pigeon-tem-comms 0.2.0__tar.gz → 0.4.0__tar.gz

{pigeon_tem_comms-0.2.0/pigeon_tem_comms.egg-info → pigeon_tem_comms-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pigeon-tem-comms
-Version: 0.2.0
+Version: 0.4.0
 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-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/__init__.py

@@ -4,11 +4,8 @@ from . import scope
 from . import stage
 from . import tile
 from . import ui
+from . import montage
 
-import importlib.metadata
-
-
-__version__ = importlib.metadata.version("pigeon-tem-comms")
 
 topics = {
     "buffer.status": buffer.Status,
@@ -35,7 +32,6 @@ topics = {
     "ui.edit": ui.Edit,
     "ui.run": ui.Run,
     "ui.setup": ui.Setup,
+    "montage.start": montage.Start,
+    "montage.finished": montage.Finished,
 }
-
-
-msgs = (topics, __version__)

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/camera.py

@@ -1,23 +1,30 @@
 from pigeon import BaseMessage
+from typing import Optional
+
 
 class Command(BaseMessage):
     tile_id: str
 
+
 class Image(BaseMessage):
     tile_id: str
     path: str
 
+
 class Settings(BaseMessage):
     exposure: float | None = None
+    gain: Optional[float] = None
     width: int | None = None
     height: int | None = None
 
+
 class Status(BaseMessage):
     exposure: float
+    gain: float
     width: int
     height: int
     temp: float
     target_temp: float
     device_name: str
     device_model_id: int
-    device_sn: str
+    device_sn: str

pigeon_tem_comms-0.4.0/TEM_comms/montage.py

@@ -0,0 +1,15 @@
+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-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/scope.py

@@ -2,6 +2,7 @@ from pigeon import BaseMessage
 from typing import Literal
 from pydantic import model_validator
 
+
 class Command(BaseMessage):
     focus: int | None = None
     mag_mode: Literal["LM", "MAG1", "MAG2"] | None = None
@@ -18,4 +19,4 @@ class Status(BaseMessage):
     aperture: str | None
     mag_mode: str
     mag: int
-    tank_voltage: int
+    tank_voltage: int

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/stage/__init__.py

@@ -1,3 +1,3 @@
 from . import aperture
 from . import motion
-from . import rotation
+from . import rotation

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/stage/aperture.py

@@ -1,10 +1,12 @@
 from pigeon import BaseMessage
 
+
 class Command(BaseMessage):
     aperture_id: int | None = None
     calibrate: bool = False
 
+
 class Status(BaseMessage):
     current_aperture: int
     calibrated: bool
-    error: str = ""
+    error: str = ""

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/stage/motion.py

@@ -1,12 +1,14 @@
 from pigeon import BaseMessage
 
+
 class Command(BaseMessage):
     x: int | None = None
     y: int | None = None
     calibrate: bool = False
 
+
 class Status(BaseMessage):
     x: int
     y: int
     in_motion: bool
-    error: str = ""
+    error: str = ""

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/stage/rotation.py

@@ -1,12 +1,14 @@
 from pigeon import BaseMessage
 
+
 class Command(BaseMessage):
     angle_x: float | None = None
     angle_y: float | None = None
     calibrate: bool = False
 
+
 class Status(BaseMessage):
     angle_x: float
     angle_y: float
     in_motion: bool
-    error: str = ""
+    error: str = ""

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/tile/__init__.py

@@ -12,22 +12,24 @@ class Minimap(BaseMessage):
     path: str
 
 
-class Processed(BaseMessage):
-    tile_id: str
-    path: str
-
-
 class Raw(BaseMessage):
     tile_id: str
     montage_id: str
     path: str
     row: int
     column: int
-    overlap: float
+    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-0.2.0 → pigeon_tem_comms-0.4.0}/TEM_comms/tile/statistics.py

@@ -1,15 +1,22 @@
 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
+    mean: int
+

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0/pigeon_tem_comms.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pigeon-tem-comms
-Version: 0.2.0
+Version: 0.4.0
 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-0.2.0 → pigeon_tem_comms-0.4.0}/pigeon_tem_comms.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ pyproject.toml
 TEM_comms/__init__.py
 TEM_comms/buffer.py
 TEM_comms/camera.py
+TEM_comms/montage.py
 TEM_comms/scope.py
 TEM_comms/ui.py
 TEM_comms/stage/__init__.py

pigeon_tem_comms-0.4.0/pigeon_tem_comms.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[pigeon.msgs]
+msgs = TEM_comms:topics

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pigeon-tem-comms"
-version = "0.2.0"
+version = "0.4.0"
 authors = [
   { name="Cameron Devine", email="cameron.devine@alleninstitute.org" },
 ]
@@ -21,7 +21,7 @@ classifiers = [
 ]
 
 [project.entry-points."pigeon.msgs"]
-msgs = "TEM_comms:msgs"
+msgs = "TEM_comms:topics"
 
