@opentrons/shared-data 0.0.0-alpha.2

package/python/opentrons_shared_data/pipette/scripts/build_json_script.py

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+import argparse
+import csv
+import json
+from ast import literal_eval
+from typing import Optional, Dict, Union, Any, List
+from pathlib import Path
+from pydantic import BaseModel
+import math
+
+from ... import get_shared_data_root
+from ..pipette_definition import (
+    PipetteGeometryDefinition,
+    PipetteLiquidPropertiesDefinition,
+    PipettePhysicalPropertiesDefinition,
+    PlungerPositions,
+    SupportedTipsDefinition,
+    MotorConfigurations,
+    PartialTipDefinition,
+    AvailableSensorDefinition,
+    PickUpTipConfigurations,
+    PressFitPickUpTipConfiguration,
+    DropTipConfigurations,
+    PlungerEjectDropTipConfiguration,
+)
+
+from ..dev_types import PipetteModelSpec
+
+
+PIPETTE_DEFINITION_ROOT = Path("pipette") / "definitions" / "2"
+GEOMETRY_ROOT = get_shared_data_root() / PIPETTE_DEFINITION_ROOT / "geometry"
+GENERAL_ROOT = get_shared_data_root() / PIPETTE_DEFINITION_ROOT / "general"
+LIQUID_ROOT = get_shared_data_root() / PIPETTE_DEFINITION_ROOT / "liquid"
+
+GENERAL_SCHEMA = "#/pipette/schemas/2/pipettePropertiesSchema.json"
+LIQUID_SCHEMA = "#/pipette/schemas/2/pipetteLiquidPropertiesSchema.json"
+GEOMETRY_SCHEMA = "#/pipette/schemas/2/pipetteGeometryPropertiesSchema.json"
+
+
+def _build_pickup_tip_data(
+    model_configurations: Optional[PipetteModelSpec] = None,
+) -> PickUpTipConfigurations:
+    presses = 0
+    increment = 0
+    distance = 0.0
+    if model_configurations:
+        current = model_configurations["pickUpCurrent"]["value"]
+        speed = model_configurations["pickUpSpeed"]["value"]
+        presses = model_configurations["pickUpPresses"]["value"]
+        increment = int(model_configurations["pickUpIncrement"]["value"])
+        distance = model_configurations["pickUpDistance"]["value"]
+    else:
+        print("Handling pick up tip configurations\n")
+        speed = float(input("please provide the speed\n"))
+        presses = int(input("please provide the number of presses for force pick up\n"))
+        increment = int(
+            input(
+                "please provide the increment to move the pipette down for force pickup\n"
+            )
+        )
+        distance = float(
+            input("please provide the starting distance for pick up tip\n")
+        )
+    print(f"TODO: Current {current} is not used yet")
+    return PickUpTipConfigurations(
+        pressFit=PressFitPickUpTipConfiguration(
+            speed=speed,
+            presses=presses,
+            increment=increment,
+            distance=distance,
+            currentByTipCount={},
+        )
+    )
+
+
+def _build_drop_tip_data(
+    model_configurations: Optional[PipetteModelSpec] = None,
+) -> DropTipConfigurations:
+    if model_configurations:
+        current = model_configurations["dropTipCurrent"]["value"]
+        speed = model_configurations["dropTipSpeed"]["value"]
+    else:
+        print("Handling drop tip configurations\n")
+        speed = float(input("please provide the speed\n"))
+    return DropTipConfigurations(
+        plungerEject=PlungerEjectDropTipConfiguration(
+            current=current,
+            speed=speed,
+        )
+    )
+
+
+def _build_plunger_positions(
+    model_configurations: Optional[PipetteModelSpec] = None,
+) -> PlungerPositions:
+    if model_configurations:
+        top = model_configurations["top"]["value"]
+        bottom = model_configurations["bottom"]["value"]
+        blow_out = model_configurations["blowout"]["value"]
+        drop_tip = model_configurations["dropTip"]["value"]
+    else:
+        print("Handling plunger motor positions\n")
+        top = float(input("Please provide the top plunger position\n"))
+        bottom = float(input("Please provide the bottom plunger position\n"))
+        blow_out = float(input("Please provide the blow out plunger position\n"))
+        drop_tip = float(input("Please provide the drop tip plunger position\n"))
+    return PlungerPositions(top=top, bottom=bottom, blowout=blow_out, drop=drop_tip)
+
+
+def _build_motor_configurations(
+    model_configurations: Optional[PipetteModelSpec] = None,
+) -> MotorConfigurations:
+    if model_configurations:
+        run = model_configurations["plungerCurrent"]["value"]
+        idle = model_configurations.get("idleCurrent", run)
+    else:
+        print("Handling default plunger motor currents\n")
+        idle = float(
+            input("Please provide the default idle current of the plunger motor\n")
+        )
+        run = float(
+            input("Please provide the default run current of the plunger motor\n")
+        )
+    return MotorConfigurations(idle=idle, run=run)
+
+
+def _build_partial_tip_configurations(channels: int) -> PartialTipDefinition:
+    if channels == 8:
+        return PartialTipDefinition(
+            partialTipSupported=True, availableConfigurations=[1, 2, 3, 4, 5, 6, 7, 8]
+        )
+    elif channels == 96:
+        return PartialTipDefinition(
+            partialTipSupported=True, availableConfigurations=[1, 8, 12, 96]
