pigeon-tem-comms 1.3.0__tar.gz → 1.4.0__tar.gz

{pigeon_tem_comms-1.3.0/pigeon_tem_comms.egg-info → pigeon_tem_comms-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 1.3.0
+Version: 1.4.0
 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-1.3.0 → pigeon_tem_comms-1.4.0}/TEM_comms/__init__.py

@@ -27,7 +27,7 @@ topics = {
     "tile.statistics.focus": tile.statistics.Focus,
     "tile.statistics.histogram": tile.statistics.Histogram,
     "tile.statistics.min_max_mean": tile.statistics.MinMaxMean,
-    "tile.transform": tile.Transform,
+    "tile.matches": tile.Matches,
     "ui.edit": ui.Edit,
     "ui.run": ui.Run,
     "ui.setup": ui.Setup,
@@ -36,6 +36,7 @@ topics = {
     "roi.load": roi.LoadROI,
     "roi.create": roi.CreateROI,
     "roi.current": roi.ROI,
+    "roi.status": roi.ROIStatus,
     "montage.minimaps": montage.Minimaps,
     "calibration.resolution": calibration.Resolution,
     "calibration.centroid": calibration.Centroid,

pigeon_tem_comms-1.4.0/TEM_comms/roi.py

@@ -0,0 +1,64 @@
+from pigeon import BaseMessage
+from typing import List, Tuple, Optional
+from pydantic import Field
+
+
+class Vertex(BaseMessage):
+    x: float
+    y: float
+
+
+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
+    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
+    queue_position: Optional[int] = Field(
+        None, description="Position in queue, None means set as current"
+    )
+
+
+class CreateROI(ROI):
+    center: Optional[Vertex] = None
+    tilt_angles: Optional[List[float]] = Field(
+        default=[0.0],
+        description="List of tilt angles in degrees for tomography series",
+    )
+    aperture_centroid_pixel: Optional[Vertex] = Field(
+        None, description="Aperture centroid in pixel coordinates"
+    )
+    aperture_centroid_physical: Optional[Vertex] = Field(
+        None, description="Aperture centroid in physical coordinates (nm)"
+    )
+    overview_nm_per_pixel: Optional[float] = Field(
+        None, description="Overview image scale in nm per pixel"
+    )
+
+
+class ROIStatus(BaseMessage):
+    type: str = Field(
+        description="Event type: roi_added, roi_advanced, queue_cleared, queue_empty"
+    )
+    timestamp: int = Field(description="Timestamp")
+    roi_count: int = Field(description="Total number of active ROIs (queue + current)")
+    has_active_rois: bool = Field(description="Whether there are any ROIs available")
+    source: Optional[str] = Field(
+        None, description="Source of last ROI submission: UI or external"
+    )
+    montage_id: Optional[str] = Field(None, description="Current montage ID")
+    queue_info: Optional[dict] = Field(
+        None, description="Queue statistics: total, completed, remaining"
+    )

{pigeon_tem_comms-1.3.0 → pigeon_tem_comms-1.4.0}/TEM_comms/scope.py

@@ -21,7 +21,7 @@ class Command(BaseMessage):
 class Status(BaseMessage):
     focus: int
     aperture: str | None
-    mag_mode: str
+    mag_mode: Literal["MAG", "LOWMAG"]
     mag: int
     tank_voltage: int
     brightness: int

pigeon_tem_comms-1.4.0/TEM_comms/tile/__init__.py

@@ -0,0 +1,42 @@
+from .metadata import TileMetadata
+from . import statistics
+from pydantic import BaseModel
+from typing import Literal, List
+
+
+class Preview(TileMetadata):
+    image: str
+
+
+class Mini(TileMetadata):
+    image: str
+
+
+class Raw(TileMetadata):
+    path: str
+
+
+class Match(BaseModel):
+    model_config = {"extra": "forbid"}
+    row: int
+    column: int
+    dX: float
+    dY: float
+    dXsd: float
+    dYsd: float
+    distance: float
+    rotation: float
+    match_quality: float
+    position: Literal["top", "bottom", "left", "right"]
+    pX: List[int]
+    pY: List[int]
+    qX: List[int]
+    qY: List[int]
+
+
+class Matches(TileMetadata):
+    matches: List[Match]
+
+
+class Processed(TileMetadata):
+    path: str

