pigeon-tem-comms 0.4.11__py3-none-any.whl → 1.0.0__py3-none-any.whl

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,
 }

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):

TEM_comms/montage.py

@@ -1,5 +1,5 @@
 from pigeon import BaseMessage
-from typing import Mapping, List, Any
+from typing import Mapping, List, Any, Optional
 
 
 class Start(BaseMessage):
@@ -13,3 +13,16 @@ class Finished(BaseMessage):
     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

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"
+    )

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 = ""

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 = ""

TEM_comms/tile/__init__.py

@@ -1,35 +1,24 @@
-from pigeon import BaseMessage
+from .metadata import TileMetadata
 from . import statistics
 
 
-class Preview(BaseMessage):
-    tile_id: str
+class Preview(TileMetadata):
     image: str
 
 
-class Minimap(BaseMessage):
-    tile_id: str
-    path: str
+class Mini(TileMetadata):
+    image: str
 
 
-class Raw(BaseMessage):
-    tile_id: str
-    montage_id: str
+class Raw(TileMetadata):
     path: str
-    row: int
-    column: int
-    overlap: int
 
 
-class Transform(BaseMessage):
-    montage_id: str
-    tile_id: str
+class Transform(TileMetadata):
     rotation: float
     x: float
     y: float
 
 
-class Processed(BaseMessage):
-    montage_id: str
-    tile_id: str
+class Processed(TileMetadata):
     path: str

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

TEM_comms/tile/statistics.py

@@ -1,22 +1,16 @@
-from pigeon import BaseMessage
+from .metadata import TileMetadata
+from typing import List
 
 
-class Focus(BaseMessage):
-    montage_id: str
-    tile_id: str
+class Focus(TileMetadata):
     focus: float
 
 
-class Histogram(BaseMessage):
-    montage_id: str
-    tile_id: str
-    path: str
+class Histogram(TileMetadata):
+    hist: List[int]
 
 
-class MinMaxMean(BaseMessage):
-    montage_id: str
-    tile_id: str
+class MinMaxMean(TileMetadata):
     min: int
     max: int
     mean: int
-

{pigeon_tem_comms-0.4.11.dist-info → pigeon_tem_comms-1.0.0.dist-info}/METADATA

@@ -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-1.0.0.dist-info/RECORD

@@ -0,0 +1,21 @@
+TEM_comms/__init__.py,sha256=ujCgc64ihXYl3uvwxW6zfQGIAxiMBoV-betCiMMBuCQ,1300
+TEM_comms/buffer.py,sha256=Jr6fUIbUPreQSSGKWR7jkA1McyZZv3lVE8uQSER8VL4,123
+TEM_comms/camera.py,sha256=uOw8uEfNc0DqhOyNce4-OBHcLpdZU24zG06ibHvehHQ,669
+TEM_comms/montage.py,sha256=H4bpqSfJLroR3WBoSY2KdPrE8A2WXrDgzp0wAA0M0oE,505
+TEM_comms/qc.py,sha256=sujy2i0wimMvrHDPEXKdaiO7xxvRcHiy83mVpATLyqA,141
+TEM_comms/roi.py,sha256=37fKMT-KNJfWOwWvFAPTFHuBzkV1h6RS42kQsU00teQ,1145
+TEM_comms/scope.py,sha256=lPEKzWT2raR6ailiAitvWXH-Xu6fxWwYBf3GPfVIizc,761
+TEM_comms/ui.py,sha256=Yxd0i4wjmddDl9sVzcFHHu5b6n0ICzaO0b_8SmAysxg,1459
+TEM_comms/stage/__init__.py,sha256=UVtYKzMBI01FUADS24xSItNIjhqdZtlDeJdqsDJNVIc,67
+TEM_comms/stage/aperture.py,sha256=lyJO34_K76MKrZ-o2izd5V7eEN55d3lGu__RvZq-NlA,227
+TEM_comms/stage/motion.py,sha256=CqP-BS7mRP5Z9VkFT9-ePiICg6HQiviUubaO1qSioxo,287
+TEM_comms/stage/rotation.py,sha256=tUcf6IpQ2ooRDYb51Zb4pi7pQUrBuLPiLKSg8Ebb2DY,332
+TEM_comms/tile/__init__.py,sha256=ID3b4VAHqVXAkxTYOZ7H2oTSrnVdUYt4Xb6gpQ0I3qo,316
+TEM_comms/tile/metadata.py,sha256=pUxmi_C02e5nwTm51rIULkKaRz6ij5mlXylzAcDU-9c,149
+TEM_comms/tile/statistics.py,sha256=ij0ggk15J_jikIkuSDmhvY96yjliofFRN5SNdsGA0lA,232
+pigeon_tem_comms-1.0.0.dist-info/licenses/LICENSE,sha256=tZfQIUX7uNGacTb751ZWInVenJl6OwYQihcGbYrKSts,1463
+pigeon_tem_comms-1.0.0.dist-info/METADATA,sha256=L-ZnoBYgyiEYm9_XL6Qj23R8Jmju4EdXDGtjM3LgUb4,1575
+pigeon_tem_comms-1.0.0.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
+pigeon_tem_comms-1.0.0.dist-info/entry_points.txt,sha256=X2WfBCDgfH9XVVqiI4rLu7BLyMNuLW6WWckqXxfbrgk,38
+pigeon_tem_comms-1.0.0.dist-info/top_level.txt,sha256=3_1RcQ7xvS2dJEYnPIigo9snoKcSXSNJzPqunY0qydI,10
+pigeon_tem_comms-1.0.0.dist-info/RECORD,,

