Merge feature/virtual microscope

pyclm_config.toml

@@ -1,7 +1,7 @@
 # MicroManager Configuration Path
-config_path = "C:\\Program Files\\Micro-Manager-2.0\\Ti2MightexCrestSolaSpectra.cfg"
+config_path = "C:\\Program Files\\Micro-Manager-2.0\\Ti2MightexCrestSolaSpectra_newlab.cfg"
 
 # SLM Configuration
-affine_transform = [[-0.289, 0.006, 959.025], [-0.012, -0.579, 1540.03]]
+affine_transform = [[-0.29, -0.002, 939.891], [0.004, -0.579, 1505.235]]
 slm_shape_h =  1140
 slm_shape_w =  912

src/pyclm/__main__.py

@@ -7,7 +7,7 @@
 def main():
     args = process_args()
     base_path = Path(args.directory)
-    run_pyclm(base_path, args.config)
+    run_pyclm(base_path, args.config, dry=args.dry)
 
 
 def process_args():
@@ -16,6 +16,9 @@ def process_args():
     parser.add_argument(
         "--config", type=str, help="path to pyclm_config.toml file", default=None
     )
+    parser.add_argument(
+        "--dry", action="store_true", help="run without executing the experiment"
+    )
 
     return parser.parse_args()
 

src/pyclm/controller.py

@@ -26,17 +26,29 @@
     SegmentationProcess,
     SLMBuffer,
 )
+from .core.real_core import RealMicroscopeCore
+from .core.virtual_microscope.simulated_core import SimulatedMicroscopeCore
+from .core.virtual_microscope.simulated_source import TimeSeriesImageSource
 
 logger = logging.getLogger(__name__)
 
 
 class Controller:
-    def __init__(self, config="MMConfig_demo.cfg"):
-        self.stop_event = Event()
-        self.core = CMMCorePlus()
+    def __init__(self, config="MMConfig_demo.cfg", dry=False):
+        if not dry:
+            # Applies if config specifies that a real microscope is in use
+            self.core = RealMicroscopeCore()
+        else:
+            # image_source = TimeSeriesImageSource.from_tiff_stack(Path("path/to/stack.tif"), loop=True)
+            image_source = TimeSeriesImageSource.from_folder(
+                Path("tif-source"), pattern="*.tif", loop=True
+            )
+            self.core = SimulatedMicroscopeCore(image_source, slm_device=None)
         self.core.loadSystemConfiguration(config)
         self.all_queues = AllQueues()
 
+        self.stop_event = Event()
+
         self.microscope = MicroscopeProcess(
             core=self.core, aq=self.all_queues, stop_event=self.stop_event
         )
@@ -192,7 +204,6 @@ def run(self):
                     for f in future_to_process:
                         f.cancel()
 
-                self.core.unloadAllDevices()
                 self.all_queues.close()
 
                 logger.info("Controller run finished.")

src/pyclm/core/core_interface.py

@@ -0,0 +1,45 @@
+from __future__ import annotations
+
+from collections.abc import Sequence
+from typing import Any, Protocol
+
+
+class MicroscopeCoreInterface(Protocol):
+    def loadSystemConfiguration(self, configuration): ...
+
+    # SLM-related
+    def getSLMDevice(self) -> str: ...
+    def getSLMHeight(self, device: str) -> int: ...
+    def getSLMWidth(self, device: str) -> int: ...
+    def setSLMImage(self, device: str, image: Any) -> None: ...
+
+    # Config/device properties
+    def setConfig(self, group: str, config: str) -> None: ...
+    def setProperty(self, label: str, name: str, value: Any) -> None: ...
+    def getProperty(self, label: str, name: str) -> str: ...
+    def getAllowedPropertyValues(
+        self, device: str, prop_name: str
+    ) -> Sequence[str]: ...
+    def describe(self) -> str: ...
+    def setFocusDevice(self, label: str) -> None: ...
+    def getAvailableConfigGroups(self) -> Sequence[str]: ...
+    def getConfigGroupObject(
+        self, group: str, include_read_only: bool = False
+    ) -> Any: ...
+
+    # Camera-related
+    def getCameraDevice(self) -> str: ...
+    def setExposure(self, exposure_ms: float) -> None: ...
+    def snapImage(self) -> None: ...
+    def getImage(self) -> Any: ...
+    def getPixelSizeUm(self) -> float: ...
+    def getROI(self): ...
+
+    # Stage/focus/positioning
+    def getZPosition(self) -> float: ...
+    def setPosition(self, z: float) -> None: ...
+    def setXYPosition(self, x: float, y: float) -> None: ...
+    def setAutoFocusOffset(self, offset: float) -> None: ...
+
+    # Synchronization
+    def waitForSystem(self) -> None: ...

