Contents

• write_zen_tiles_experiment

  • class PositionWriter(object)

write_zen_tiles_experiment

Module which contains class PositionWriter(object), whose methods convert positions to stage coordinates and save the results.

class PositionWriter(object)

class microscope_automation.orchestrator.write_zen_tiles_experiment.PositionWriter(zsd, plate, production_path, testing_mode=False)

Converts positions to stage coordinates, saves positions to .czsh file

Requirements:

1) Ensure the dummy_tile_positions.czsh path is specified in preferences under key “PathDummy”

convert_to_stage_coords(offset_x=0, offset_y=0, positions_list=[], header=False)

Converts the distance of points from center of image to x-y coordinates in stage with 10 to 100x objective offsets.

Input:

offset_x: x_offset to account for in stage coordinate conversion

offset_y: y_offset to accoutn for in stage coordinate conversion

positions_list: center of well positions to convert to stage coordinates

header: boolean of whether positions_list includes a header. Skips the first row if True. Default: False

Output:

converted_list: stage coordinates of positions converted from center of well positions

get_next_pos_name(test_mode=False, test_file_names=[])

Find the next available letter label, but dont backfill files.

Input:

test_mode: False by default. Runs in test mode if True.

test_file_names: list of test file names to use if running in test mode

Output:

label: unused alphabetical label for new positions list

write(converted=[], dummy='', name_czsh='positions_output.czsh')

Writes coordinates to a dummy.czsh file, and saves it

Input:

converted: positions to write to the czsh file

dummy: empty (no coordinates) .czsh file to use for writing

name_czsh: name to save written .czsh file as

Output:

none