pigeon-tem-comms 1.4.1__tar.gz → 2.1.0__tar.gz

{pigeon_tem_comms-1.4.1/pigeon_tem_comms.egg-info → pigeon_tem_comms-2.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 1.4.1
+Version: 2.1.0
 Summary: Pigeon messages for the next generation TEM imaging system.
 Author-email: Cameron Devine <cameron.devine@alleninstitute.org>
 License: BSD 3 Clause

{pigeon_tem_comms-1.4.1 → pigeon_tem_comms-2.1.0}/TEM_comms/__init__.py

@@ -1,9 +1,17 @@
-from pigeon import BaseMessage
-from . import buffer, camera, montage, qc, roi, scope, stage, tile, ui, calibration
-
-
-class State(BaseMessage):
-    state: str
+from . import (
+    buffer,
+    camera,
+    montage,
+    qc,
+    roi,
+    scope,
+    stage,
+    tile,
+    ui,
+    calibration,
+    state,
+    lens_correction,
+)
 
 
 topics = {
@@ -14,6 +22,9 @@ topics = {
     "camera.status": camera.Status,
     "scope.command": scope.Command,
     "scope.status": scope.Status,
+    "scope.image_shift.status": scope.image_shift.Status,
+    "scope.image_shift.command": scope.image_shift.Command,
+    "scope.image_shift.calibrate": scope.image_shift.Calibrate,
     "stage.aperture.command": stage.aperture.Command,
     "stage.aperture.status": stage.aperture.Status,
     "stage.motion.command": stage.motion.Command,
@@ -28,6 +39,7 @@ topics = {
     "tile.statistics.histogram": tile.statistics.Histogram,
     "tile.statistics.min_max_mean": tile.statistics.MinMaxMean,
     "tile.matches": tile.Matches,
+    "tile.template_matches": tile.TemplateMatches,
     "ui.edit": ui.Edit,
     "ui.run": ui.Run,
     "ui.setup": ui.Setup,
@@ -40,5 +52,7 @@ topics = {
     "montage.minimaps": montage.Minimaps,
     "calibration.resolution": calibration.Resolution,
     "calibration.centroid": calibration.Centroid,
-    "state": State,
+    "state.current": state.Current,
+    "state.change": state.Change,
+    "lens_correction.transform": lens_correction.Transform,
 }

pigeon_tem_comms-2.1.0/TEM_comms/buffer.py

@@ -0,0 +1,18 @@
+from pigeon import BaseMessage
+from pydantic import Field
+
+
+class Status(BaseMessage):
+    """
+    This message contains information about the status of the tile upload buffer.
+    """
+
+    queue_length: int = Field(
+        description="The number of tiles currently stored and waiting to be uploaded."
+    )
+    free_space: int = Field(
+        description="The amount of free space on the tile storage disk in bytes."
+    )
+    upload_rate: int = Field(
+        description="The rate at which data is being uploaded in bits per second."
+    )

pigeon_tem_comms-2.1.0/TEM_comms/calibration.py

@@ -0,0 +1,42 @@
+from pigeon import BaseMessage
+from typing import Mapping
+from pydantic import Field
+
+
+class _Resolution(BaseMessage):
+    nm_per_px: tuple[float, float] = Field(
+        description="The X-Y size of each pixel in the processed camera image in nanometers.",
+        examples=[(3.97, 4.03)],
+    )
+    rotation: float = Field(
+        description="The rotation required to match a right-handed image coordinate system to the coordinate system of the stage in radians."
+    )
+
+
+class Resolution(BaseMessage):
+    """
+    This message contains the resolutions of all the calibrated magnifications of the microscope.
+    """
+
+    lowmag: Mapping[int, _Resolution] = Field(
+        description="A mapping of calibrated low-mag magnifications to thier calibration values."
+    )
+    mag: Mapping[int, _Resolution] = Field(
+        description="A mapping of calibrated high-mag magnifications to their calibration values."
+    )
+
+
+class Centroid(BaseMessage):
+    """
+    This message contains the location of the centroid of the specified aperture.
+    """
+
+    aperture_id: int = Field(
+        description="The ID of the aperture that this centroid pertains to."
+    )
+    x: int = Field(
+        description="The stage coordinate system X axis location of the centroid."
+    )
+    y: int = Field(
+        description="The stage coordinate system Y axis location of the centroid."
+    )

