Getting Started with PyHamilton

Stefan · January 17, 2023, 8:36pm

Oh shoot! Thanks!

TechsupportCLS · December 13, 2023, 5:16pm

Hi!

I’m excited to try Pyhamilton, but I am having some trouble getting started. I’m running this in simulation on my PC to get it working before I try to use it connected to a Hamilton. The script runs, and opens Run control, but it fails while analyzing the method due to “syntax errors: 0x23 0x2 0x35”. I’ve had this error previously, when I was first installing Hamilton and it came down to not having the correct Hamilton libraries installed. In this case, I can see that the library is installed. Has anyone else encountered this issue?

Thank you, any help would be appreciated.

Stefan · December 13, 2023, 10:38pm

Did you run pyhamilton-configure and proceed with all the executables? One thing you can check is whether you can run a test Venus method that just imports the HTTP library and runs some HTTP functions as a test. If that doesn’t work, this is a Venus issue.

Check out the library downloads thread and see if there’s an HTTP installer in there that works. If not, tag one of the Hamilton folks and ask for an updated installer for your combination of Windows and Venus versions.

Thanks for trying PyHamilton! Let me know if there’s anything else I can do to help you get started.

TechsupportCLS · December 14, 2023, 10:09pm

I did start with pyahmilton-configure. As far as I can tell, everything installed.

I will try running a test method to import the HTTP library, thank you!

TechsupportCLS · January 3, 2024, 11:23pm

I had to get IT to give me permission to install the library, but I finally did and it worked. I’m so excited to try this out. Now I can finally get started.

Thank you so much!

partyparrot · January 24, 2024, 11:23pm

Trying to get PyHamilton to work and whenever I run the default ‘robot_method.py’ file that was auto-created, I am getting some JSON errors (‘Class not registered’, ‘Bad argument’), but then it repeatedly sends back a ‘response status code: 200’ in the trace file and hangs.

Anyone else experience this? How do I move forward from this?
I have made sure that the JSON library was downloaded correctly in the Library folder.
Thanks!

Stefan · January 25, 2024, 3:10am

Did you run pyhamilton-configure and accept all the prompts? This is a sign that the JSON library didn’t install correctly.

Check out this post with a link to an installer known to fix this issue: Library Downloads? (Requests) - #141 by DanHartman_Hamilton

partyparrot · January 29, 2024, 5:32pm

I did! However, I am running VENUS 6 and getting the updated HSL Json Library from the link you provided fixed my issue. Thank you!

partyparrot · January 30, 2024, 9:02pm

Is there a way to programmatically create a deck layout file without using VENUS?

Stefan · January 30, 2024, 9:05pm

I’ve been slowly working on something that allows you to do programmatic deck generation in PyLabRobot and import this into Venus, if it’s something you’re interested in maybe I can go a little faster lol. You do ultimately have to use Venus though (or use PLR instead).

RobertR · February 15, 2024, 4:34pm

Hi not sure if this is the correct place for this question. Nor do I know if this question is answered by the docs, I ahve looked and I havent seen anything obvious.

However, how does one use CORE grippers to move plates?
Are their code exampels on how to use these grippers as well as how to use HHS?

i am excited to learn more and would appreciate it if someone can point me to more information.

Stefan · February 15, 2024, 4:44pm

Check out liquid_handling_wrappers.py

All the “gripper” functions are for the CO-RE grippers

def get_plate_gripper_seq(ham, source_plate_seq,  gripHeight, gripWidth, openWidth, lid, tool_sequence, **more_options):
    logging.info('get_plate: Getting plate ' + source_plate_seq )
    
    if lid:
        cid = ham.send_command(GRIP_GET, plateSequence=source_plate_seq, transportMode=1, gripHeight=gripHeight, gripWidth=gripWidth, widthBefore=openWidth, toolSequence=tool_sequence)
    else:
        cid = ham.send_command(GRIP_GET, plateSequence=source_plate_seq, transportMode=0, gripHeight=gripHeight, gripWidth=gripWidth, widthBefore=openWidth, toolSequence=tool_sequence)
    ham.wait_on_response(cid, raise_first_exception=True, timeout=120)

