pigeon-tem-comms 0.4.11__tar.gz → 1.0.0__tar.gz

{pigeon_tem_comms-0.4.11/pigeon_tem_comms.egg-info → pigeon_tem_comms-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 0.4.11
+Version: 1.0.0
 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-0.4.11 → pigeon_tem_comms-1.0.0}/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-0.4.11 → pigeon_tem_comms-1.0.0}/TEM_comms/camera.py

@@ -4,11 +4,15 @@ from typing import Optional
 
 class Command(BaseMessage):
     tile_id: str
+    montage_id: str
+    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-1.0.0/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-0.4.11 → pigeon_tem_comms-1.0.0}/TEM_comms/roi.py

@@ -2,10 +2,12 @@ from pigeon import BaseMessage
 from typing import List, Tuple, Optional
 from pydantic import Field
 
+
 class Vertex(BaseMessage):
-    x: float 
+    x: float
     y: float
 
+
 class ROI(BaseMessage):
     vertices: List[Vertex]
     rotation_angle: float
@@ -15,13 +17,19 @@ class ROI(BaseMessage):
     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")
+    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")
+    queue_position: Optional[int] = Field(
+        None, description="Position in queue, None means set as current"
+    )
+
 
 class CreateROI(BaseMessage):
     center: Vertex
@@ -32,5 +40,6 @@ class CreateROI(BaseMessage):
     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")
-
+    queue_position: Optional[int] = Field(
+        None, description="Position in queue, None means set as current"
+    )

{pigeon_tem_comms-0.4.11 → pigeon_tem_comms-1.0.0}/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-0.4.11 → pigeon_tem_comms-1.0.0}/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-1.0.0/TEM_comms/tile/__init__.py

@@ -0,0 +1,24 @@
+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

pigeon_tem_comms-1.0.0/TEM_comms/tile/metadata.py

@@ -0,0 +1,9 @@
+from pigeon import BaseMessage
+
+
+class TileMetadata(BaseMessage):
+    tile_id: str
+    montage_id: str
+    row: int
+    column: int
+    overlap: int

pigeon_tem_comms-1.0.0/TEM_comms/tile/statistics.py

@@ -0,0 +1,16 @@
+from .metadata import TileMetadata
+from typing import List
+
+
+class Focus(TileMetadata):
+    focus: float
+
+
+class Histogram(TileMetadata):
+    hist: List[int]
+
+
+class MinMaxMean(TileMetadata):
+    min: int
+    max: int
+    mean: int

{pigeon_tem_comms-0.4.11 → pigeon_tem_comms-1.0.0/pigeon_tem_comms.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: pigeon-tem-comms
-Version: 0.4.11
+Version: 1.0.0
 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-0.4.11 → pigeon_tem_comms-1.0.0}/pigeon_tem_comms.egg-info/SOURCES.txt

@@ -14,6 +14,7 @@ TEM_comms/stage/aperture.py
 TEM_comms/stage/motion.py
 TEM_comms/stage/rotation.py
 TEM_comms/tile/__init__.py
+TEM_comms/tile/metadata.py
 TEM_comms/tile/statistics.py
 pigeon_tem_comms.egg-info/PKG-INFO
 pigeon_tem_comms.egg-info/SOURCES.txt

{pigeon_tem_comms-0.4.11 → pigeon_tem_comms-1.0.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pigeon-tem-comms"
-version = "0.4.11"
+version = "1.0.0"
 authors = [
   { name="Cameron Devine", email="cameron.devine@alleninstitute.org" },
 ]

pigeon_tem_comms-0.4.11/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]

pigeon_tem_comms-0.4.11/TEM_comms/tile/__init__.py

@@ -1,35 +0,0 @@
-from pigeon import BaseMessage
-from . import statistics
-
-
-class Preview(BaseMessage):
-    tile_id: str
-    image: str
-
-
-class Minimap(BaseMessage):
-    tile_id: str
-    path: str
-
-
-class Raw(BaseMessage):
-    tile_id: str
-    montage_id: str
-    path: str
-    row: int
-    column: int
-    overlap: int
-
-
-class Transform(BaseMessage):
-    montage_id: str
-    tile_id: str
-    rotation: float
-    x: float
-    y: float
-
-
-class Processed(BaseMessage):
-    montage_id: str
-    tile_id: str
-    path: str

pigeon_tem_comms-0.4.11/TEM_comms/tile/statistics.py

@@ -1,22 +0,0 @@
-from pigeon import BaseMessage
-
-
-class Focus(BaseMessage):
-    montage_id: str
-    tile_id: str
-    focus: float
-
-
-class Histogram(BaseMessage):
-    montage_id: str
-    tile_id: str
-    path: str
-
-
-class MinMaxMean(BaseMessage):
-    montage_id: str
-    tile_id: str
-    min: int
-    max: int
-    mean: int
-