pigeon_tem_comms-2.1.0/TEM_comms/camera.py

@@ -0,0 +1,64 @@
+from pigeon import BaseMessage
+from .tile.metadata import TileMetadata, ProcessingOptions
+from typing import Optional
+from pydantic import Field
+
+
+class Command(TileMetadata, ProcessingOptions):
+    """
+    This message is used to instruct the camera to capture an image.
+    """
+
+
+class Image(BaseMessage):
+    """
+    This message is sent after the camera exposure is complete.
+    """
+
+    tile_id: str = Field(
+        description="The tile ID", examples=["69005602-15b0-4407-bf5b-4bddd6629141"]
+    )
+    montage_id: str = Field(
+        description="The montage ID. If a zero length string, the tile is for UI display or calibration purposes only.",
+        examples=["4330c7cf-e45b-4950-89cf-82dc0f815fe9"],
+    )
+
+
+class Settings(BaseMessage):
+    """
+    This message is used to change camera settings.
+    """
+
+    exposure: float | None = Field(
+        default=None, description="The length of the camera exposure in microseconds."
+    )
+    gain: Optional[float] = Field(
+        default=None, description="The camera gain in decibels."
+    )
+    width: int | None = Field(
+        default=None, description="The width of the camera frame."
+    )
+    height: int | None = Field(
+        default=None, description="The height of the camera frame."
+    )
+
+
+class Status(BaseMessage):
+    """
+    This message contains information about the state of the camera.
+    """
+
+    exposure: float = Field(
+        description="The length of the camera exposure in microseconds."
+    )
+    gain: float = Field(description="The camera gain in decibels.")
+    width: int = Field(description="The camera frame width.")
+    height: int = Field(description="The camera frame height.")
+    temp: float = Field(description="The camera temperature.")
+    target_temp: float = Field(
+        description="The target temperature of the camera cooling system."
+    )
+    device_name: str = Field(description="The human readable device name.")
+    device_model_id: str = Field(description="The device model identifier.")
+    device_sn: str = Field(description="The camera serial number.")
+    bit_depth: int | str = Field(description="The bit depth of the camera sensor.")

pigeon_tem_comms-2.1.0/TEM_comms/lens_correction.py

@@ -0,0 +1,10 @@
+from pigeon import BaseMessage
+from pydantic import Field
+
+
+class Transform(BaseMessage):
+    """
+    This message contains a compact representation of the generated lens correction transform.
+    """
+
+    transform: str = Field(description="The base64 encoded lens correction transform.")

pigeon_tem_comms-2.1.0/TEM_comms/montage.py

@@ -0,0 +1,55 @@
+from pigeon import BaseMessage
+from typing import Mapping, Dict, Any, Optional, Tuple
+from datetime import datetime
+from pydantic import Field
+
+
+class Tile(BaseMessage):
+    raster_index: int = Field(
+        description="The index of the tile incremented for each subsequent tile in the montage."
+    )
+    stage_position: Tuple[int, int] = Field(
+        description="The X-Y stage position of the tile in nanometers."
+    )
+    raster_position: Tuple[int, int] = Field(
+        description="The X-Y indicies of the tile in the montage."
+    )
+
+
+class Complete(BaseMessage):
+    """
+    This message is sent after a montage is completed.
+    """
+
+    montage_id: str = Field(description="The unique montage ID.")
+    tiles: Dict[str, Tile] = Field(
+        description="A mapping from tile IDs to tile metadata."
+    )
+    acquisition_id: str = Field(description="The corresponding TEMdb acqusition ID.")
+    start_time: datetime = Field(
+        description="The timestamp when the montage was started."
+    )
+    pixel_size: float = Field(description="The average size ofee")
+    rotation_angle: float = Field(
+        description="The necessary tile rotation in radians to line up the right-handed image coordinate system with the Stage x-y coordinate system."
+    )
+    aperture_centroid: Tuple[int, int] = Field(
+        description="The X-Y coordinates of the centroid of the imaged aperture in nanometers."
+    )
+
+
+class Minimap(BaseMessage):
+    image: Optional[str] = Field(description="The map as a base 64 encoded image.")
+    colorbar: str = Field(description="The colorbar as a base 64 encoded image.")
+    min: Optional[float] = Field(description="The minimum value of the colorbar.")
+    max: Optional[float] = Field(description="The maximum value of the colorbar.")
+
+
+class Minimaps(BaseMessage):
+    """
+    This message contains multiple overview maps including a low resolution version of the montage, along with various statistics.
+    """
+
+    montage_id: str = Field(description="The unique montage ID.")
+    montage: Minimap = Field(description="The montage minimap.")
+    focus: Minimap = Field(description="The focus score map.")