{pigeon_tem_comms-0.4.11.dist-info → pigeon_tem_comms-1.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (77.0.3)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pigeon_tem_comms-0.4.11.dist-info/RECORD

@@ -1,20 +0,0 @@
-TEM_comms/__init__.py,sha256=YCjLxCTzYjlYToUwPCuUeTUWIi3yrEPb0P6h_gJJ_Po,1263
-TEM_comms/buffer.py,sha256=Jr6fUIbUPreQSSGKWR7jkA1McyZZv3lVE8uQSER8VL4,123
-TEM_comms/camera.py,sha256=L9ebaZra-M3g571PUzQCAuC92Auw4ox3gRceJ2uKRhs,522
-TEM_comms/montage.py,sha256=PCfve__0M3S2RSmBtrDRlDlmIW_qJffDRE8gnlEHoxY,281
-TEM_comms/qc.py,sha256=sujy2i0wimMvrHDPEXKdaiO7xxvRcHiy83mVpATLyqA,141
-TEM_comms/roi.py,sha256=RWLy9xb12cGCkvnZ9wO9kheoof0aRzg9py7sGgrT7Qo,1101
-TEM_comms/scope.py,sha256=lPEKzWT2raR6ailiAitvWXH-Xu6fxWwYBf3GPfVIizc,761
-TEM_comms/ui.py,sha256=Yxd0i4wjmddDl9sVzcFHHu5b6n0ICzaO0b_8SmAysxg,1459
-TEM_comms/stage/__init__.py,sha256=UVtYKzMBI01FUADS24xSItNIjhqdZtlDeJdqsDJNVIc,67
-TEM_comms/stage/aperture.py,sha256=lyJO34_K76MKrZ-o2izd5V7eEN55d3lGu__RvZq-NlA,227
-TEM_comms/stage/motion.py,sha256=1NSuGQvPjlxwnkaV410VGDBBtmsISQn_XjZcPuUXvQg,244
-TEM_comms/stage/rotation.py,sha256=J7tAIP2nskjInhZmdIbqwrvxTFXihEynVOAyxbDDfjU,262
-TEM_comms/tile/__init__.py,sha256=RlmgJt3ELn3PWlv1kIr0dRAgMaSaMcsy6fgtsQ3hMr0,500
-TEM_comms/tile/statistics.py,sha256=big7ydZe18RaT_B_sh1ust7MiGITOZ1aJdH7mY9T2BY,307
-pigeon_tem_comms-0.4.11.dist-info/LICENSE,sha256=tZfQIUX7uNGacTb751ZWInVenJl6OwYQihcGbYrKSts,1463
-pigeon_tem_comms-0.4.11.dist-info/METADATA,sha256=6PXKNAqmZAibC6lg2dK7lg2XkrHShn_B-3BqCs0GJuE,1554
-pigeon_tem_comms-0.4.11.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-pigeon_tem_comms-0.4.11.dist-info/entry_points.txt,sha256=X2WfBCDgfH9XVVqiI4rLu7BLyMNuLW6WWckqXxfbrgk,38
-pigeon_tem_comms-0.4.11.dist-info/top_level.txt,sha256=3_1RcQ7xvS2dJEYnPIigo9snoKcSXSNJzPqunY0qydI,10
-pigeon_tem_comms-0.4.11.dist-info/RECORD,,