+        )
+    else:
+        return PartialTipDefinition(partialTipSupported=False)
+
+
+def build_geometry_model_v2(
+    input_dictionary: Dict[str, Any]
+) -> PipetteGeometryDefinition:
+    return PipetteGeometryDefinition.parse_obj(input_dictionary)
+
+
+def build_liquid_model_v2(
+    input_dictionary: Dict[str, Any],
+    supported_tip_configurations: Dict[str, SupportedTipsDefinition],
+) -> PipetteLiquidPropertiesDefinition:
+    if input_dictionary:
+        if input_dictionary.get("partialTipConfigurations"):
+            return PipetteLiquidPropertiesDefinition.parse_obj(
+                {**input_dictionary, "supportedTips": supported_tip_configurations}
+            )
+        else:
+            return PipetteLiquidPropertiesDefinition.parse_obj(
+                {
+                    **input_dictionary,
+                    "supportedTips": supported_tip_configurations,
+                }
+            )
+    max_volume = int(input("please provide the max volume of the pipette\n"))
+    min_volume = float(input("please provide the min volume of the pipette\n"))
+    default_tipracks = input(
+        "please input the load names of default tipracks separated by commas\n"
+    )
+    list_default_tipracks = default_tipracks.split(",")
+    return PipetteLiquidPropertiesDefinition.parse_obj(
+        {
+            "supportedTips": supported_tip_configurations,
+            "maxVolume": max_volume,
+            "minVolume": min_volume,
+            "defaultTipracks": list_default_tipracks,
+        }
+    )
+
+
+def build_physical_model_v2(
+    input_dictionary: Optional[Dict[str, Any]], pipette_type: Optional[str] = None
+) -> PipettePhysicalPropertiesDefinition:
+    if input_dictionary:
+        available_sensors = AvailableSensorDefinition(
+            sensors=input_dictionary.pop("availableSensors", [])
+        )
+        back_compat_names = input_dictionary.pop("backCompatNames", [])
+        return PipettePhysicalPropertiesDefinition.parse_obj(
+            {
+                **input_dictionary,
+                "availableSensors": available_sensors,
+                "backCompatNames": back_compat_names,
+            }
+        )
+    print(f"Handling general pipette information for {pipette_type}\n")
+    display_name = input("please provide the product name of the pipette\n")
+
+    display_category = input("please provide the model generation of the pipette\n")
+    input_available_sensors = input(
+        "Please provide a list of available sensors, separated by comma\n"
+    )
+    channels = input(f"Please provide the number of channels your {pipette_type} has\n")
+    shaft_diam = float(input(f"Please provide the shaft diameter of {pipette_type}\n"))
+    shaft_ul_per_mm = float(
+        input(f"Please provide the uL to mm conversion for {pipette_type}\n")
+    )
+    pick_up_tip_configurations = _build_pickup_tip_data()
+    drop_tip_configurations = _build_drop_tip_data()
+    plunger_positions = _build_plunger_positions()
+    plunger_motor_configurations = _build_motor_configurations()
+    partial_tip_configurations = _build_partial_tip_configurations(int(channels))
+
+    back_compat_names_str = input(
+        "Please list compatible pipette names separated by commas or hit enter if none"
+    )
+    if back_compat_names_str:
+        back_compat_names = [i.strip() for i in back_compat_names_str.split(",")]
+    else:
+        back_compat_names = []
+    return PipettePhysicalPropertiesDefinition.parse_obj(
+        {
+            "displayName": display_name,
+            "model": pipette_type,
+            "displayCategory": display_category,
+            "pickUpTipConfigurations": pick_up_tip_configurations,
+            "dropTipConfigurations": drop_tip_configurations,
+            "plungerMotorConfigurations": plunger_motor_configurations,
+            "plungerPositionsConfigurations": plunger_positions,
+            "availableSensors": AvailableSensorDefinition(
+                sensors=input_available_sensors.split(",")
+            ),
+            "partialTipConfigurations": partial_tip_configurations,
+            "channels": channels,
+            "shaftDiameter": shaft_diam,
+            "shaftULperMM": shaft_ul_per_mm,
+            "backCompatNames": back_compat_names,
+        }
+    )
+
+
+def build_supported_tips(input_dictionary: Dict[str, Any]) -> SupportedTipsDefinition:
+    return SupportedTipsDefinition.parse_obj(input_dictionary)
+
+
+def save_to_file(
+    directorypath: Path,
+    file_name: str,
+    data: Union[BaseModel, Dict[str, Any]],
+    schema_path: str,
+) -> None:
+    """
+    Function used to save data to a file
+    """
+
+    directorypath.mkdir(parents=True, exist_ok=True)
+    filepath = directorypath / f"{file_name}.json"
+    if isinstance(data, BaseModel):
+        # We have to rely on the json serialization of the
+        # pydantic model to properly convert special objects
+        # such as (pipetteModelType) to a string. However,
+        # we also want to add in a new key on top of the
+        # data in the pydantic model so we need to convert it
+        # back to a dictionary before saving to file.