pigeon_tem_comms-2.1.0/TEM_comms/qc.py

@@ -0,0 +1,17 @@
+from pigeon import BaseMessage
+from typing import Literal, Optional
+from pydantic import Field
+
+
+class Status(BaseMessage):
+    """
+    This message contains the overall QC status of the system.
+    """
+
+    status: Literal["GOOD", "STOP_AT_END", "STOP_NOW"] = Field(
+        description='The QC status, "GOOD" if imaging should continue, "STOP_AT_END" if imaging should be stopped at the end of the current montage, and "STOP_NOW" if imaging should be stopped immediately.'
+    )
+    reason: Optional[str] = Field(
+        default=None,
+        description="Optionally, a human readable reason for the current status.",
+    )

{pigeon_tem_comms-1.4.1 → pigeon_tem_comms-2.1.0}/TEM_comms/roi.py

@@ -9,30 +9,61 @@ class Vertex(BaseMessage):
 
 
 class ROI(BaseMessage):
-    vertices: List[Vertex]
-    rotation_angle: float
-    buffer_size: float = 0.0
-    montage_id: str
-    specimen_id: Optional[str] = None
-    grid_id: Optional[str] = None
-    section_id: Optional[str] = None
-    metadata: Optional[dict] = None
+    """
+    Information about the current ROI being imaged.
+    """
+
+    vertices: List[Vertex] = Field(
+        description="A list of points defining a polygonal ROI."
+    )
+    rotation_angle: float = Field(
+        description="The rotation angle of the ROI in radians."
+    )
+    buffer_size: float = Field(
+        default=0.0,
+        description="The amount to dialate the ROI in nanometers when imaging.",
+    )
+    montage_id: str = Field(description="The montage ID to use when imaging the ROI.")
+    specimen_id: Optional[str] = Field(
+        default=None, description="The specimen ID corresponding to this ROI."
+    )
+    grid_id: Optional[str] = Field(
+        default=None, description="The grid ID where this ROI should be imaged."
+    )
+    section_id: Optional[str] = Field(
+        default=None, description="The section ID corresponding to this ROI."
+    )
+    metadata: Optional[dict] = Field(
+        default=None, description="Extra metadata about this ROI."
+    )
     queue_position: Optional[int] = Field(
         None, description="Position in queue, None means set as current"
     )
 
 
 class LoadROI(BaseMessage):
-    specimen_id: str
-    section_id: str
-    grid_id: Optional[str] = None
+    """
+    This message can be used to load an ROI from the database into the ROI queue.
+    """
+
+    specimen_id: str = Field(description="The specimen ID to load from the database.")
+    section_id: str = Field(description="The section ID to load from the database.")
+    grid_id: Optional[str] = Field(
+        default=None, description="The the grid ID where the section is loaded."
+    )
     queue_position: Optional[int] = Field(
         None, description="Position in queue, None means set as current"
     )
 
 
 class CreateROI(ROI):
-    center: Optional[Vertex] = None
+    """
+    This message can be used to create an ROI and add it to the ROI queue.
+    """
+
+    center: Optional[Vertex] = Field(
+        default=None, description="The center point of the ROI."
+    )
     tilt_angles: Optional[List[float]] = Field(
         default=[0.0],
         description="List of tilt angles in degrees for tomography series",
@@ -49,6 +80,10 @@ class CreateROI(ROI):
 
 
 class ROIStatus(BaseMessage):
+    """
+    This message contains information on the status of an individual ROI.
+    """
+
     type: str = Field(
         description="Event type: roi_added, roi_advanced, queue_cleared, queue_empty"
     )

