opentrons 8.6.0a1__py3-none-any.whl

opentrons/calibration_storage/ot3/gripper_offset.py

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+import json
+from pydantic import ValidationError
+from typing import Optional, Union
+
+from opentrons import config, types
+from dataclasses import asdict
+from opentrons.util.helpers import utc_now
+
+
+from .. import file_operators as io, types as local_types
+
+from .models import v1
+
+
+# Delete Gripper Offset Calibrations
+
+
+def delete_gripper_calibration_file(gripper: str) -> None:
+    """
+    Delete gripper calibration offset file based on gripper serial number
+
+    :param gripper: gripper serial number
+    """
+    offset_path = (
+        config.get_opentrons_path("gripper_calibration_dir") / f"{gripper}.json"
+    )
+
+    io.delete_file(offset_path)
+
+
+def clear_gripper_calibration_offsets() -> None:
+    """
+    Delete all gripper calibration data files.
+    """
+
+    offset_dir = config.get_opentrons_path("gripper_calibration_dir")
+    io._remove_json_files_in_directories(offset_dir)
+
+
+# Delete Gripper Jaw Width Calibration
+
+
+def delete_gripper_jaw_width_data_file(gripper: str) -> None:
+    """
+    Delete gripper jaw width data file based on gripper serial number
+
+    :param gripper: gripper serial number
+    """
+    offset_path = config.get_opentrons_path("gripper_jaw_width_dir") / f"{gripper}.json"
+    io.delete_file(offset_path)
+
+
+def clear_gripper_jaw_width_data() -> None:
+    """
+    Delete all gripper jaw width data files.
+    """
+    offset_dir = config.get_opentrons_path("gripper_jaw_width_dir")
+    io._remove_json_files_in_directories(offset_dir)
+
+
+# Save Gripper Offset Calibrations
+
+
+def save_gripper_calibration(
+    offset: types.Point,
+    gripper_id: str,
+    cal_status: Optional[
+        Union[local_types.CalibrationStatus, v1.CalibrationStatus]
+    ] = None,
+) -> None:
+    gripper_dir = config.get_opentrons_path("gripper_calibration_dir")
+
+    if isinstance(cal_status, local_types.CalibrationStatus):
+        cal_status_model = v1.CalibrationStatus(**asdict(cal_status))
+    elif isinstance(cal_status, v1.CalibrationStatus):
+        cal_status_model = cal_status
+    else:
+        cal_status_model = v1.CalibrationStatus()
+
+    gripper_calibration = v1.InstrumentOffsetModel(
+        offset=offset,
+        lastModified=utc_now(),
+        source=local_types.SourceType.user,
+        status=cal_status_model,
+    )
+    io.save_to_file(gripper_dir, gripper_id, gripper_calibration)
+
+
+# Save Gripper Jaw Width Data
+
+
+def save_gripper_jaw_width_data(
+    encoder_position_at_jaw_closed: float,
+    gripper_id: str,
+    cal_status: Optional[
+        Union[local_types.CalibrationStatus, v1.CalibrationStatus]
+    ] = None,
+) -> None:
+    gripper_jaw_width_dir = config.get_opentrons_path("gripper_jaw_width_dir")
+
+    if isinstance(cal_status, local_types.CalibrationStatus):
+        cal_status_model = v1.CalibrationStatus(**asdict(cal_status))
+    elif isinstance(cal_status, v1.CalibrationStatus):
+        cal_status_model = cal_status
+    else:
+        cal_status_model = v1.CalibrationStatus()
+
+    gripper_jaw_width = v1.GripperJawWidthModel(
+        encoderPositionAtJawClosed=encoder_position_at_jaw_closed,
+        lastModified=utc_now(),
+        source=local_types.SourceType.user,
+        status=cal_status_model,
+    )
+    io.save_to_file(gripper_jaw_width_dir, gripper_id, gripper_jaw_width)
+
+
+# Get Gripper Offset Calibrations
+
+
+def get_gripper_calibration_offset(
+    gripper_id: str,
+) -> Optional[v1.InstrumentOffsetModel]:
+    """
+    Return the requested gripper offset data.
+    """
+    if not config.feature_flags.enable_ot3_hardware_controller():
+        raise NotImplementedError("Gripper calibrations are only valid on the OT-3")
+    try:
+        gripper_calibration_filepath = (
+            config.get_opentrons_path("gripper_calibration_dir") / f"{gripper_id}.json"
+        )
+        return v1.InstrumentOffsetModel(
+            **io.read_cal_file(gripper_calibration_filepath)
+        )
+    except FileNotFoundError:
+        return None
+    except (json.JSONDecodeError, ValidationError):
+        return None
+
+
+# Get Gripper Jaw Width
+
+
+def get_gripper_jaw_width_data(gripper_id: str) -> Optional[v1.GripperJawWidthModel]:
+    """Return the requested gripper jaw width data."""
+    if not config.feature_flags.enable_ot3_hardware_controller():
+        raise NotImplementedError("Gripper jaw width data only available on the OT-3.")
+    try:
+        gripper_jaw_width_filepath = (
+            config.get_opentrons_path("gripper_jaw_width_dir") / f"{gripper_id}.json"
+        )
+        return v1.GripperJawWidthModel(**io.read_cal_file(gripper_jaw_width_filepath))
+    except FileNotFoundError:
+        return None
+    except (json.JSONDecodeError, ValidationError):
+        return None

