pigeon-tem-comms 1.0.0__tar.gz → 1.1.1__tar.gz

{pigeon_tem_comms-1.0.0/pigeon_tem_comms.egg-info → pigeon_tem_comms-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 1.0.0
+Version: 1.1.1
 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-1.0.0 → pigeon_tem_comms-1.1.1}/TEM_comms/__init__.py

@@ -26,8 +26,7 @@ topics = {
     "ui.edit": ui.Edit,
     "ui.run": ui.Run,
     "ui.setup": ui.Setup,
-    "montage.start": montage.Start,
-    "montage.finished": montage.Finished,
+    "montage.complete": montage.Complete,
     "qc.status": qc.Status,
     "roi.load": roi.LoadROI,
     "roi.create": roi.CreateROI,

{pigeon_tem_comms-1.0.0 → pigeon_tem_comms-1.1.1}/TEM_comms/camera.py

@@ -1,10 +1,9 @@
 from pigeon import BaseMessage
+from .tile.metadata import TileMetadata
 from typing import Optional
 
 
-class Command(BaseMessage):
-    tile_id: str
-    montage_id: str
+class Command(TileMetadata):
     brightfield: Optional[bool] = False
     darkfield: Optional[bool] = False
     lens_correction: Optional[bool] = True
@@ -32,3 +31,4 @@ class Status(BaseMessage):
     device_name: str
     device_model_id: int
     device_sn: str
+    bit_depth: int

pigeon_tem_comms-1.1.1/TEM_comms/montage.py

@@ -0,0 +1,26 @@
+from pigeon import BaseMessage
+from typing import Mapping, List, Any, Optional, Tuple
+from datetime import datetime
+
+
+class Complete(BaseMessage):
+    montage_id: str
+    tile_ids: List[str]
+    acquisition_id: str
+    start_time: datetime
+    pixel_size: float
+    rotation_angle: float
+    aperture_centroid: Tuple[int, int]
+
+
+class Minimap(BaseMessage):
+    image: Optional[str]
+    colorbar: str
+    min: Optional[float]
+    max: Optional[float]
+
+
+class Minimaps(BaseMessage):
+    montage_id: str
+    montage: Minimap
+    focus: Minimap

{pigeon_tem_comms-1.0.0 → pigeon_tem_comms-1.1.1}/TEM_comms/scope.py

@@ -9,6 +9,7 @@ class Command(BaseMessage):
     mag: Optional[int] = None
     brightness: Optional[int] = None
     beam_offset: Optional[Tuple[int, int]] = None
+    spot_size: Optional[int] = None
     screen: Optional[Literal["up", "down"]] = None
 
     @model_validator(mode="after")
@@ -25,4 +26,5 @@ class Status(BaseMessage):
     tank_voltage: int
     brightness: int
     beam_offset: Tuple[int, int]
+    spot_size: int
     screen: Literal["up", "down"] | None

{pigeon_tem_comms-1.0.0 → pigeon_tem_comms-1.1.1}/TEM_comms/tile/statistics.py

@@ -14,3 +14,4 @@ class MinMaxMean(TileMetadata):
     min: int
     max: int
     mean: int
+    std: int

{pigeon_tem_comms-1.0.0 → pigeon_tem_comms-1.1.1/pigeon_tem_comms.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 1.0.0
+Version: 1.1.1
 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-1.0.0 → pigeon_tem_comms-1.1.1}/pigeon_tem_comms.egg-info/SOURCES.txt

@@ -23,6 +23,7 @@ pigeon_tem_comms.egg-info/entry_points.txt
 pigeon_tem_comms.egg-info/requires.txt
 pigeon_tem_comms.egg-info/top_level.txt
 tests/test_buffer.py
+tests/test_camera.py
 tests/test_qc.py
 tests/test_scope_command.py
 tests/test_ui.py

{pigeon_tem_comms-1.0.0 → pigeon_tem_comms-1.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pigeon-tem-comms"
-version = "1.0.0"
+version = "1.1.1"
 authors = [
   { name="Cameron Devine", email="cameron.devine@alleninstitute.org" },
 ]

pigeon_tem_comms-1.1.1/tests/test_camera.py

@@ -0,0 +1,42 @@
+from TEM_comms.camera import Command
+from pytest import mark
+
+
+@mark.parametrize(
+    "data",
+    [
+        {
+            "montage_id": "a montage id",
+            "tile_id": "a tile id",
+            "row": 1,
+            "column": 2,
+            "overlap": 100,
+        },
+        {
+            "montage_id": "a montage id",
+            "tile_id": "a tile id",
+            "row": 1,
+            "column": 2,
+            "overlap": 100,
+            "darkfield": True,
+        },
+        {
+            "montage_id": "a montage id",
+            "tile_id": "a tile id",
+            "row": 1,
+            "column": 2,
+            "overlap": 100,
+            "brightfield": True,
+        },
+        {
+            "montage_id": "a montage id",
+            "tile_id": "a tile id",
+            "row": 1,
+            "column": 2,
+            "overlap": 100,
+            "lens_correction": False,
+        },
+    ],
+)
+def test_command(data):
+    Command(**data)

pigeon_tem_comms-1.0.0/TEM_comms/montage.py

@@ -1,28 +0,0 @@
-from pigeon import BaseMessage
-from typing import Mapping, List, Any, Optional
-
-
-class Start(BaseMessage):
-    montage_id: str
-    num_tiles: int
-
-
-class Finished(BaseMessage):
-    montage_id: str
-    num_tiles: int
-    roi: str
-    specimen: str
-    metadata: Mapping[str, Any] | List[Any]
-
-
-class Minimap(BaseMessage):
-    image: Optional[str]
-    colorbar: str
-    min: Optional[float]
-    max: Optional[float]
-
-
-class Minimaps(BaseMessage):
-    montage_id: str
-    montage: Minimap
-    focus: Minimap