pigeon_tem_comms-2.1.0/TEM_comms/scope/__init__.py

@@ -0,0 +1,68 @@
+from pigeon import BaseMessage
+from typing import Literal, Optional, Tuple
+from pydantic import model_validator, Field
+from . import image_shift
+
+
+class Command(BaseMessage):
+    """
+    This message is used to change microscope settings.
+    """
+
+    focus: Optional[int] = Field(
+        default=None,
+        description="The desired focus value for the microscope, or None to keep the current value.",
+    )
+    mag_mode: Optional[Literal["LM", "MAG1", "MAG2"]] = Field(
+        default=None,
+        description="The desired magnification mode for the microscope, or None to keep the current value.",
+    )
+    mag: Optional[int] = Field(
+        default=None,
+        description="The desired magnification for the microscope, or None to keep the current value.",
+    )
+    brightness: Optional[int] = Field(
+        default=None,
+        description="The desired beam spread for the microscope, or None to keep the current value.",
+    )
+    beam_offset: Optional[Tuple[int, int]] = Field(
+        default=None,
+        description="The desired beam shift values, or None to keep the current value.",
+    )
+    spot_size: Optional[int] = Field(
+        default=None,
+        description="The desired spot size, or None to keep the current value.",
+    )
+    screen: Optional[Literal["up", "down"]] = Field(
+        default=None,
+        description='"up" to raise the microscope viewscreen, "down" to lower the microscope viewscreen, or None to keep the viewscreen in the current position.',
+    )
+
+    @model_validator(mode="after")
+    def check_mag(self):
+        assert (self.mag_mode is None) == (self.mag is None)
+        return self
+
+
+class Status(BaseMessage):
+    """
+    This message contains the state of the microscope.
+    """
+
+    focus: int = Field(description="The current focus value.")
+    aperture: str | None = Field(
+        description="The current status of the objective aperture, or None if unknown."
+    )
+    mag_mode: Literal["MAG", "LOWMAG"] = Field(
+        description="The curreng magnification mode."
+    )
+    mag: int = Field(description="The current magnification.")
+    tank_voltage: int = Field(
+        description="The current voltage of the tank in kilo-volts."
+    )
+    brightness: int = Field(description="The current beam spread.")
+    beam_offset: Tuple[int, int] = Field(description="The current beam shift values.")
+    spot_size: int = Field(description="The current spot size.")
+    screen: Literal["up", "down"] | None = Field(
+        description='Whether the viewscreen is currently "up", "down", or None for an unknown position.'
+    )

pigeon_tem_comms-2.1.0/TEM_comms/scope/image_shift.py

@@ -0,0 +1,57 @@
+from pigeon import BaseMessage
+from typing import Optional, List, Tuple, Mapping
+from pydantic import model_validator, Field
+
+
+class Calibrate(BaseMessage):
+    """
+    This message is used to calibrate the image shifting system.
+    """
+
+    position: int = Field(description="The image shift position index to calibrate.")
+    image_shift: Tuple[int, int] = Field(
+        description="The new calibration values for this position index."
+    )
+
+
+class Status(BaseMessage):
+    """
+    This message conatins the status of the image shifting system.
+    """
+
+    enabled: bool = Field(
+        description="If the image shifting system is currently enabled."
+    )
+    current_position: int | None = Field(
+        default=None, description="The current position index, or None if disabled."
+    )
+    image_shift: Tuple[int, int] = Field(
+        description="The current image shift calibration values."
+    )
+    calibration: Mapping[int, Tuple[int, int]] = Field(
+        description="The calibration values for each position index."
+    )
+
+    @model_validator(mode="after")
+    def check_current_position(self):
+        assert self.enabled == (self.current_position is not None)
+        return self
+
+
+class Command(BaseMessage):
+    """
+    This message is used to enable and disable the image shifting system, and to switch to a predefined position.
+    """
+
+    enable: bool = Field(
+        description="Used to enable and disable the image shifting system."
+    )
+    position: Optional[int] = Field(
+        default=None,
+        description="The calibrated position index to use, or None if disabled.",
+    )
+
+    @model_validator(mode="after")
+    def check_position(self):
+        assert self.enable == (self.position is not None)
+        return self

pigeon_tem_comms-2.1.0/TEM_comms/stage/aperture.py

@@ -0,0 +1,35 @@
+from pigeon import BaseMessage
+from pydantic import ConfigDict, Field
+
+
+class Command(BaseMessage):
+    """
+    This message is uesd to change between apertures on a substrate.
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    aperture_id: int | None = Field(
+        default=None,
+        description="The ID of the aperture to change to, or None to remain at the current aperture.",
+    )
+    calibrate: bool = Field(
+        default=False,
+        description="Set to True to initiate aperture changing hardware calibration.",
+    )
+
+
+class Status(BaseMessage):
+    """
+    This message includes status information about the aperture changing system.
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    current_aperture: int | None = Field(
+        description="The ID of the current aperture, or None if unknown."
+    )
+    calibrated: bool = Field(
+        description="True if the aperture changing hardware is calibrated."
+    )
+    error: str = Field(default="", description="An optional error message.")