 [project.urls]
 Homepage = "https://github.com/AllenInstitute/TEM_comms"

pigeon_tem_comms-0.4.0/tests/test_buffer.py

@@ -0,0 +1,64 @@
+import re
+
+import pytest
+from TEM_comms.buffer import Status
+
+from pydantic import ValidationError
+
+
+# Test cases for the Status class
+@pytest.mark.parametrize(
+    "queue_length, free_space, upload_rate, test_id",
+    [
+        (10, 100, 20, "test_id_01"),  # Happy path: normal values
+        (0, 0, 0, "test_id_02"),  # Edge case: zero values
+        (100, 500, 100, "test_id_03"),  # Happy path: higher values
+        (-1, -100, -10, "test_id_04"),  # Error case: negative values
+        (1e6, 1e6, 1e4, "test_id_05"),  # Edge case: very large values
+    ],
+)
+def test_status_initialization(queue_length, free_space, upload_rate, test_id):
+    # Act
+    status = Status(
+        queue_length=queue_length, free_space=free_space, upload_rate=upload_rate
+    )
+
+    # Assert
+    assert (
+        status.queue_length == queue_length
+    ), f"{test_id}: queue_length does not match"
+    assert status.free_space == free_space, f"{test_id}: free_space does not match"
+    assert status.upload_rate == upload_rate, f"{test_id}: upload_rate does not match"
+
+
+# Test cases for handling type errors
+@pytest.mark.parametrize(
+    "queue_length, free_space, upload_rate, test_id",
+    [
+        (
+            "ten",
+            100,
+            20,
+            "test_id_06",
+        ),  # Error case: string instead of int for queue_length
+        (
+            10,
+            "hundred",
+            20,
+            "test_id_07",
+        ),  # Error case: string instead of int for free_space
+        (
+            10,
+            100,
+            "twenty",
+            "test_id_08",
+        ),  # Error case: string instead of int for upload_rate
+    ],
+)
+def test_status_type_errors(queue_length, free_space, upload_rate, test_id):
+    # Act and Assert
+    expected_error_pattern = re.escape("validation error")
+    with pytest.raises(ValidationError, match=expected_error_pattern):
+        Status(
+            queue_length=queue_length, free_space=free_space, upload_rate=upload_rate
+        )

{pigeon_tem_comms-0.2.0 → pigeon_tem_comms-0.4.0}/tests/test_scope_command.py

@@ -2,20 +2,22 @@ from TEM_comms.scope import Command
 from pydantic import ValidationError
 import pytest
 
+
 def test_mag():
     with pytest.raises(ValidationError):
         Command(mag_mode="LM")
-    
+
     with pytest.raises(ValidationError):
         Command(mag=10)
 
     Command()
     Command(mag_mode="LM", mag=1)
 
+
 def test_mag_mode():
     with pytest.raises(ValidationError):
         Command(mag_mode="test", mag=1)
 
     Command(mag_mode="LM", mag=1)
     Command(mag_mode="MAG2", mag=1)
-    Command(mag_mode="MAG2", mag=1)
+    Command(mag_mode="MAG2", mag=1)

pigeon_tem_comms-0.2.0/pigeon_tem_comms.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[pigeon.msgs]
-msgs = TEM_comms:msgs

pigeon_tem_comms-0.2.0/tests/test_buffer.py

@@ -1,41 +0,0 @@
-import re
-
-import pytest
-from TEM_comms.buffer import Status
-
-from pydantic import ValidationError
-
-# Test cases for the Status class
-@pytest.mark.parametrize(
-    "queue_length, free_space, upload_rate, test_id",
-    [
-        (10, 100, 20, "test_id_01"),  # Happy path: normal values
-        (0, 0, 0, "test_id_02"),      # Edge case: zero values
-        (100, 500, 100, "test_id_03"), # Happy path: higher values
-        (-1, -100, -10, "test_id_04"), # Error case: negative values
-        (1e6, 1e6, 1e4, "test_id_05"), # Edge case: very large values
-    ]
-)
-def test_status_initialization(queue_length, free_space, upload_rate, test_id):
-    # Act
-    status = Status(queue_length=queue_length, free_space=free_space, upload_rate=upload_rate)
-
-    # Assert
-    assert status.queue_length == queue_length, f"{test_id}: queue_length does not match"
-    assert status.free_space == free_space, f"{test_id}: free_space does not match"
-    assert status.upload_rate == upload_rate, f"{test_id}: upload_rate does not match"
-
-# Test cases for handling type errors
-@pytest.mark.parametrize(
-    "queue_length, free_space, upload_rate, test_id",
-    [
-        ("ten", 100, 20, "test_id_06"),  # Error case: string instead of int for queue_length
-        (10, "hundred", 20, "test_id_07"), # Error case: string instead of int for free_space
-        (10, 100, "twenty", "test_id_08"), # Error case: string instead of int for upload_rate
-    ]
-)
-def test_status_type_errors(queue_length, free_space, upload_rate, test_id):
-    # Act and Assert
-    expected_error_pattern = re.escape("validation error")
-    with pytest.raises(ValidationError, match=expected_error_pattern):
-        Status(queue_length=queue_length, free_space=free_space, upload_rate=upload_rate)