fpga

Illumina HiSeq 2500 System :: FPGA

The FPGA arms triggers for the TDI cameras. The FPGA also controls the z stage, objective stage, optics, LEDS, and stage temperature.

Commands from hackteria

Example:

#Create FPGA object
import pyseq
fpga = pyseq.fpga.FPGA('COM12','COM15')
#Initialize FPGA
fpga.initialize()
# Read write encoder position (to sync with y stage).
fpga.read_position()
0
fpga.write_position(0)
# Arm y stage triggers for TDI imgaging.
fpga.TDIYPOS(3000000)
fpga.TDIYPOS3(4096,3000000)
# Set LEDs to nightride mode (blue sweep)
fpga.led('A', 'sweep blue')
fpga.led('B', 'sweep blue')

Classes

FPGA(com_port_command, com_port_response[, …])

HiSeq 2500 System :: FPGA
class pyseq.fpga.FPGA(com_port_command, com_port_response, baudrate=115200, logger=None)

HiSeq 2500 System :: FPGA

Attributes

  • led_dict (dict): Dictionary of command options for different LED modes.

  • y_offset (int): FPGA offset of ystage position

  • logger (logger): Logger used for messaging

LED(AorB, mode, **kwargs)

Set front LEDs.

Parameters:

  • AorB (int/str): A or 1 for the left LED, B or 2 for the right LED.

  • mode (str): Color / mode to set the LED to, see list below.

  • kwargs: sweep (1-255): sweep rate

    pulse (1-255): pulse rate

Available Colors/Modes:

  • off

  • yellow

  • green

  • pulse green

  • blue

  • pulse blue

  • sweep blue

Returns:

  • bool: True if AorB and mode are valid, False if not.

TDIYARM3(n_triggers, y_pos)

Arm the y stage triggers for TDI imaging.

Parameters:

  • n_triggers (int): Number of triggers to send to the cameras.

  • y_pos (int): The initial y position of the image.

TDIYPOS(y_pos)

Set the y position for TDI imaging.

Parameters:

  • y_pos (int): The initial y position of the image.

command(text, instrument='FPGA')

Send commands to the FPGA and return the response.

Parameters:

  • text (str): A command to send to the FPGA.

  • instrument (str): Specify instrument (FPGA,OBJstage,Zstage,optics)

Returns:

  • str: The response from the FPGA.

initialize()

Initialize the FPGA.

read_position()

Read the y position of the encoder for TDI imaging.

Returns:

  • int: The y position of the encoder.

write_position(position)

Write the position of the y stage to the encoder.

Allows for a 5 step (50 nm) error.

Parameters:

  • position (int) = The position of the y stage.