opentrons/calibration_storage/ot3/models/v1.py

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+import typing
+
+from typing_extensions import Literal
+from opentrons.hardware_control.modules.types import ModuleType
+from opentrons.hardware_control.types import OT3Mount
+from pydantic import field_validator, BaseModel, Field, PlainSerializer
+from datetime import datetime
+
+from opentrons_shared_data.pipette.types import LabwareUri
+
+from opentrons.types import Point
+from opentrons.calibration_storage import types
+
+
+DatetimeType = typing.Annotated[
+    datetime,
+    PlainSerializer(lambda x: x.isoformat(), when_used="json"),
+]
+
+
+class CalibrationStatus(BaseModel):
+    markedBad: bool = False
+    source: typing.Optional[types.SourceType] = None
+    markedAt: typing.Optional[DatetimeType] = None
+
+
+class TipLengthModel(BaseModel):
+    tipLength: float = Field(..., description="Tip length data found from calibration.")
+    lastModified: DatetimeType = Field(
+        ..., description="The last time this tip length was calibrated."
+    )
+    uri: typing.Union[LabwareUri, Literal[""]] = Field(
+        ..., description="The tiprack URI associated with the tip length data."
+    )
+    source: types.SourceType = Field(
+        default=types.SourceType.factory, description="The source of calibration."
+    )
+    status: CalibrationStatus = Field(
+        default_factory=CalibrationStatus,
+        description="The status of the calibration data.",
+    )
+
+    @field_validator("tipLength")
+    @classmethod
+    def ensure_tip_length_positive(cls, tipLength: float) -> float:
+        if tipLength < 0.0:
+            raise ValueError("Tip Length must be a positive number")
+        return tipLength
+
+
+class BeltCalibrationModel(BaseModel):
+    attitude: types.AttitudeMatrix = Field(
+        ..., description="Attitude matrix for belts found from calibration."
+    )
+    lastModified: DatetimeType = Field(
+        ..., description="The last time this deck was calibrated."
+    )
+    source: types.SourceType = Field(
+        default=types.SourceType.factory, description="The source of calibration."
+    )
+    pipetteCalibratedWith: typing.Optional[str] = Field(
+        default=None, description="The pipette id used to calibrate the deck."
+    )
+    status: CalibrationStatus = Field(
+        default_factory=CalibrationStatus,
+        description="The status of the calibration data.",
+    )
+
+
+class InstrumentOffsetModel(BaseModel):
+    offset: Point = Field(..., description="Instrument offset found from calibration.")
+    lastModified: DatetimeType = Field(
+        ..., description="The last time this instrument was calibrated."
+    )
+    source: types.SourceType = Field(
+        default=types.SourceType.factory, description="The source of calibration."
+    )
+    status: CalibrationStatus = Field(
+        default_factory=CalibrationStatus,
+        description="The status of the calibration data.",
+    )
+
+
+class GripperJawWidthModel(BaseModel):
+    encoderPositionAtJawClosed: float = Field(
+        ..., description="The encoder position when the gripper jaw is closed."
+    )
+    lastModified: DatetimeType = Field(
+        ..., description="The last time this instrument was calibrated."
+    )
+    source: types.SourceType = Field(
+        default=types.SourceType.factory, description="The source of calibration."
+    )
+    status: CalibrationStatus = Field(
+        default_factory=CalibrationStatus,
+        description="The status of the calibration data.",
+    )
+
+
+class ModuleOffsetModel(BaseModel):
+    offset: Point = Field(..., description="Module offset found from calibration.")
+    mount: OT3Mount = Field(..., description="The mount used to calibrate this module.")
+    slot: str = Field(
+        ...,
+        description=("The slot this module was calibrated in."),
+    )
+    module: ModuleType = Field(..., description="The module type of this module.")
+    module_id: str = Field(..., description="The unique id of this module.")
+    instrument_id: str = Field(
+        ...,
+        description="The unique id of the instrument used to calibrate this module.",
+    )
+    lastModified: DatetimeType = Field(
+        ..., description="The last time this module was calibrated."
+    )
+    source: types.SourceType = Field(
+        default=types.SourceType.factory, description="The source of calibration."
+    )
+    status: CalibrationStatus = Field(
+        default_factory=CalibrationStatus,
+        description="The status of the calibration data.",
+    )