src/pyclm/core/microscope.py

@@ -5,6 +5,7 @@
 import numpy as np
 from pymmcore_plus import CMMCorePlus
 
+from .core_interface import MicroscopeCoreInterface
 from .datatypes import AcquisitionData, EventSLMPattern, StimulationData
 from .events import AcquisitionEvent, UpdatePatternEvent, UpdateStagePositionEvent
 from .experiments import ConfigGroup, DeviceProperty, PositionWithAutoFocus
@@ -19,7 +20,10 @@
 
 class MicroscopeProcess(BaseProcess):
     def __init__(
-        self, core: CMMCorePlus, aq: AllQueues, stop_event: Event | None = None
+        self,
+        core: MicroscopeCoreInterface,
+        aq: AllQueues,
+        stop_event: Event | None = None,
     ):
         super().__init__(stop_event, name="microscope")
         self.core = core

src/pyclm/core/real_core.py

@@ -0,0 +1,94 @@
+from __future__ import annotations
+
+from collections.abc import Sequence
+from typing import Any
+
+from pymmcore_plus import CMMCorePlus
+
+from .core_interface import MicroscopeCoreInterface
+
+
+class RealMicroscopeCore(MicroscopeCoreInterface):
+    """
+    Delegates everything to an internal CMMCorePlus.
+    """
+
+    def __init__(self):
+        self._core = CMMCorePlus()
+
+    def loadSystemConfiguration(self, configuration):
+        self._core.loadSystemConfiguration(str(configuration))
+
+    # SLM-related
+    def getSLMDevice(self) -> str:
+        return self._core.getSLMDevice()
+
+    def getSLMHeight(self, device: str) -> int:
+        return self._core.getSLMHeight(device)
+
+    def getSLMWidth(self, device: str) -> int:
+        return self._core.getSLMWidth(device)
+
+    def setSLMImage(self, device: str, image: Any) -> None:
+        self._core.setSLMImage(device, image)
+
+    # Config/device properties
+    def setConfig(self, group: str, config: str) -> None:
+        self._core.setConfig(group, config)
+
+    def setProperty(self, label: str, name: str, value: Any) -> None:
+        self._core.setProperty(label, name, value)
+
+    def getProperty(self, label: str, name: str) -> str:
+        return self._core.getProperty(label, name)
+
+    def getAllowedPropertyValues(self, device: str, prop_name: str) -> Sequence[str]:
+        return self._core.getAllowedPropertyValues(device, prop_name)
+
+    def describe(self) -> str:
+        return self._core.describe()
+
+    def setFocusDevice(self, label: str) -> None:
+        self._core.setFocusDevice(label)
+
+    def getAvailableConfigGroups(self) -> Sequence[str]:
+        return self._core.getAvailableConfigGroups()
+
+    def getConfigGroupObject(self, group: str, include_read_only: bool = False):
+        return self._core.getConfigGroupObject(group, include_read_only)
+
+    # Camera-related
+    def getCameraDevice(self) -> str:
+        return self._core.getCameraDevice()
+
+    def setExposure(self, exposure_ms: float) -> None:
+        self._core.setExposure(exposure_ms)
+
+    def snapImage(self) -> None:
+        self._core.snapImage()
+
+    def getImage(self) -> Any:
+        return self._core.getImage()
+
+    def getPixelSizeUm(self) -> float:
+        return self._core.getPixelSizeUm()
+
+    def getROI(self):
+        return self._core.getROI()
+
+    # Stage/focus/positioning
+    def getZPosition(self) -> float:
+        return self._core.getZPosition()
+
+    def setPosition(self, z: float) -> None:
+        self._core.setPosition(z)
+
+    def setXYPosition(self, x: float, y: float) -> None:
+        self._core.setXYPosition(x, y)
+
+    def setAutoFocusOffset(self, offset: float) -> None:
+        self._core.setAutoFocusOffset(offset)
+
+    # Synchronization
+    def waitForSystem(self) -> None:
+        self._core.waitForSystem()