+        json_basemodel = data.json(by_alias=True)
+        dict_basemodel = json.loads(json_basemodel)
+        dict_basemodel["$otSharedSchema"] = schema_path
+        filepath.write_text(
+            json.dumps(dict_basemodel, ensure_ascii=False), encoding="utf-8"
+        )
+    else:
+        data["$otSharedSchema"] = schema_path
+        filepath.write_text(json.dumps(data, ensure_ascii=False), encoding="utf-8")
+
+
+def migrate_new_blow_out_configs_v2() -> None:
+    pipette_volumes = {
+        1: ["p10", "p50", "p300", "p1000"],
+        2: ["p20", "p300", "p1000"],
+        3: ["p50", "p1000"],
+    }
+
+    for pipette_gen in range(1, 4):  # gen 1, gen 2, gen 3
+        print(f"\nTaking data for gen{pipette_gen} pipettes:")
+        # overwrite and pass in dict with user input for each gen
+        shaft_diameters = {
+            vol: float(input(f"Enter shaft diameter for gen{pipette_gen} {vol}: "))
+            for vol in pipette_volumes[pipette_gen]
+        }
+        fill_blowout_configs(pipette_gen, shaft_diameters, pipette_volumes[pipette_gen])
+
+
+def fill_blowout_configs(
+    pipette_gen: int, shaft_diameters: Dict[str, float], volumes: List[str]
+) -> None:
+
+    general_config_files = Path(GENERAL_ROOT).glob("*")
+    for pipette_type in general_config_files:  # single, eight, 96-channel
+        for volume in volumes:  # pipette max volume- p10, p20, p50, etc.
+            shaft_diameter = shaft_diameters[volume]
+            # calculate uL per mm, default blowout vol
+            ul_per_mm = math.pi * (shaft_diameter / 2) ** 2
+            # get path for every file version for the pipette gen at hand
+            volume_path = Path(pipette_type / volume)
+            for general_file_version in volume_path.glob(f"{str(pipette_gen)}_*.json"):
+                with open(general_file_version, "r") as file:
+                    general_config_dict = json.load(file)
+                general_config_dict["shaftDiameter"] = round(shaft_diameter, 3)
+                general_config_dict["shaftULperMM"] = round(ul_per_mm, 3)
+
+                # get file path to pass into save_to_file
+                gen_path = GENERAL_ROOT / pipette_type / volume
+                version_str = str(general_file_version).split("/")[-1][:-5]
+                save_to_file(gen_path, version_str, general_config_dict, GENERAL_SCHEMA)
+
+
+def build_new_pipette_model_v2(
+    pipette_functions_dict: Dict[str, Any], pipette_model_csv: str
+) -> None:
+    """
+    Build a brand new pipette model from user inputted data.
