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MADSci 0.6 REST node tested and working, cleanup needed
1 parent bba3133 commit e5f8667

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Lines changed: 2439 additions & 285 deletions

‎pyproject.toml‎

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@@ -7,16 +7,17 @@ authors = [
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{name = "Doga Ozgulbas", email="dozgulbas@anl.gov"},
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{name = "Abe Stroka", email="astroka@anl.gov"},
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{name = "Tobias Ginsburg", email = "tginsburg@anl.gov"},
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{name = "Casey Stone", email = "cstone@anl.gov"},
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]
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dependencies = [
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"fastapi>=0.103",
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"uvicorn>=0.14.0",
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"pyusb",
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"libusb",
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"pyserial",
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"madsci-node-module~=0.5.0",
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"madsci-client~=0.5.0",
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"madsci-common~=0.5.0",
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"madsci-node-module~=0.6.0",
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"madsci-client~=0.6.0",
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"madsci-common~=0.6.0",
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"pydantic>=2.7",
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"pytest"
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]

‎src/default.node.yaml‎

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node_name: sciclops_node
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node_id: 01KMZZ7ESXANZZP024R2Y98TYP
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node_description: null
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node_type: device
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module_name: hudson_sciclops_node
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module_version: 0.0.1
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capabilities: null

‎src/resource_helpers/resource_types.py‎

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"""This module contains the Pydantic models for the PlateCrane resource types"""
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from typing import Optional
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from pydantic import BaseModel
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class PlateCraneLocation(BaseModel):
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"""A location accessible by the PlateCrane EX"""
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name: str
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"""Internal name of the location"""
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joint_angles: list[int]
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"""List of 4 joint angles (unit: integer stepper values)"""
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location_type: str
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"""Type of location, either stack or nest. This will be used to determine gripper path for interactions with the location"""
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safe_approach_height: Optional[int] = None
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"""A safe height (unit: integer stepper value for Z axis) from which
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to extend the arm when approaching this location."""
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class SciClopsLocation(BaseModel):
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"""A location accessible by the PlateCrane EX"""
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name: str
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"""Internal name of the location"""
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joint_angles: dict
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"""List of 4 joint angles (unit: integer stepper values)"""
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location_type: str
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"""Type of location, either stack or nest. This will be used to determine gripper path for interactions with the location"""
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safe_approach_height: Optional[float] = None
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"""A safe height (unit: integer stepper value for Z axis) from which
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to extend the arm when approaching this location."""
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class PlateResource(BaseModel):
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"""A plate resource that can be manipulated by the PlateCrane EX"""
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# Plate Properties
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plate_height: float
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"""The height measured from the bottom of the plate to the top"""
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grip_height: float
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"""The height at which to grip the plate, measured from the bottom of the plate"""
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plate_height_with_lid: Optional[float] = None
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"""The height of the plate when lidded, measured from the bottom of the plate to the top of the lid.
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Only required if the resource supports lids"""
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# Lid Properties
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lid_height: Optional[float] = None
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"""The height of the lid alone, measured from the bottom of the lid to the top of the lid"""
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lid_grip_height: Optional[float] = None
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"""The height at which to grip the lid itself, measured from the bottom of the lid"""
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lid_removal_grip_height: Optional[float] = None
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"""The height at which to grip the lid when removing it, measured from the bottom of the lidded plate"""
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@staticmethod
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def convert_to_steps(plate_measurement_in_mm: float) -> int:
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"""Converts plate measurements in mm to PlateCrane EX motor steps on the z-axis"""
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steps_per_mm = 80.5
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return int(plate_measurement_in_mm * steps_per_mm)