pigeon_tem_comms-2.1.0/TEM_comms/stage/motion.py

@@ -0,0 +1,51 @@
+from typing import Optional
+from pigeon import BaseMessage
+from pydantic import ConfigDict, Field
+
+
+class Command(BaseMessage):
+    """
+    This message is used to specify how the stage should move the sample.
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    x: int | None = Field(
+        default=None,
+        description="The desired absolute X position of the stage in nanometers, or None to keep the current position.",
+    )
+    y: int | None = Field(
+        default=None,
+        description="The desired absolute Y position of the stage in nanometers, or None to keep the current position.",
+    )
+    z: Optional[int] = Field(
+        default=None,
+        description="The desired absolute Z position of the stage in nanometers, or None to keep the current position.",
+    )
+    calibrate: bool = Field(
+        default=False, description="Set to True to initiate stage calibration."
+    )
+
+
+class Status(BaseMessage):
+    """
+    This message includes stage motion status information.
+    """
+
+    model_config = ConfigDict(extra="allow")
+
+    x: int | None = Field(
+        description="The current X position of the stage in nanometers, or None if unknown."
+    )
+    y: int | None = Field(
+        description="The current Y position of the stage in nanometers, or None if unknown."
+    )
+    z: Optional[int] = Field(
+        default=None,
+        description="The current Z position of the stage in nanometers, or None if unknown.",
+    )
+    in_motion: bool = Field(
+        description="This value is True if the stage is currently moving."
+    )
+    calibrated: bool = Field(description="True if the stage is calibrated.")
+    error: str = Field(default="", description="An optional error message.")

pigeon_tem_comms-2.1.0/TEM_comms/stage/rotation.py

@@ -0,0 +1,44 @@
+from pigeon import BaseMessage
+from pydantic import Field
+
+
+class Command(BaseMessage):
+    """
+    This message is used to rotate the sample, and to calibrate this rotation.
+    """
+
+    angle_x: float | None = Field(
+        default=None,
+        description="The desired rotation angle around the X axis in radians, or None to keep the current value.",
+    )
+    angle_y: float | None = Field(
+        default=None,
+        description="The desired rotation angle around the Y axis in radians, or None to keep the current value.",
+    )
+    eucentric_height: float | None = Field(
+        default=None,
+        description="The eucentric height of the stage in nanometers for calibration, or None to keep the current value.",
+    )
+    calibrate: bool = Field(
+        default=False, description="If True, calibrate the sample rotation hardware."
+    )
+
+
+class Status(BaseMessage):
+    """
+    This message contains the status of the sample rotation system.
+    """
+
+    angle_x: float = Field(
+        description="The current angle around the X axis in radians."
+    )
+    angle_y: float = Field(
+        description="The current angle around the Y axis in radians."
+    )
+    eucentric_height: float = Field(
+        description="The current enucentric height value in nanometers."
+    )
+    in_motion: bool = Field(
+        description="True if the rotation stage is currently moving."
+    )
+    error: str = Field(default="", description="An optional error message.")

pigeon_tem_comms-2.1.0/TEM_comms/state.py

@@ -0,0 +1,23 @@
+from pigeon import BaseMessage
+from pydantic import Field
+
+
+class Current(BaseMessage):
+    """
+    This message contains the current state of the orchastration state machine.
+    """
+
+    state: str = Field(
+        description="The current state of the orchastration state machine."
+    )
+
+
+class Change(BaseMessage):
+    """
+    This message is sent on a state change of the orchastration state machine.
+    """
+
+    old: str = Field(
+        description="The previous state of the orchastration state machine."
+    )
+    new: str = Field(description="The new state of the orchastration state machine.")