Contents

• positions_list

  • class CreateTilePositions(object)

positions_list

This module contains just one class, which is used in the samples module to create a list of positions for tiling images.

class CreateTilePositions(object)

class microscope_automation.samples.positions_list.CreateTilePositions(tile_type='none', tile_number=(2, 2), tile_size=(1, 1), degrees=0)

Create position lists for tiling and multi-position imaging.

create_ellipse(nx, ny)

Return positions for ellipse with step size of one.

Input:

nx, ny: number of tiles in x and y

Output:

ellipse_list: list for rectangle positions, centered around zero and with step size of one

create_rectangle(nx, ny)

Return positions for rectangle with step size of one.

Input:

nx, ny: number of tiles in x and y

Output:

rect_list: list for rectangle positions, centered around zero and with step size of one

get_field_rotation()

Set size of tiles in x and y.

Input:

none

Output:

degrees: Angle the tile field is rotated counterclockwise in degrees

get_pos_list(center=(0, 0, 0))

Return list with positions.

Input:

center: Center position for tiles as tuple (x, y, z)

Output:

pos_list: list with tuples (x,y) for tile centers.

get_tile_number()

Return number of tiles in x and y.

Input:

none

Output:

tile_number: tuple with number of tiles in x and y direction

get_tile_size()

Retrieve size of tiles in x and y.

Input:

none

Output:

tile_size: tuple with size of tiles in x and y direction

get_tile_type()

Return type of tiling.

Input:

none

Output:

tile_type: string to describe type of tiling. Allowed values:

‘none’: do not tile

‘rectangle’: tiles are arranged to form a rectangle

‘ellipse’: tiles are arranged to form an ellipse

rotate_pos_list(pos_list, degrees)

Rotate all coordinates in pos_list counterclockwise by angle degree around center = (0, 0, 0).

Input:

pos_list: list with (x, y, z) coordinates

degrees: amount of counterclock rotation around origin in degree

Output:

rot_list: list with (x, y, z) coordinates after rotation.

set_field_rotation(degrees=0)

Set size of tiles in x and y.

Input:

degrees: Angle the tile field is rotated counterclockwise in degrees

Output:

none

set_tile_number(tile_number=(2, 2))

Set number of tiles in x and y.

Input:

tile_number: tuple with number of tiles in x and y direction

Output:

none

set_tile_size(tile_size=(1, 1))

Set size of tiles in x and y.

Input:

tile_size: tuple with size of tiles in x and y direction

Output:

none

set_tile_type(tile_type='none')

Set type of tiling.

Input:

tile_type: string to describe type of tiling. Allowed values:

‘none’: do not tile

‘rectangle’: tiles are arranged to form a rectangle

‘ellipse’: tiles are arranged to form an ellipse

Output:

none

show(center=(0, 0, 0))

Display positions.

Input:

center: Center position for tiles

Output:

none