opentrons/calibration_storage/ot3/module_offset.py

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+import json
+import logging
+import os
+from functools import lru_cache
+from pathlib import Path
+from opentrons.hardware_control.modules.types import ModuleType
+from opentrons.hardware_control.types import OT3Mount
+from pydantic import ValidationError
+from typing import List, Optional, Union, no_type_check
+from dataclasses import asdict
+
+from opentrons import config, types
+
+
+from .. import file_operators as io, types as local_types
+from opentrons.util.helpers import utc_now
+
+from .models import v1
+
+log = logging.getLogger(__name__)
+# Delete Module Offset Calibrations
+
+
+@no_type_check
+def delete_module_offset_file(module_id: str) -> None:
+    """
+    Delete module offset file for the given module id.
+
+    :param module: module id serial number
+    """
+    offset_dir = config.get_opentrons_path("module_calibration_dir")
+    offset_path = offset_dir / f"{module_id}.json"
+    io.delete_file(offset_path)
+    # something changed, clear lru cache
+    get_module_offset.cache_clear()
+    load_all_module_offsets.cache_clear()
+
+
+def clear_module_offset_calibrations() -> None:
+    """
+    Delete all module offset calibration files.
+    """
+
+    offset_dir = config.get_opentrons_path("module_calibration_dir")
+    io._remove_json_files_in_directories(offset_dir)
+    # something changed, clear lru cache
+    get_module_offset.cache_clear()
+    load_all_module_offsets.cache_clear()
+
+
+# Save Module Offset Calibrations
+
+
+@no_type_check
+def save_module_calibration(
+    offset: types.Point,
+    mount: OT3Mount,
+    slot: str,
+    module: ModuleType,
+    module_id: str,
+    instrument_id: Optional[str] = None,
+    cal_status: Optional[
+        Union[local_types.CalibrationStatus, v1.CalibrationStatus]
+    ] = None,
+) -> None:
+    module_dir = config.get_opentrons_path("module_calibration_dir")
+    if isinstance(cal_status, local_types.CalibrationStatus):
+        cal_status_model = v1.CalibrationStatus(**asdict(cal_status))
+    elif isinstance(cal_status, v1.CalibrationStatus):
+        cal_status_model = cal_status
+    else:
+        cal_status_model = v1.CalibrationStatus()
+
+    module_calibration = v1.ModuleOffsetModel(
+        offset=offset,
+        mount=mount,
+        slot=slot,
+        module=module,
+        module_id=module_id,
+        instrument_id=instrument_id,
+        lastModified=utc_now(),
+        source=local_types.SourceType.user,
+        status=cal_status_model,
+    )
+    io.save_to_file(module_dir, module_id, module_calibration)
+    # something changed, clear lru cache
+    get_module_offset.cache_clear()
+    load_all_module_offsets.cache_clear()
+
+
+# Get Module Offset Calibrations
+
+
+@no_type_check
+@lru_cache(maxsize=10)
+def get_module_offset(
+    module: ModuleType, module_id: str, slot: Optional[str] = None
+) -> Optional[v1.ModuleOffsetModel]:
+    try:
+        module_calibration_filepath = (
+            config.get_opentrons_path("module_calibration_dir") / f"{module_id}.json"
+        )
+        return v1.ModuleOffsetModel(**io.read_cal_file(module_calibration_filepath))
+    except FileNotFoundError:
+        log.warning(
+            f"Calibrations for {module} {module_id} on slot {slot} does not exist."
+        )
+        return None
+    except (json.JSONDecodeError, ValidationError):
+        log.warning(
+            f"Malformed calibrations for {module_id} on slot {slot}. Please factory reset your calibrations.",
+            exc_info=True,
+        )
+        return None
+
+
+@lru_cache(maxsize=10)
+def load_all_module_offsets() -> List[v1.ModuleOffsetModel]:
+    """Load all module offsets from the disk."""
+
+    calibrations: List[v1.ModuleOffsetModel] = []
+    files = os.listdir(config.get_opentrons_path("module_calibration_dir"))
+    for file in files:
+        try:
+            calibrations.append(
+                v1.ModuleOffsetModel(
+                    **io.read_cal_file(
+                        Path(config.get_opentrons_path("module_calibration_dir") / file)
+                    )
+                )
+            )
+        except (json.JSONDecodeError, ValidationError):
+            log.warning(
+                f"Malformed module calibrations for {file}. Please factory reset your calibrations.",
+                exc_info=True,
+            )
+            continue
+    return calibrations

