

Parameters:

file_path (PathType) – Path to Suite2p output path.

Returns:

plane_names – List of plane names.

Return type:

list

_load_npy(file_name: str, mmap_mode=None, transpose: bool = False)

Load a .npy file with specified filename. Returns None if file is missing.

Parameters:

• file_name (str) – The name of the .npy file to load.

• mmap_mode (str) – The mode to use for memory mapping. See numpy.load for details.

• transpose (bool, optional) – Whether to transpose the loaded array.

Return type:

The loaded .npy file.

get_num_frames() → int

Get the number of frames in the recording (duration of recording).

Returns:

num_frames – Number of frames in the recording.

Return type:

int

get_accepted_list()

Get a list of accepted ROI ids.

Returns:

accepted_list – List of accepted ROI ids.

Return type:

list

get_rejected_list()

Get a list of rejected ROI ids.

Returns:

rejected_list – List of rejected ROI ids.

Return type:

list

_correlation_image_read()

Read correlation image from ops (settings) dict.

Returns:

img – The correlation image.

Return type:

numpy.ndarray | None

property roi_locations

Returns the center locations (x, y) of each ROI.

get_roi_pixel_masks(roi_ids=None)

Get the weights applied to each of the pixels of the mask.

Parameters:

roi_ids (array_like) – A list or 1D array of ids of the ROIs. Length is the number of ROIs requested.

Returns:

pixel_masks – List of length number of rois, each element is a 2-D array with shape (number_of_non_zero_pixels, 3). Columns 1 and 2 are the x and y coordinates of the pixel, while the third column represents the weight of the pixel.

Return type:

list

get_image_size()

Get frame size of movie (height, width).

Returns:

no_rois – 2-D array: image height x image width

Return type:

array_like

_abc_impl = <_abc._abc_data object>

static write_segmentation(segmentation_object: SegmentationExtractor, save_path: str | Path, overwrite=True)

Write a SegmentationExtractor to a folder specified by save_path.

Parameters:

• segmentation_object (SegmentationExtractor) – The SegmentationExtractor object to be written.

• save_path (str or Path) – The folder path where to write the segmentation.

• overwrite (bool) – If True, overwrite the folder if it already exists.

Raises:

• AssertionError – If save_path is not a folder.

• FileExistsError – If the folder already exists and overwrite is False.

Notes

The folder structure is as follows: save_path └── plane<plane_num>

├── F.npy ├── Fneu.npy ├── spks.npy ├── stat.npy ├── iscell.npy └── ops.npy

Module contents

A segmentation extractor for Suite2p.

Modules

suite2psegmentationextractor

A segmentation extractor for Suite2p.

Classes

Suite2pSegmentationExtractor

A segmentation extractor for Suite2p.