{pigeon_tem_comms-1.3.0 → pigeon_tem_comms-1.4.0/pigeon_tem_comms.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 1.3.0
+Version: 1.4.0
 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-1.3.0 → pigeon_tem_comms-1.4.0}/pigeon_tem_comms.egg-info/SOURCES.txt

@@ -29,4 +29,5 @@ tests/test_camera.py
 tests/test_qc.py
 tests/test_scope_command.py
 tests/test_stage.py
+tests/test_tile.py
 tests/test_ui.py

{pigeon_tem_comms-1.3.0 → pigeon_tem_comms-1.4.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pigeon-tem-comms"
-version = "1.3.0"
+version = "1.4.0"
 authors = [
   { name="Cameron Devine", email="cameron.devine@alleninstitute.org" },
 ]

pigeon_tem_comms-1.4.0/tests/test_tile.py

@@ -0,0 +1,56 @@
+from TEM_comms.tile import Matches
+
+
+def test_matches_empty():
+    matches = Matches(
+        row=2,
+        column=5,
+        overlap=128,
+        tile_id="a_tile_id",
+        montage_id="a_montage_id",
+        matches=(),
+    )
+
+
+def test_matches():
+    matches = Matches(
+        row=2,
+        column=5,
+        overlap=128,
+        tile_id="a_tile_id",
+        montage_id="a_montage_id",
+        matches=(
+            {
+                "row": 3,
+                "column": 5,
+                "dX": 24.3,
+                "dY": 37.8,
+                "distance": 55.7,
+                "rotation": 0.1,
+                "position": "bottom",
+                "match_quality": 0.5,
+                "dXsd": 0.47,
+                "dYsd": 0.35,
+                "pX": [1, 2, 3, 4],
+                "pY": [5, 6, 7, 8],
+                "qX": [9, 10, 11, 12],
+                "qY": [13, 14, 15, 16],
+            },
+            {
+                "row": 2,
+                "column": 6,
+                "dX": 14.9,
+                "dY": 32.3,
+                "distance": 42.1,
+                "rotation": -0.04,
+                "position": "right",
+                "match_quality": 0.59,
+                "dXsd": 0.59,
+                "dYsd": 0.21,
+                "pX": [4, 3, 2, 1],
+                "pY": [8, 7, 6, 5],
+                "qX": [12, 11, 10, 9],
+                "qY": [16, 15, 14, 13],
+            },
+        ),
+    )

pigeon_tem_comms-1.3.0/TEM_comms/roi.py

@@ -1,45 +0,0 @@
-from pigeon import BaseMessage
-from typing import List, Tuple, Optional
-from pydantic import Field
-
-
-class Vertex(BaseMessage):
-    x: float
-    y: float
-
-
-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
-    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
-    queue_position: Optional[int] = Field(
-        None, description="Position in queue, None means set as current"
-    )
-
-
-class CreateROI(BaseMessage):
-    center: Vertex
-    width: float
-    height: float
-    rotation_angle: float = 0.0
-    montage_id: str
-    specimen_id: Optional[str] = None
-    grid_id: Optional[str] = None
-    section_id: Optional[str] = None
-    queue_position: Optional[int] = Field(
-        None, description="Position in queue, None means set as current"
-    )

pigeon_tem_comms-1.3.0/TEM_comms/tile/__init__.py

@@ -1,24 +0,0 @@
-from .metadata import TileMetadata
-from . import statistics
-
-
-class Preview(TileMetadata):
-    image: str
-
-
-class Mini(TileMetadata):
-    image: str
-
-
-class Raw(TileMetadata):
-    path: str
-
-
-class Transform(TileMetadata):
-    rotation: float
-    x: float
-    y: float
-
-
-class Processed(TileMetadata):
-    path: str