hnccorr.utils module¶

Helper functions for HNCcorr.

hnccorr.utils.add_offset_set_coordinates(iterable, offset)[source]¶

Adds a fixed offset to all pixel coordinates in a set.

Parameters

coordinates (set) – Set of pixel coordinates. Each pixel coordinate is a tuple.
offset (tuple) – Offset to add to each pixel coordinate. Tuple should be of the same length as the tuples in coordinates.

Returns

Set of updated coordinates.

Return type

set

Example

>>> add_offset_set_coordinates({(5, 2), (4, 7)}, (2, 2))
{(7, 4), (6, 9)}

hnccorr.utils.add_offset_to_coordinate(coordinate, offset)[source]¶

Offsets pixel coordinate by another coordinate.

Parameters

coordinate (tuple) – Pixel coordinate to offset.
offset (tuple) – Offset to add to coordinate. Must be of the same length.

Example

>>> add_offset_to_coordinate((5, 3, 4), (1, -1, 3))
(6, 2, 7)

hnccorr.utils.add_time_index(index)[source]¶

Inserts a full slice as the first dimension of an index for e.g. numpy.

Parameters: index (tuple) – Index for e.g. numpy array.
Returns: New index with additional dimension.
Return type: tuple

Example

>>> add_time_index((5, :3))
(:, 5, :3)

hnccorr.utils.eight_neighborhood(num_dims, max_radius)[source]¶

Returns all coordinates within a given L-infinity distance of zero.

Includes zero coordinate itself.

Parameters

num_dims (int) – Number of dimensions for the coordinates.
max_radius (int) – Largest L-infinity distance allowed.

Returns

Set of pixel coordinates.

Return type

set

Example

>>> eight_neighborhood(1, 1)
[(-1,), (0,), (1,)]
>>> eight_neighborhood(2, 1)
[
    (-1, -1), (-1, 0), (-1, 1), (0, -1), (0, 0),
    (0, 1), (1, -1), (1, 0), (1, 1)
]

hnccorr.utils.four_neighborhood(num_dims)[source]¶

Returns all neighboring pixels of zero that differ in at most one coordinate.

Includes zero coordinate itself.

Parameters: num_dims (int) – Number of dimensions for the coordinates.
Returns: Set of pixel coordinates.
Return type: set

Example

>>> four_neighborhood(1)
[(-1,), (0,), (1,)]
>>> eight_neighborhood(2)
[(-1, 0), (0, -1), (0, 0), (0, 1), (1, 0)]

hnccorr.utils.generate_pixels(shape)[source]¶

Enumerate all pixel coordinates for a movie/patch.

Parameters: shape (tuple) – Shape of movie. Number of pixels in each dimension.
Returns: Iterates over all pixels.
Return type: Iterator

Example

>>> generate_pixels((2,2))
[(0, 0), (0, 1), (1, 0), (1, 1)]

hnccorr.utils.list_images(folder)[source]¶

Lists and sorts tiff images in a folder.

Images are sorted in ascending order based on filename.

Caution

Filenames are sorted as strings. Note that 200.tiff is sorted before 5.tiff. Pad image filenames with zeros to prevent this: 005.tiff.

Parameters: folder – folder containing tiff image files.
Returns: Sorted list of paths of tiff files in folder.
Return type: list