+    """
+    top_level_pipette_model = {}
+    with open(pipette_model_csv, "r") as f:
+        reader = csv.reader(f)
+        current_key = None
+        for row in reader:
+            if row[0]:
+                current_key = row[0]
+                top_level_pipette_model[current_key] = {row[1]: literal_eval(row[2])}
+            elif current_key:
+                top_level_pipette_model[current_key][row[1]] = literal_eval(row[2])
+            else:
+                continue
+    geometry_model = build_geometry_model_v2(top_level_pipette_model["geometry"])
+    liquid_model = build_liquid_model_v2(
+        top_level_pipette_model["liquid"],
+        pipette_functions_dict,
+    )
+    liquid_model_dict = liquid_model.dict(by_alias=True)
+    liquid_model_dict["supportedTips"] = {
+        k.name: v for k, v in liquid_model_dict["supportedTips"].items()
+    }
+    pipette_type = f"p{liquid_model.max_volume}"
+    physical_model = build_physical_model_v2(
+        {
+            **top_level_pipette_model["general"],
+            "plungerMotorConfigurations": top_level_pipette_model[
+                "plungerMotorConfigurations"
+            ],
+            "plungerPositionsConfigurations": top_level_pipette_model[
+                "plungerPositionsConfigurations"
+            ],
+            "pickUpTipConfigurations": top_level_pipette_model[
+                "pickUpTipConfigurations"
+            ],
+            "dropTipConfigurations": top_level_pipette_model["dropTipConfigurations"],
+            "partialTipConfigurations": _build_partial_tip_configurations(
+                top_level_pipette_model["general"]["channels"]
+            ),
+        },
+        pipette_type,
+    )
+
+    major_version = input("please provide the major version of this pipette model\n")
+    minor_version = input("please provide the minor version of this pipette model\n")
+
+    file_name = f"{major_version}_{minor_version}"
+    current_pipette_path = Path(physical_model.channels.name.lower()) / pipette_type
+
+    save_to_file(
+        GEOMETRY_ROOT / current_pipette_path, file_name, geometry_model, GEOMETRY_SCHEMA
+    )
+    save_to_file(
+        GENERAL_ROOT / current_pipette_path, file_name, physical_model, GENERAL_SCHEMA
+    )
+    save_to_file(
+        LIQUID_ROOT / current_pipette_path, file_name, liquid_model_dict, LIQUID_SCHEMA
+    )
+
+
+def main() -> None:
+    """Entry point."""
+    parser = argparse.ArgumentParser(
+        description="96 channel tip handling testing script."
+    )
+    parser.add_argument(
+        "--path_to_pipette_model",
+        type=str,
+        help="the csv filled with data to build a pipette model",
+        default=None,
+    )
+    parser.add_argument(
+        "--migrate_blowout_configs",
+        type=bool,
+        help="If true, migrate new blowout configs to existing json files",
+        default=False,
+    )
+
+    args = parser.parse_args()
+    if args.migrate_blowout_configs:
+        migrate_new_blow_out_configs_v2()
+    else:
+        using_csv = "" if args.path_to_pipette_model else "out"
+        print(f"Building new pipette function with{using_csv} using csv")
+
+        next_tip = True
+        pipette_functions_dict: Dict[str, Any] = {}
+        while next_tip:
+            print("Preparing pipetting function table from csv\n")
+            tip_volume = input("Please provide the next tip volume\n")
+            tiprack = input(
+                "Please provide the tiprack/tip type associated with this data\n"
+            )
+            path_to_data = input("Please provide the data path to the csv\n")
+            csv_dict = pipette_functions_dict.get(f"t{tip_volume}", {})
+            with open(path_to_data, "r") as f:
+                reader = csv.reader(f)
+                pipetting_key = None
+                for row in reader:
+                    current_key_exists = csv_dict.get(row[0])
+                    if row[0] == "aspirate" or row[0] == "dispense":
+                        pipetting_key = row[0]
+                        if current_key_exists:
+                            csv_dict[pipetting_key][f"{tiprack}"].append(
+                                [float(row[1]), float(row[2]), float(row[3])]
+                            )
+                        else:
+                            csv_dict[pipetting_key] = {
+                                f"{tiprack}": [
+                                    [float(row[1]), float(row[2]), float(row[3])]
+                                ]
+                            }
+                    elif pipetting_key and not row[0]:
+                        csv_dict[pipetting_key][f"{tiprack}"].append(
+                            [float(row[1]), float(row[2]), float(row[3])]
+                        )
+                    else:
+                        pipetting_key = None
+                        if current_key_exists:
+                            continue
+                        csv_dict[row[0]] = row[1]
+            pipette_functions_dict[f"t{tip_volume}"] = csv_dict
+            cont = input("Additional tips? Please enter y/n")
+
+            next_tip = cont == "y" or cont == "yes"
+        converted_pipette_functions_dict = {
+            k: build_supported_tips(d) for k, d in pipette_functions_dict.items()
+        }
+
+        print(
+            "Please review the aspirate and dispense functions once the pipette model is built.\n"
+        )
+        build_new_pipette_model_v2(
+            converted_pipette_functions_dict, args.path_to_pipette_model
+        )
+
+
+if __name__ == "__main__":
+    """
+    A script to automate building a pipette configuration definition.
+
+    This script can either perform migrations from a v1 -> v2 schema format
+    or build a brand new script from scratch.
+
+    When building a new pipette configuration model, you will either need
+    to provide CSVs or use command line inputs.
+
+    If you choose CSVs you will need one CSV for the general pipette configuration
+    data (such as pipette model or number of channels) and one for every tip
+    type that this pipette model can support.
+    """
+    main()