‎src/resource_helpers/sciclops_resource_defs.py‎

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"""Resource definitions for the platecrane in BIO 350."""
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from resource_helpers.resource_types import PlateResource, SciClopsLocation
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# Locations accessible by the PlateCrane EX. [R (base), Z (vertical axis), P (gripper rotation), Y (arm extension)]
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# Locations accessible by the SciClops. [Z (vertical axis), P (gripper rotation), Y (arm extension)]
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# NOTE: THIS IS NOT THE SAME ORDER AS THE PLATE CRANE!
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# NOTE: Running get location in the SciClops won't return the values in the right order!
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locations = {
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"Safe": SciClopsLocation(
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name="Safe",
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joint_angles={"Z": 23.5188, "R": 109.2741, "Y": 32.7484, "P": 98.2955},
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location_type="nest",
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safe_approach_height=0,
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),
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"Stack1": SciClopsLocation(
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name="Stack1",
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joint_angles={"Z": -397.1688, "R": 137.1106, "Y": 173.0127, "P": 9.6875},
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location_type="stack",
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safe_approach_height=0,
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),
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"Stack2": SciClopsLocation(
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name="Stack2",
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joint_angles={"Z": -397.2875, "R": 154.9712, "Y": 172.5352, "P": 9.6875},
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location_type="stack",
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safe_approach_height=0,
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),
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"LidNest1": SciClopsLocation(
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name="LidNest1",
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joint_angles={"Z": -386.8563, "R": 173.1300, "Y": 26.1751, "P": 10.3409},
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location_type="nest",
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safe_approach_height=0,
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),
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"Home": SciClopsLocation(
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name="Home",
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joint_angles={"Z": -1.0188, "R": 0.0, "Y": 0.0, "P": -0.0284},
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location_type="stack",
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safe_approach_height=0,
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),
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}
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# OLD PLATE DEFINITIONS
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# # Dictionary for plate information
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# locations = {
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# "stack1": {
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# "pos": {"Z": -397.1688, "R": 137.1106, "Y": 173.0127, "P": 9.6875},
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# "type": "stack",
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# },
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# "stack2": {
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# "pos": {"Z": -397.2875, "R": 154.9712, "Y": 172.5352, "P": 9.6875},
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# "type": "stack",
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# },
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# "stack3": {
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# "pos": {"Z": -397.3563, "R": 173.0506, "Y": 172.7398, "P": 9.6875},
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# "type": "stack",
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# },
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# "stack4": {
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# "pos": {"Z": -396.1000, "R": 191.1141, "Y": 172.4918, "P": 9.6875},
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# "type": "stack",
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# },
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# "stack5": {
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# "pos": {"Z": -394.4875, "R": 209.0771, "Y": 172.5104, "P": 9.6875},
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# "type": "stack",
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# },
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# "lidnest1": { # Z:-381.0938, R:173.1300, Y:26.1751, P:10.3409
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# # "pos": {"Z": -388.8563, "R": 172.8812, "Y": 26.9317, "P": 10.3409},
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# "pos": {"Z": -386.8563, "R": 173.1300, "Y": 26.1751, "P": 10.3409},
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# "type": "nest",
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# },
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# "lidnest2": { # Z:-379.2313, R:205.2971, Y:26.4480, P:10.2841
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# # "pos": {"Z": -388.4625, "R": 205.2900, "Y": 26.8139, "P": 10.2841},
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# "pos": {"Z": -386.8563, "R": 205.2971, "Y": 26.4480, "P": 10.2841},
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# "type": "nest",
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# },
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# "exchange": {
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# "pos": {"Z": -416.8438, "R": 299.8747, "Y": 153.6526, "P": 21.5057},
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# "type": "nest",
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# },
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# "neutral": {
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# "pos": {"Z": 23.5188, "R": 109.2741, "Y": 32.7484, "P": 98.2955},
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# "type": "point",
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# },
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# }
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# locations = {
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# "Safe": PlateCraneLocation(
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# name="Safe",
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# joint_angles=[182220, 2500, 460, -308],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Stack1": PlateCraneLocation( # After vibration table
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# name="Stack1",
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# joint_angles=[164713, -32703, 450, 5472],
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# location_type="stack",
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# safe_approach_height=0,
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# ),
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# "Stack2": PlateCraneLocation(
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# name="Stack2",
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# joint_angles=[182201, -32703, 486, 5445],
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# location_type="stack",
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# safe_approach_height=0,
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# ),
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# "Stack3": PlateCraneLocation(
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# name="Stack3",
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# joint_angles=[199696, -32703, 486, 5445],
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# location_type="stack",
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# safe_approach_height=0,
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# ),
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# "Stack4": PlateCraneLocation( # After vibration table
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# name="Stack4",
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# joint_angles=[217301, -32703, 486, 5445],
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# location_type="stack",
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# safe_approach_height=0,
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# ),
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# "Stack5": PlateCraneLocation( # After vibration table
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# name="Stack5",
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# joint_angles=[235004, -32703, 486, 5445],
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# location_type="stack",
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# safe_approach_height=0,
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# ),
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# "LidNest1": PlateCraneLocation( # After vibration table
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# name="LidNest1",
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# joint_angles=[168367, -31725, 470, -329],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "LidNest2": PlateCraneLocation(
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# name="LidNest2",
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# joint_angles=[199862, -31725, 462, -328],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "LidNest3": PlateCraneLocation(
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# name="LidNest3",
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# joint_angles=[231449, -31800, 484, -306],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Solo.Position1": PlateCraneLocation(
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# name="Solo.Position1",
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# joint_angles=[41665, -27455, -830, 5046],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Solo.Position2": PlateCraneLocation( # After vibration table
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# name="Solo.Position2",
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# joint_angles=[57372, -27457, -233, 2613],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Solo.Position2AfterPeeler": PlateCraneLocation( # no longer needed
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# name="Solo.Position2",
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# joint_angles=[53225, -27960, -431, 855],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Hidex.Nest": PlateCraneLocation( # After vibration table
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# name="Hidex.Nest",
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# joint_angles=[102406, -31090, -5901, 2373],
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# location_type="nest",
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# safe_approach_height=-27033,
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# ),
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# "Sealer.Nest": PlateCraneLocation( # After vibration table
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# name="Sealer.Nest",
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# joint_angles=[118212, -998, -4758, 4071],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Sealer.DeepWell.Nest": PlateCraneLocation( # After vibration table
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# name="Sealer.DeepWell.Nest",
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# joint_angles=[118212, -2498, -4758, 4071],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Peeler.Nest": PlateCraneLocation( # After vibration table
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# name="Peeler.Nest",
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# joint_angles=[302738, -30340, -4142, 2351],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# "Liconic.Nest": PlateCraneLocation( # After vibration table
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# name="Liconic.Nest",
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# joint_angles=[267724, -24666, -5357, 1591],
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# location_type="nest",
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# safe_approach_height=0,
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# ),
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# }
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# Dimensions of labware used on the BIO_Workcells
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plate_definitions = {
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"flat_bottom_96well": PlateResource(
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plate_height=14,
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grip_height=1,
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plate_height_with_lid=16,
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lid_height=10,
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lid_grip_height=4,
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lid_removal_grip_height=12,
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),
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"tip_box_180uL": PlateResource(
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plate_height=0,
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grip_height=0,
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plate_height_with_lid=0,
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lid_height=0,
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lid_grip_height=0,
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lid_removal_grip_height=0,
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),
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"pcr_96well": PlateResource(
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plate_height=0,
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grip_height=0,
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plate_height_with_lid=0,
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lid_height=0,
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lid_grip_height=0,
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lid_removal_grip_height=0,
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),
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"deep_96well": PlateResource(
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plate_height=40,
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grip_height=30,
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plate_height_with_lid=46,
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lid_height=9,
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lid_grip_height=4,
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lid_removal_grip_height=42,
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),
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}

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