pigeon-tem-comms 0.5.0__tar.gz → 1.1.0__tar.gz

{pigeon_tem_comms-0.5.0/pigeon_tem_comms.egg-info → pigeon_tem_comms-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 0.5.0
+Version: 1.1.0
 Summary: Pigeon messages for the next generation TEM imaging system.
 Author-email: Cameron Devine <cameron.devine@alleninstitute.org>
 License: BSD 3 Clause
@@ -18,6 +18,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pigeon-client
 Requires-Dist: pydantic
+Dynamic: license-file
 
 [![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/AllenInstitute/TEM_comms/main.yaml)](https://github.com/AllenInstitute/TEM_comms/actions)
 [![PyPI - Version](https://img.shields.io/pypi/v/pigeon-tem-comms)](https://pypi.org/project/pigeon-tem-comms/)

{pigeon_tem_comms-0.5.0 → pigeon_tem_comms-1.1.0}/TEM_comms/__init__.py

@@ -1,5 +1,6 @@
 from . import buffer, camera, montage, qc, roi, scope, stage, tile, ui
 
+
 topics = {
     "buffer.status": buffer.Status,
     "camera.command": camera.Command,
@@ -15,7 +16,7 @@ topics = {
     "stage.rotation.command": stage.rotation.Command,
     "stage.rotation.status": stage.rotation.Status,
     "tile.preview": tile.Preview,
-    "tile.minimap": tile.Minimap,
+    "tile.mini": tile.Mini,
     "tile.processed": tile.Processed,
     "tile.raw": tile.Raw,
     "tile.statistics.focus": tile.statistics.Focus,
@@ -31,4 +32,5 @@ topics = {
     "roi.load": roi.LoadROI,
     "roi.create": roi.CreateROI,
     "roi.current": roi.ROI,
+    "montage.minimaps": montage.Minimaps,
 }

{pigeon_tem_comms-0.5.0 → pigeon_tem_comms-1.1.0}/TEM_comms/camera.py

@@ -1,14 +1,17 @@
 from pigeon import BaseMessage
+from .tile.metadata import TileMetadata
 from typing import Optional
 
 
-class Command(BaseMessage):
-    tile_id: str
+class Command(TileMetadata):
+    brightfield: Optional[bool] = False
+    darkfield: Optional[bool] = False
+    lens_correction: Optional[bool] = True
 
 
 class Image(BaseMessage):
     tile_id: str
-    path: str
+    montage_id: str
 
 
 class Settings(BaseMessage):

pigeon_tem_comms-1.1.0/TEM_comms/montage.py

@@ -0,0 +1,28 @@
+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

{pigeon_tem_comms-0.5.0 → pigeon_tem_comms-1.1.0}/TEM_comms/stage/motion.py

@@ -4,11 +4,13 @@ from pigeon import BaseMessage
 class Command(BaseMessage):
     x: int | None = None
     y: int | None = None
+    z: int | None = None
     calibrate: bool = False
 
 
 class Status(BaseMessage):
     x: int | None
     y: int | None
+    z: int | None
     in_motion: bool
     error: str = ""

{pigeon_tem_comms-0.5.0 → pigeon_tem_comms-1.1.0}/TEM_comms/stage/rotation.py

@@ -4,11 +4,13 @@ from pigeon import BaseMessage
 class Command(BaseMessage):
     angle_x: float | None = None
     angle_y: float | None = None
+    eucentric_height: float | None = None
     calibrate: bool = False
 
 
 class Status(BaseMessage):
     angle_x: float
     angle_y: float
+    eucentric_height: float
     in_motion: bool
     error: str = ""

{pigeon_tem_comms-0.5.0 → pigeon_tem_comms-1.1.0}/TEM_comms/tile/__init__.py

@@ -6,7 +6,7 @@ class Preview(TileMetadata):
     image: str
 
 
-class Minimap(TileMetadata):
+class Mini(TileMetadata):
     image: str
 
 

{pigeon_tem_comms-0.5.0 → pigeon_tem_comms-1.1.0/pigeon_tem_comms.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 0.5.0
+Version: 1.1.0
 Summary: Pigeon messages for the next generation TEM imaging system.
 Author-email: Cameron Devine <cameron.devine@alleninstitute.org>
 License: BSD 3 Clause
@@ -18,6 +18,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pigeon-client
 Requires-Dist: pydantic
+Dynamic: license-file
 
 [![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/AllenInstitute/TEM_comms/main.yaml)](https://github.com/AllenInstitute/TEM_comms/actions)
 [![PyPI - Version](https://img.shields.io/pypi/v/pigeon-tem-comms)](https://pypi.org/project/pigeon-tem-comms/)

{pigeon_tem_comms-0.5.0 → pigeon_tem_comms-1.1.0}/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-0.5.0 → pigeon_tem_comms-1.1.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pigeon-tem-comms"
-version = "0.5.0"
+version = "1.1.0"
 authors = [
   { name="Cameron Devine", email="cameron.devine@alleninstitute.org" },
 ]

pigeon_tem_comms-1.1.0/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-0.5.0/TEM_comms/montage.py

@@ -1,15 +0,0 @@
-from pigeon import BaseMessage
-from typing import Mapping, List, Any
-
-
-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]