opentrons/calibration_storage/ot3/pipette_offset.py

@@ -0,0 +1,95 @@
+import json
+import logging
+from pydantic import ValidationError
+from typing import Optional, Union, no_type_check
+from dataclasses import asdict
+
+from opentrons import config, types
+
+
+from .. import file_operators as io, types as local_types
+from opentrons.util.helpers import utc_now
+
+from .models import v1
+
+log = logging.getLogger(__name__)
+# Delete Pipette Offset Calibrations
+
+
+@no_type_check
+def delete_pipette_offset_file(pipette: str, mount: types.Mount) -> None:
+    """
+    Delete pipette offset file based on mount and pipette serial number
+
+    :param pipette: pipette serial number
+    :param mount: pipette mount
+    """
+    offset_dir = config.get_opentrons_path("pipette_calibration_dir")
+    offset_path = offset_dir / mount.name.lower() / f"{pipette}.json"
+    io.delete_file(offset_path)
+
+
+def clear_pipette_offset_calibrations() -> None:
+    """
+    Delete all pipette offset calibration files.
+    """
+
+    offset_dir = config.get_opentrons_path("pipette_calibration_dir")
+    io._remove_json_files_in_directories(offset_dir)
+
+
+# Save Pipette Offset Calibrations
+
+
+@no_type_check
+def save_pipette_calibration(
+    offset: types.Point,
+    pip_id: str,
+    mount: types.Mount,
+    cal_status: Optional[
+        Union[local_types.CalibrationStatus, v1.CalibrationStatus]
+    ] = None,
+) -> None:
+    pip_dir = config.get_opentrons_path("pipette_calibration_dir") / mount.name.lower()
+
+    if isinstance(cal_status, local_types.CalibrationStatus):
+        cal_status_model = v1.CalibrationStatus(**asdict(cal_status))
+    elif isinstance(cal_status, v1.CalibrationStatus):
+        cal_status_model = cal_status
+    else:
+        cal_status_model = v1.CalibrationStatus()
+
+    pipette_calibration = v1.InstrumentOffsetModel(
+        offset=offset,
+        lastModified=utc_now(),
+        source=local_types.SourceType.user,
+        status=cal_status_model,
+    )
+    io.save_to_file(pip_dir, pip_id, pipette_calibration)
+
+
+# Get Pipette Offset Calibrations
+
+
+@no_type_check
+def get_pipette_offset(
+    pipette_id: str, mount: types.Mount
+) -> Optional[v1.InstrumentOffsetModel]:
+    try:
+        pipette_calibration_filepath = (
+            config.get_opentrons_path("pipette_calibration_dir")
+            / mount.name.lower()
+            / f"{pipette_id}.json"
+        )
+        return v1.InstrumentOffsetModel(
+            **io.read_cal_file(pipette_calibration_filepath)
+        )
+    except FileNotFoundError:
+        log.debug(f"Calibrations for {pipette_id} on {mount} does not exist.")
+        return None
+    except (json.JSONDecodeError, ValidationError):
+        log.warning(
+            f"Malformed calibrations for {pipette_id} on {mount}. Please factory reset your calibrations.",
+            exc_info=True,
+        )
+        return None

opentrons/calibration_storage/types.py

@@ -0,0 +1,45 @@
+import typing
+
+from dataclasses import dataclass
+from datetime import datetime
+from enum import Enum
+
+AttitudeMatrix = typing.List[typing.List[float]]
+
+
+class SourceType(str, Enum):
+    """Calibration source type"""
+
+    default = "default"
+    factory = "factory"
+    user = "user"
+    calibration_check = "calibration_check"
+    legacy = "legacy"
+    unknown = "unknown"
+
+
+class TipLengthCalNotFound(Exception):
+    pass
+
+
+@dataclass
+class CalibrationStatus:
+    markedBad: bool = False
+    source: typing.Optional[SourceType] = None
+    markedAt: typing.Optional[datetime] = None
+
+
+@dataclass
+class UriDetails:
+    namespace: str
+    load_name: str
+    version: int
+
+
+# TODO(mm, 2023-11-20): Deduplicate this with similar types in robot_server
+# and opentrons.protocol_engine.
+@dataclass
+class CutoutFixturePlacement:
+    cutout_fixture_id: str
+    cutout_id: str
+    opentrons_module_serial_number: typing.Optional[str]

opentrons/cli/__init__.py

@@ -0,0 +1,21 @@
+"""Opentrons command-line interface.
+
+This CLI application is not yet public-facing.
+It is currently used by the Opentrons App to analyze protocols.
+"""
+
+import click
+
+from .analyze import analyze
+
+
+@click.group()
+def main() -> None:
+    """Welcome to the `opentrons` command-line application.
+
+    This application is not yet public facing.
+    Please check back in a future software version.
+    """
+
+
+main.add_command(analyze)

opentrons/cli/__main__.py

@@ -0,0 +1,5 @@
+"""Opentrons CLI application entry point."""
+
+from . import main
+
+main()