def move_plate_gripper_seq(ham, dest_plate_seq, **more_options):
    logging.info('move_plate: Moving plate ' + dest_plate_seq)
    cid = ham.send_command(GRIP_MOVE, plateSequence=dest_plate_seq)
    ham.wait_on_response(cid, raise_first_exception=True, timeout=120)
    
def place_plate_gripper_seq(ham, dest_plate_seq, tool_sequence, **more_options):
    logging.info('place_plate: Placing plate ' + dest_plate_seq )
    cid = ham.send_command(GRIP_PLACE, plateSequence=dest_plate_seq, toolSequence=tool_sequence)
    ham.wait_on_response(cid, raise_first_exception=True, timeout=120)

def move_plate_gripper(ham, dest_poss, **more_options):
    labware_poss = compound_pos_str(dest_poss)
    #logging.info('move_plate: Moving plate ' + dest_plate_seq)
    cid = ham.send_command(GRIP_MOVE, plateLabwarePositions=labware_poss, **more_options)
    ham.wait_on_response(cid, raise_first_exception=True, timeout=120)

RobertR · February 16, 2024, 7:57am

Excellent, thanks for your quick response and pointing me in the right direction.

Nikolay · March 1, 2024, 10:38am

Hi @Stefan
thank you for developing pyHamilton. It looks great and I’m keen to use it but have a number of questions - from general script behaviour to specific equipment integration. Is there any guidance on how to structure questions / where to post them within PyHamilton section?

I feel that some may have already been covered but at the technical level which I struggle to comprehend (e.g. sections Extending the API, references to wrappers etc). I’d imagine the problem is not unique to me I’m interested in understanding this properly and making a ‘dummies’ guide to share with the community and enhance the outreach. Is this something you could support?

samiraoudjane · May 7, 2024, 2:23pm

@Stefan

thanks for this write up. where is liquid_handling_wrappers.py? i am also interested in using the core grippers with pyhamilton

Stefan · May 7, 2024, 3:05pm

github.com

dgretton/pyhamilton/blob/master/pyhamilton/liquid_handling_wrappers.py

# -*- coding: utf-8 -*-
"""
Created on Wed Mar  9 12:01:01 2022

@author: stefa
@author: yang
"""

import sys, os, time, logging, importlib
from threading import Thread

from .interface import HamiltonInterface
from .deckresource import LayoutManager, ResourceType, Plate24, Plate96, Tip96
from .oemerr import PositionError
from .interface import (INITIALIZE, PICKUP, EJECT, ASPIRATE, DISPENSE, ISWAP_GET, ISWAP_PLACE, HEPA,
WASH96_EMPTY, PICKUP96, EJECT96, ASPIRATE96, DISPENSE96, ISWAP_MOVE, MOVE_SEQ, TILT_INIT, TILT_MOVE, GRIP_GET,
GRIP_MOVE, GRIP_PLACE, SET_ASP_PARAM, SET_DISP_PARAM)
from .liquid_class_dict import liquidclass_params_asp, liquidclass_params_dsp

def resource_list_with_prefix(layout_manager, prefix, res_class, num_ress, order_key=None, reverse=False):

This file has been truncated. show original

bryank · October 18, 2024, 10:30pm

Sorry not very familiar with the HSL editor. How is this done, assuming the prior step is already completed where you added new sub-method to STAR_OEM_toolkit.smt. Thanks!

bryank · October 18, 2024, 11:23pm

Looks like there are 2 STAR_OEM_toolkit.smt files, one in the star-oem folder and one in the star-oem/VENUS_Method folder. I added custom function to wrong one

cbcbcbc · October 27, 2024, 5:35pm

Having issues installing this on a new instrument. On running pyhamilton-configure it successfully ran the installers for json, http, ph, centrifuge, but an unnamed installer is failing with a prompt to check with the vendor that it’s a valid installer. Lots of undeclared identifier errors when I try to make a test method having to do with HSLMPElib. Any suggestions?

Stefan · October 27, 2024, 5:50pm

Check out Library Downloads (Links) in case there is an updated version of the MPE installer that works. If not, let Hamilton know along with the version of Venus you are running and what kind of robot you have.

If you don’t have an MPE you can also delete that import from the universal method.